Starting phenix.real_space_refine on Sun Feb 18 20:28:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9t_35283/02_2024/8i9t_35283_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9t_35283/02_2024/8i9t_35283.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9t_35283/02_2024/8i9t_35283.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9t_35283/02_2024/8i9t_35283.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9t_35283/02_2024/8i9t_35283_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9t_35283/02_2024/8i9t_35283_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 2391 5.49 5 S 273 5.16 5 C 75141 2.51 5 N 24640 2.21 5 O 31342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "CA TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA GLU 125": "OE1" <-> "OE2" Residue "CA TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CB TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CB PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CB PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CB TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CB TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CC TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CC TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE PHE 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE ASP 386": "OD1" <-> "OD2" Residue "CE TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE TYR 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CF ASP 62": "OD1" <-> "OD2" Residue "CF TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CG TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH ASP 6": "OD1" <-> "OD2" Residue "CH ASP 86": "OD1" <-> "OD2" Residue "CH TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH GLU 300": "OE1" <-> "OE2" Residue "CH ASP 307": "OD1" <-> "OD2" Residue "CH TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CI TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CI PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CJ TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CJ GLU 75": "OE1" <-> "OE2" Residue "CJ PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CJ PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CJ TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CJ TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CJ PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CJ PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CJ GLU 384": "OE1" <-> "OE2" Residue "CK TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CL ASP 52": "OD1" <-> "OD2" Residue "CM TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CM PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CN PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CP PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CP TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CP TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CP GLU 538": "OE1" <-> "OE2" Residue "CQ PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CQ ASP 25": "OD1" <-> "OD2" Residue "CQ PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CR ASP 205": "OD1" <-> "OD2" Residue "CS ASP 694": "OD1" <-> "OD2" Residue "Cb GLU 14": "OE1" <-> "OE2" Residue "Cb ASP 431": "OD1" <-> "OD2" Residue "Cb PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cb GLU 529": "OE1" <-> "OE2" Residue "Cb PHE 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB GLU 298": "OE1" <-> "OE2" Residue "LB GLU 356": "OE1" <-> "OE2" Residue "LC PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LE TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LE PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LF PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LF PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LF TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LF PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LF PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LF PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LF PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LF PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG GLU 249": "OE1" <-> "OE2" Residue "LH PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LH TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LH TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LH PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LH TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LM PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LM PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LQ ASP 117": "OD1" <-> "OD2" Residue "LS PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LV TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LV GLU 123": "OE1" <-> "OE2" Residue "LY TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LY ASP 113": "OD1" <-> "OD2" Residue "Le PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lf PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Li PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lq PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cc PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cc PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cc GLU 157": "OE1" <-> "OE2" Residue "Cd ASP 88": "OD1" <-> "OD2" Residue "Cd TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cd TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cd TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cd PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cd PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cd ASP 405": "OD1" <-> "OD2" Residue "Ce PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cg PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cg PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 133790 Number of models: 1 Model: "" Number of chains: 59 Chain: "C1" Number of atoms: 45600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2132, 45600 Classifications: {'RNA': 2132} Modifications used: {'rna2p_pur': 217, 'rna2p_pyr': 150, 'rna3p_pur': 952, 'rna3p_pyr': 813} Link IDs: {'rna2p': 366, 'rna3p': 1765} Chain breaks: 15 Chain: "C2" Number of atoms: 3359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3359 Classifications: {'RNA': 158} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 13, 'rna3p_pur': 63, 'rna3p_pyr': 65} Link IDs: {'rna2p': 29, 'rna3p': 128} Chain: "C3" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2097 Classifications: {'RNA': 98} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 8, 'rna3p_pur': 40, 'rna3p_pyr': 39} Link IDs: {'rna2p': 19, 'rna3p': 78} Chain breaks: 1 Chain: "CA" Number of atoms: 2144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2144 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 11, 'TRANS': 248} Chain breaks: 2 Chain: "CB" Number of atoms: 2063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2063 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 20, 'TRANS': 239} Chain breaks: 1 Chain: "CC" Number of atoms: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2388 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 38, 'TRANS': 250} Chain breaks: 2 Chain: "CE" Number of atoms: 3673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3673 Classifications: {'peptide': 463} Link IDs: {'PTRANS': 21, 'TRANS': 441} Chain breaks: 1 Chain: "CF" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1945 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 11, 'TRANS': 233} Chain: "CG" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1396 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 7, 'TRANS': 169} Chain: "CH" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3851 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 23, 'TRANS': 452} Chain: "CI" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1196 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "CJ" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3109 Classifications: {'peptide': 380} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 354} Chain breaks: 2 Chain: "CK" Number of atoms: 1778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1778 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 9, 'TRANS': 212} Chain breaks: 3 Chain: "CL" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2173 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 255} Link IDs: {'CIS': 1, 'PTRANS': 33, 'TRANS': 355} Chain breaks: 2 Unresolved chain link angles: 27 Unresolved non-hydrogen bonds: 891 Unresolved non-hydrogen angles: 1142 Unresolved non-hydrogen dihedrals: 732 Unresolved non-hydrogen chiralities: 96 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 5, 'TYR:plan': 6, 'ASN:plan1': 9, 'TRP:plan': 3, 'ASP:plan': 17, 'PHE:plan': 8, 'GLU:plan': 8, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 416 Chain: "CM" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1525 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain breaks: 1 Chain: "CN" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1856 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 8, 'TRANS': 237} Chain: "CO" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 468 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain breaks: 2 Chain: "CP" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2535 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 19, 'TRANS': 304} Chain: "CQ" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 960 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "CR" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1354 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 8, 'TRANS': 158} Chain breaks: 3 Chain: "CS" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 734 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 1 Chain: "CU" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1415 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain breaks: 1 Chain: "CX" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 701 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 3, 'TRANS': 84} Chain: "Cz" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 592 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "Cb" Number of atoms: 4397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4397 Classifications: {'peptide': 560} Link IDs: {'PTRANS': 29, 'TRANS': 530} Chain breaks: 4 Chain: "Ch" Number of atoms: 562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 562 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "LB" Number of atoms: 2708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2708 Classifications: {'peptide': 341} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 328} Chain breaks: 1 Chain: "LC" Number of atoms: 2752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2752 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 24, 'TRANS': 337} Chain: "LE" Number of atoms: 1338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1338 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 158} Chain breaks: 1 Chain: "LF" Number of atoms: 1967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1967 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 12, 'TRANS': 227} Chain: "LG" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1574 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 8, 'TRANS': 186} Chain breaks: 1 Chain: "LH" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1496 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain: "LK" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1112 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain breaks: 1 Chain: "LL" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 964 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "LM" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1101 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 7, 'TRANS': 129} Chain: "LN" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1563 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 177} Chain breaks: 1 Chain: "LO" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1618 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 10, 'TRANS': 193} Chain: "LP" Number of atoms: 1212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1212 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 6, 'TRANS': 147} Chain breaks: 1 Chain: "LQ" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 7, 'TRANS': 121} Chain: "LS" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1433 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 10, 'TRANS': 163} Chain: "LT" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1014 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain: "LV" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 995 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 125} Chain: "LX" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 148 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Chain: "LY" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1065 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 6, 'TRANS': 127} Chain: "Le" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1055 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "Lf" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 862 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "Lh" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 995 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "Li" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 731 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "Lj" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 595 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "Lq" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1600 Classifications: {'peptide': 207} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 197} Chain: "Cc" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1898 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 7, 'TRANS': 228} Chain breaks: 1 Chain: "Cd" Number of atoms: 2763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2763 Classifications: {'peptide': 342} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 319} Chain breaks: 3 Chain: "Ce" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1609 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 8, 'TRANS': 185} Chain: "Cf" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 845 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "Cg" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1850 Classifications: {'peptide': 233} Link IDs: {'PCIS': 4, 'PTRANS': 12, 'TRANS': 216} Chain breaks: 1 Chain: "CH" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "CQ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Lj" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Ce" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 83451 SG CYSCQ 36 138.665 50.615 204.988 1.00109.20 S ATOM A0HGV SG CYSLj 19 169.724 122.491 138.265 1.00 89.83 S ATOM A0HHN SG CYSLj 22 171.273 123.859 141.438 1.00 85.06 S ATOM A0HKD SG CYSLj 34 167.540 124.047 141.014 1.00 86.66 S ATOM A0HKU SG CYSLj 37 169.682 126.263 138.872 1.00 86.91 S ATOM A0MYF SG CYSCe 38 200.468 171.436 196.739 1.00 76.07 S Time building chain proxies: 50.04, per 1000 atoms: 0.37 Number of scatterers: 133790 At special positions: 0 Unit cell: (260.205, 262.295, 318.725, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 273 16.00 P 2391 15.00 O 31342 8.00 N 24640 7.00 C 75141 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYSCQ 6 " - pdb=" SG CYSCQ 9 " distance=2.03 Simple disulfide: pdb=" SG CYSCQ 9 " - pdb=" SG CYSCQ 32 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 50.03 Conformation dependent library (CDL) restraints added in 11.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNCQ1000 " pdb="ZN ZNCQ1000 " - pdb=" SG CYSCQ 36 " pdb=" ZNCe1000 " pdb="ZN ZNCe1000 " - pdb=" SG CYSCe 38 " pdb=" ZNLj 101 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 34 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 22 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 37 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 19 " Number of angles added : 6 20556 Ramachandran restraints generated. 10278 Oldfield, 0 Emsley, 10278 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 19634 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 391 helices and 86 sheets defined 49.8% alpha, 12.8% beta 784 base pairs and 1188 stacking pairs defined. Time for finding SS restraints: 73.59 Creating SS restraints... Processing helix chain 'CA' and resid 45 through 60 Proline residue: CA 60 - end of helix Processing helix chain 'CA' and resid 73 through 85 Processing helix chain 'CA' and resid 143 through 149 removed outlier: 3.824A pdb=" N GLUCA 147 " --> pdb=" O ASPCA 143 " (cutoff:3.500A) Processing helix chain 'CA' and resid 150 through 164 Processing helix chain 'CA' and resid 263 through 295 Processing helix chain 'CA' and resid 310 through 316 removed outlier: 3.752A pdb=" N ALACA 316 " --> pdb=" O ARGCA 312 " (cutoff:3.500A) Processing helix chain 'CB' and resid 19 through 40 Processing helix chain 'CB' and resid 52 through 60 removed outlier: 4.290A pdb=" N GLUCB 59 " --> pdb=" O SERCB 55 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N THRCB 60 " --> pdb=" O THRCB 56 " (cutoff:3.500A) Processing helix chain 'CB' and resid 74 through 80 Proline residue: CB 80 - end of helix Processing helix chain 'CB' and resid 104 through 115 Processing helix chain 'CB' and resid 118 through 124 removed outlier: 4.404A pdb=" N ALACB 122 " --> pdb=" O GLUCB 118 " (cutoff:3.500A) Processing helix chain 'CB' and resid 129 through 137 Processing helix chain 'CB' and resid 139 through 151 removed outlier: 5.260A pdb=" N ASPCB 151 " --> pdb=" O PHECB 147 " (cutoff:3.500A) Processing helix chain 'CB' and resid 156 through 167 removed outlier: 4.464A pdb=" N ASNCB 161 " --> pdb=" O THRCB 157 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARGCB 162 " --> pdb=" O ARGCB 158 " (cutoff:3.500A) Proline residue: CB 164 - end of helix Processing helix chain 'CB' and resid 168 through 173 Processing helix chain 'CB' and resid 216 through 230 Processing helix chain 'CB' and resid 251 through 269 Processing helix chain 'CC' and resid 202 through 213 Processing helix chain 'CC' and resid 232 through 245 Processing helix chain 'CC' and resid 277 through 282 removed outlier: 4.448A pdb=" N PHECC 281 " --> pdb=" O PROCC 277 " (cutoff:3.500A) Processing helix chain 'CC' and resid 284 through 301 Processing helix chain 'CC' and resid 308 through 316 Processing helix chain 'CC' and resid 357 through 362 removed outlier: 3.943A pdb=" N LEUCC 361 " --> pdb=" O PROCC 357 " (cutoff:3.500A) Proline residue: CC 362 - end of helix No H-bonds generated for 'chain 'CC' and resid 357 through 362' Processing helix chain 'CC' and resid 363 through 374 removed outlier: 5.413A pdb=" N ASPCC 374 " --> pdb=" O TRPCC 370 " (cutoff:3.500A) Processing helix chain 'CC' and resid 389 through 394 Proline residue: CC 394 - end of helix Processing helix chain 'CC' and resid 398 through 412 Processing helix chain 'CE' and resid 112 through 117 removed outlier: 4.841A pdb=" N ASNCE 117 " --> pdb=" O PHECE 113 " (cutoff:3.500A) Processing helix chain 'CE' and resid 119 through 130 Processing helix chain 'CE' and resid 135 through 148 removed outlier: 4.202A pdb=" N ILECE 142 " --> pdb=" O GLNCE 138 " (cutoff:3.500A) Proline residue: CE 143 - end of helix Processing helix chain 'CE' and resid 160 through 177 Proline residue: CE 168 - end of helix Processing helix chain 'CE' and resid 192 through 208 Processing helix chain 'CE' and resid 222 through 233 Processing helix chain 'CE' and resid 240 through 250 Processing helix chain 'CE' and resid 265 through 273 Processing helix chain 'CE' and resid 274 through 285 Processing helix chain 'CE' and resid 300 through 311 Processing helix chain 'CE' and resid 343 through 356 Processing helix chain 'CE' and resid 366 through 381 Processing helix chain 'CE' and resid 392 through 406 Processing helix chain 'CE' and resid 414 through 422 removed outlier: 3.949A pdb=" N GLYCE 420 " --> pdb=" O VALCE 416 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ASPCE 422 " --> pdb=" O ALACE 418 " (cutoff:3.500A) Processing helix chain 'CE' and resid 437 through 451 Processing helix chain 'CE' and resid 467 through 477 removed outlier: 4.204A pdb=" N ALACE 471 " --> pdb=" O LEUCE 467 " (cutoff:3.500A) Processing helix chain 'CE' and resid 493 through 504 Processing helix chain 'CE' and resid 505 through 525 Processing helix chain 'CE' and resid 532 through 537 removed outlier: 4.319A pdb=" N LEUCE 536 " --> pdb=" O ASPCE 532 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ASPCE 537 " --> pdb=" O VALCE 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'CE' and resid 532 through 537' Processing helix chain 'CE' and resid 538 through 546 Processing helix chain 'CF' and resid 19 through 35 Proline residue: CF 35 - end of helix Processing helix chain 'CF' and resid 50 through 61 removed outlier: 4.927A pdb=" N LYSCF 54 " --> pdb=" O ASNCF 50 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASPCF 55 " --> pdb=" O ASNCF 51 " (cutoff:3.500A) Processing helix chain 'CF' and resid 69 through 78 Processing helix chain 'CF' and resid 88 through 97 removed outlier: 4.986A pdb=" N THRCF 97 " --> pdb=" O THRCF 93 " (cutoff:3.500A) Processing helix chain 'CF' and resid 108 through 120 removed outlier: 5.776A pdb=" N SERCF 120 " --> pdb=" O PHECF 116 " (cutoff:3.500A) Processing helix chain 'CF' and resid 158 through 169 Proline residue: CF 163 - end of helix Processing helix chain 'CF' and resid 202 through 213 Processing helix chain 'CF' and resid 237 through 243 removed outlier: 4.725A pdb=" N LYSCF 241 " --> pdb=" O LEUCF 237 " (cutoff:3.500A) Processing helix chain 'CG' and resid 5 through 20 Processing helix chain 'CG' and resid 22 through 28 Processing helix chain 'CG' and resid 49 through 58 removed outlier: 4.365A pdb=" N CYSCG 58 " --> pdb=" O ASNCG 54 " (cutoff:3.500A) Processing helix chain 'CG' and resid 60 through 65 removed outlier: 5.650A pdb=" N LEUCG 65 " --> pdb=" O ARGCG 61 " (cutoff:3.500A) Processing helix chain 'CG' and resid 83 through 94 Proline residue: CG 88 - end of helix Processing helix chain 'CG' and resid 101 through 111 Proline residue: CG 107 - end of helix Processing helix chain 'CG' and resid 150 through 157 Processing helix chain 'CG' and resid 170 through 177 removed outlier: 4.013A pdb=" N LEUCG 174 " --> pdb=" O CYSCG 170 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASPCG 176 " --> pdb=" O GLUCG 172 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLUCG 177 " --> pdb=" O TYRCG 173 " (cutoff:3.500A) Processing helix chain 'CH' and resid 12 through 27 Processing helix chain 'CH' and resid 37 through 68 Proline residue: CH 68 - end of helix Processing helix chain 'CH' and resid 74 through 85 Processing helix chain 'CH' and resid 86 through 118 removed outlier: 3.733A pdb=" N SERCH 98 " --> pdb=" O LEUCH 94 " (cutoff:3.500A) Processing helix chain 'CH' and resid 120 through 143 Processing helix chain 'CH' and resid 144 through 159 Processing helix chain 'CH' and resid 178 through 187 Processing helix chain 'CH' and resid 232 through 245 Processing helix chain 'CH' and resid 262 through 278 Proline residue: CH 275 - end of helix Processing helix chain 'CH' and resid 298 through 311 removed outlier: 4.552A pdb=" N SERCH 311 " --> pdb=" O ASPCH 307 " (cutoff:3.500A) Processing helix chain 'CH' and resid 326 through 352 removed outlier: 4.595A pdb=" N GLYCH 350 " --> pdb=" O LYSCH 346 " (cutoff:3.500A) Processing helix chain 'CH' and resid 358 through 369 Processing helix chain 'CH' and resid 384 through 390 Processing helix chain 'CH' and resid 403 through 412 Processing helix chain 'CH' and resid 420 through 426 removed outlier: 4.394A pdb=" N ASPCH 424 " --> pdb=" O ASPCH 420 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ILECH 426 " --> pdb=" O ARGCH 422 " (cutoff:3.500A) Processing helix chain 'CH' and resid 445 through 450 Processing helix chain 'CH' and resid 453 through 472 Processing helix chain 'CH' and resid 429 through 434 removed outlier: 5.279A pdb=" N TYRCH 434 " --> pdb=" O GLUCH 431 " (cutoff:3.500A) Processing helix chain 'CI' and resid 199 through 211 Processing helix chain 'CI' and resid 237 through 249 Processing helix chain 'CI' and resid 284 through 296 Proline residue: CI 296 - end of helix Processing helix chain 'CI' and resid 298 through 321 Processing helix chain 'CJ' and resid 6 through 11 removed outlier: 4.014A pdb=" N SERCJ 10 " --> pdb=" O LYSCJ 6 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLYCJ 11 " --> pdb=" O LYSCJ 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'CJ' and resid 6 through 11' Processing helix chain 'CJ' and resid 18 through 27 Processing helix chain 'CJ' and resid 29 through 41 Processing helix chain 'CJ' and resid 49 through 55 Processing helix chain 'CJ' and resid 65 through 75 Processing helix chain 'CJ' and resid 76 through 98 Processing helix chain 'CJ' and resid 99 through 111 Processing helix chain 'CJ' and resid 112 through 117 removed outlier: 4.480A pdb=" N GLYCJ 117 " --> pdb=" O PROCJ 113 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 123 through 132 Proline residue: CJ 132 - end of helix Processing helix chain 'CJ' and resid 133 through 155 removed outlier: 4.111A pdb=" N ASPCJ 142 " --> pdb=" O LEUCJ 138 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ASPCJ 143 " --> pdb=" O ARGCJ 139 " (cutoff:3.500A) Proline residue: CJ 155 - end of helix Processing helix chain 'CJ' and resid 161 through 183 Processing helix chain 'CJ' and resid 223 through 250 removed outlier: 3.589A pdb=" N METCJ 227 " --> pdb=" O ASPCJ 223 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 258 through 265 Processing helix chain 'CJ' and resid 362 through 368 removed outlier: 4.800A pdb=" N PHECJ 367 " --> pdb=" O PROCJ 363 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 379 through 391 Processing helix chain 'CJ' and resid 457 through 468 Processing helix chain 'CJ' and resid 472 through 477 Processing helix chain 'CK' and resid 5 through 14 Processing helix chain 'CK' and resid 19 through 42 removed outlier: 4.763A pdb=" N GLYCK 32 " --> pdb=" O ALACK 28 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N HISCK 33 " --> pdb=" O ALACK 29 " (cutoff:3.500A) Processing helix chain 'CK' and resid 44 through 75 removed outlier: 5.987A pdb=" N LYSCK 48 " --> pdb=" O GLYCK 44 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N GLYCK 75 " --> pdb=" O ARGCK 71 " (cutoff:3.500A) Processing helix chain 'CK' and resid 98 through 116 Processing helix chain 'CK' and resid 128 through 139 Processing helix chain 'CK' and resid 206 through 213 Processing helix chain 'CK' and resid 248 through 253 Processing helix chain 'CL' and resid 17 through 42 Processing helix chain 'CL' and resid 61 through 80 Processing helix chain 'CL' and resid 193 through 205 removed outlier: 5.059A pdb=" N VALCL 197 " --> pdb=" O ALACL 193 " (cutoff:3.500A) Processing helix chain 'CL' and resid 216 through 221 Processing helix chain 'CL' and resid 223 through 232 removed outlier: 4.984A pdb=" N ALACL 228 " --> pdb=" O ASPCL 224 " (cutoff:3.500A) Processing helix chain 'CL' and resid 245 through 250 removed outlier: 4.841A pdb=" N VALCL 249 " --> pdb=" O LYSCL 245 " (cutoff:3.500A) Proline residue: CL 250 - end of helix No H-bonds generated for 'chain 'CL' and resid 245 through 250' Processing helix chain 'CL' and resid 251 through 265 removed outlier: 4.688A pdb=" N PHECL 264 " --> pdb=" O TYRCL 260 " (cutoff:3.500A) Processing helix chain 'CL' and resid 292 through 308 Processing helix chain 'CL' and resid 324 through 335 Processing helix chain 'CL' and resid 396 through 403 removed outlier: 5.159A pdb=" N ASNCL 403 " --> pdb=" O LEUCL 399 " (cutoff:3.500A) Processing helix chain 'CL' and resid 413 through 428 removed outlier: 5.660A pdb=" N VALCL 417 " --> pdb=" O PROCL 413 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N THRCL 427 " --> pdb=" O ARGCL 423 " (cutoff:3.500A) Proline residue: CL 428 - end of helix Processing helix chain 'CL' and resid 429 through 439 Processing helix chain 'CL' and resid 450 through 466 removed outlier: 4.440A pdb=" N THRCL 454 " --> pdb=" O GLYCL 450 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N METCL 455 " --> pdb=" O GLYCL 451 " (cutoff:3.500A) Processing helix chain 'CL' and resid 475 through 490 Processing helix chain 'CM' and resid 53 through 78 removed outlier: 4.758A pdb=" N GLNCM 78 " --> pdb=" O ILECM 74 " (cutoff:3.500A) Processing helix chain 'CM' and resid 102 through 113 Processing helix chain 'CM' and resid 126 through 137 Processing helix chain 'CM' and resid 146 through 157 Processing helix chain 'CM' and resid 171 through 180 Processing helix chain 'CM' and resid 186 through 197 Processing helix chain 'CM' and resid 200 through 209 removed outlier: 5.236A pdb=" N TRPCM 209 " --> pdb=" O ALACM 205 " (cutoff:3.500A) Processing helix chain 'CM' and resid 239 through 249 removed outlier: 4.544A pdb=" N ALACM 243 " --> pdb=" O GLUCM 239 " (cutoff:3.500A) Processing helix chain 'CN' and resid 12 through 17 Processing helix chain 'CN' and resid 32 through 43 Processing helix chain 'CN' and resid 58 through 63 Processing helix chain 'CN' and resid 77 through 88 Processing helix chain 'CN' and resid 103 through 108 Processing helix chain 'CN' and resid 122 through 134 Processing helix chain 'CN' and resid 147 through 152 Processing helix chain 'CN' and resid 166 through 178 Processing helix chain 'CN' and resid 192 through 197 Processing helix chain 'CN' and resid 211 through 223 Processing helix chain 'CN' and resid 230 through 238 removed outlier: 6.845A pdb=" N ASNCN 234 " --> pdb=" O PROCN 230 " (cutoff:3.500A) Processing helix chain 'CN' and resid 239 through 246 Processing helix chain 'CO' and resid 7 through 21 Processing helix chain 'CO' and resid 22 through 43 Processing helix chain 'CO' and resid 83 through 88 Processing helix chain 'CP' and resid 262 through 274 Processing helix chain 'CP' and resid 277 through 289 Proline residue: CP 289 - end of helix Processing helix chain 'CP' and resid 290 through 303 Proline residue: CP 303 - end of helix Processing helix chain 'CP' and resid 316 through 328 Processing helix chain 'CP' and resid 354 through 360 Processing helix chain 'CP' and resid 366 through 377 Proline residue: CP 372 - end of helix removed outlier: 4.571A pdb=" N CYSCP 377 " --> pdb=" O VALCP 373 " (cutoff:3.500A) Processing helix chain 'CP' and resid 392 through 403 Processing helix chain 'CP' and resid 414 through 429 Processing helix chain 'CP' and resid 439 through 447 Proline residue: CP 444 - end of helix Processing helix chain 'CP' and resid 464 through 469 Proline residue: CP 469 - end of helix Processing helix chain 'CP' and resid 476 through 499 Proline residue: CP 484 - end of helix removed outlier: 5.848A pdb=" N ASNCP 499 " --> pdb=" O ILECP 495 " (cutoff:3.500A) Processing helix chain 'CP' and resid 516 through 532 removed outlier: 4.535A pdb=" N GLUCP 521 " --> pdb=" O VALCP 517 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLUCP 522 " --> pdb=" O GLUCP 518 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N VALCP 523 " --> pdb=" O GLUCP 519 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VALCP 524 " --> pdb=" O ASNCP 520 " (cutoff:3.500A) Proline residue: CP 532 - end of helix Processing helix chain 'CP' and resid 470 through 475 removed outlier: 4.777A pdb=" N ARGCP 475 " --> pdb=" O SERCP 470 " (cutoff:3.500A) No H-bonds generated for 'chain 'CP' and resid 470 through 475' Processing helix chain 'CQ' and resid 33 through 43 removed outlier: 3.779A pdb=" N LYSCQ 43 " --> pdb=" O ASNCQ 39 " (cutoff:3.500A) Processing helix chain 'CQ' and resid 45 through 50 removed outlier: 5.208A pdb=" N LYSCQ 50 " --> pdb=" O PROCQ 46 " (cutoff:3.500A) Processing helix chain 'CQ' and resid 52 through 60 removed outlier: 3.974A pdb=" N GLYCQ 60 " --> pdb=" O ARGCQ 56 " (cutoff:3.500A) Processing helix chain 'CQ' and resid 66 through 73 removed outlier: 3.504A pdb=" N ALACQ 72 " --> pdb=" O THRCQ 68 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ALACQ 73 " --> pdb=" O LEUCQ 69 " (cutoff:3.500A) Processing helix chain 'CQ' and resid 82 through 112 Processing helix chain 'CR' and resid 3 through 12 Processing helix chain 'CR' and resid 33 through 39 Processing helix chain 'CR' and resid 44 through 53 Processing helix chain 'CR' and resid 131 through 137 removed outlier: 4.222A pdb=" N GLNCR 135 " --> pdb=" O VALCR 131 " (cutoff:3.500A) Processing helix chain 'CR' and resid 166 through 178 Processing helix chain 'CR' and resid 188 through 203 Processing helix chain 'CR' and resid 205 through 213 removed outlier: 5.840A pdb=" N ARGCR 213 " --> pdb=" O METCR 209 " (cutoff:3.500A) Processing helix chain 'CR' and resid 221 through 233 Processing helix chain 'CS' and resid 465 through 483 Processing helix chain 'CS' and resid 657 through 669 removed outlier: 4.983A pdb=" N GLYCS 669 " --> pdb=" O GLNCS 665 " (cutoff:3.500A) Processing helix chain 'CS' and resid 672 through 682 removed outlier: 5.338A pdb=" N ASNCS 682 " --> pdb=" O ASPCS 678 " (cutoff:3.500A) Processing helix chain 'CS' and resid 693 through 705 removed outlier: 4.808A pdb=" N LYSCS 705 " --> pdb=" O ALACS 701 " (cutoff:3.500A) Processing helix chain 'CS' and resid 711 through 723 Processing helix chain 'CU' and resid 192 through 204 Processing helix chain 'CU' and resid 213 through 218 Processing helix chain 'CU' and resid 225 through 231 removed outlier: 6.338A pdb=" N SERCU 229 " --> pdb=" O ARGCU 225 " (cutoff:3.500A) Proline residue: CU 231 - end of helix Processing helix chain 'CU' and resid 235 through 262 Processing helix chain 'CU' and resid 278 through 312 Processing helix chain 'CU' and resid 313 through 344 Processing helix chain 'CU' and resid 357 through 369 removed outlier: 3.707A pdb=" N ALACU 361 " --> pdb=" O PROCU 357 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VALCU 362 " --> pdb=" O PHECU 358 " (cutoff:3.500A) Processing helix chain 'CX' and resid 65 through 70 removed outlier: 4.810A pdb=" N GLYCX 70 " --> pdb=" O GLUCX 66 " (cutoff:3.500A) Processing helix chain 'CX' and resid 97 through 114 Processing helix chain 'CX' and resid 118 through 150 Processing helix chain 'Cz' and resid 47 through 92 Processing helix chain 'Cb' and resid 16 through 22 removed outlier: 4.833A pdb=" N SERCb 20 " --> pdb=" O ASPCb 16 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LEUCb 21 " --> pdb=" O ILECb 17 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N PHECb 22 " --> pdb=" O ALACb 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'Cb' and resid 16 through 22' Processing helix chain 'Cb' and resid 91 through 96 Processing helix chain 'Cb' and resid 98 through 109 Processing helix chain 'Cb' and resid 114 through 127 Proline residue: Cb 122 - end of helix Processing helix chain 'Cb' and resid 139 through 153 Proline residue: Cb 147 - end of helix Processing helix chain 'Cb' and resid 169 through 185 Processing helix chain 'Cb' and resid 199 through 210 Processing helix chain 'Cb' and resid 217 through 229 Processing helix chain 'Cb' and resid 242 through 250 Processing helix chain 'Cb' and resid 251 through 263 Proline residue: Cb 263 - end of helix Processing helix chain 'Cb' and resid 276 through 287 Processing helix chain 'Cb' and resid 316 through 327 Processing helix chain 'Cb' and resid 375 through 390 Processing helix chain 'Cb' and resid 401 through 415 Processing helix chain 'Cb' and resid 423 through 430 removed outlier: 5.765A pdb=" N ALACb 427 " --> pdb=" O THRCb 423 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 446 through 459 removed outlier: 4.551A pdb=" N THRCb 457 " --> pdb=" O ARGCb 453 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ALACb 458 " --> pdb=" O VALCb 454 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ARGCb 459 " --> pdb=" O GLYCb 455 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 471 through 486 Proline residue: Cb 476 - end of helix Processing helix chain 'Cb' and resid 510 through 528 Processing helix chain 'Cb' and resid 529 through 549 Processing helix chain 'Cb' and resid 553 through 567 removed outlier: 4.983A pdb=" N LYSCb 567 " --> pdb=" O VALCb 563 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 577 through 597 removed outlier: 4.293A pdb=" N ASNCb 589 " --> pdb=" O GLNCb 585 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LEUCb 590 " --> pdb=" O VALCb 586 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEUCb 591 " --> pdb=" O ARGCb 587 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYRCb 597 " --> pdb=" O LYSCb 593 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 615 through 629 Processing helix chain 'Cb' and resid 865 through 880 Processing helix chain 'Ch' and resid 270 through 311 removed outlier: 4.983A pdb=" N ALACh 311 " --> pdb=" O ALACh 307 " (cutoff:3.500A) Processing helix chain 'Ch' and resid 319 through 340 removed outlier: 6.574A pdb=" N GLUCh 323 " --> pdb=" O SERCh 319 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYSCh 325 " --> pdb=" O GLNCh 321 " (cutoff:3.500A) Processing helix chain 'LB' and resid 111 through 120 removed outlier: 4.595A pdb=" N LYSLB 120 " --> pdb=" O ARGLB 116 " (cutoff:3.500A) Processing helix chain 'LB' and resid 130 through 140 removed outlier: 4.336A pdb=" N ASNLB 140 " --> pdb=" O LYSLB 136 " (cutoff:3.500A) Processing helix chain 'LB' and resid 141 through 155 Processing helix chain 'LB' and resid 166 through 171 Proline residue: LB 171 - end of helix Processing helix chain 'LB' and resid 188 through 200 Processing helix chain 'LB' and resid 205 through 210 Processing helix chain 'LB' and resid 348 through 353 removed outlier: 4.773A pdb=" N LEULB 352 " --> pdb=" O SERLB 348 " (cutoff:3.500A) Processing helix chain 'LB' and resid 373 through 382 Processing helix chain 'LB' and resid 384 through 391 Processing helix chain 'LC' and resid 24 through 29 removed outlier: 4.207A pdb=" N SERLC 28 " --> pdb=" O PROLC 24 " (cutoff:3.500A) Processing helix chain 'LC' and resid 32 through 48 removed outlier: 4.048A pdb=" N ARGLC 48 " --> pdb=" O ALALC 44 " (cutoff:3.500A) Processing helix chain 'LC' and resid 115 through 133 removed outlier: 4.967A pdb=" N ALALC 133 " --> pdb=" O ALALC 129 " (cutoff:3.500A) Processing helix chain 'LC' and resid 134 through 140 Processing helix chain 'LC' and resid 154 through 159 Processing helix chain 'LC' and resid 160 through 165 removed outlier: 4.458A pdb=" N ALALC 164 " --> pdb=" O GLYLC 160 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYSLC 165 " --> pdb=" O ASPLC 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'LC' and resid 160 through 165' Processing helix chain 'LC' and resid 166 through 177 Processing helix chain 'LC' and resid 178 through 189 Processing helix chain 'LC' and resid 195 through 200 Processing helix chain 'LC' and resid 220 through 230 removed outlier: 4.497A pdb=" N LYSLC 224 " --> pdb=" O LYSLC 220 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILELC 229 " --> pdb=" O GLYLC 225 " (cutoff:3.500A) Proline residue: LC 230 - end of helix Processing helix chain 'LC' and resid 241 through 247 Proline residue: LC 247 - end of helix Processing helix chain 'LC' and resid 258 through 272 removed outlier: 3.594A pdb=" N ALALC 267 " --> pdb=" O LYSLC 263 " (cutoff:3.500A) Processing helix chain 'LC' and resid 286 through 293 removed outlier: 3.738A pdb=" N SERLC 293 " --> pdb=" O ARGLC 289 " (cutoff:3.500A) Processing helix chain 'LC' and resid 294 through 300 Processing helix chain 'LC' and resid 318 through 323 Processing helix chain 'LC' and resid 324 through 330 Processing helix chain 'LC' and resid 331 through 340 removed outlier: 4.669A pdb=" N THRLC 335 " --> pdb=" O PROLC 331 " (cutoff:3.500A) Processing helix chain 'LC' and resid 355 through 364 Processing helix chain 'LC' and resid 214 through 219 Processing helix chain 'LE' and resid 98 through 103 removed outlier: 4.991A pdb=" N ILELE 103 " --> pdb=" O ALALE 99 " (cutoff:3.500A) Processing helix chain 'LE' and resid 115 through 124 Processing helix chain 'LE' and resid 125 through 130 Processing helix chain 'LE' and resid 138 through 145 Processing helix chain 'LE' and resid 155 through 174 removed outlier: 5.681A pdb=" N LYSLE 163 " --> pdb=" O ALALE 159 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ALALE 168 " --> pdb=" O ALALE 164 " (cutoff:3.500A) Processing helix chain 'LE' and resid 178 through 186 removed outlier: 5.441A pdb=" N SERLE 186 " --> pdb=" O TYRLE 182 " (cutoff:3.500A) Processing helix chain 'LF' and resid 15 through 79 Processing helix chain 'LF' and resid 102 through 113 Processing helix chain 'LF' and resid 126 through 137 Processing helix chain 'LF' and resid 146 through 156 Processing helix chain 'LF' and resid 171 through 179 Processing helix chain 'LF' and resid 186 through 197 Processing helix chain 'LF' and resid 200 through 209 removed outlier: 5.014A pdb=" N TRPLF 209 " --> pdb=" O ALALF 205 " (cutoff:3.500A) Processing helix chain 'LF' and resid 238 through 249 removed outlier: 4.838A pdb=" N ASNLF 242 " --> pdb=" O GLULF 238 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ALALF 243 " --> pdb=" O GLULF 239 " (cutoff:3.500A) Processing helix chain 'LG' and resid 56 through 72 Processing helix chain 'LG' and resid 75 through 84 removed outlier: 5.023A pdb=" N THRLG 84 " --> pdb=" O GLNLG 80 " (cutoff:3.500A) Processing helix chain 'LG' and resid 86 through 101 Processing helix chain 'LG' and resid 104 through 121 Processing helix chain 'LG' and resid 138 through 149 Processing helix chain 'LG' and resid 162 through 177 removed outlier: 4.823A pdb=" N VALLG 166 " --> pdb=" O PROLG 162 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N PHELG 168 " --> pdb=" O GLULG 164 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEULG 169 " --> pdb=" O LEULG 165 " (cutoff:3.500A) Proline residue: LG 170 - end of helix Processing helix chain 'LG' and resid 185 through 194 removed outlier: 4.022A pdb=" N HISLG 194 " --> pdb=" O GLYLG 190 " (cutoff:3.500A) Processing helix chain 'LG' and resid 207 through 233 removed outlier: 3.627A pdb=" N LYSLG 211 " --> pdb=" O ARGLG 207 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ASNLG 212 " --> pdb=" O SERLG 208 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLULG 213 " --> pdb=" O GLULG 209 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEULG 226 " --> pdb=" O LYSLG 222 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LYSLG 228 " --> pdb=" O GLYLG 224 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N THRLG 232 " --> pdb=" O LYSLG 228 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARGLG 233 " --> pdb=" O VALLG 229 " (cutoff:3.500A) Processing helix chain 'LG' and resid 242 through 252 Processing helix chain 'LH' and resid 61 through 84 Processing helix chain 'LH' and resid 152 through 168 removed outlier: 4.601A pdb=" N LYSLH 168 " --> pdb=" O GLNLH 164 " (cutoff:3.500A) Processing helix chain 'LH' and resid 173 through 178 removed outlier: 4.761A pdb=" N LEULH 178 " --> pdb=" O ILELH 174 " (cutoff:3.500A) Processing helix chain 'LK' and resid 31 through 36 Processing helix chain 'LK' and resid 38 through 51 Processing helix chain 'LK' and resid 76 through 86 Processing helix chain 'LK' and resid 105 through 121 removed outlier: 5.164A pdb=" N PHELK 118 " --> pdb=" O ARGLK 114 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LYSLK 119 " --> pdb=" O THRLK 115 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N PHELK 121 " --> pdb=" O ARGLK 117 " (cutoff:3.500A) Processing helix chain 'LK' and resid 124 through 140 Processing helix chain 'LK' and resid 147 through 158 Processing helix chain 'LL' and resid 17 through 22 Processing helix chain 'LL' and resid 27 through 47 Processing helix chain 'LL' and resid 76 through 84 Processing helix chain 'LL' and resid 86 through 94 Proline residue: LL 91 - end of helix Processing helix chain 'LL' and resid 105 through 123 Processing helix chain 'LM' and resid 58 through 63 removed outlier: 5.169A pdb=" N LEULM 63 " --> pdb=" O LEULM 59 " (cutoff:3.500A) Processing helix chain 'LM' and resid 77 through 89 Processing helix chain 'LM' and resid 90 through 97 Processing helix chain 'LM' and resid 98 through 112 Processing helix chain 'LM' and resid 114 through 138 Processing helix chain 'LN' and resid 2 through 14 Processing helix chain 'LN' and resid 16 through 34 removed outlier: 4.569A pdb=" N ASNLN 34 " --> pdb=" O TYRLN 30 " (cutoff:3.500A) Processing helix chain 'LN' and resid 44 through 52 Processing helix chain 'LN' and resid 97 through 111 Processing helix chain 'LN' and resid 139 through 146 Proline residue: LN 146 - end of helix Processing helix chain 'LN' and resid 147 through 154 removed outlier: 6.034A pdb=" N ILELN 151 " --> pdb=" O ARGLN 147 " (cutoff:3.500A) Proline residue: LN 154 - end of helix Processing helix chain 'LN' and resid 158 through 163 Processing helix chain 'LN' and resid 165 through 173 Processing helix chain 'LN' and resid 186 through 196 Processing helix chain 'LO' and resid 16 through 31 Processing helix chain 'LO' and resid 38 through 43 removed outlier: 5.834A pdb=" N ASNLO 43 " --> pdb=" O CYSLO 39 " (cutoff:3.500A) Processing helix chain 'LO' and resid 47 through 62 removed outlier: 5.178A pdb=" N METLO 62 " --> pdb=" O TYRLO 58 " (cutoff:3.500A) Processing helix chain 'LO' and resid 77 through 91 Proline residue: LO 91 - end of helix Processing helix chain 'LO' and resid 94 through 105 removed outlier: 4.929A pdb=" N LYSLO 105 " --> pdb=" O LEULO 101 " (cutoff:3.500A) Processing helix chain 'LO' and resid 111 through 118 removed outlier: 4.518A pdb=" N LYSLO 117 " --> pdb=" O PROLO 113 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LYSLO 118 " --> pdb=" O TYRLO 114 " (cutoff:3.500A) Processing helix chain 'LO' and resid 126 through 131 Processing helix chain 'LO' and resid 139 through 148 Processing helix chain 'LO' and resid 153 through 189 Processing helix chain 'LO' and resid 192 through 203 Processing helix chain 'LP' and resid 10 through 15 removed outlier: 4.685A pdb=" N ALALP 15 " --> pdb=" O PROLP 11 " (cutoff:3.500A) Processing helix chain 'LP' and resid 25 through 37 Processing helix chain 'LP' and resid 40 through 54 Processing helix chain 'LP' and resid 84 through 106 Processing helix chain 'LP' and resid 70 through 76 removed outlier: 3.677A pdb=" N GLYLP 73 " --> pdb=" O THRLP 70 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLNLP 75 " --> pdb=" O GLNLP 72 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 51 through 68 Processing helix chain 'LQ' and resid 70 through 83 removed outlier: 5.285A pdb=" N SERLQ 83 " --> pdb=" O ARGLQ 79 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 91 through 101 removed outlier: 5.147A pdb=" N ASNLQ 101 " --> pdb=" O ARGLQ 97 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 134 through 145 Processing helix chain 'LQ' and resid 150 through 158 Processing helix chain 'LS' and resid 33 through 49 Processing helix chain 'LS' and resid 98 through 114 Processing helix chain 'LS' and resid 117 through 122 removed outlier: 5.421A pdb=" N HISLS 122 " --> pdb=" O PHELS 118 " (cutoff:3.500A) Processing helix chain 'LS' and resid 137 through 145 removed outlier: 4.827A pdb=" N LEULS 143 " --> pdb=" O TYRLS 139 " (cutoff:3.500A) Processing helix chain 'LT' and resid 54 through 59 removed outlier: 5.754A pdb=" N GLYLT 59 " --> pdb=" O LYSLT 55 " (cutoff:3.500A) Processing helix chain 'LT' and resid 101 through 123 removed outlier: 4.494A pdb=" N PHELT 105 " --> pdb=" O SERLT 101 " (cutoff:3.500A) Processing helix chain 'LV' and resid 121 through 129 Proline residue: LV 129 - end of helix Processing helix chain 'LV' and resid 130 through 135 Processing helix chain 'LX' and resid 12 through 29 Processing helix chain 'LY' and resid 10 through 21 Processing helix chain 'LY' and resid 22 through 31 Processing helix chain 'LY' and resid 35 through 43 Processing helix chain 'LY' and resid 99 through 104 removed outlier: 4.865A pdb=" N VALLY 104 " --> pdb=" O PROLY 100 " (cutoff:3.500A) Processing helix chain 'LY' and resid 111 through 134 Processing helix chain 'Le' and resid 22 through 27 removed outlier: 4.528A pdb=" N LYSLe 27 " --> pdb=" O SERLe 23 " (cutoff:3.500A) Processing helix chain 'Le' and resid 41 through 46 Processing helix chain 'Le' and resid 55 through 60 removed outlier: 5.275A pdb=" N SERLe 60 " --> pdb=" O ILELe 56 " (cutoff:3.500A) Processing helix chain 'Le' and resid 79 through 88 removed outlier: 4.957A pdb=" N METLe 88 " --> pdb=" O GLULe 84 " (cutoff:3.500A) Processing helix chain 'Le' and resid 102 through 117 Processing helix chain 'Lf' and resid 39 through 47 Processing helix chain 'Lh' and resid 8 through 16 removed outlier: 5.444A pdb=" N ASNLh 16 " --> pdb=" O LEULh 12 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 17 through 39 Processing helix chain 'Lh' and resid 43 through 76 Processing helix chain 'Lh' and resid 82 through 87 Proline residue: Lh 87 - end of helix Processing helix chain 'Lh' and resid 90 through 96 Processing helix chain 'Lh' and resid 98 through 104 Processing helix chain 'Lh' and resid 106 through 116 Processing helix chain 'Li' and resid 43 through 58 Processing helix chain 'Li' and resid 60 through 73 Processing helix chain 'Li' and resid 74 through 87 Processing helix chain 'Li' and resid 88 through 110 Processing helix chain 'Lj' and resid 50 through 58 Processing helix chain 'Lj' and resid 65 through 77 removed outlier: 4.767A pdb=" N THRLj 69 " --> pdb=" O ARGLj 65 " (cutoff:3.500A) Proline residue: Lj 71 - end of helix Processing helix chain 'Lq' and resid 5 through 25 removed outlier: 3.542A pdb=" N ASPLq 18 " --> pdb=" O ALALq 14 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYRLq 19 " --> pdb=" O GLULq 15 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASNLq 21 " --> pdb=" O LEULq 17 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 72 through 81 removed outlier: 5.490A pdb=" N ARGLq 76 " --> pdb=" O HISLq 72 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 86 through 97 removed outlier: 4.243A pdb=" N ASNLq 96 " --> pdb=" O LYSLq 92 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LYSLq 97 " --> pdb=" O LEULq 93 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 98 through 108 removed outlier: 4.987A pdb=" N ASPLq 108 " --> pdb=" O ALALq 104 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 113 through 121 removed outlier: 3.679A pdb=" N ILELq 117 " --> pdb=" O SERLq 113 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LYSLq 118 " --> pdb=" O GLULq 114 " (cutoff:3.500A) Proline residue: Lq 121 - end of helix Processing helix chain 'Lq' and resid 122 through 130 Proline residue: Lq 126 - end of helix removed outlier: 4.722A pdb=" N LYSLq 130 " --> pdb=" O PROLq 126 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 143 through 153 removed outlier: 6.342A pdb=" N ASNLq 149 " --> pdb=" O SERLq 145 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N SERLq 153 " --> pdb=" O ASNLq 149 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 175 through 195 removed outlier: 5.286A pdb=" N LYSLq 195 " --> pdb=" O VALLq 191 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 9 through 16 removed outlier: 4.511A pdb=" N HISCc 13 " --> pdb=" O PROCc 9 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 18 through 36 removed outlier: 5.160A pdb=" N ARGCc 36 " --> pdb=" O PHECc 32 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 37 through 42 Processing helix chain 'Cc' and resid 43 through 62 removed outlier: 5.392A pdb=" N ASPCc 62 " --> pdb=" O LEUCc 58 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 63 through 82 removed outlier: 4.853A pdb=" N ILECc 78 " --> pdb=" O LEUCc 74 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TRPCc 79 " --> pdb=" O ALACc 75 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLNCc 80 " --> pdb=" O ASPCc 76 " (cutoff:3.500A) Proline residue: Cc 82 - end of helix Processing helix chain 'Cc' and resid 83 through 101 removed outlier: 4.586A pdb=" N ALACc 87 " --> pdb=" O ARGCc 83 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N THRCc 88 " --> pdb=" O GLUCc 84 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 106 through 128 removed outlier: 4.503A pdb=" N LYSCc 111 " --> pdb=" O LEUCc 107 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYSCc 128 " --> pdb=" O PHECc 124 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 151 through 165 Processing helix chain 'Cc' and resid 190 through 209 removed outlier: 5.238A pdb=" N VALCc 202 " --> pdb=" O LEUCc 198 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ASPCc 203 " --> pdb=" O ASPCc 199 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 215 through 236 Processing helix chain 'Cc' and resid 238 through 251 Processing helix chain 'Cd' and resid 13 through 18 Processing helix chain 'Cd' and resid 20 through 54 Proline residue: Cd 54 - end of helix Processing helix chain 'Cd' and resid 55 through 64 Processing helix chain 'Cd' and resid 68 through 73 Processing helix chain 'Cd' and resid 88 through 98 Processing helix chain 'Cd' and resid 180 through 188 Proline residue: Cd 188 - end of helix Processing helix chain 'Cd' and resid 211 through 223 Proline residue: Cd 223 - end of helix Processing helix chain 'Cd' and resid 240 through 252 Processing helix chain 'Cd' and resid 294 through 299 Proline residue: Cd 299 - end of helix Processing helix chain 'Cd' and resid 318 through 333 Proline residue: Cd 333 - end of helix Processing helix chain 'Cd' and resid 409 through 414 removed outlier: 5.267A pdb=" N GLUCd 414 " --> pdb=" O ARGCd 410 " (cutoff:3.500A) Processing helix chain 'Cd' and resid 424 through 429 Processing helix chain 'Ce' and resid 2 through 12 Processing helix chain 'Ce' and resid 43 through 48 removed outlier: 5.083A pdb=" N SERCe 48 " --> pdb=" O PROCe 44 " (cutoff:3.500A) Processing helix chain 'Ce' and resid 86 through 99 Processing helix chain 'Ce' and resid 102 through 134 Processing helix chain 'Ce' and resid 142 through 161 Processing helix chain 'Ce' and resid 162 through 177 Processing helix chain 'Ce' and resid 187 through 195 removed outlier: 6.253A pdb=" N LYSCe 193 " --> pdb=" O GLNCe 189 " (cutoff:3.500A) Processing helix chain 'Cf' and resid 440 through 459 Proline residue: Cf 459 - end of helix Processing helix chain 'Cf' and resid 460 through 481 Processing helix chain 'Cf' and resid 487 through 537 Processing helix chain 'Cg' and resid 45 through 60 Processing helix chain 'Cg' and resid 74 through 86 Proline residue: Cg 84 - end of helix Processing helix chain 'Cg' and resid 123 through 132 removed outlier: 5.207A pdb=" N ARGCg 132 " --> pdb=" O ARGCg 128 " (cutoff:3.500A) Processing helix chain 'Cg' and resid 138 through 144 removed outlier: 4.845A pdb=" N METCg 142 " --> pdb=" O GLYCg 138 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THRCg 143 " --> pdb=" O LYSCg 139 " (cutoff:3.500A) Proline residue: Cg 144 - end of helix No H-bonds generated for 'chain 'Cg' and resid 138 through 144' Processing helix chain 'Cg' and resid 160 through 180 Proline residue: Cg 164 - end of helix removed outlier: 5.957A pdb=" N SERCg 169 " --> pdb=" O ARGCg 165 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEUCg 170 " --> pdb=" O HISCg 166 " (cutoff:3.500A) Proline residue: Cg 180 - end of helix Processing helix chain 'Cg' and resid 188 through 193 removed outlier: 5.123A pdb=" N ARGCg 193 " --> pdb=" O LEUCg 189 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'CA' and resid 61 through 66 removed outlier: 6.665A pdb=" N LYSCA 114 " --> pdb=" O ILECA 243 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VALCA 239 " --> pdb=" O GLNCA 118 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASNCA 119 " --> pdb=" O VALCA 239 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'CA' and resid 138 through 142 removed outlier: 6.426A pdb=" N ASPCA 177 " --> pdb=" O ILECA 196 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'CA' and resid 111 through 114 Processing sheet with id= 4, first strand: chain 'CA' and resid 193 through 200 removed outlier: 7.628A pdb=" N ASNCA 193 " --> pdb=" O ILECA 234 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'CB' and resid 125 through 128 removed outlier: 3.950A pdb=" N ARGCB 126 " --> pdb=" O VALCB 97 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'CB' and resid 239 through 244 removed outlier: 5.757A pdb=" N THRCB 239 " --> pdb=" O THRCB 68 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'CC' and resid 137 through 141 Processing sheet with id= 8, first strand: chain 'CE' and resid 150 through 154 Processing sheet with id= 9, first strand: chain 'CE' and resid 213 through 217 Processing sheet with id= 10, first strand: chain 'CE' and resid 408 through 413 removed outlier: 4.023A pdb=" N GLYCE 409 " --> pdb=" O LYSCE 358 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N SERCE 458 " --> pdb=" O GLUCE 333 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N VALCE 338 " --> pdb=" O TYRCE 483 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'CF' and resid 63 through 67 removed outlier: 6.701A pdb=" N VALCF 42 " --> pdb=" O LEUCF 224 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'CF' and resid 39 through 42 Processing sheet with id= 13, first strand: chain 'CG' and resid 37 through 40 removed outlier: 6.676A pdb=" N VALCG 45 " --> pdb=" O LEUCG 71 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'CG' and resid 96 through 100 removed outlier: 4.674A pdb=" N TYRCG 96 " --> pdb=" O GLYCG 131 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'CH' and resid 203 through 209 removed outlier: 5.011A pdb=" N ARGCH 167 " --> pdb=" O ARGCH 214 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLYCH 173 " --> pdb=" O THRCH 220 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N METCH 281 " --> pdb=" O ALACH 247 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'CI' and resid 214 through 218 removed outlier: 4.712A pdb=" N VALCI 188 " --> pdb=" O VALCI 263 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'CJ' and resid 186 through 191 Processing sheet with id= 18, first strand: chain 'CJ' and resid 394 through 397 Processing sheet with id= 19, first strand: chain 'CK' and resid 190 through 195 removed outlier: 3.934A pdb=" N VALCK 191 " --> pdb=" O HISCK 186 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N TYRCK 242 " --> pdb=" O LEUCK 260 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'CL' and resid 267 through 270 removed outlier: 5.712A pdb=" N ILECL 208 " --> pdb=" O ARGCL 238 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLYCL 319 " --> pdb=" O SERCL 373 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'CM' and resid 139 through 144 removed outlier: 5.058A pdb=" N TRPCM 139 " --> pdb=" O ILECM 95 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASNCM 119 " --> pdb=" O ARGCM 94 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ASNCM 118 " --> pdb=" O LEUCM 213 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'CN' and resid 1 through 4 Processing sheet with id= 23, first strand: chain 'CN' and resid 23 through 27 Processing sheet with id= 24, first strand: chain 'CN' and resid 69 through 73 Processing sheet with id= 25, first strand: chain 'CN' and resid 114 through 117 Processing sheet with id= 26, first strand: chain 'CN' and resid 158 through 161 Processing sheet with id= 27, first strand: chain 'CP' and resid 330 through 334 removed outlier: 6.618A pdb=" N THRCP 330 " --> pdb=" O PHECP 345 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VALCP 334 " --> pdb=" O GLYCP 341 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLYCP 341 " --> pdb=" O VALCP 334 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VALCP 340 " --> pdb=" O THRCP 310 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VALCP 306 " --> pdb=" O VALCP 344 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N HISCP 361 " --> pdb=" O ASNCP 311 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'CP' and resid 432 through 438 removed outlier: 5.922A pdb=" N ASNCP 432 " --> pdb=" O GLYCP 406 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ASPCP 456 " --> pdb=" O METCP 387 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VALCP 453 " --> pdb=" O TYRCP 507 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N CYSCP 513 " --> pdb=" O ALACP 457 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ASNCP 533 " --> pdb=" O ILECP 584 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'CP' and resid 544 through 547 No H-bonds generated for sheet with id= 29 Processing sheet with id= 30, first strand: chain 'CP' and resid 563 through 568 removed outlier: 4.248A pdb=" N ARGCP 564 " --> pdb=" O VALCP 578 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VALCP 578 " --> pdb=" O ARGCP 564 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ASPCP 574 " --> pdb=" O PROCP 568 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'CQ' and resid 3 through 6 removed outlier: 4.426A pdb=" N ARGCQ 11 " --> pdb=" O CYSCQ 6 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'CQ' and resid 18 through 23 Processing sheet with id= 33, first strand: chain 'Cb' and resid 190 through 194 Processing sheet with id= 34, first strand: chain 'Cb' and resid 392 through 396 removed outlier: 7.641A pdb=" N ASPCb 503 " --> pdb=" O LEUCb 305 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N SERCb 307 " --> pdb=" O ASPCb 503 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N VALCb 505 " --> pdb=" O SERCb 307 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'LB' and resid 55 through 58 removed outlier: 4.473A pdb=" N ARGLB 335 " --> pdb=" O LYSLB 50 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ILELB 336 " --> pdb=" O VALLB 221 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VALLB 221 " --> pdb=" O ILELB 336 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N GLYLB 224 " --> pdb=" O GLYLB 272 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLYLB 272 " --> pdb=" O GLYLB 224 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'LB' and resid 84 through 87 removed outlier: 6.369A pdb=" N LEULB 162 " --> pdb=" O VALLB 87 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VALLB 158 " --> pdb=" O TYRLB 92 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLYLB 91 " --> pdb=" O LEULB 102 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'LB' and resid 285 through 288 Processing sheet with id= 38, first strand: chain 'LB' and resid 75 through 80 removed outlier: 6.851A pdb=" N ALALB 75 " --> pdb=" O GLYLB 327 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'LB' and resid 88 through 91 Processing sheet with id= 40, first strand: chain 'LB' and resid 159 through 165 removed outlier: 5.006A pdb=" N VALLB 159 " --> pdb=" O ILELB 184 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'LB' and resid 214 through 217 Processing sheet with id= 42, first strand: chain 'LC' and resid 6 through 9 removed outlier: 4.825A pdb=" N ALALC 19 " --> pdb=" O VALLC 9 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'LC' and resid 209 through 212 Processing sheet with id= 44, first strand: chain 'LE' and resid 56 through 61 removed outlier: 4.470A pdb=" N THRLE 56 " --> pdb=" O LEULE 72 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'LE' and resid 81 through 84 Processing sheet with id= 46, first strand: chain 'LF' and resid 140 through 144 removed outlier: 5.484A pdb=" N ASNLF 118 " --> pdb=" O LEULF 213 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'LG' and resid 178 through 184 Processing sheet with id= 48, first strand: chain 'LH' and resid 5 through 12 removed outlier: 6.105A pdb=" N GLYLH 51 " --> pdb=" O VALLH 12 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'LH' and resid 17 through 20 removed outlier: 6.478A pdb=" N ARGLH 23 " --> pdb=" O LEULH 38 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'LH' and resid 100 through 107 removed outlier: 4.824A pdb=" N TYRLH 112 " --> pdb=" O METLH 130 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'LH' and resid 134 through 139 removed outlier: 5.443A pdb=" N GLULH 145 " --> pdb=" O SERLH 139 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ASPLH 144 " --> pdb=" O TYRLH 92 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'LK' and resid 11 through 16 Processing sheet with id= 53, first strand: chain 'LL' and resid 56 through 59 Processing sheet with id= 54, first strand: chain 'LM' and resid 18 through 22 removed outlier: 4.851A pdb=" N ARGLM 18 " --> pdb=" O ILELM 30 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N SERLM 26 " --> pdb=" O LEULM 22 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'LM' and resid 31 through 34 removed outlier: 3.564A pdb=" N GLULM 32 " --> pdb=" O LEULM 40 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ARGLM 38 " --> pdb=" O ILELM 34 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'LN' and resid 35 through 40 removed outlier: 6.252A pdb=" N VALLN 35 " --> pdb=" O ARGLN 65 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLYLN 58 " --> pdb=" O ASPLN 136 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILELN 133 " --> pdb=" O LEULN 116 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'LN' and resid 117 through 121 removed outlier: 6.865A pdb=" N TYRLN 129 " --> pdb=" O VALLN 121 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'LO' and resid 7 through 11 Processing sheet with id= 59, first strand: chain 'LP' and resid 16 through 20 removed outlier: 6.616A pdb=" N ILELP 149 " --> pdb=" O LYSLP 115 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'LP' and resid 57 through 60 removed outlier: 5.199A pdb=" N ARGLP 80 " --> pdb=" O METLP 60 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'LP' and resid 116 through 122 Processing sheet with id= 62, first strand: chain 'LQ' and resid 146 through 149 removed outlier: 4.956A pdb=" N GLULQ 127 " --> pdb=" O LYSLQ 106 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'LS' and resid 55 through 59 removed outlier: 8.076A pdb=" N THRLS 55 " --> pdb=" O LEULS 14 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILELS 10 " --> pdb=" O VALLS 59 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLULS 6 " --> pdb=" O ILELS 64 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'LS' and resid 86 through 95 removed outlier: 3.530A pdb=" N GLYLS 86 " --> pdb=" O SERLS 83 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ASNLS 74 " --> pdb=" O LEULS 129 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'LT' and resid 39 through 42 removed outlier: 6.661A pdb=" N ILELT 39 " --> pdb=" O SERLT 99 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'LT' and resid 71 through 79 No H-bonds generated for sheet with id= 66 Processing sheet with id= 67, first strand: chain 'LV' and resid 22 through 26 Processing sheet with id= 68, first strand: chain 'LV' and resid 58 through 62 removed outlier: 4.390A pdb=" N ASPLV 58 " --> pdb=" O ILELV 80 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASPLV 99 " --> pdb=" O ALALV 84 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'LV' and resid 86 through 89 Processing sheet with id= 70, first strand: chain 'LY' and resid 55 through 58 removed outlier: 4.400A pdb=" N LYSLY 65 " --> pdb=" O ILELY 57 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'LY' and resid 71 through 74 Processing sheet with id= 72, first strand: chain 'LY' and resid 84 through 88 removed outlier: 6.756A pdb=" N VALLY 84 " --> pdb=" O ILELY 96 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLNLY 92 " --> pdb=" O LYSLY 88 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'Le' and resid 72 through 78 No H-bonds generated for sheet with id= 73 Processing sheet with id= 74, first strand: chain 'Lf' and resid 12 through 16 removed outlier: 5.867A pdb=" N LYSLf 12 " --> pdb=" O GLULf 35 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEULf 31 " --> pdb=" O LEULf 16 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARGLf 84 " --> pdb=" O THRLf 74 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ARGLf 50 " --> pdb=" O METLf 103 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'Lf' and resid 10 through 16 Processing sheet with id= 76, first strand: chain 'Lq' and resid 49 through 54 removed outlier: 6.091A pdb=" N PHELq 49 " --> pdb=" O LEULq 159 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'Lq' and resid 65 through 68 Processing sheet with id= 78, first strand: chain 'Lq' and resid 164 through 171 removed outlier: 4.348A pdb=" N VALLq 32 " --> pdb=" O VALLq 169 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASNLq 171 " --> pdb=" O GLULq 30 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N GLULq 30 " --> pdb=" O ASNLq 171 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'Cc' and resid 172 through 175 Processing sheet with id= 80, first strand: chain 'Cd' and resid 224 through 228 removed outlier: 4.835A pdb=" N THRCd 205 " --> pdb=" O ILECd 228 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLYCd 206 " --> pdb=" O VALCd 259 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLUCd 261 " --> pdb=" O GLYCd 206 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THRCd 254 " --> pdb=" O LEUCd 274 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SERCd 267 " --> pdb=" O ILECd 289 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THRCd 286 " --> pdb=" O ARGCd 402 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYSCd 400 " --> pdb=" O THRCd 288 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N THRCd 398 " --> pdb=" O ARGCd 290 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'Cd' and resid 307 through 314 removed outlier: 5.467A pdb=" N TYRCd 308 " --> pdb=" O GLYCd 340 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N GLNCd 342 " --> pdb=" O TYRCd 308 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ARGCd 341 " --> pdb=" O TYRCd 360 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARGCd 357 " --> pdb=" O ILECd 393 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARGCd 359 " --> pdb=" O GLNCd 391 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLNCd 391 " --> pdb=" O ARGCd 359 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'Cd' and resid 283 through 286 Processing sheet with id= 83, first strand: chain 'Ce' and resid 17 through 22 removed outlier: 6.899A pdb=" N PHECe 17 " --> pdb=" O ARGCe 29 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLNCe 25 " --> pdb=" O THRCe 21 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'Ce' and resid 49 through 56 removed outlier: 4.052A pdb=" N THRCe 60 " --> pdb=" O SERCe 56 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ILECe 61 " --> pdb=" O LEUCe 83 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'Cg' and resid 33 through 38 removed outlier: 5.131A pdb=" N VALCg 101 " --> pdb=" O VALCg 118 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ARGCg 117 " --> pdb=" O METCg 337 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N METCg 337 " --> pdb=" O ARGCg 117 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'Cg' and resid 216 through 223 removed outlier: 6.753A pdb=" N HISCg 216 " --> pdb=" O LEUCg 329 " (cutoff:3.500A) 4203 hydrogen bonds defined for protein. 12480 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1980 hydrogen bonds 3278 hydrogen bond angles 0 basepair planarities 784 basepair parallelities 1188 stacking parallelities Total time for adding SS restraints: 127.42 Time building geometry restraints manager: 54.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 18414 1.32 - 1.45: 49431 1.45 - 1.57: 68255 1.57 - 1.69: 4766 1.69 - 1.82: 456 Bond restraints: 141322 Sorted by residual: bond pdb=" C PROCd 280 " pdb=" O PROCd 280 " ideal model delta sigma weight residual 1.246 1.203 0.042 8.50e-03 1.38e+04 2.49e+01 bond pdb=" C VALCd 279 " pdb=" N PROCd 280 " ideal model delta sigma weight residual 1.331 1.362 -0.031 8.70e-03 1.32e+04 1.28e+01 bond pdb=" O3' CC1 480 " pdb=" P UC1 481 " ideal model delta sigma weight residual 1.607 1.658 -0.051 1.50e-02 4.44e+03 1.17e+01 bond pdb=" C SERCH 98 " pdb=" O SERCH 98 " ideal model delta sigma weight residual 1.236 1.200 0.037 1.16e-02 7.43e+03 1.02e+01 bond pdb=" N VALCd 272 " pdb=" CA VALCd 272 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.12e-02 7.97e+03 9.99e+00 ... (remaining 141317 not shown) Histogram of bond angle deviations from ideal: 81.39 - 92.22: 2 92.22 - 103.05: 5054 103.05 - 113.88: 94890 113.88 - 124.71: 91555 124.71 - 135.54: 10793 Bond angle restraints: 202294 Sorted by residual: angle pdb=" O3' UC11084 " pdb=" P AC11085 " pdb=" OP1 AC11085 " ideal model delta sigma weight residual 108.00 81.39 26.61 3.00e+00 1.11e-01 7.87e+01 angle pdb=" O3' UC11084 " pdb=" P AC11085 " pdb=" OP2 AC11085 " ideal model delta sigma weight residual 108.00 84.49 23.51 3.00e+00 1.11e-01 6.14e+01 angle pdb=" CA PROLS 170 " pdb=" N PROLS 170 " pdb=" CD PROLS 170 " ideal model delta sigma weight residual 112.00 103.20 8.80 1.40e+00 5.10e-01 3.95e+01 angle pdb=" CA ARGCf 463 " pdb=" CB ARGCf 463 " pdb=" CG ARGCf 463 " ideal model delta sigma weight residual 114.10 126.50 -12.40 2.00e+00 2.50e-01 3.84e+01 angle pdb=" CB ARGCh 331 " pdb=" CG ARGCh 331 " pdb=" CD ARGCh 331 " ideal model delta sigma weight residual 111.30 125.38 -14.08 2.30e+00 1.89e-01 3.75e+01 ... (remaining 202289 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 82273 35.84 - 71.68: 6323 71.68 - 107.52: 738 107.52 - 143.36: 15 143.36 - 179.20: 28 Dihedral angle restraints: 89377 sinusoidal: 59088 harmonic: 30289 Sorted by residual: dihedral pdb=" CA ARGLq 60 " pdb=" C ARGLq 60 " pdb=" N PROLq 61 " pdb=" CA PROLq 61 " ideal model delta harmonic sigma weight residual -180.00 -128.15 -51.85 0 5.00e+00 4.00e-02 1.08e+02 dihedral pdb=" C4' AC1 702 " pdb=" C3' AC1 702 " pdb=" C2' AC1 702 " pdb=" C1' AC1 702 " ideal model delta sinusoidal sigma weight residual -35.00 34.88 -69.88 1 8.00e+00 1.56e-02 9.84e+01 dihedral pdb=" CA HISCL 223 " pdb=" C HISCL 223 " pdb=" N ASPCL 224 " pdb=" CA ASPCL 224 " ideal model delta harmonic sigma weight residual 180.00 131.29 48.71 0 5.00e+00 4.00e-02 9.49e+01 ... (remaining 89374 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.407: 24460 0.407 - 0.814: 0 0.814 - 1.222: 0 1.222 - 1.629: 0 1.629 - 2.036: 1 Chirality restraints: 24461 Sorted by residual: chirality pdb=" P AC11085 " pdb=" OP1 AC11085 " pdb=" OP2 AC11085 " pdb=" O5' AC11085 " both_signs ideal model delta sigma weight residual True 2.41 0.37 2.04 2.00e-01 2.50e+01 1.04e+02 chirality pdb=" CB VALCH 69 " pdb=" CA VALCH 69 " pdb=" CG1 VALCH 69 " pdb=" CG2 VALCH 69 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" CA ASPLG 161 " pdb=" N ASPLG 161 " pdb=" C ASPLG 161 " pdb=" CB ASPLG 161 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 24458 not shown) Planarity restraints: 16966 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARGLS 169 " 0.092 5.00e-02 4.00e+02 1.33e-01 2.83e+01 pdb=" N PROLS 170 " -0.230 5.00e-02 4.00e+02 pdb=" CA PROLS 170 " 0.069 5.00e-02 4.00e+02 pdb=" CD PROLS 170 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLNCb 446 " 0.086 5.00e-02 4.00e+02 1.25e-01 2.51e+01 pdb=" N PROCb 447 " -0.217 5.00e-02 4.00e+02 pdb=" CA PROCb 447 " 0.065 5.00e-02 4.00e+02 pdb=" CD PROCb 447 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASPCB 103 " 0.080 5.00e-02 4.00e+02 1.24e-01 2.45e+01 pdb=" N PROCB 104 " -0.214 5.00e-02 4.00e+02 pdb=" CA PROCB 104 " 0.069 5.00e-02 4.00e+02 pdb=" CD PROCB 104 " 0.066 5.00e-02 4.00e+02 ... (remaining 16963 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 1084 2.55 - 3.14: 102154 3.14 - 3.73: 241639 3.73 - 4.31: 326547 4.31 - 4.90: 478719 Nonbonded interactions: 1150143 Sorted by model distance: nonbonded pdb=" O4 UC11055 " pdb=" C4 CC11063 " model vdw 1.963 3.260 nonbonded pdb=" O SERLE 156 " pdb=" O ALALE 159 " model vdw 1.981 2.432 nonbonded pdb=" OE2 GLUCd 310 " pdb=" OH TYRCd 360 " model vdw 2.007 2.440 nonbonded pdb=" O6 GC1 974 " pdb=" O4 UC11038 " model vdw 2.039 2.432 nonbonded pdb=" O2 UC12389 " pdb=" O6 GC12560 " model vdw 2.054 2.432 ... (remaining 1150138 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.180 Extract box with map and model: 18.540 Check model and map are aligned: 1.430 Set scattering table: 0.910 Process input model: 420.020 Find NCS groups from input model: 3.580 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 450.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 141322 Z= 0.193 Angle : 0.701 26.615 202294 Z= 0.387 Chirality : 0.042 2.036 24461 Planarity : 0.007 0.133 16966 Dihedral : 20.776 179.200 69737 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.69 % Favored : 95.12 % Rotamer: Outliers : 0.17 % Allowed : 0.38 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.02 % Twisted Proline : 0.56 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.08), residues: 10278 helix: 1.01 (0.08), residues: 4585 sheet: -0.25 (0.14), residues: 1286 loop : -0.83 (0.09), residues: 4407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRPCe 191 HIS 0.009 0.001 HISCA 169 PHE 0.041 0.002 PHECN 34 TYR 0.041 0.002 TYRLO 170 ARG 0.034 0.001 ARGCh 331 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20556 Ramachandran restraints generated. 10278 Oldfield, 0 Emsley, 10278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20556 Ramachandran restraints generated. 10278 Oldfield, 0 Emsley, 10278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3587 residues out of total 8922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 3572 time to evaluate : 8.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CA 67 LYS cc_start: 0.7163 (mttp) cc_final: 0.6680 (mttm) REVERT: CA 76 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7091 (tp30) REVERT: CA 80 LEU cc_start: 0.8559 (tp) cc_final: 0.8074 (mp) REVERT: CA 107 VAL cc_start: 0.9170 (t) cc_final: 0.8961 (t) REVERT: CA 122 THR cc_start: 0.8897 (p) cc_final: 0.8633 (p) REVERT: CA 131 ASN cc_start: 0.7820 (t0) cc_final: 0.7572 (t0) REVERT: CA 157 GLU cc_start: 0.8575 (mm-30) cc_final: 0.7055 (mm-30) REVERT: CA 229 ILE cc_start: 0.9032 (mt) cc_final: 0.8762 (mt) REVERT: CA 259 LYS cc_start: 0.8349 (mmtt) cc_final: 0.8146 (mtmt) REVERT: CA 262 ILE cc_start: 0.8024 (mp) cc_final: 0.7632 (tp) REVERT: CA 284 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7521 (mt-10) REVERT: CB 33 HIS cc_start: 0.8048 (t-170) cc_final: 0.7796 (t70) REVERT: CB 98 CYS cc_start: 0.8185 (t) cc_final: 0.7982 (t) REVERT: CB 147 PHE cc_start: 0.8640 (t80) cc_final: 0.8397 (t80) REVERT: CB 282 TYR cc_start: 0.5602 (m-80) cc_final: 0.5326 (m-80) REVERT: CC 121 PHE cc_start: 0.7699 (m-80) cc_final: 0.6943 (m-10) REVERT: CC 137 TYR cc_start: 0.8412 (p90) cc_final: 0.8149 (p90) REVERT: CC 276 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7455 (tt0) REVERT: CC 287 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7205 (tt0) REVERT: CC 408 MET cc_start: 0.9308 (mtm) cc_final: 0.8787 (mtt) REVERT: CE 138 GLN cc_start: 0.8407 (mt0) cc_final: 0.7961 (mt0) REVERT: CE 246 ASP cc_start: 0.7970 (t70) cc_final: 0.7409 (t0) REVERT: CE 255 PHE cc_start: 0.7890 (p90) cc_final: 0.7668 (p90) REVERT: CE 573 TYR cc_start: 0.7476 (t80) cc_final: 0.7190 (t80) REVERT: CF 11 HIS cc_start: 0.7284 (m-70) cc_final: 0.7058 (m-70) REVERT: CF 159 HIS cc_start: 0.8697 (p-80) cc_final: 0.8488 (p90) REVERT: CF 228 ASN cc_start: 0.7217 (t0) cc_final: 0.6880 (t0) REVERT: CG 82 LEU cc_start: 0.8383 (pt) cc_final: 0.8124 (pp) REVERT: CG 149 ARG cc_start: 0.7273 (pmt170) cc_final: 0.6789 (pmt170) REVERT: CH 36 PHE cc_start: 0.5927 (m-10) cc_final: 0.4710 (m-80) REVERT: CH 69 VAL cc_start: 0.8879 (OUTLIER) cc_final: 0.8365 (m) REVERT: CH 150 ASP cc_start: 0.8735 (t0) cc_final: 0.8288 (t0) REVERT: CH 165 THR cc_start: 0.7993 (p) cc_final: 0.7681 (p) REVERT: CH 231 MET cc_start: 0.8431 (mmt) cc_final: 0.8134 (mmt) REVERT: CH 236 MET cc_start: 0.8479 (mmm) cc_final: 0.7981 (tpp) REVERT: CH 297 LEU cc_start: 0.7295 (pt) cc_final: 0.7031 (pt) REVERT: CH 389 ASN cc_start: 0.7483 (p0) cc_final: 0.7278 (p0) REVERT: CI 189 MET cc_start: 0.7564 (ttp) cc_final: 0.7233 (ttt) REVERT: CI 242 ASP cc_start: 0.8048 (m-30) cc_final: 0.7775 (m-30) REVERT: CJ 24 LYS cc_start: 0.8342 (mttt) cc_final: 0.7943 (tppt) REVERT: CJ 173 HIS cc_start: 0.6429 (m170) cc_final: 0.5182 (m-70) REVERT: CJ 196 TYR cc_start: 0.8645 (m-80) cc_final: 0.8279 (m-80) REVERT: CJ 225 ARG cc_start: 0.8448 (mtm180) cc_final: 0.7826 (ttt-90) REVERT: CJ 462 TRP cc_start: 0.8395 (t-100) cc_final: 0.8041 (t-100) REVERT: CK 13 LEU cc_start: 0.9025 (mt) cc_final: 0.8807 (mm) REVERT: CK 36 SER cc_start: 0.7394 (t) cc_final: 0.6982 (p) REVERT: CK 67 GLN cc_start: 0.8096 (mt0) cc_final: 0.7751 (tm-30) REVERT: CK 201 LYS cc_start: 0.8496 (mmpt) cc_final: 0.8288 (mttp) REVERT: CK 206 ASN cc_start: 0.8824 (t0) cc_final: 0.8230 (m-40) REVERT: CL 23 LYS cc_start: 0.7328 (ttmm) cc_final: 0.6702 (tttp) REVERT: CM 89 LEU cc_start: 0.8211 (tp) cc_final: 0.7922 (tp) REVERT: CM 175 ILE cc_start: 0.7647 (mm) cc_final: 0.7396 (mm) REVERT: CM 211 PHE cc_start: 0.8487 (m-80) cc_final: 0.7525 (m-80) REVERT: CM 240 HIS cc_start: 0.8642 (m90) cc_final: 0.7727 (m90) REVERT: CN 93 ARG cc_start: 0.7642 (mtp180) cc_final: 0.7401 (mtp-110) REVERT: CN 136 GLU cc_start: 0.7280 (pp20) cc_final: 0.6238 (pp20) REVERT: CN 176 LEU cc_start: 0.9087 (pp) cc_final: 0.8816 (tp) REVERT: CN 237 MET cc_start: 0.8726 (mpp) cc_final: 0.8497 (mpp) REVERT: CO 3 LYS cc_start: 0.7425 (mmmt) cc_final: 0.7046 (mtmm) REVERT: CO 87 SER cc_start: 0.7233 (p) cc_final: 0.6883 (m) REVERT: CP 265 GLN cc_start: 0.8457 (tp40) cc_final: 0.8122 (tm-30) REVERT: CP 269 ASP cc_start: 0.7346 (m-30) cc_final: 0.6413 (m-30) REVERT: CP 284 LEU cc_start: 0.9190 (mt) cc_final: 0.8920 (tt) REVERT: CP 374 MET cc_start: 0.7953 (mtp) cc_final: 0.7621 (mtp) REVERT: CP 439 ASP cc_start: 0.6941 (t0) cc_final: 0.5960 (t0) REVERT: CP 459 CYS cc_start: 0.9126 (p) cc_final: 0.8892 (p) REVERT: CP 574 ASP cc_start: 0.7901 (m-30) cc_final: 0.7644 (m-30) REVERT: CQ 8 PHE cc_start: 0.8452 (t80) cc_final: 0.7711 (t80) REVERT: CQ 34 SER cc_start: 0.8563 (p) cc_final: 0.8313 (t) REVERT: CQ 45 ASN cc_start: 0.8434 (t0) cc_final: 0.7571 (t0) REVERT: CQ 51 TRP cc_start: 0.8091 (p-90) cc_final: 0.7654 (p-90) REVERT: CR 18 ARG cc_start: 0.7572 (ttm-80) cc_final: 0.7296 (ttt180) REVERT: CR 73 LEU cc_start: 0.5466 (tp) cc_final: 0.5231 (tp) REVERT: CR 151 LEU cc_start: 0.8238 (mp) cc_final: 0.7958 (mt) REVERT: CS 475 MET cc_start: 0.7917 (mtt) cc_final: 0.7541 (mtp) REVERT: CU 217 HIS cc_start: 0.8020 (p90) cc_final: 0.7817 (p-80) REVERT: CU 219 SER cc_start: 0.9388 (p) cc_final: 0.8110 (p) REVERT: CU 233 ILE cc_start: 0.9030 (mt) cc_final: 0.8473 (tp) REVERT: CU 288 LYS cc_start: 0.8670 (ttmt) cc_final: 0.8409 (ttmt) REVERT: CU 360 VAL cc_start: 0.8287 (t) cc_final: 0.7959 (t) REVERT: CU 369 ASP cc_start: 0.6786 (m-30) cc_final: 0.6276 (m-30) REVERT: CX 75 ASN cc_start: 0.8541 (t0) cc_final: 0.8282 (t0) REVERT: Cb 3 LYS cc_start: 0.7170 (ptpp) cc_final: 0.6510 (mmtt) REVERT: Cb 225 LYS cc_start: 0.9488 (tttt) cc_final: 0.9277 (pttm) REVERT: Cb 241 ASP cc_start: 0.8951 (t0) cc_final: 0.8677 (t0) REVERT: Cb 249 MET cc_start: 0.8806 (mmp) cc_final: 0.8004 (ttm) REVERT: Cb 309 PHE cc_start: 0.8911 (m-80) cc_final: 0.8583 (m-80) REVERT: Cb 323 HIS cc_start: 0.8444 (t70) cc_final: 0.8165 (t70) REVERT: Cb 412 PHE cc_start: 0.8039 (t80) cc_final: 0.7791 (t80) REVERT: Cb 420 LEU cc_start: 0.9599 (tp) cc_final: 0.9389 (tp) REVERT: Ch 295 ASN cc_start: 0.8442 (p0) cc_final: 0.8075 (m-40) REVERT: Ch 331 ARG cc_start: 0.7951 (mpp-170) cc_final: 0.7494 (ptt180) REVERT: LB 135 LYS cc_start: 0.8415 (mtmt) cc_final: 0.8215 (tttt) REVERT: LB 168 ARG cc_start: 0.8004 (ptt90) cc_final: 0.7492 (ppt90) REVERT: LC 46 ASN cc_start: 0.5829 (m-40) cc_final: 0.5502 (m-40) REVERT: LC 56 LYS cc_start: 0.6775 (mtmt) cc_final: 0.5920 (mmtm) REVERT: LC 224 LYS cc_start: 0.6103 (mtmm) cc_final: 0.5783 (mttm) REVERT: LC 283 SER cc_start: 0.7890 (m) cc_final: 0.7553 (m) REVERT: LC 304 LYS cc_start: 0.7811 (mttp) cc_final: 0.7525 (tttt) REVERT: LC 343 GLU cc_start: 0.7498 (pt0) cc_final: 0.7275 (pt0) REVERT: LC 350 LYS cc_start: 0.8803 (ttpt) cc_final: 0.8452 (ttpp) REVERT: LE 56 THR cc_start: 0.9503 (m) cc_final: 0.9295 (m) REVERT: LF 134 LYS cc_start: 0.8485 (tttt) cc_final: 0.8137 (tptt) REVERT: LF 174 ILE cc_start: 0.8171 (mt) cc_final: 0.7882 (mt) REVERT: LG 112 LEU cc_start: 0.9358 (mm) cc_final: 0.9112 (mp) REVERT: LG 148 ASN cc_start: 0.8281 (m-40) cc_final: 0.7716 (m-40) REVERT: LG 232 THR cc_start: 0.7131 (t) cc_final: 0.6882 (t) REVERT: LH 173 ASP cc_start: 0.8262 (t0) cc_final: 0.7491 (t70) REVERT: LK 129 VAL cc_start: 0.8265 (t) cc_final: 0.8032 (t) REVERT: LL 55 ARG cc_start: 0.8104 (mtt-85) cc_final: 0.7658 (mtt-85) REVERT: LL 87 ARG cc_start: 0.7784 (ttt90) cc_final: 0.7553 (ttt180) REVERT: LM 5 ASN cc_start: 0.8074 (m110) cc_final: 0.7818 (m-40) REVERT: LN 106 VAL cc_start: 0.7717 (t) cc_final: 0.7451 (t) REVERT: LO 32 GLN cc_start: 0.8003 (tp40) cc_final: 0.7753 (tp40) REVERT: LO 204 TYR cc_start: 0.7636 (m-80) cc_final: 0.6662 (m-80) REVERT: LP 3 ARG cc_start: 0.6237 (ptm160) cc_final: 0.5911 (ttp-170) REVERT: LP 74 LYS cc_start: 0.7793 (mtpt) cc_final: 0.7315 (pptt) REVERT: LP 89 GLN cc_start: 0.8148 (tm-30) cc_final: 0.7677 (tt0) REVERT: LQ 45 LYS cc_start: 0.6854 (mmtm) cc_final: 0.6571 (pttp) REVERT: LQ 113 THR cc_start: 0.9272 (m) cc_final: 0.8878 (p) REVERT: LQ 132 ARG cc_start: 0.7659 (ttp80) cc_final: 0.7429 (ttp80) REVERT: LQ 147 ARG cc_start: 0.7027 (mtp-110) cc_final: 0.6744 (ttm-80) REVERT: LS 27 MET cc_start: 0.8665 (mtm) cc_final: 0.8457 (mtp) REVERT: LS 65 SER cc_start: 0.8614 (m) cc_final: 0.8381 (t) REVERT: LS 81 TYR cc_start: 0.8093 (p90) cc_final: 0.7273 (p90) REVERT: LS 96 GLU cc_start: 0.7627 (mp0) cc_final: 0.6519 (mp0) REVERT: LS 141 LYS cc_start: 0.8509 (ttmt) cc_final: 0.8302 (tttm) REVERT: LT 43 LYS cc_start: 0.8363 (tttt) cc_final: 0.8126 (tptt) REVERT: LT 52 MET cc_start: 0.5152 (ptm) cc_final: 0.3545 (mtt) REVERT: LT 75 ILE cc_start: 0.8446 (mt) cc_final: 0.7552 (mt) REVERT: LT 99 SER cc_start: 0.8434 (t) cc_final: 0.7820 (m) REVERT: LT 104 ASP cc_start: 0.9037 (t0) cc_final: 0.8711 (t0) REVERT: LT 107 ARG cc_start: 0.8773 (ttp80) cc_final: 0.8514 (ttt-90) REVERT: LT 116 LYS cc_start: 0.8786 (ttmt) cc_final: 0.8001 (tptt) REVERT: LV 70 GLU cc_start: 0.7735 (tp30) cc_final: 0.7526 (tp30) REVERT: LV 86 PRO cc_start: 0.8975 (Cg_exo) cc_final: 0.8623 (Cg_endo) REVERT: LV 122 LYS cc_start: 0.7639 (mmtp) cc_final: 0.7344 (mmmt) REVERT: LY 7 VAL cc_start: 0.8664 (t) cc_final: 0.8384 (m) REVERT: LY 46 SER cc_start: 0.8857 (p) cc_final: 0.8647 (p) REVERT: LY 93 THR cc_start: 0.7670 (p) cc_final: 0.7387 (p) REVERT: Le 6 LYS cc_start: 0.7890 (ttmm) cc_final: 0.7093 (tptt) REVERT: Le 31 SER cc_start: 0.7733 (p) cc_final: 0.7342 (p) REVERT: Le 114 LYS cc_start: 0.8602 (tptt) cc_final: 0.8373 (tttt) REVERT: Lf 60 GLU cc_start: 0.7333 (mt-10) cc_final: 0.7009 (mt-10) REVERT: Lh 16 ASN cc_start: 0.7463 (p0) cc_final: 0.6670 (p0) REVERT: Lh 29 THR cc_start: 0.9072 (p) cc_final: 0.8382 (p) REVERT: Li 59 LEU cc_start: 0.8751 (mt) cc_final: 0.8532 (mp) REVERT: Lq 63 MET cc_start: 0.6753 (mpp) cc_final: 0.6462 (mpp) REVERT: Lq 99 LEU cc_start: 0.9273 (mt) cc_final: 0.9068 (pp) REVERT: Lq 188 ASN cc_start: 0.8490 (m-40) cc_final: 0.8188 (m-40) REVERT: Cc 18 ASP cc_start: 0.7935 (t0) cc_final: 0.7646 (t0) REVERT: Cc 37 GLN cc_start: 0.7438 (mm110) cc_final: 0.6630 (tm-30) REVERT: Cc 46 ASP cc_start: 0.8342 (m-30) cc_final: 0.8126 (m-30) REVERT: Cc 157 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7954 (mm-30) REVERT: Cc 165 TRP cc_start: 0.8390 (m100) cc_final: 0.7593 (m100) REVERT: Cc 166 PRO cc_start: 0.8286 (Cg_exo) cc_final: 0.7939 (Cg_endo) REVERT: Cc 230 ASP cc_start: 0.8511 (t0) cc_final: 0.7601 (t0) REVERT: Cc 234 GLN cc_start: 0.7874 (mp10) cc_final: 0.7153 (mp10) REVERT: Cd 76 ASP cc_start: 0.6649 (m-30) cc_final: 0.5924 (m-30) REVERT: Cd 224 ASN cc_start: 0.7402 (t0) cc_final: 0.7175 (t0) REVERT: Cd 242 ARG cc_start: 0.8195 (mtp85) cc_final: 0.7823 (mtm180) REVERT: Cd 260 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7827 (mt0) REVERT: Cd 267 SER cc_start: 0.7986 (OUTLIER) cc_final: 0.7562 (t) REVERT: Cd 288 THR cc_start: 0.8054 (OUTLIER) cc_final: 0.7841 (p) REVERT: Cd 343 VAL cc_start: 0.8919 (m) cc_final: 0.8366 (p) REVERT: Cd 429 LYS cc_start: 0.7573 (mtpp) cc_final: 0.6801 (mttt) REVERT: Cd 433 ARG cc_start: 0.8467 (mmm160) cc_final: 0.8107 (tpt170) REVERT: Ce 96 GLN cc_start: 0.8336 (mp10) cc_final: 0.8001 (mp10) REVERT: Ce 149 GLU cc_start: 0.7689 (mp0) cc_final: 0.6831 (mp0) REVERT: Ce 185 ASN cc_start: 0.8350 (m110) cc_final: 0.7738 (m110) REVERT: Cf 446 MET cc_start: 0.2948 (ttt) cc_final: 0.2624 (ptm) REVERT: Cg 90 LEU cc_start: 0.8994 (tp) cc_final: 0.8577 (tp) REVERT: Cg 105 LEU cc_start: 0.9271 (tp) cc_final: 0.9033 (pp) REVERT: Cg 116 PHE cc_start: 0.8388 (m-80) cc_final: 0.8164 (m-80) REVERT: Cg 151 ASN cc_start: 0.7723 (m-40) cc_final: 0.7503 (m-40) REVERT: Cg 162 LYS cc_start: 0.8334 (ptpp) cc_final: 0.7764 (pttp) REVERT: Cg 209 LYS cc_start: 0.5479 (mmpt) cc_final: 0.4654 (mtmm) REVERT: Cg 333 MET cc_start: 0.8948 (tpt) cc_final: 0.8517 (mpp) REVERT: Cg 335 LEU cc_start: 0.8578 (mt) cc_final: 0.8242 (mt) outliers start: 15 outliers final: 2 residues processed: 3579 average time/residue: 1.2942 time to fit residues: 7760.4268 Evaluate side-chains 1995 residues out of total 8922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1989 time to evaluate : 8.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CH residue 69 VAL Chi-restraints excluded: chain LM residue 131 GLU Chi-restraints excluded: chain Cd residue 260 GLN Chi-restraints excluded: chain Cd residue 267 SER Chi-restraints excluded: chain Cd residue 288 THR Chi-restraints excluded: chain Cd residue 290 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1262 random chunks: chunk 1065 optimal weight: 5.9990 chunk 956 optimal weight: 6.9990 chunk 530 optimal weight: 10.0000 chunk 326 optimal weight: 2.9990 chunk 645 optimal weight: 3.9990 chunk 511 optimal weight: 10.0000 chunk 989 optimal weight: 3.9990 chunk 382 optimal weight: 9.9990 chunk 601 optimal weight: 10.0000 chunk 736 optimal weight: 40.0000 chunk 1146 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 25 ASN CA 48 HIS ** CA 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 285 GLN CB 73 HIS CB 105 GLN CB 213 ASN ** CB 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 174 ASN CC 286 ASN CE 182 ASN CE 210 HIS ** CE 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CE 250 ASN ** CE 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CF 51 ASN ** CG 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CH 151 GLN ** CH 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CH 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 15 ASN CJ 54 ASN ** CJ 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 124 ASN CJ 183 HIS ** CJ 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CK 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CK 203 ASN CM 110 GLN CN 9 ASN CN 83 HIS ** CN 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CP 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CP 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CP 485 HIS CR 28 ASN ** CR 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CU 232 GLN CU 287 GLN CU 305 GLN CU 335 ASN CU 336 GLN LB 68 HIS LB 178 HIS ** LB 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LB 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LB 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LC 60 GLN LC 84 HIS LC 142 GLN ** LE 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 10 ASN LF 118 ASN LG 194 HIS LH 35 GLN LH 76 ASN ** LH 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LK 100 HIS LL 17 HIS LL 25 HIS LN 194 HIS LN 195 ASN LO 43 ASN LP 28 ASN ** LQ 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 98 ASN ** LS 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LV 30 ASN LV 100 ASN LY 116 ASN Li 72 ASN ** Lq 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cc 187 GLN ** Cc 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cd 25 GLN Cd 26 GLN Cd 263 GLN Cd 315 ASN Ce 12 GLN Cf 524 GLN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 141322 Z= 0.395 Angle : 0.766 27.907 202294 Z= 0.388 Chirality : 0.046 1.902 24461 Planarity : 0.007 0.151 16966 Dihedral : 22.221 177.459 48701 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.91 % Favored : 94.86 % Rotamer: Outliers : 3.65 % Allowed : 14.70 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.02 % Twisted Proline : 0.38 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.08), residues: 10278 helix: 1.02 (0.08), residues: 4595 sheet: -0.18 (0.14), residues: 1338 loop : -0.92 (0.09), residues: 4345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRPCI 302 HIS 0.014 0.002 HISCK 55 PHE 0.038 0.003 PHECh 334 TYR 0.037 0.003 TYRLG 58 ARG 0.014 0.001 ARGCc 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20556 Ramachandran restraints generated. 10278 Oldfield, 0 Emsley, 10278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20556 Ramachandran restraints generated. 10278 Oldfield, 0 Emsley, 10278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2305 residues out of total 8922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 316 poor density : 1989 time to evaluate : 8.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CA 76 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7517 (tp30) REVERT: CA 246 GLN cc_start: 0.9183 (pt0) cc_final: 0.8951 (pt0) REVERT: CA 262 ILE cc_start: 0.8111 (mp) cc_final: 0.7615 (tt) REVERT: CB 147 PHE cc_start: 0.8755 (t80) cc_final: 0.8461 (t80) REVERT: CC 137 TYR cc_start: 0.8290 (p90) cc_final: 0.7857 (p90) REVERT: CC 147 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8269 (tt) REVERT: CC 193 LYS cc_start: 0.9015 (pptt) cc_final: 0.8766 (pptt) REVERT: CC 194 LYS cc_start: 0.8526 (ptpp) cc_final: 0.8224 (mttp) REVERT: CC 381 ASP cc_start: 0.8592 (m-30) cc_final: 0.8119 (p0) REVERT: CC 408 MET cc_start: 0.9311 (mtm) cc_final: 0.8803 (mtt) REVERT: CE 226 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7994 (mt-10) REVERT: CE 255 PHE cc_start: 0.8140 (p90) cc_final: 0.7858 (p90) REVERT: CF 41 PHE cc_start: 0.7391 (m-80) cc_final: 0.7000 (m-80) REVERT: CF 115 TYR cc_start: 0.8338 (t80) cc_final: 0.7986 (t80) REVERT: CF 228 ASN cc_start: 0.7264 (t0) cc_final: 0.6771 (t0) REVERT: CG 121 ARG cc_start: 0.7496 (mpp-170) cc_final: 0.7087 (mpp-170) REVERT: CH 139 ILE cc_start: 0.8972 (mm) cc_final: 0.8664 (mm) REVERT: CH 150 ASP cc_start: 0.8759 (t0) cc_final: 0.8428 (t0) REVERT: CH 231 MET cc_start: 0.8413 (mmt) cc_final: 0.7087 (mmt) REVERT: CH 236 MET cc_start: 0.8566 (mmm) cc_final: 0.8053 (tpp) REVERT: CH 361 LEU cc_start: 0.8803 (tp) cc_final: 0.8535 (tp) REVERT: CI 191 ILE cc_start: 0.9390 (tt) cc_final: 0.9130 (tt) REVERT: CI 223 LYS cc_start: 0.8742 (mttm) cc_final: 0.8516 (mttm) REVERT: CI 243 ILE cc_start: 0.9514 (mm) cc_final: 0.9215 (tt) REVERT: CI 288 MET cc_start: 0.8520 (mtm) cc_final: 0.8263 (mtt) REVERT: CJ 24 LYS cc_start: 0.8321 (mttt) cc_final: 0.7936 (tppt) REVERT: CJ 111 ASN cc_start: 0.6815 (m110) cc_final: 0.6128 (t0) REVERT: CJ 124 ASN cc_start: 0.1802 (OUTLIER) cc_final: 0.1470 (m110) REVERT: CJ 164 MET cc_start: 0.8424 (ptm) cc_final: 0.8120 (ppp) REVERT: CJ 196 TYR cc_start: 0.8700 (m-80) cc_final: 0.8317 (m-80) REVERT: CK 36 SER cc_start: 0.7786 (t) cc_final: 0.7472 (p) REVERT: CK 37 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7434 (tt0) REVERT: CK 67 GLN cc_start: 0.8264 (mt0) cc_final: 0.7703 (tm-30) REVERT: CK 132 MET cc_start: 0.6510 (ttm) cc_final: 0.6285 (tpt) REVERT: CK 201 LYS cc_start: 0.8703 (mmpt) cc_final: 0.8332 (mtmt) REVERT: CK 212 LEU cc_start: 0.9608 (OUTLIER) cc_final: 0.9273 (mm) REVERT: CL 23 LYS cc_start: 0.7533 (ttmm) cc_final: 0.6710 (tptt) REVERT: CM 209 TRP cc_start: 0.7998 (m100) cc_final: 0.7587 (m100) REVERT: CN 57 ARG cc_start: 0.7992 (ttm-80) cc_final: 0.7676 (mtp85) REVERT: CN 147 LEU cc_start: 0.7934 (mt) cc_final: 0.7513 (mt) REVERT: CN 180 PRO cc_start: 0.8398 (Cg_exo) cc_final: 0.8132 (Cg_endo) REVERT: CN 245 PHE cc_start: 0.8997 (m-80) cc_final: 0.8671 (m-80) REVERT: CO 3 LYS cc_start: 0.7511 (mmmt) cc_final: 0.7274 (mttt) REVERT: CP 314 ARG cc_start: 0.8382 (mtm-85) cc_final: 0.7754 (mtm180) REVERT: CP 316 HIS cc_start: 0.8898 (t-90) cc_final: 0.8689 (t-90) REVERT: CP 374 MET cc_start: 0.7905 (mtp) cc_final: 0.7624 (mtp) REVERT: CP 402 MET cc_start: 0.6386 (ptp) cc_final: 0.5916 (ptt) REVERT: CP 574 ASP cc_start: 0.7951 (m-30) cc_final: 0.7649 (m-30) REVERT: CP 581 PHE cc_start: 0.7778 (m-80) cc_final: 0.7522 (m-80) REVERT: CQ 8 PHE cc_start: 0.8748 (t80) cc_final: 0.8211 (t80) REVERT: CQ 25 ASP cc_start: 0.8231 (p0) cc_final: 0.7785 (p0) REVERT: CQ 45 ASN cc_start: 0.8567 (t0) cc_final: 0.7757 (t0) REVERT: CQ 55 TYR cc_start: 0.8837 (t80) cc_final: 0.8483 (t80) REVERT: CQ 93 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.7227 (mmt) REVERT: CR 18 ARG cc_start: 0.8107 (ttm-80) cc_final: 0.7501 (ttt180) REVERT: CR 21 ASN cc_start: 0.8497 (t0) cc_final: 0.8256 (t0) REVERT: CR 73 LEU cc_start: 0.5618 (tp) cc_final: 0.5292 (tp) REVERT: CR 135 GLN cc_start: 0.7714 (tm-30) cc_final: 0.7505 (tm-30) REVERT: CR 201 LYS cc_start: 0.9058 (tptp) cc_final: 0.8834 (tptp) REVERT: CS 475 MET cc_start: 0.7997 (mtt) cc_final: 0.7707 (mtp) REVERT: CU 217 HIS cc_start: 0.7959 (p90) cc_final: 0.7493 (p-80) REVERT: CU 219 SER cc_start: 0.9370 (p) cc_final: 0.8022 (p) REVERT: CU 235 ASP cc_start: 0.8753 (t0) cc_final: 0.8430 (t0) REVERT: Cz 55 ARG cc_start: 0.8332 (mmm-85) cc_final: 0.8088 (mmm-85) REVERT: Cb 110 PHE cc_start: 0.7736 (m-80) cc_final: 0.7305 (t80) REVERT: Cb 228 MET cc_start: 0.7119 (mmp) cc_final: 0.6770 (mmp) REVERT: Cb 249 MET cc_start: 0.8819 (mmp) cc_final: 0.7969 (ttm) REVERT: Cb 381 TYR cc_start: 0.8835 (t80) cc_final: 0.8579 (t80) REVERT: Cb 413 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7057 (mtt-85) REVERT: Cb 546 MET cc_start: 0.8278 (tpp) cc_final: 0.8063 (tpt) REVERT: Cb 559 ARG cc_start: 0.7878 (mtm-85) cc_final: 0.7556 (ptp-170) REVERT: Cb 561 ARG cc_start: 0.6114 (mtt-85) cc_final: 0.5834 (mtt90) REVERT: Cb 866 TYR cc_start: 0.7542 (t80) cc_final: 0.7129 (t80) REVERT: Ch 295 ASN cc_start: 0.8309 (p0) cc_final: 0.7861 (m-40) REVERT: LB 119 TYR cc_start: 0.8246 (m-80) cc_final: 0.8046 (m-80) REVERT: LB 135 LYS cc_start: 0.8605 (mtmt) cc_final: 0.8286 (mmmt) REVERT: LC 56 LYS cc_start: 0.6687 (mtmt) cc_final: 0.5575 (mmtm) REVERT: LC 137 MET cc_start: 0.8335 (mpp) cc_final: 0.7850 (mtm) REVERT: LC 283 SER cc_start: 0.8278 (m) cc_final: 0.8024 (m) REVERT: LC 301 ARG cc_start: 0.7746 (ptt90) cc_final: 0.7496 (ptt90) REVERT: LC 304 LYS cc_start: 0.8148 (mttp) cc_final: 0.7876 (tttt) REVERT: LC 327 LEU cc_start: 0.8562 (mt) cc_final: 0.8322 (mp) REVERT: LC 350 LYS cc_start: 0.8844 (ttpt) cc_final: 0.8515 (ttpp) REVERT: LE 33 GLU cc_start: 0.6975 (tm-30) cc_final: 0.6240 (tp30) REVERT: LE 56 THR cc_start: 0.9451 (m) cc_final: 0.9202 (m) REVERT: LE 101 TYR cc_start: 0.9006 (m-80) cc_final: 0.8800 (m-80) REVERT: LF 134 LYS cc_start: 0.8724 (tttt) cc_final: 0.8318 (tptt) REVERT: LF 172 ASN cc_start: 0.8487 (m-40) cc_final: 0.7836 (p0) REVERT: LG 64 GLN cc_start: 0.8641 (mt0) cc_final: 0.8422 (mt0) REVERT: LH 100 ASN cc_start: 0.8494 (t0) cc_final: 0.8271 (t0) REVERT: LH 170 ARG cc_start: 0.8038 (mtp180) cc_final: 0.7619 (ttp80) REVERT: LH 173 ASP cc_start: 0.8512 (t0) cc_final: 0.8211 (t70) REVERT: LH 176 LYS cc_start: 0.8538 (tptt) cc_final: 0.8306 (tppt) REVERT: LK 121 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.7920 (t80) REVERT: LN 41 ARG cc_start: 0.7667 (ptp-110) cc_final: 0.7459 (ptp-110) REVERT: LN 140 LYS cc_start: 0.8204 (pttt) cc_final: 0.7973 (ttpt) REVERT: LO 43 ASN cc_start: 0.7501 (OUTLIER) cc_final: 0.7258 (m110) REVERT: LO 170 TYR cc_start: 0.9152 (t80) cc_final: 0.8936 (t80) REVERT: LP 3 ARG cc_start: 0.6570 (ptm160) cc_final: 0.6195 (ttp-170) REVERT: LP 75 GLN cc_start: 0.6681 (pt0) cc_final: 0.6255 (mm-40) REVERT: LP 89 GLN cc_start: 0.8564 (tm-30) cc_final: 0.8189 (tt0) REVERT: LQ 45 LYS cc_start: 0.6626 (mmtm) cc_final: 0.6245 (tptt) REVERT: LQ 101 ASN cc_start: 0.7193 (t0) cc_final: 0.6897 (t0) REVERT: LS 5 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7602 (mp10) REVERT: LS 21 ASN cc_start: 0.7731 (t0) cc_final: 0.7284 (t0) REVERT: LS 55 THR cc_start: 0.8779 (p) cc_final: 0.8216 (t) REVERT: LS 65 SER cc_start: 0.8597 (m) cc_final: 0.8387 (t) REVERT: LS 141 LYS cc_start: 0.8609 (ttmt) cc_final: 0.8354 (tttm) REVERT: LT 52 MET cc_start: 0.5150 (ptm) cc_final: 0.3560 (mtt) REVERT: LT 107 ARG cc_start: 0.8756 (ttp80) cc_final: 0.8192 (ttt-90) REVERT: LT 146 ASN cc_start: 0.8317 (m-40) cc_final: 0.8011 (m-40) REVERT: LV 65 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8425 (tmtt) REVERT: LY 54 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7925 (tp30) REVERT: LY 92 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7903 (tm-30) REVERT: LY 93 THR cc_start: 0.7554 (p) cc_final: 0.7241 (t) REVERT: LY 126 GLU cc_start: 0.8303 (mp0) cc_final: 0.8060 (mp0) REVERT: Le 6 LYS cc_start: 0.8035 (ttmm) cc_final: 0.7198 (tptt) REVERT: Le 37 LYS cc_start: 0.7717 (mmtt) cc_final: 0.7058 (mmtp) REVERT: Le 114 LYS cc_start: 0.8832 (tptt) cc_final: 0.8468 (tttt) REVERT: Lf 46 TYR cc_start: 0.8521 (m-80) cc_final: 0.8288 (m-80) REVERT: Lf 60 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7088 (mt-10) REVERT: Lq 63 MET cc_start: 0.6733 (mpp) cc_final: 0.5861 (mpp) REVERT: Lq 99 LEU cc_start: 0.9281 (mt) cc_final: 0.9014 (pp) REVERT: Lq 184 MET cc_start: 0.6348 (mmm) cc_final: 0.5812 (mmm) REVERT: Lq 188 ASN cc_start: 0.8508 (m-40) cc_final: 0.8239 (m-40) REVERT: Cc 37 GLN cc_start: 0.7467 (mm110) cc_final: 0.6688 (tm-30) REVERT: Cc 171 GLU cc_start: 0.8287 (pm20) cc_final: 0.8017 (pm20) REVERT: Cc 172 GLU cc_start: 0.8515 (pm20) cc_final: 0.8282 (pm20) REVERT: Cc 219 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7648 (ttm110) REVERT: Cc 234 GLN cc_start: 0.7962 (mp10) cc_final: 0.7464 (mp10) REVERT: Cd 26 GLN cc_start: 0.7898 (mm-40) cc_final: 0.7663 (mm-40) REVERT: Cd 37 ARG cc_start: 0.8049 (ttm110) cc_final: 0.7627 (mtt90) REVERT: Cd 76 ASP cc_start: 0.6921 (m-30) cc_final: 0.6031 (m-30) REVERT: Cd 224 ASN cc_start: 0.7699 (t0) cc_final: 0.7259 (t0) REVERT: Cd 263 GLN cc_start: 0.7451 (mm110) cc_final: 0.7141 (mt0) REVERT: Cd 267 SER cc_start: 0.8404 (OUTLIER) cc_final: 0.8132 (t) REVERT: Cd 433 ARG cc_start: 0.8718 (mmm160) cc_final: 0.8289 (tpt170) REVERT: Ce 195 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6790 (mm) REVERT: Cf 446 MET cc_start: 0.2668 (ttt) cc_final: 0.2436 (ptm) REVERT: Cg 116 PHE cc_start: 0.8721 (m-80) cc_final: 0.8271 (m-80) REVERT: Cg 151 ASN cc_start: 0.7881 (m-40) cc_final: 0.7668 (m-40) REVERT: Cg 335 LEU cc_start: 0.8793 (mt) cc_final: 0.8398 (mt) outliers start: 316 outliers final: 184 residues processed: 2179 average time/residue: 1.2252 time to fit residues: 4595.8852 Evaluate side-chains 1895 residues out of total 8922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1699 time to evaluate : 8.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 47 ARG Chi-restraints excluded: chain CA residue 65 ASP Chi-restraints excluded: chain CA residue 70 THR Chi-restraints excluded: chain CA residue 113 VAL Chi-restraints excluded: chain CA residue 184 VAL Chi-restraints excluded: chain CA residue 227 THR Chi-restraints excluded: chain CA residue 310 ASP Chi-restraints excluded: chain CB residue 44 ASP Chi-restraints excluded: chain CB residue 48 ASN Chi-restraints excluded: chain CB residue 131 SER Chi-restraints excluded: chain CB residue 174 THR Chi-restraints excluded: chain CB residue 283 VAL Chi-restraints excluded: chain CC residue 118 LEU Chi-restraints excluded: chain CC residue 147 ILE Chi-restraints excluded: chain CC residue 167 VAL Chi-restraints excluded: chain CC residue 182 SER Chi-restraints excluded: chain CC residue 220 LEU Chi-restraints excluded: chain CC residue 234 ASP Chi-restraints excluded: chain CC residue 258 THR Chi-restraints excluded: chain CC residue 265 VAL Chi-restraints excluded: chain CE residue 442 ILE Chi-restraints excluded: chain CE residue 496 GLN Chi-restraints excluded: chain CE residue 555 ILE Chi-restraints excluded: chain CF residue 26 LEU Chi-restraints excluded: chain CF residue 139 THR Chi-restraints excluded: chain CF residue 142 VAL Chi-restraints excluded: chain CF residue 153 HIS Chi-restraints excluded: chain CF residue 215 CYS Chi-restraints excluded: chain CG residue 59 VAL Chi-restraints excluded: chain CG residue 65 LEU Chi-restraints excluded: chain CG residue 67 LEU Chi-restraints excluded: chain CG residue 106 GLN Chi-restraints excluded: chain CH residue 56 CYS Chi-restraints excluded: chain CH residue 203 LEU Chi-restraints excluded: chain CH residue 268 ASN Chi-restraints excluded: chain CH residue 338 LEU Chi-restraints excluded: chain CH residue 473 PHE Chi-restraints excluded: chain CI residue 224 THR Chi-restraints excluded: chain CI residue 326 GLU Chi-restraints excluded: chain CJ residue 124 ASN Chi-restraints excluded: chain CK residue 37 GLU Chi-restraints excluded: chain CK residue 130 GLU Chi-restraints excluded: chain CK residue 155 THR Chi-restraints excluded: chain CK residue 212 LEU Chi-restraints excluded: chain CL residue 63 GLU Chi-restraints excluded: chain CM residue 147 LEU Chi-restraints excluded: chain CM residue 148 LYS Chi-restraints excluded: chain CM residue 153 LEU Chi-restraints excluded: chain CN residue 144 ASP Chi-restraints excluded: chain CN residue 166 SER Chi-restraints excluded: chain CN residue 215 LEU Chi-restraints excluded: chain CO residue 19 LYS Chi-restraints excluded: chain CO residue 34 SER Chi-restraints excluded: chain CO residue 37 LEU Chi-restraints excluded: chain CO residue 40 ILE Chi-restraints excluded: chain CO residue 94 LYS Chi-restraints excluded: chain CP residue 267 LEU Chi-restraints excluded: chain CP residue 277 ASN Chi-restraints excluded: chain CP residue 306 VAL Chi-restraints excluded: chain CP residue 524 VAL Chi-restraints excluded: chain CQ residue 89 THR Chi-restraints excluded: chain CQ residue 91 LYS Chi-restraints excluded: chain CQ residue 93 MET Chi-restraints excluded: chain CR residue 128 SER Chi-restraints excluded: chain CR residue 177 THR Chi-restraints excluded: chain CR residue 221 THR Chi-restraints excluded: chain CS residue 673 LYS Chi-restraints excluded: chain CS residue 692 LEU Chi-restraints excluded: chain CS residue 699 ASP Chi-restraints excluded: chain CU residue 228 ASP Chi-restraints excluded: chain CU residue 315 VAL Chi-restraints excluded: chain CU residue 366 LEU Chi-restraints excluded: chain CX residue 105 LEU Chi-restraints excluded: chain Cb residue 231 ASP Chi-restraints excluded: chain Cb residue 301 VAL Chi-restraints excluded: chain Cb residue 328 ILE Chi-restraints excluded: chain Cb residue 395 TYR Chi-restraints excluded: chain Cb residue 400 LEU Chi-restraints excluded: chain Cb residue 413 ARG Chi-restraints excluded: chain Cb residue 550 ASN Chi-restraints excluded: chain LB residue 104 THR Chi-restraints excluded: chain LB residue 145 ILE Chi-restraints excluded: chain LB residue 206 ILE Chi-restraints excluded: chain LB residue 225 HIS Chi-restraints excluded: chain LB residue 277 THR Chi-restraints excluded: chain LB residue 318 VAL Chi-restraints excluded: chain LB residue 364 SER Chi-restraints excluded: chain LC residue 17 THR Chi-restraints excluded: chain LC residue 37 LYS Chi-restraints excluded: chain LC residue 61 THR Chi-restraints excluded: chain LC residue 79 SER Chi-restraints excluded: chain LC residue 185 VAL Chi-restraints excluded: chain LC residue 277 LEU Chi-restraints excluded: chain LC residue 294 THR Chi-restraints excluded: chain LC residue 300 LEU Chi-restraints excluded: chain LF residue 24 SER Chi-restraints excluded: chain LF residue 89 LEU Chi-restraints excluded: chain LF residue 100 LYS Chi-restraints excluded: chain LF residue 126 THR Chi-restraints excluded: chain LF residue 170 THR Chi-restraints excluded: chain LG residue 113 LEU Chi-restraints excluded: chain LG residue 117 THR Chi-restraints excluded: chain LG residue 129 SER Chi-restraints excluded: chain LG residue 134 THR Chi-restraints excluded: chain LG residue 191 THR Chi-restraints excluded: chain LG residue 201 VAL Chi-restraints excluded: chain LG residue 203 ILE Chi-restraints excluded: chain LG residue 204 THR Chi-restraints excluded: chain LG residue 218 ILE Chi-restraints excluded: chain LH residue 16 LEU Chi-restraints excluded: chain LH residue 55 LEU Chi-restraints excluded: chain LH residue 56 GLU Chi-restraints excluded: chain LH residue 137 GLU Chi-restraints excluded: chain LH residue 167 CYS Chi-restraints excluded: chain LH residue 171 ASN Chi-restraints excluded: chain LK residue 100 HIS Chi-restraints excluded: chain LK residue 101 ASN Chi-restraints excluded: chain LK residue 121 PHE Chi-restraints excluded: chain LK residue 147 SER Chi-restraints excluded: chain LL residue 17 HIS Chi-restraints excluded: chain LL residue 46 LEU Chi-restraints excluded: chain LL residue 51 VAL Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LM residue 131 GLU Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LN residue 101 THR Chi-restraints excluded: chain LN residue 125 SER Chi-restraints excluded: chain LN residue 178 HIS Chi-restraints excluded: chain LO residue 43 ASN Chi-restraints excluded: chain LO residue 106 VAL Chi-restraints excluded: chain LO residue 147 VAL Chi-restraints excluded: chain LO residue 175 LEU Chi-restraints excluded: chain LP residue 12 THR Chi-restraints excluded: chain LP residue 20 SER Chi-restraints excluded: chain LP residue 25 SER Chi-restraints excluded: chain LP residue 29 THR Chi-restraints excluded: chain LP residue 52 ILE Chi-restraints excluded: chain LQ residue 69 GLU Chi-restraints excluded: chain LQ residue 123 VAL Chi-restraints excluded: chain LS residue 13 HIS Chi-restraints excluded: chain LS residue 59 VAL Chi-restraints excluded: chain LS residue 120 SER Chi-restraints excluded: chain LS residue 171 SER Chi-restraints excluded: chain LT residue 42 ILE Chi-restraints excluded: chain LT residue 72 VAL Chi-restraints excluded: chain LV residue 30 ASN Chi-restraints excluded: chain LV residue 65 LYS Chi-restraints excluded: chain LY residue 1 MET Chi-restraints excluded: chain LY residue 70 THR Chi-restraints excluded: chain LY residue 71 SER Chi-restraints excluded: chain LY residue 128 VAL Chi-restraints excluded: chain Le residue 24 ASP Chi-restraints excluded: chain Le residue 121 THR Chi-restraints excluded: chain Le residue 129 THR Chi-restraints excluded: chain Lf residue 37 VAL Chi-restraints excluded: chain Lf residue 83 VAL Chi-restraints excluded: chain Lf residue 99 SER Chi-restraints excluded: chain Lf residue 108 SER Chi-restraints excluded: chain Lh residue 20 LEU Chi-restraints excluded: chain Lh residue 36 ILE Chi-restraints excluded: chain Lh residue 61 THR Chi-restraints excluded: chain Li residue 27 THR Chi-restraints excluded: chain Li residue 70 LEU Chi-restraints excluded: chain Li residue 97 GLU Chi-restraints excluded: chain Li residue 106 SER Chi-restraints excluded: chain Lj residue 61 THR Chi-restraints excluded: chain Lj residue 68 SER Chi-restraints excluded: chain Lj residue 82 VAL Chi-restraints excluded: chain Cc residue 17 SER Chi-restraints excluded: chain Cc residue 30 HIS Chi-restraints excluded: chain Cc residue 96 THR Chi-restraints excluded: chain Cc residue 161 LEU Chi-restraints excluded: chain Cc residue 210 LEU Chi-restraints excluded: chain Cc residue 219 ARG Chi-restraints excluded: chain Cc residue 236 THR Chi-restraints excluded: chain Cd residue 70 ASP Chi-restraints excluded: chain Cd residue 86 VAL Chi-restraints excluded: chain Cd residue 220 SER Chi-restraints excluded: chain Cd residue 231 THR Chi-restraints excluded: chain Cd residue 267 SER Chi-restraints excluded: chain Cd residue 269 LEU Chi-restraints excluded: chain Cd residue 274 LEU Chi-restraints excluded: chain Cd residue 286 THR Chi-restraints excluded: chain Cd residue 290 ARG Chi-restraints excluded: chain Cd residue 311 LEU Chi-restraints excluded: chain Cd residue 386 ILE Chi-restraints excluded: chain Ce residue 37 LEU Chi-restraints excluded: chain Ce residue 61 ILE Chi-restraints excluded: chain Ce residue 84 SER Chi-restraints excluded: chain Ce residue 95 ASP Chi-restraints excluded: chain Ce residue 114 THR Chi-restraints excluded: chain Ce residue 165 THR Chi-restraints excluded: chain Ce residue 195 LEU Chi-restraints excluded: chain Cf residue 484 VAL Chi-restraints excluded: chain Cg residue 177 SER Chi-restraints excluded: chain Cg residue 213 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1262 random chunks: chunk 636 optimal weight: 10.0000 chunk 355 optimal weight: 0.6980 chunk 953 optimal weight: 5.9990 chunk 780 optimal weight: 5.9990 chunk 316 optimal weight: 9.9990 chunk 1148 optimal weight: 0.0270 chunk 1240 optimal weight: 7.9990 chunk 1022 optimal weight: 3.9990 chunk 1138 optimal weight: 8.9990 chunk 391 optimal weight: 5.9990 chunk 921 optimal weight: 5.9990 overall best weight: 3.3444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** CA 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 279 HIS ** CB 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 174 ASN CC 286 ASN CE 138 GLN ** CE 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CE 250 ASN CE 463 GLN ** CE 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CF 51 ASN ** CF 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CG 118 HIS CH 354 ASN ** CH 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CI 256 HIS ** CI 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 173 HIS ** CJ 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CK 3 GLN ** CK 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CP 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CP 474 ASN CP 485 HIS ** CP 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CR 28 ASN ** CR 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CX 125 GLN Cz 30 GLN ** Cb 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LB 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 274 HIS ** LB 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 379 GLN LC 60 GLN LC 228 ASN ** LE 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LG 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 194 HIS ** LH 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LH 165 GLN ** LK 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LK 101 ASN ** LK 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LL 17 HIS LN 112 ASN ** LO 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LQ 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 98 ASN ** LT 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LV 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LV 100 ASN LY 116 ASN Lf 44 ASN Li 72 ASN Lq 27 ASN ** Cc 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cd 315 ASN Ce 41 GLN ** Ce 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cf 524 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 141322 Z= 0.316 Angle : 0.687 27.806 202294 Z= 0.349 Chirality : 0.043 1.919 24461 Planarity : 0.006 0.103 16966 Dihedral : 22.131 175.992 48696 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.96 % Favored : 94.84 % Rotamer: Outliers : 4.15 % Allowed : 17.45 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.02 % Twisted Proline : 0.38 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.08), residues: 10278 helix: 1.12 (0.08), residues: 4596 sheet: -0.15 (0.14), residues: 1338 loop : -0.92 (0.09), residues: 4344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPCI 302 HIS 0.014 0.002 HISLL 17 PHE 0.040 0.002 PHECK 133 TYR 0.039 0.002 TYRCG 110 ARG 0.015 0.001 ARGCP 318 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20556 Ramachandran restraints generated. 10278 Oldfield, 0 Emsley, 10278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20556 Ramachandran restraints generated. 10278 Oldfield, 0 Emsley, 10278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2147 residues out of total 8922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 360 poor density : 1787 time to evaluate : 8.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CA 76 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7517 (tp30) REVERT: CA 143 ASP cc_start: 0.7981 (OUTLIER) cc_final: 0.7718 (m-30) REVERT: CA 246 GLN cc_start: 0.9164 (pt0) cc_final: 0.8920 (pt0) REVERT: CA 262 ILE cc_start: 0.8178 (mp) cc_final: 0.7715 (tt) REVERT: CB 44 ASP cc_start: 0.7121 (OUTLIER) cc_final: 0.6807 (p0) REVERT: CB 91 THR cc_start: 0.6743 (OUTLIER) cc_final: 0.6535 (p) REVERT: CB 147 PHE cc_start: 0.8808 (t80) cc_final: 0.8501 (t80) REVERT: CC 137 TYR cc_start: 0.8255 (p90) cc_final: 0.7755 (p90) REVERT: CC 147 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8322 (tt) REVERT: CC 193 LYS cc_start: 0.9000 (pptt) cc_final: 0.8763 (pptt) REVERT: CC 194 LYS cc_start: 0.8531 (ptpp) cc_final: 0.8139 (mttp) REVERT: CC 381 ASP cc_start: 0.8705 (m-30) cc_final: 0.8141 (p0) REVERT: CE 226 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7963 (mt-10) REVERT: CE 255 PHE cc_start: 0.8407 (p90) cc_final: 0.8128 (p90) REVERT: CE 279 ARG cc_start: 0.8261 (mtm-85) cc_final: 0.8031 (mtm110) REVERT: CE 280 GLN cc_start: 0.8410 (mt0) cc_final: 0.8202 (mt0) REVERT: CE 390 LYS cc_start: 0.7665 (mmtp) cc_final: 0.7417 (mmtp) REVERT: CF 41 PHE cc_start: 0.7453 (m-80) cc_final: 0.7073 (m-80) REVERT: CG 137 MET cc_start: 0.6995 (pmm) cc_final: 0.6781 (pmm) REVERT: CH 69 VAL cc_start: 0.8671 (m) cc_final: 0.8436 (p) REVERT: CH 150 ASP cc_start: 0.8671 (t0) cc_final: 0.8321 (t0) REVERT: CH 199 THR cc_start: 0.8737 (m) cc_final: 0.8385 (p) REVERT: CH 231 MET cc_start: 0.8356 (mmt) cc_final: 0.7840 (mmt) REVERT: CH 236 MET cc_start: 0.8543 (mmm) cc_final: 0.7966 (tpp) REVERT: CH 333 HIS cc_start: 0.8359 (t70) cc_final: 0.8143 (t-170) REVERT: CI 250 LYS cc_start: 0.8370 (mptt) cc_final: 0.8106 (mmtm) REVERT: CI 274 LYS cc_start: 0.8308 (ptmm) cc_final: 0.8046 (ptmm) REVERT: CJ 24 LYS cc_start: 0.8130 (mttt) cc_final: 0.7775 (tppt) REVERT: CJ 111 ASN cc_start: 0.6886 (m110) cc_final: 0.6165 (t0) REVERT: CJ 196 TYR cc_start: 0.8684 (m-80) cc_final: 0.8316 (m-80) REVERT: CJ 230 PHE cc_start: 0.9129 (m-80) cc_final: 0.8570 (m-80) REVERT: CK 36 SER cc_start: 0.7796 (t) cc_final: 0.7529 (p) REVERT: CK 37 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7384 (tt0) REVERT: CK 67 GLN cc_start: 0.8242 (mt0) cc_final: 0.7738 (tm-30) REVERT: CK 179 TYR cc_start: 0.9163 (m-80) cc_final: 0.8899 (m-10) REVERT: CK 201 LYS cc_start: 0.8750 (mmpt) cc_final: 0.8436 (mtmt) REVERT: CL 23 LYS cc_start: 0.7586 (ttmm) cc_final: 0.6958 (tptt) REVERT: CL 63 GLU cc_start: 0.9013 (tp30) cc_final: 0.8802 (mm-30) REVERT: CM 112 LEU cc_start: 0.8593 (mt) cc_final: 0.8366 (mt) REVERT: CM 209 TRP cc_start: 0.7838 (m100) cc_final: 0.7437 (m100) REVERT: CN 41 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8212 (mm-30) REVERT: CN 57 ARG cc_start: 0.8118 (ttm-80) cc_final: 0.7775 (ttm-80) REVERT: CN 245 PHE cc_start: 0.9038 (m-80) cc_final: 0.8717 (m-80) REVERT: CO 3 LYS cc_start: 0.7604 (mmmt) cc_final: 0.7286 (mttt) REVERT: CP 284 LEU cc_start: 0.9153 (mm) cc_final: 0.8715 (tt) REVERT: CP 314 ARG cc_start: 0.8442 (mtm-85) cc_final: 0.8036 (ptp-170) REVERT: CP 374 MET cc_start: 0.8063 (mtp) cc_final: 0.7720 (mtp) REVERT: CP 398 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7842 (ppp) REVERT: CP 402 MET cc_start: 0.6188 (ptp) cc_final: 0.5728 (ptt) REVERT: CP 438 TYR cc_start: 0.6930 (m-10) cc_final: 0.6683 (m-10) REVERT: CP 441 ARG cc_start: 0.8813 (ptp90) cc_final: 0.8523 (ptm-80) REVERT: CQ 8 PHE cc_start: 0.8770 (t80) cc_final: 0.8192 (t80) REVERT: CQ 45 ASN cc_start: 0.8529 (t0) cc_final: 0.7717 (t0) REVERT: CQ 55 TYR cc_start: 0.8858 (t80) cc_final: 0.8428 (t80) REVERT: CQ 93 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7477 (mmt) REVERT: CR 18 ARG cc_start: 0.8248 (ttm-80) cc_final: 0.7523 (ttt180) REVERT: CR 73 LEU cc_start: 0.5905 (tp) cc_final: 0.5593 (tp) REVERT: CR 133 GLN cc_start: 0.8222 (mm-40) cc_final: 0.7584 (mm-40) REVERT: CR 135 GLN cc_start: 0.7742 (tm-30) cc_final: 0.7442 (tm-30) REVERT: CS 475 MET cc_start: 0.7936 (mtt) cc_final: 0.7722 (mtp) REVERT: CS 688 GLN cc_start: 0.4895 (mt0) cc_final: 0.4428 (mt0) REVERT: CU 244 MET cc_start: 0.8449 (tpp) cc_final: 0.7992 (mmm) REVERT: CU 282 MET cc_start: 0.9205 (mmp) cc_final: 0.8982 (mmp) REVERT: CU 320 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.7387 (mp10) REVERT: CU 337 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8234 (tt) REVERT: Cb 110 PHE cc_start: 0.7783 (m-80) cc_final: 0.7409 (t80) REVERT: Cb 228 MET cc_start: 0.6969 (mmp) cc_final: 0.6384 (mmm) REVERT: Cb 249 MET cc_start: 0.8815 (mmp) cc_final: 0.7994 (ttm) REVERT: Cb 381 TYR cc_start: 0.8895 (t80) cc_final: 0.8694 (t80) REVERT: Cb 559 ARG cc_start: 0.7742 (mtm-85) cc_final: 0.7475 (ptp-170) REVERT: Cb 597 TYR cc_start: 0.7740 (t80) cc_final: 0.7271 (t80) REVERT: Cb 866 TYR cc_start: 0.7539 (t80) cc_final: 0.7109 (t80) REVERT: Ch 295 ASN cc_start: 0.8247 (p0) cc_final: 0.7817 (m-40) REVERT: Ch 331 ARG cc_start: 0.8229 (mmt180) cc_final: 0.7318 (ptt180) REVERT: LB 118 PHE cc_start: 0.8128 (m-80) cc_final: 0.7836 (m-80) REVERT: LB 119 TYR cc_start: 0.8276 (m-80) cc_final: 0.8012 (m-80) REVERT: LB 135 LYS cc_start: 0.8507 (mtmt) cc_final: 0.8227 (mmmt) REVERT: LB 227 PHE cc_start: 0.5865 (OUTLIER) cc_final: 0.4660 (m-10) REVERT: LC 56 LYS cc_start: 0.6703 (mtmt) cc_final: 0.5654 (mmtm) REVERT: LC 301 ARG cc_start: 0.7730 (ptt90) cc_final: 0.7472 (ptt90) REVERT: LC 304 LYS cc_start: 0.8173 (mttp) cc_final: 0.7888 (tttt) REVERT: LC 350 LYS cc_start: 0.8866 (ttpt) cc_final: 0.8527 (ttpp) REVERT: LE 33 GLU cc_start: 0.6993 (tm-30) cc_final: 0.6120 (tp30) REVERT: LE 56 THR cc_start: 0.9457 (m) cc_final: 0.9203 (m) REVERT: LF 134 LYS cc_start: 0.8724 (tttt) cc_final: 0.8333 (tptt) REVERT: LF 172 ASN cc_start: 0.8438 (m-40) cc_final: 0.7824 (p0) REVERT: LG 159 ASP cc_start: 0.8778 (p0) cc_final: 0.8489 (p0) REVERT: LH 100 ASN cc_start: 0.8523 (t0) cc_final: 0.8288 (t0) REVERT: LH 173 ASP cc_start: 0.8487 (t0) cc_final: 0.8055 (t70) REVERT: LK 83 ARG cc_start: 0.8312 (mmm160) cc_final: 0.7961 (mmm160) REVERT: LK 121 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.7995 (t80) REVERT: LL 78 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7180 (tt0) REVERT: LL 114 GLN cc_start: 0.7731 (tp40) cc_final: 0.7268 (tp40) REVERT: LM 42 ASP cc_start: 0.8750 (t0) cc_final: 0.8055 (t0) REVERT: LO 55 TYR cc_start: 0.8673 (t80) cc_final: 0.7917 (t80) REVERT: LO 146 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7085 (mp0) REVERT: LO 170 TYR cc_start: 0.9164 (t80) cc_final: 0.8943 (t80) REVERT: LP 3 ARG cc_start: 0.6637 (ptm160) cc_final: 0.6316 (ttp-170) REVERT: LP 40 LYS cc_start: 0.8584 (mmmt) cc_final: 0.8349 (mmmt) REVERT: LP 75 GLN cc_start: 0.6795 (pt0) cc_final: 0.6247 (mm110) REVERT: LP 89 GLN cc_start: 0.8564 (tm-30) cc_final: 0.8136 (tt0) REVERT: LP 147 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.6802 (tm-30) REVERT: LQ 45 LYS cc_start: 0.6734 (mmtm) cc_final: 0.6318 (tptt) REVERT: LS 5 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7749 (mp10) REVERT: LS 21 ASN cc_start: 0.7933 (t0) cc_final: 0.7529 (t0) REVERT: LS 55 THR cc_start: 0.8798 (p) cc_final: 0.8283 (t) REVERT: LT 52 MET cc_start: 0.4891 (ptm) cc_final: 0.3523 (mtt) REVERT: LT 103 GLU cc_start: 0.9211 (pt0) cc_final: 0.8894 (pm20) REVERT: LT 112 ASN cc_start: 0.8637 (m110) cc_final: 0.8343 (p0) REVERT: LT 146 ASN cc_start: 0.8526 (m-40) cc_final: 0.8191 (m-40) REVERT: LV 65 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8227 (tmtt) REVERT: LV 72 ARG cc_start: 0.8301 (ttm110) cc_final: 0.8017 (mtt-85) REVERT: LY 54 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7954 (tp30) REVERT: LY 92 GLN cc_start: 0.8225 (tm-30) cc_final: 0.7439 (tm-30) REVERT: LY 93 THR cc_start: 0.7582 (p) cc_final: 0.7379 (t) REVERT: LY 126 GLU cc_start: 0.8189 (mp0) cc_final: 0.7887 (mt-10) REVERT: Le 6 LYS cc_start: 0.8033 (ttmm) cc_final: 0.7094 (tptt) REVERT: Le 114 LYS cc_start: 0.8875 (tptt) cc_final: 0.8568 (tttt) REVERT: Lf 60 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7102 (mt-10) REVERT: Lh 16 ASN cc_start: 0.7536 (p0) cc_final: 0.7079 (p0) REVERT: Lh 95 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6825 (mtt180) REVERT: Lq 63 MET cc_start: 0.6773 (mpp) cc_final: 0.6107 (mpp) REVERT: Lq 66 CYS cc_start: 0.9055 (p) cc_final: 0.8827 (p) REVERT: Lq 83 ASP cc_start: 0.5470 (p0) cc_final: 0.5227 (p0) REVERT: Lq 103 LEU cc_start: 0.9553 (tp) cc_final: 0.9054 (pp) REVERT: Lq 184 MET cc_start: 0.6619 (mmm) cc_final: 0.6061 (mmm) REVERT: Lq 188 ASN cc_start: 0.8537 (m-40) cc_final: 0.8261 (m-40) REVERT: Cc 37 GLN cc_start: 0.7681 (mm110) cc_final: 0.7155 (tm-30) REVERT: Cc 171 GLU cc_start: 0.8410 (pm20) cc_final: 0.8171 (pm20) REVERT: Cc 172 GLU cc_start: 0.8520 (pm20) cc_final: 0.8273 (pm20) REVERT: Cc 189 ILE cc_start: 0.9193 (mm) cc_final: 0.8936 (mm) REVERT: Cd 26 GLN cc_start: 0.7909 (mm-40) cc_final: 0.7669 (mm-40) REVERT: Cd 37 ARG cc_start: 0.8156 (ttm110) cc_final: 0.7742 (mtt90) REVERT: Cd 224 ASN cc_start: 0.7585 (t0) cc_final: 0.7296 (t0) REVERT: Cd 267 SER cc_start: 0.8378 (OUTLIER) cc_final: 0.8167 (t) REVERT: Ce 149 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.6768 (mp0) REVERT: Cf 513 ILE cc_start: 0.8666 (mm) cc_final: 0.8401 (mt) REVERT: Cf 524 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.7162 (mt0) REVERT: Cf 526 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7816 (pttt) REVERT: Cf 529 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7069 (mm-30) REVERT: Cg 116 PHE cc_start: 0.8756 (m-80) cc_final: 0.8387 (m-80) REVERT: Cg 151 ASN cc_start: 0.7836 (m-40) cc_final: 0.7578 (m-40) REVERT: Cg 335 LEU cc_start: 0.8799 (mt) cc_final: 0.8583 (mt) REVERT: Cg 337 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.7346 (pmm) outliers start: 360 outliers final: 229 residues processed: 2000 average time/residue: 1.1809 time to fit residues: 4082.4975 Evaluate side-chains 1876 residues out of total 8922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 1626 time to evaluate : 8.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 47 ARG Chi-restraints excluded: chain CA residue 65 ASP Chi-restraints excluded: chain CA residue 70 THR Chi-restraints excluded: chain CA residue 72 SER Chi-restraints excluded: chain CA residue 74 LEU Chi-restraints excluded: chain CA residue 113 VAL Chi-restraints excluded: chain CA residue 118 GLN Chi-restraints excluded: chain CA residue 143 ASP Chi-restraints excluded: chain CA residue 184 VAL Chi-restraints excluded: chain CA residue 186 ASP Chi-restraints excluded: chain CA residue 227 THR Chi-restraints excluded: chain CA residue 310 ASP Chi-restraints excluded: chain CB residue 44 ASP Chi-restraints excluded: chain CB residue 91 THR Chi-restraints excluded: chain CB residue 131 SER Chi-restraints excluded: chain CB residue 170 THR Chi-restraints excluded: chain CB residue 185 MET Chi-restraints excluded: chain CB residue 283 VAL Chi-restraints excluded: chain CC residue 118 LEU Chi-restraints excluded: chain CC residue 147 ILE Chi-restraints excluded: chain CC residue 258 THR Chi-restraints excluded: chain CC residue 265 VAL Chi-restraints excluded: chain CC residue 286 ASN Chi-restraints excluded: chain CE residue 184 THR Chi-restraints excluded: chain CE residue 237 LEU Chi-restraints excluded: chain CE residue 304 GLU Chi-restraints excluded: chain CE residue 342 ASP Chi-restraints excluded: chain CE residue 382 LEU Chi-restraints excluded: chain CE residue 442 ILE Chi-restraints excluded: chain CE residue 485 PHE Chi-restraints excluded: chain CE residue 496 GLN Chi-restraints excluded: chain CE residue 503 THR Chi-restraints excluded: chain CE residue 555 ILE Chi-restraints excluded: chain CF residue 139 THR Chi-restraints excluded: chain CF residue 142 VAL Chi-restraints excluded: chain CF residue 174 MET Chi-restraints excluded: chain CF residue 194 ILE Chi-restraints excluded: chain CF residue 215 CYS Chi-restraints excluded: chain CG residue 59 VAL Chi-restraints excluded: chain CG residue 65 LEU Chi-restraints excluded: chain CG residue 67 LEU Chi-restraints excluded: chain CG residue 106 GLN Chi-restraints excluded: chain CH residue 56 CYS Chi-restraints excluded: chain CH residue 165 THR Chi-restraints excluded: chain CH residue 203 LEU Chi-restraints excluded: chain CH residue 281 MET Chi-restraints excluded: chain CH residue 338 LEU Chi-restraints excluded: chain CH residue 425 TRP Chi-restraints excluded: chain CI residue 210 PHE Chi-restraints excluded: chain CI residue 224 THR Chi-restraints excluded: chain CI residue 260 CYS Chi-restraints excluded: chain CJ residue 158 THR Chi-restraints excluded: chain CJ residue 374 LEU Chi-restraints excluded: chain CK residue 37 GLU Chi-restraints excluded: chain CK residue 130 GLU Chi-restraints excluded: chain CK residue 152 THR Chi-restraints excluded: chain CK residue 155 THR Chi-restraints excluded: chain CK residue 193 VAL Chi-restraints excluded: chain CK residue 216 THR Chi-restraints excluded: chain CL residue 18 THR Chi-restraints excluded: chain CL residue 38 LEU Chi-restraints excluded: chain CM residue 147 LEU Chi-restraints excluded: chain CM residue 148 LYS Chi-restraints excluded: chain CM residue 153 LEU Chi-restraints excluded: chain CM residue 244 LEU Chi-restraints excluded: chain CN residue 166 SER Chi-restraints excluded: chain CN residue 215 LEU Chi-restraints excluded: chain CO residue 19 LYS Chi-restraints excluded: chain CO residue 34 SER Chi-restraints excluded: chain CO residue 37 LEU Chi-restraints excluded: chain CO residue 40 ILE Chi-restraints excluded: chain CO residue 94 LYS Chi-restraints excluded: chain CP residue 267 LEU Chi-restraints excluded: chain CP residue 277 ASN Chi-restraints excluded: chain CP residue 306 VAL Chi-restraints excluded: chain CP residue 319 ASP Chi-restraints excluded: chain CP residue 398 MET Chi-restraints excluded: chain CP residue 454 LEU Chi-restraints excluded: chain CP residue 524 VAL Chi-restraints excluded: chain CQ residue 6 CYS Chi-restraints excluded: chain CQ residue 34 SER Chi-restraints excluded: chain CQ residue 89 THR Chi-restraints excluded: chain CQ residue 93 MET Chi-restraints excluded: chain CR residue 33 ASN Chi-restraints excluded: chain CR residue 46 SER Chi-restraints excluded: chain CR residue 128 SER Chi-restraints excluded: chain CR residue 177 THR Chi-restraints excluded: chain CR residue 221 THR Chi-restraints excluded: chain CS residue 699 ASP Chi-restraints excluded: chain CU residue 228 ASP Chi-restraints excluded: chain CU residue 315 VAL Chi-restraints excluded: chain CU residue 320 GLN Chi-restraints excluded: chain CU residue 335 ASN Chi-restraints excluded: chain CU residue 337 LEU Chi-restraints excluded: chain CX residue 105 LEU Chi-restraints excluded: chain Cz residue 50 LEU Chi-restraints excluded: chain Cb residue 237 TYR Chi-restraints excluded: chain Cb residue 255 LEU Chi-restraints excluded: chain Cb residue 301 VAL Chi-restraints excluded: chain Cb residue 328 ILE Chi-restraints excluded: chain Cb residue 395 TYR Chi-restraints excluded: chain Cb residue 400 LEU Chi-restraints excluded: chain Cb residue 474 ASP Chi-restraints excluded: chain Cb residue 564 ILE Chi-restraints excluded: chain Cb residue 565 VAL Chi-restraints excluded: chain LB residue 57 VAL Chi-restraints excluded: chain LB residue 104 THR Chi-restraints excluded: chain LB residue 167 ILE Chi-restraints excluded: chain LB residue 225 HIS Chi-restraints excluded: chain LB residue 227 PHE Chi-restraints excluded: chain LB residue 277 THR Chi-restraints excluded: chain LB residue 297 THR Chi-restraints excluded: chain LB residue 318 VAL Chi-restraints excluded: chain LB residue 320 ASN Chi-restraints excluded: chain LB residue 364 SER Chi-restraints excluded: chain LC residue 60 GLN Chi-restraints excluded: chain LC residue 61 THR Chi-restraints excluded: chain LC residue 79 SER Chi-restraints excluded: chain LC residue 185 VAL Chi-restraints excluded: chain LC residue 277 LEU Chi-restraints excluded: chain LC residue 294 THR Chi-restraints excluded: chain LC residue 300 LEU Chi-restraints excluded: chain LE residue 103 ILE Chi-restraints excluded: chain LE residue 198 MET Chi-restraints excluded: chain LF residue 10 ASN Chi-restraints excluded: chain LF residue 24 SER Chi-restraints excluded: chain LF residue 89 LEU Chi-restraints excluded: chain LF residue 100 LYS Chi-restraints excluded: chain LF residue 126 THR Chi-restraints excluded: chain LF residue 170 THR Chi-restraints excluded: chain LG residue 89 LEU Chi-restraints excluded: chain LG residue 113 LEU Chi-restraints excluded: chain LG residue 117 THR Chi-restraints excluded: chain LG residue 129 SER Chi-restraints excluded: chain LG residue 139 LEU Chi-restraints excluded: chain LG residue 191 THR Chi-restraints excluded: chain LG residue 197 THR Chi-restraints excluded: chain LG residue 201 VAL Chi-restraints excluded: chain LG residue 203 ILE Chi-restraints excluded: chain LG residue 204 THR Chi-restraints excluded: chain LG residue 218 ILE Chi-restraints excluded: chain LH residue 16 LEU Chi-restraints excluded: chain LH residue 47 VAL Chi-restraints excluded: chain LH residue 55 LEU Chi-restraints excluded: chain LH residue 56 GLU Chi-restraints excluded: chain LH residue 101 VAL Chi-restraints excluded: chain LH residue 128 VAL Chi-restraints excluded: chain LH residue 137 GLU Chi-restraints excluded: chain LH residue 149 SER Chi-restraints excluded: chain LH residue 165 GLN Chi-restraints excluded: chain LH residue 167 CYS Chi-restraints excluded: chain LH residue 171 ASN Chi-restraints excluded: chain LK residue 121 PHE Chi-restraints excluded: chain LK residue 147 SER Chi-restraints excluded: chain LL residue 17 HIS Chi-restraints excluded: chain LL residue 46 LEU Chi-restraints excluded: chain LL residue 78 GLU Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LM residue 98 ASN Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LN residue 97 SER Chi-restraints excluded: chain LN residue 101 THR Chi-restraints excluded: chain LN residue 110 CYS Chi-restraints excluded: chain LN residue 112 ASN Chi-restraints excluded: chain LN residue 181 ASN Chi-restraints excluded: chain LO residue 106 VAL Chi-restraints excluded: chain LO residue 128 VAL Chi-restraints excluded: chain LO residue 146 GLU Chi-restraints excluded: chain LO residue 147 VAL Chi-restraints excluded: chain LO residue 196 SER Chi-restraints excluded: chain LP residue 12 THR Chi-restraints excluded: chain LP residue 20 SER Chi-restraints excluded: chain LP residue 29 THR Chi-restraints excluded: chain LP residue 52 ILE Chi-restraints excluded: chain LP residue 147 GLU Chi-restraints excluded: chain LQ residue 52 VAL Chi-restraints excluded: chain LQ residue 69 GLU Chi-restraints excluded: chain LQ residue 108 VAL Chi-restraints excluded: chain LQ residue 123 VAL Chi-restraints excluded: chain LS residue 13 HIS Chi-restraints excluded: chain LS residue 59 VAL Chi-restraints excluded: chain LS residue 72 VAL Chi-restraints excluded: chain LS residue 87 THR Chi-restraints excluded: chain LS residue 133 GLU Chi-restraints excluded: chain LS residue 171 SER Chi-restraints excluded: chain LT residue 42 ILE Chi-restraints excluded: chain LT residue 66 ASN Chi-restraints excluded: chain LT residue 72 VAL Chi-restraints excluded: chain LT residue 97 LYS Chi-restraints excluded: chain LT residue 143 ILE Chi-restraints excluded: chain LT residue 145 ASP Chi-restraints excluded: chain LV residue 21 VAL Chi-restraints excluded: chain LV residue 65 LYS Chi-restraints excluded: chain LY residue 1 MET Chi-restraints excluded: chain LY residue 6 THR Chi-restraints excluded: chain LY residue 51 LYS Chi-restraints excluded: chain LY residue 55 VAL Chi-restraints excluded: chain LY residue 70 THR Chi-restraints excluded: chain LY residue 71 SER Chi-restraints excluded: chain LY residue 128 VAL Chi-restraints excluded: chain Le residue 8 VAL Chi-restraints excluded: chain Le residue 24 ASP Chi-restraints excluded: chain Le residue 121 THR Chi-restraints excluded: chain Le residue 129 THR Chi-restraints excluded: chain Lf residue 32 ILE Chi-restraints excluded: chain Lf residue 37 VAL Chi-restraints excluded: chain Lf residue 108 SER Chi-restraints excluded: chain Lh residue 36 ILE Chi-restraints excluded: chain Lh residue 61 THR Chi-restraints excluded: chain Lh residue 95 ARG Chi-restraints excluded: chain Li residue 27 THR Chi-restraints excluded: chain Li residue 64 ARG Chi-restraints excluded: chain Li residue 66 VAL Chi-restraints excluded: chain Li residue 70 LEU Chi-restraints excluded: chain Li residue 97 GLU Chi-restraints excluded: chain Li residue 106 SER Chi-restraints excluded: chain Lj residue 59 THR Chi-restraints excluded: chain Lj residue 61 THR Chi-restraints excluded: chain Lj residue 68 SER Chi-restraints excluded: chain Lj residue 69 THR Chi-restraints excluded: chain Lj residue 82 VAL Chi-restraints excluded: chain Cc residue 17 SER Chi-restraints excluded: chain Cc residue 30 HIS Chi-restraints excluded: chain Cc residue 96 THR Chi-restraints excluded: chain Cc residue 102 THR Chi-restraints excluded: chain Cc residue 106 VAL Chi-restraints excluded: chain Cc residue 161 LEU Chi-restraints excluded: chain Cc residue 236 THR Chi-restraints excluded: chain Cd residue 70 ASP Chi-restraints excluded: chain Cd residue 86 VAL Chi-restraints excluded: chain Cd residue 220 SER Chi-restraints excluded: chain Cd residue 231 THR Chi-restraints excluded: chain Cd residue 267 SER Chi-restraints excluded: chain Cd residue 290 ARG Chi-restraints excluded: chain Cd residue 311 LEU Chi-restraints excluded: chain Cd residue 404 VAL Chi-restraints excluded: chain Ce residue 10 ILE Chi-restraints excluded: chain Ce residue 39 ASN Chi-restraints excluded: chain Ce residue 41 GLN Chi-restraints excluded: chain Ce residue 84 SER Chi-restraints excluded: chain Ce residue 114 THR Chi-restraints excluded: chain Ce residue 149 GLU Chi-restraints excluded: chain Ce residue 165 THR Chi-restraints excluded: chain Cf residue 484 VAL Chi-restraints excluded: chain Cf residue 524 GLN Chi-restraints excluded: chain Cf residue 526 LYS Chi-restraints excluded: chain Cg residue 67 LEU Chi-restraints excluded: chain Cg residue 173 THR Chi-restraints excluded: chain Cg residue 337 MET Chi-restraints excluded: chain Cg residue 352 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1262 random chunks: chunk 1134 optimal weight: 30.0000 chunk 863 optimal weight: 3.9990 chunk 595 optimal weight: 20.0000 chunk 127 optimal weight: 5.9990 chunk 547 optimal weight: 30.0000 chunk 770 optimal weight: 5.9990 chunk 1152 optimal weight: 0.9990 chunk 1219 optimal weight: 3.9990 chunk 601 optimal weight: 8.9990 chunk 1092 optimal weight: 0.8980 chunk 328 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** CA 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 174 ASN CC 339 HIS ** CE 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CF 51 ASN ** CF 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CH 155 HIS CH 369 HIS CI 256 HIS ** CI 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 124 ASN ** CJ 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CK 10 HIS CK 57 GLN ** CK 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CN 168 GLN ** CP 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CP 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CP 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CP 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CP 485 HIS ** CP 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CR 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CU 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cb 384 ASN Cb 582 ASN ** LB 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 60 GLN ** LE 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 48 GLN ** LG 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LH 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LH 165 GLN LK 100 HIS ** LK 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LL 17 HIS LM 24 ASN LN 112 ASN ** LQ 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 98 ASN LS 62 ASN ** LT 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LV 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LV 100 ASN LY 116 ASN Le 50 ASN Lf 44 ASN Li 72 ASN ** Cc 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cd 58 GLN Ce 85 GLN Cf 524 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 141322 Z= 0.238 Angle : 0.646 27.516 202294 Z= 0.326 Chirality : 0.041 1.945 24461 Planarity : 0.005 0.098 16966 Dihedral : 22.062 175.556 48693 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.82 % Favored : 94.98 % Rotamer: Outliers : 4.32 % Allowed : 18.85 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.02 % Twisted Proline : 0.38 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.08), residues: 10278 helix: 1.20 (0.08), residues: 4625 sheet: -0.12 (0.14), residues: 1306 loop : -0.90 (0.09), residues: 4347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRPCc 79 HIS 0.010 0.001 HISCI 256 PHE 0.041 0.002 PHECh 334 TYR 0.026 0.002 TYRLB 123 ARG 0.008 0.001 ARGCd 47 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20556 Ramachandran restraints generated. 10278 Oldfield, 0 Emsley, 10278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20556 Ramachandran restraints generated. 10278 Oldfield, 0 Emsley, 10278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2101 residues out of total 8922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 374 poor density : 1727 time to evaluate : 8.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CA 76 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7342 (tp30) REVERT: CA 143 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7819 (m-30) REVERT: CA 246 GLN cc_start: 0.9167 (pt0) cc_final: 0.8931 (pt0) REVERT: CA 262 ILE cc_start: 0.8190 (mp) cc_final: 0.7753 (tt) REVERT: CB 44 ASP cc_start: 0.7114 (OUTLIER) cc_final: 0.6698 (p0) REVERT: CB 147 PHE cc_start: 0.8809 (t80) cc_final: 0.8445 (t80) REVERT: CC 137 TYR cc_start: 0.8227 (p90) cc_final: 0.7692 (p90) REVERT: CC 194 LYS cc_start: 0.8493 (ptpp) cc_final: 0.8028 (mttp) REVERT: CC 246 LEU cc_start: 0.5250 (OUTLIER) cc_final: 0.4814 (mp) REVERT: CC 381 ASP cc_start: 0.8777 (m-30) cc_final: 0.8162 (p0) REVERT: CE 226 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7905 (mt-10) REVERT: CE 280 GLN cc_start: 0.8423 (mt0) cc_final: 0.8202 (mt0) REVERT: CE 355 MET cc_start: 0.8205 (mmt) cc_final: 0.7493 (mmt) REVERT: CF 41 PHE cc_start: 0.7428 (m-80) cc_final: 0.7110 (m-80) REVERT: CH 33 ARG cc_start: 0.3905 (mmt180) cc_final: 0.3375 (mtm180) REVERT: CH 150 ASP cc_start: 0.8616 (t0) cc_final: 0.8332 (t0) REVERT: CH 199 THR cc_start: 0.8688 (m) cc_final: 0.8284 (p) REVERT: CH 231 MET cc_start: 0.8320 (mmt) cc_final: 0.7890 (mmt) REVERT: CH 236 MET cc_start: 0.8527 (mmm) cc_final: 0.8080 (tpp) REVERT: CH 253 MET cc_start: 0.7712 (pmm) cc_final: 0.7410 (pmm) REVERT: CH 297 LEU cc_start: 0.7183 (pt) cc_final: 0.6879 (pt) REVERT: CH 333 HIS cc_start: 0.8334 (t70) cc_final: 0.8103 (t-170) REVERT: CI 250 LYS cc_start: 0.8378 (mptt) cc_final: 0.8043 (mmtm) REVERT: CI 274 LYS cc_start: 0.8270 (ptmm) cc_final: 0.8049 (ptmm) REVERT: CJ 17 MET cc_start: 0.7200 (OUTLIER) cc_final: 0.6665 (pmm) REVERT: CJ 190 LEU cc_start: 0.3964 (OUTLIER) cc_final: 0.3737 (pp) REVERT: CJ 196 TYR cc_start: 0.8763 (m-80) cc_final: 0.8361 (m-80) REVERT: CJ 230 PHE cc_start: 0.9076 (m-80) cc_final: 0.8810 (m-80) REVERT: CK 67 GLN cc_start: 0.8110 (mt0) cc_final: 0.7676 (tm-30) REVERT: CK 179 TYR cc_start: 0.9151 (m-80) cc_final: 0.8871 (m-10) REVERT: CK 201 LYS cc_start: 0.8805 (mmpt) cc_final: 0.8415 (mtmt) REVERT: CK 212 LEU cc_start: 0.9578 (OUTLIER) cc_final: 0.9265 (mm) REVERT: CL 23 LYS cc_start: 0.7679 (ttmm) cc_final: 0.7022 (tptt) REVERT: CM 142 TYR cc_start: 0.7094 (p90) cc_final: 0.6875 (p90) REVERT: CM 209 TRP cc_start: 0.7865 (m100) cc_final: 0.7389 (m100) REVERT: CN 57 ARG cc_start: 0.8069 (ttm-80) cc_final: 0.7746 (mtp85) REVERT: CN 197 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7672 (tmm) REVERT: CN 245 PHE cc_start: 0.9039 (m-80) cc_final: 0.8711 (m-80) REVERT: CO 3 LYS cc_start: 0.7558 (mmmt) cc_final: 0.7260 (mtmt) REVERT: CP 374 MET cc_start: 0.8141 (mtp) cc_final: 0.7807 (mtp) REVERT: CP 438 TYR cc_start: 0.6885 (m-10) cc_final: 0.6666 (m-10) REVERT: CP 441 ARG cc_start: 0.8846 (ptp90) cc_final: 0.8507 (ptm-80) REVERT: CP 552 MET cc_start: 0.8123 (mmm) cc_final: 0.7676 (mmm) REVERT: CQ 8 PHE cc_start: 0.8716 (t80) cc_final: 0.8180 (t80) REVERT: CQ 45 ASN cc_start: 0.8555 (t0) cc_final: 0.7842 (t0) REVERT: CQ 55 TYR cc_start: 0.8867 (t80) cc_final: 0.8481 (t80) REVERT: CR 18 ARG cc_start: 0.8264 (ttm-80) cc_final: 0.8033 (ttp-170) REVERT: CR 73 LEU cc_start: 0.5957 (tp) cc_final: 0.5670 (tp) REVERT: CR 135 GLN cc_start: 0.7672 (tm-30) cc_final: 0.7353 (tm-30) REVERT: CS 475 MET cc_start: 0.7978 (mtt) cc_final: 0.7549 (mtp) REVERT: CS 689 LYS cc_start: 0.7318 (mmpt) cc_final: 0.6092 (mmtt) REVERT: CS 699 ASP cc_start: 0.7356 (OUTLIER) cc_final: 0.7129 (t0) REVERT: CU 244 MET cc_start: 0.8355 (tpp) cc_final: 0.8092 (mmm) REVERT: CU 282 MET cc_start: 0.9136 (mmp) cc_final: 0.8876 (mmp) REVERT: CU 320 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.7537 (mp10) REVERT: CU 364 ASN cc_start: 0.8778 (p0) cc_final: 0.8518 (p0) REVERT: Cz 26 ARG cc_start: 0.7512 (ttm-80) cc_final: 0.7163 (ttm-80) REVERT: Cz 67 GLU cc_start: 0.5911 (mp0) cc_final: 0.5682 (mp0) REVERT: Cb 110 PHE cc_start: 0.7802 (m-80) cc_final: 0.7465 (t80) REVERT: Cb 249 MET cc_start: 0.8780 (mmp) cc_final: 0.7972 (ttm) REVERT: Ch 331 ARG cc_start: 0.8235 (mmt180) cc_final: 0.7260 (ptt180) REVERT: LB 119 TYR cc_start: 0.8221 (m-80) cc_final: 0.7930 (m-80) REVERT: LB 135 LYS cc_start: 0.8443 (mtmt) cc_final: 0.8212 (tttt) REVERT: LB 227 PHE cc_start: 0.6036 (OUTLIER) cc_final: 0.4788 (m-10) REVERT: LC 56 LYS cc_start: 0.6550 (mtmt) cc_final: 0.5524 (mmtm) REVERT: LC 228 ASN cc_start: 0.6611 (t160) cc_final: 0.6256 (t0) REVERT: LC 304 LYS cc_start: 0.8163 (mttp) cc_final: 0.7897 (tttt) REVERT: LC 350 LYS cc_start: 0.8849 (ttpt) cc_final: 0.8623 (ttpp) REVERT: LE 33 GLU cc_start: 0.7006 (tm-30) cc_final: 0.6047 (tp30) REVERT: LE 56 THR cc_start: 0.9507 (m) cc_final: 0.9247 (m) REVERT: LF 134 LYS cc_start: 0.8704 (tttt) cc_final: 0.8310 (tptt) REVERT: LF 172 ASN cc_start: 0.8496 (m-40) cc_final: 0.8029 (p0) REVERT: LG 55 TRP cc_start: 0.7308 (m100) cc_final: 0.6925 (m100) REVERT: LG 64 GLN cc_start: 0.8633 (mt0) cc_final: 0.8289 (mt0) REVERT: LG 159 ASP cc_start: 0.8720 (p0) cc_final: 0.8454 (p0) REVERT: LH 100 ASN cc_start: 0.8527 (t0) cc_final: 0.8258 (t0) REVERT: LH 170 ARG cc_start: 0.7877 (mtp180) cc_final: 0.7545 (ttp80) REVERT: LH 173 ASP cc_start: 0.8465 (t0) cc_final: 0.8054 (t70) REVERT: LK 121 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.7975 (t80) REVERT: LK 132 ILE cc_start: 0.9286 (OUTLIER) cc_final: 0.9024 (tp) REVERT: LL 78 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7143 (tt0) REVERT: LL 114 GLN cc_start: 0.7796 (tp40) cc_final: 0.7303 (tp40) REVERT: LM 42 ASP cc_start: 0.8639 (t0) cc_final: 0.7916 (t0) REVERT: LO 146 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7080 (mp0) REVERT: LO 170 TYR cc_start: 0.9129 (t80) cc_final: 0.8909 (t80) REVERT: LP 3 ARG cc_start: 0.6612 (ptm160) cc_final: 0.6308 (ttp-170) REVERT: LP 40 LYS cc_start: 0.8702 (mmmt) cc_final: 0.8486 (mmmt) REVERT: LP 75 GLN cc_start: 0.6715 (pt0) cc_final: 0.6212 (mm110) REVERT: LP 89 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8134 (tt0) REVERT: LP 147 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7154 (tm-30) REVERT: LQ 117 ASP cc_start: 0.8850 (t0) cc_final: 0.8465 (t0) REVERT: LS 5 GLN cc_start: 0.8246 (mm-40) cc_final: 0.7715 (mp10) REVERT: LS 21 ASN cc_start: 0.7973 (t0) cc_final: 0.7370 (t0) REVERT: LS 55 THR cc_start: 0.8759 (p) cc_final: 0.8220 (t) REVERT: LS 75 PHE cc_start: 0.8941 (m-80) cc_final: 0.8712 (m-80) REVERT: LS 81 TYR cc_start: 0.8479 (p90) cc_final: 0.8248 (p90) REVERT: LS 117 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.7228 (mtt180) REVERT: LT 52 MET cc_start: 0.4881 (ptm) cc_final: 0.3509 (mtt) REVERT: LT 103 GLU cc_start: 0.9192 (pt0) cc_final: 0.8865 (pm20) REVERT: LT 146 ASN cc_start: 0.8504 (m-40) cc_final: 0.7919 (m-40) REVERT: LV 65 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8290 (tmtt) REVERT: LV 72 ARG cc_start: 0.8264 (ttm110) cc_final: 0.8024 (mtt-85) REVERT: LY 54 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7936 (tp30) REVERT: LY 92 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7508 (tm-30) REVERT: LY 93 THR cc_start: 0.7676 (p) cc_final: 0.7379 (t) REVERT: LY 126 GLU cc_start: 0.8273 (mp0) cc_final: 0.7928 (mt-10) REVERT: Le 6 LYS cc_start: 0.8009 (ttmm) cc_final: 0.7034 (tptt) REVERT: Le 114 LYS cc_start: 0.8863 (tptt) cc_final: 0.8552 (tttt) REVERT: Lf 60 GLU cc_start: 0.7412 (mt-10) cc_final: 0.7086 (mt-10) REVERT: Lh 16 ASN cc_start: 0.7658 (p0) cc_final: 0.7336 (p0) REVERT: Lh 108 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7641 (ptpt) REVERT: Lj 30 GLN cc_start: 0.8228 (mm-40) cc_final: 0.8005 (mm-40) REVERT: Lq 63 MET cc_start: 0.6927 (mpp) cc_final: 0.6148 (mpp) REVERT: Lq 66 CYS cc_start: 0.8944 (p) cc_final: 0.8529 (p) REVERT: Lq 103 LEU cc_start: 0.9491 (tp) cc_final: 0.9107 (pp) REVERT: Lq 174 MET cc_start: 0.5245 (ppp) cc_final: 0.4344 (ppp) REVERT: Lq 184 MET cc_start: 0.6623 (mmm) cc_final: 0.6088 (mmm) REVERT: Lq 188 ASN cc_start: 0.8545 (m-40) cc_final: 0.8269 (m-40) REVERT: Cc 37 GLN cc_start: 0.7724 (mm110) cc_final: 0.7132 (tm-30) REVERT: Cc 105 ASP cc_start: 0.6906 (OUTLIER) cc_final: 0.6233 (m-30) REVERT: Cc 171 GLU cc_start: 0.8429 (pm20) cc_final: 0.8225 (pm20) REVERT: Cc 172 GLU cc_start: 0.8518 (pm20) cc_final: 0.8311 (pm20) REVERT: Cc 189 ILE cc_start: 0.9165 (mm) cc_final: 0.8921 (mm) REVERT: Cd 26 GLN cc_start: 0.7889 (mm-40) cc_final: 0.7640 (mm-40) REVERT: Cd 37 ARG cc_start: 0.8154 (ttm110) cc_final: 0.7749 (mtt90) REVERT: Cd 224 ASN cc_start: 0.7552 (t0) cc_final: 0.7183 (t0) REVERT: Cd 338 LEU cc_start: 0.9105 (mm) cc_final: 0.8813 (mm) REVERT: Ce 10 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7570 (pt) REVERT: Ce 149 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.6786 (mp0) REVERT: Cf 446 MET cc_start: 0.2540 (ptm) cc_final: 0.2227 (ptt) REVERT: Cf 513 ILE cc_start: 0.8714 (mm) cc_final: 0.8466 (mt) REVERT: Cg 116 PHE cc_start: 0.8800 (m-80) cc_final: 0.8333 (m-80) REVERT: Cg 337 MET cc_start: 0.7691 (mpp) cc_final: 0.7254 (pmm) outliers start: 374 outliers final: 233 residues processed: 1947 average time/residue: 1.1919 time to fit residues: 4020.2324 Evaluate side-chains 1864 residues out of total 8922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 1610 time to evaluate : 8.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 47 ARG Chi-restraints excluded: chain CA residue 65 ASP Chi-restraints excluded: chain CA residue 70 THR Chi-restraints excluded: chain CA residue 72 SER Chi-restraints excluded: chain CA residue 113 VAL Chi-restraints excluded: chain CA residue 118 GLN Chi-restraints excluded: chain CA residue 143 ASP Chi-restraints excluded: chain CA residue 148 GLN Chi-restraints excluded: chain CA residue 184 VAL Chi-restraints excluded: chain CA residue 186 ASP Chi-restraints excluded: chain CA residue 227 THR Chi-restraints excluded: chain CA residue 295 GLN Chi-restraints excluded: chain CB residue 44 ASP Chi-restraints excluded: chain CB residue 131 SER Chi-restraints excluded: chain CB residue 151 ASP Chi-restraints excluded: chain CB residue 170 THR Chi-restraints excluded: chain CB residue 185 MET Chi-restraints excluded: chain CB residue 283 VAL Chi-restraints excluded: chain CC residue 118 LEU Chi-restraints excluded: chain CC residue 182 SER Chi-restraints excluded: chain CC residue 246 LEU Chi-restraints excluded: chain CC residue 258 THR Chi-restraints excluded: chain CC residue 265 VAL Chi-restraints excluded: chain CE residue 184 THR Chi-restraints excluded: chain CE residue 209 TYR Chi-restraints excluded: chain CE residue 237 LEU Chi-restraints excluded: chain CE residue 301 THR Chi-restraints excluded: chain CE residue 382 LEU Chi-restraints excluded: chain CE residue 442 ILE Chi-restraints excluded: chain CE residue 472 HIS Chi-restraints excluded: chain CE residue 485 PHE Chi-restraints excluded: chain CE residue 496 GLN Chi-restraints excluded: chain CE residue 555 ILE Chi-restraints excluded: chain CF residue 34 ILE Chi-restraints excluded: chain CF residue 139 THR Chi-restraints excluded: chain CF residue 142 VAL Chi-restraints excluded: chain CF residue 174 MET Chi-restraints excluded: chain CF residue 179 VAL Chi-restraints excluded: chain CF residue 194 ILE Chi-restraints excluded: chain CG residue 59 VAL Chi-restraints excluded: chain CG residue 65 LEU Chi-restraints excluded: chain CG residue 67 LEU Chi-restraints excluded: chain CH residue 55 THR Chi-restraints excluded: chain CH residue 56 CYS Chi-restraints excluded: chain CH residue 203 LEU Chi-restraints excluded: chain CH residue 264 LYS Chi-restraints excluded: chain CH residue 338 LEU Chi-restraints excluded: chain CH residue 359 THR Chi-restraints excluded: chain CH residue 387 VAL Chi-restraints excluded: chain CH residue 473 PHE Chi-restraints excluded: chain CI residue 210 PHE Chi-restraints excluded: chain CI residue 224 THR Chi-restraints excluded: chain CI residue 260 CYS Chi-restraints excluded: chain CJ residue 17 MET Chi-restraints excluded: chain CJ residue 158 THR Chi-restraints excluded: chain CJ residue 190 LEU Chi-restraints excluded: chain CK residue 130 GLU Chi-restraints excluded: chain CK residue 152 THR Chi-restraints excluded: chain CK residue 155 THR Chi-restraints excluded: chain CK residue 212 LEU Chi-restraints excluded: chain CK residue 227 ASP Chi-restraints excluded: chain CK residue 237 ILE Chi-restraints excluded: chain CK residue 258 VAL Chi-restraints excluded: chain CL residue 18 THR Chi-restraints excluded: chain CL residue 38 LEU Chi-restraints excluded: chain CM residue 147 LEU Chi-restraints excluded: chain CM residue 148 LYS Chi-restraints excluded: chain CM residue 153 LEU Chi-restraints excluded: chain CM residue 244 LEU Chi-restraints excluded: chain CN residue 1 MET Chi-restraints excluded: chain CN residue 166 SER Chi-restraints excluded: chain CN residue 197 MET Chi-restraints excluded: chain CN residue 198 VAL Chi-restraints excluded: chain CN residue 215 LEU Chi-restraints excluded: chain CO residue 19 LYS Chi-restraints excluded: chain CO residue 34 SER Chi-restraints excluded: chain CO residue 37 LEU Chi-restraints excluded: chain CO residue 40 ILE Chi-restraints excluded: chain CO residue 94 LYS Chi-restraints excluded: chain CP residue 267 LEU Chi-restraints excluded: chain CP residue 277 ASN Chi-restraints excluded: chain CP residue 306 VAL Chi-restraints excluded: chain CP residue 319 ASP Chi-restraints excluded: chain CP residue 349 VAL Chi-restraints excluded: chain CP residue 454 LEU Chi-restraints excluded: chain CP residue 524 VAL Chi-restraints excluded: chain CP residue 560 LEU Chi-restraints excluded: chain CQ residue 1 MET Chi-restraints excluded: chain CQ residue 6 CYS Chi-restraints excluded: chain CQ residue 34 SER Chi-restraints excluded: chain CQ residue 89 THR Chi-restraints excluded: chain CR residue 33 ASN Chi-restraints excluded: chain CR residue 46 SER Chi-restraints excluded: chain CR residue 221 THR Chi-restraints excluded: chain CS residue 673 LYS Chi-restraints excluded: chain CS residue 692 LEU Chi-restraints excluded: chain CS residue 699 ASP Chi-restraints excluded: chain CU residue 219 SER Chi-restraints excluded: chain CU residue 228 ASP Chi-restraints excluded: chain CU residue 315 VAL Chi-restraints excluded: chain CU residue 320 GLN Chi-restraints excluded: chain CU residue 335 ASN Chi-restraints excluded: chain CU residue 366 LEU Chi-restraints excluded: chain CX residue 105 LEU Chi-restraints excluded: chain CX residue 133 ARG Chi-restraints excluded: chain Cz residue 50 LEU Chi-restraints excluded: chain Cb residue 237 TYR Chi-restraints excluded: chain Cb residue 255 LEU Chi-restraints excluded: chain Cb residue 301 VAL Chi-restraints excluded: chain Cb residue 328 ILE Chi-restraints excluded: chain Cb residue 439 ILE Chi-restraints excluded: chain Cb residue 440 ASN Chi-restraints excluded: chain Cb residue 506 VAL Chi-restraints excluded: chain LB residue 109 HIS Chi-restraints excluded: chain LB residue 227 PHE Chi-restraints excluded: chain LB residue 277 THR Chi-restraints excluded: chain LB residue 294 ASN Chi-restraints excluded: chain LB residue 297 THR Chi-restraints excluded: chain LB residue 318 VAL Chi-restraints excluded: chain LB residue 320 ASN Chi-restraints excluded: chain LB residue 352 LEU Chi-restraints excluded: chain LB residue 364 SER Chi-restraints excluded: chain LC residue 61 THR Chi-restraints excluded: chain LC residue 181 ASP Chi-restraints excluded: chain LC residue 277 LEU Chi-restraints excluded: chain LC residue 294 THR Chi-restraints excluded: chain LC residue 300 LEU Chi-restraints excluded: chain LC residue 323 LYS Chi-restraints excluded: chain LE residue 129 THR Chi-restraints excluded: chain LE residue 138 SER Chi-restraints excluded: chain LE residue 186 SER Chi-restraints excluded: chain LF residue 10 ASN Chi-restraints excluded: chain LF residue 14 VAL Chi-restraints excluded: chain LF residue 89 LEU Chi-restraints excluded: chain LF residue 100 LYS Chi-restraints excluded: chain LF residue 101 ILE Chi-restraints excluded: chain LF residue 126 THR Chi-restraints excluded: chain LF residue 170 THR Chi-restraints excluded: chain LF residue 189 ASP Chi-restraints excluded: chain LG residue 89 LEU Chi-restraints excluded: chain LG residue 113 LEU Chi-restraints excluded: chain LG residue 117 THR Chi-restraints excluded: chain LG residue 129 SER Chi-restraints excluded: chain LG residue 139 LEU Chi-restraints excluded: chain LG residue 191 THR Chi-restraints excluded: chain LG residue 197 THR Chi-restraints excluded: chain LG residue 201 VAL Chi-restraints excluded: chain LG residue 203 ILE Chi-restraints excluded: chain LG residue 204 THR Chi-restraints excluded: chain LG residue 218 ILE Chi-restraints excluded: chain LG residue 229 VAL Chi-restraints excluded: chain LH residue 16 LEU Chi-restraints excluded: chain LH residue 56 GLU Chi-restraints excluded: chain LH residue 128 VAL Chi-restraints excluded: chain LH residue 134 VAL Chi-restraints excluded: chain LH residue 137 GLU Chi-restraints excluded: chain LH residue 149 SER Chi-restraints excluded: chain LH residue 165 GLN Chi-restraints excluded: chain LH residue 167 CYS Chi-restraints excluded: chain LH residue 171 ASN Chi-restraints excluded: chain LK residue 100 HIS Chi-restraints excluded: chain LK residue 121 PHE Chi-restraints excluded: chain LK residue 132 ILE Chi-restraints excluded: chain LK residue 147 SER Chi-restraints excluded: chain LL residue 17 HIS Chi-restraints excluded: chain LL residue 46 LEU Chi-restraints excluded: chain LL residue 62 THR Chi-restraints excluded: chain LL residue 78 GLU Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LM residue 98 ASN Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LN residue 97 SER Chi-restraints excluded: chain LN residue 101 THR Chi-restraints excluded: chain LN residue 110 CYS Chi-restraints excluded: chain LN residue 125 SER Chi-restraints excluded: chain LN residue 178 HIS Chi-restraints excluded: chain LN residue 181 ASN Chi-restraints excluded: chain LO residue 34 ILE Chi-restraints excluded: chain LO residue 106 VAL Chi-restraints excluded: chain LO residue 128 VAL Chi-restraints excluded: chain LO residue 146 GLU Chi-restraints excluded: chain LO residue 147 VAL Chi-restraints excluded: chain LP residue 12 THR Chi-restraints excluded: chain LP residue 20 SER Chi-restraints excluded: chain LP residue 29 THR Chi-restraints excluded: chain LP residue 52 ILE Chi-restraints excluded: chain LP residue 147 GLU Chi-restraints excluded: chain LQ residue 52 VAL Chi-restraints excluded: chain LQ residue 69 GLU Chi-restraints excluded: chain LQ residue 108 VAL Chi-restraints excluded: chain LQ residue 148 THR Chi-restraints excluded: chain LS residue 13 HIS Chi-restraints excluded: chain LS residue 59 VAL Chi-restraints excluded: chain LS residue 65 SER Chi-restraints excluded: chain LS residue 72 VAL Chi-restraints excluded: chain LS residue 87 THR Chi-restraints excluded: chain LS residue 117 ARG Chi-restraints excluded: chain LS residue 133 GLU Chi-restraints excluded: chain LS residue 171 SER Chi-restraints excluded: chain LT residue 42 ILE Chi-restraints excluded: chain LT residue 66 ASN Chi-restraints excluded: chain LT residue 72 VAL Chi-restraints excluded: chain LT residue 97 LYS Chi-restraints excluded: chain LT residue 143 ILE Chi-restraints excluded: chain LT residue 145 ASP Chi-restraints excluded: chain LV residue 21 VAL Chi-restraints excluded: chain LV residue 65 LYS Chi-restraints excluded: chain LY residue 1 MET Chi-restraints excluded: chain LY residue 55 VAL Chi-restraints excluded: chain LY residue 70 THR Chi-restraints excluded: chain LY residue 85 THR Chi-restraints excluded: chain LY residue 128 VAL Chi-restraints excluded: chain Le residue 8 VAL Chi-restraints excluded: chain Le residue 24 ASP Chi-restraints excluded: chain Le residue 31 SER Chi-restraints excluded: chain Le residue 121 THR Chi-restraints excluded: chain Le residue 129 THR Chi-restraints excluded: chain Lf residue 32 ILE Chi-restraints excluded: chain Lf residue 37 VAL Chi-restraints excluded: chain Lf residue 99 SER Chi-restraints excluded: chain Lf residue 108 SER Chi-restraints excluded: chain Lh residue 36 ILE Chi-restraints excluded: chain Lh residue 108 LYS Chi-restraints excluded: chain Li residue 27 THR Chi-restraints excluded: chain Li residue 66 VAL Chi-restraints excluded: chain Li residue 70 LEU Chi-restraints excluded: chain Li residue 106 SER Chi-restraints excluded: chain Lj residue 26 SER Chi-restraints excluded: chain Lj residue 61 THR Chi-restraints excluded: chain Lj residue 68 SER Chi-restraints excluded: chain Lj residue 69 THR Chi-restraints excluded: chain Lj residue 82 VAL Chi-restraints excluded: chain Cc residue 17 SER Chi-restraints excluded: chain Cc residue 30 HIS Chi-restraints excluded: chain Cc residue 54 LEU Chi-restraints excluded: chain Cc residue 96 THR Chi-restraints excluded: chain Cc residue 105 ASP Chi-restraints excluded: chain Cc residue 106 VAL Chi-restraints excluded: chain Cd residue 70 ASP Chi-restraints excluded: chain Cd residue 86 VAL Chi-restraints excluded: chain Cd residue 220 SER Chi-restraints excluded: chain Cd residue 231 THR Chi-restraints excluded: chain Cd residue 286 THR Chi-restraints excluded: chain Cd residue 290 ARG Chi-restraints excluded: chain Cd residue 311 LEU Chi-restraints excluded: chain Cd residue 427 MET Chi-restraints excluded: chain Ce residue 10 ILE Chi-restraints excluded: chain Ce residue 73 MET Chi-restraints excluded: chain Ce residue 149 GLU Chi-restraints excluded: chain Cf residue 484 VAL Chi-restraints excluded: chain Cg residue 67 LEU Chi-restraints excluded: chain Cg residue 91 LEU Chi-restraints excluded: chain Cg residue 213 ASN Chi-restraints excluded: chain Cg residue 352 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1262 random chunks: chunk 1015 optimal weight: 2.9990 chunk 692 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 908 optimal weight: 2.9990 chunk 503 optimal weight: 7.9990 chunk 1040 optimal weight: 4.9990 chunk 843 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 622 optimal weight: 5.9990 chunk 1094 optimal weight: 0.9980 chunk 307 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** CA 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 246 GLN ** CB 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 105 GLN ** CB 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 174 ASN ** CC 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CI 256 HIS ** CI 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CN 168 GLN ** CP 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CP 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CP 485 HIS CP 487 GLN CQ 70 GLN CR 47 GLN ** CR 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CU 336 GLN ** Cb 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 121 ASN ** LB 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 297 GLN LF 178 ASN ** LH 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LH 165 GLN LK 100 HIS LK 142 GLN LL 17 HIS LL 66 ASN LM 110 GLN ** LQ 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 98 ASN ** LT 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LT 146 ASN ** LV 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LV 100 ASN LY 116 ASN Li 72 ASN Ce 41 GLN Cf 524 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 141322 Z= 0.276 Angle : 0.661 27.709 202294 Z= 0.333 Chirality : 0.041 1.924 24461 Planarity : 0.006 0.100 16966 Dihedral : 22.013 176.000 48692 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.94 % Favored : 94.85 % Rotamer: Outliers : 4.86 % Allowed : 19.52 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.02 % Twisted Proline : 0.38 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.08), residues: 10278 helix: 1.19 (0.08), residues: 4630 sheet: -0.13 (0.14), residues: 1344 loop : -0.93 (0.09), residues: 4304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPCJ 460 HIS 0.022 0.001 HISLK 100 PHE 0.039 0.002 PHECh 334 TYR 0.028 0.002 TYRLB 123 ARG 0.012 0.001 ARGCG 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20556 Ramachandran restraints generated. 10278 Oldfield, 0 Emsley, 10278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20556 Ramachandran restraints generated. 10278 Oldfield, 0 Emsley, 10278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2061 residues out of total 8922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 421 poor density : 1640 time to evaluate : 8.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CA 76 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7376 (tp30) REVERT: CA 262 ILE cc_start: 0.8278 (mp) cc_final: 0.7863 (tt) REVERT: CB 147 PHE cc_start: 0.8859 (t80) cc_final: 0.8443 (t80) REVERT: CC 137 TYR cc_start: 0.8237 (p90) cc_final: 0.7649 (p90) REVERT: CC 141 LYS cc_start: 0.8414 (tppt) cc_final: 0.8153 (tptm) REVERT: CC 193 LYS cc_start: 0.8878 (pptt) cc_final: 0.8656 (pptt) REVERT: CC 246 LEU cc_start: 0.5104 (OUTLIER) cc_final: 0.4671 (mp) REVERT: CC 381 ASP cc_start: 0.8988 (m-30) cc_final: 0.8298 (p0) REVERT: CE 226 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7954 (mt-10) REVERT: CE 540 LYS cc_start: 0.8412 (mmmt) cc_final: 0.8195 (mmmt) REVERT: CF 41 PHE cc_start: 0.7515 (m-80) cc_final: 0.7239 (m-80) REVERT: CF 194 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8166 (mt) REVERT: CH 33 ARG cc_start: 0.3931 (mmt180) cc_final: 0.3291 (mtm180) REVERT: CH 150 ASP cc_start: 0.8730 (t0) cc_final: 0.8503 (t0) REVERT: CH 199 THR cc_start: 0.8783 (m) cc_final: 0.8427 (p) REVERT: CH 220 THR cc_start: 0.8606 (m) cc_final: 0.8033 (p) REVERT: CH 231 MET cc_start: 0.8286 (mmt) cc_final: 0.7884 (mmt) REVERT: CH 236 MET cc_start: 0.8583 (mmm) cc_final: 0.7993 (tpp) REVERT: CH 253 MET cc_start: 0.7792 (pmm) cc_final: 0.7436 (pmm) REVERT: CH 297 LEU cc_start: 0.7239 (pt) cc_final: 0.6947 (pt) REVERT: CH 333 HIS cc_start: 0.8320 (t70) cc_final: 0.8064 (t-170) REVERT: CH 437 ILE cc_start: 0.8459 (mt) cc_final: 0.8150 (mt) REVERT: CI 250 LYS cc_start: 0.8450 (mptt) cc_final: 0.8244 (mmtm) REVERT: CI 274 LYS cc_start: 0.8258 (ptmm) cc_final: 0.7974 (ptmm) REVERT: CJ 190 LEU cc_start: 0.3652 (OUTLIER) cc_final: 0.3450 (pp) REVERT: CJ 196 TYR cc_start: 0.8755 (m-80) cc_final: 0.8378 (m-80) REVERT: CJ 230 PHE cc_start: 0.9125 (m-80) cc_final: 0.8723 (m-80) REVERT: CK 67 GLN cc_start: 0.8146 (mt0) cc_final: 0.7668 (tm-30) REVERT: CK 110 ARG cc_start: 0.8853 (mtp85) cc_final: 0.8629 (mtp85) REVERT: CK 132 MET cc_start: 0.6739 (tpp) cc_final: 0.6523 (tpp) REVERT: CK 163 ARG cc_start: 0.7061 (ptt180) cc_final: 0.6325 (ptt180) REVERT: CK 179 TYR cc_start: 0.9171 (m-80) cc_final: 0.8882 (m-10) REVERT: CK 201 LYS cc_start: 0.8871 (mmpt) cc_final: 0.8476 (mtmt) REVERT: CK 212 LEU cc_start: 0.9587 (OUTLIER) cc_final: 0.9270 (mm) REVERT: CL 23 LYS cc_start: 0.7633 (ttmm) cc_final: 0.7068 (tptt) REVERT: CL 63 GLU cc_start: 0.9246 (mm-30) cc_final: 0.8969 (mm-30) REVERT: CL 73 ARG cc_start: 0.9086 (tmm-80) cc_final: 0.8565 (ttp80) REVERT: CM 139 TRP cc_start: 0.7525 (m-90) cc_final: 0.6970 (m-90) REVERT: CM 190 LEU cc_start: 0.9126 (mt) cc_final: 0.8842 (mt) REVERT: CM 209 TRP cc_start: 0.7867 (m100) cc_final: 0.7394 (m100) REVERT: CN 57 ARG cc_start: 0.8149 (ttm-80) cc_final: 0.7801 (mtp85) REVERT: CN 95 GLN cc_start: 0.8767 (tp40) cc_final: 0.8566 (tp40) REVERT: CN 245 PHE cc_start: 0.9054 (m-80) cc_final: 0.8690 (m-10) REVERT: CO 3 LYS cc_start: 0.7598 (mmmt) cc_final: 0.7241 (mttt) REVERT: CP 374 MET cc_start: 0.8129 (mtp) cc_final: 0.7811 (mtp) REVERT: CP 398 MET cc_start: 0.7864 (ppp) cc_final: 0.7448 (ppp) REVERT: CP 402 MET cc_start: 0.6703 (ptp) cc_final: 0.6321 (ptt) REVERT: CP 524 VAL cc_start: 0.9172 (OUTLIER) cc_final: 0.8943 (p) REVERT: CP 552 MET cc_start: 0.8371 (mmm) cc_final: 0.8016 (mmm) REVERT: CP 581 PHE cc_start: 0.7937 (m-10) cc_final: 0.7689 (m-10) REVERT: CQ 8 PHE cc_start: 0.8724 (t80) cc_final: 0.8117 (t80) REVERT: CQ 45 ASN cc_start: 0.8423 (t0) cc_final: 0.7720 (t0) REVERT: CQ 49 LEU cc_start: 0.8951 (mp) cc_final: 0.8646 (mp) REVERT: CQ 51 TRP cc_start: 0.8552 (p-90) cc_final: 0.7951 (p-90) REVERT: CQ 55 TYR cc_start: 0.8890 (t80) cc_final: 0.8431 (t80) REVERT: CR 18 ARG cc_start: 0.8196 (ttm-80) cc_final: 0.7894 (ttp-170) REVERT: CR 73 LEU cc_start: 0.6069 (tp) cc_final: 0.5787 (tp) REVERT: CR 135 GLN cc_start: 0.7703 (tm-30) cc_final: 0.7398 (tm-30) REVERT: CS 475 MET cc_start: 0.7959 (mtt) cc_final: 0.7506 (mtp) REVERT: CU 282 MET cc_start: 0.9149 (mmp) cc_final: 0.8866 (mmp) REVERT: CU 320 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.7421 (mp10) REVERT: CU 364 ASN cc_start: 0.8828 (p0) cc_final: 0.8562 (p0) REVERT: Cb 110 PHE cc_start: 0.7821 (m-80) cc_final: 0.7443 (t80) REVERT: Cb 249 MET cc_start: 0.8787 (mmp) cc_final: 0.8001 (ttm) REVERT: Ch 292 LYS cc_start: 0.7363 (ptpp) cc_final: 0.7141 (ptpp) REVERT: Ch 295 ASN cc_start: 0.8565 (p0) cc_final: 0.7960 (m-40) REVERT: Ch 331 ARG cc_start: 0.8218 (mmt180) cc_final: 0.7502 (ptt180) REVERT: LB 118 PHE cc_start: 0.8139 (m-80) cc_final: 0.7860 (m-80) REVERT: LB 227 PHE cc_start: 0.6051 (OUTLIER) cc_final: 0.4785 (m-10) REVERT: LB 284 TYR cc_start: 0.8166 (OUTLIER) cc_final: 0.7767 (m-10) REVERT: LC 276 PHE cc_start: 0.8220 (p90) cc_final: 0.7996 (p90) REVERT: LC 304 LYS cc_start: 0.8103 (mttp) cc_final: 0.7836 (tttt) REVERT: LC 322 ASN cc_start: 0.8733 (t0) cc_final: 0.8516 (t0) REVERT: LC 350 LYS cc_start: 0.8886 (ttpt) cc_final: 0.8634 (ttpp) REVERT: LE 33 GLU cc_start: 0.7060 (tm-30) cc_final: 0.5964 (tp30) REVERT: LE 53 GLN cc_start: 0.8386 (mm-40) cc_final: 0.7681 (mp10) REVERT: LE 56 THR cc_start: 0.9498 (m) cc_final: 0.9236 (m) REVERT: LE 127 TYR cc_start: 0.8777 (t80) cc_final: 0.8556 (t80) REVERT: LF 66 ARG cc_start: 0.7981 (mmm-85) cc_final: 0.7532 (mmm160) REVERT: LF 67 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7984 (pt0) REVERT: LF 98 ILE cc_start: 0.5692 (OUTLIER) cc_final: 0.5435 (pt) REVERT: LF 134 LYS cc_start: 0.8822 (tttt) cc_final: 0.8361 (tptt) REVERT: LF 172 ASN cc_start: 0.8506 (m-40) cc_final: 0.8001 (p0) REVERT: LG 55 TRP cc_start: 0.7307 (m100) cc_final: 0.6873 (m100) REVERT: LG 64 GLN cc_start: 0.8648 (mt0) cc_final: 0.8365 (mt0) REVERT: LG 159 ASP cc_start: 0.8761 (p0) cc_final: 0.8348 (p0) REVERT: LH 100 ASN cc_start: 0.8522 (t0) cc_final: 0.8245 (t0) REVERT: LH 137 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7762 (mt-10) REVERT: LH 170 ARG cc_start: 0.7862 (mtp180) cc_final: 0.7530 (ttp80) REVERT: LH 173 ASP cc_start: 0.8467 (t0) cc_final: 0.8087 (t70) REVERT: LK 83 ARG cc_start: 0.8415 (mmm160) cc_final: 0.8170 (mmm160) REVERT: LK 121 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.8024 (t80) REVERT: LK 132 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.9007 (tp) REVERT: LL 66 ASN cc_start: 0.8635 (OUTLIER) cc_final: 0.8282 (m110) REVERT: LL 78 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7139 (tt0) REVERT: LL 114 GLN cc_start: 0.7837 (tp40) cc_final: 0.7317 (tp40) REVERT: LM 42 ASP cc_start: 0.8622 (t0) cc_final: 0.7918 (t0) REVERT: LO 146 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7140 (mp0) REVERT: LO 170 TYR cc_start: 0.9090 (t80) cc_final: 0.8760 (t80) REVERT: LP 40 LYS cc_start: 0.8837 (mmmt) cc_final: 0.8545 (mmmt) REVERT: LP 75 GLN cc_start: 0.6774 (pt0) cc_final: 0.6162 (mm110) REVERT: LQ 117 ASP cc_start: 0.8865 (t0) cc_final: 0.8539 (t0) REVERT: LS 5 GLN cc_start: 0.8253 (mm-40) cc_final: 0.7689 (mp10) REVERT: LS 21 ASN cc_start: 0.8103 (t0) cc_final: 0.7487 (t0) REVERT: LS 55 THR cc_start: 0.8768 (p) cc_final: 0.8243 (t) REVERT: LS 60 SER cc_start: 0.9095 (t) cc_final: 0.8773 (m) REVERT: LS 75 PHE cc_start: 0.9059 (m-80) cc_final: 0.8564 (m-80) REVERT: LS 79 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7636 (mt) REVERT: LS 81 TYR cc_start: 0.8589 (p90) cc_final: 0.8133 (p90) REVERT: LS 117 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.7213 (mtt180) REVERT: LT 52 MET cc_start: 0.4725 (ptm) cc_final: 0.3463 (mtt) REVERT: LT 103 GLU cc_start: 0.9150 (pt0) cc_final: 0.8805 (pm20) REVERT: LV 65 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8221 (tmtt) REVERT: LV 72 ARG cc_start: 0.8255 (ttm110) cc_final: 0.8021 (mtt-85) REVERT: LY 51 LYS cc_start: 0.8884 (ttpp) cc_final: 0.8583 (ttpt) REVERT: LY 54 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7944 (tp30) REVERT: LY 92 GLN cc_start: 0.8226 (tm-30) cc_final: 0.7483 (tm-30) REVERT: LY 93 THR cc_start: 0.7750 (p) cc_final: 0.7496 (p) REVERT: LY 126 GLU cc_start: 0.8265 (mt-10) cc_final: 0.8034 (mt-10) REVERT: Le 6 LYS cc_start: 0.8025 (ttmm) cc_final: 0.7068 (tptt) REVERT: Le 30 ASP cc_start: 0.7631 (t70) cc_final: 0.7234 (t0) REVERT: Le 96 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6104 (tp30) REVERT: Le 114 LYS cc_start: 0.8853 (tptt) cc_final: 0.8533 (tttt) REVERT: Lf 24 ASN cc_start: 0.6726 (t0) cc_final: 0.5872 (m-40) REVERT: Lh 16 ASN cc_start: 0.7709 (p0) cc_final: 0.7487 (p0) REVERT: Lh 108 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7654 (ptpt) REVERT: Lj 30 GLN cc_start: 0.8325 (mm-40) cc_final: 0.8093 (mm-40) REVERT: Lq 63 MET cc_start: 0.7111 (mpp) cc_final: 0.6158 (mpp) REVERT: Lq 66 CYS cc_start: 0.9107 (p) cc_final: 0.8770 (p) REVERT: Lq 103 LEU cc_start: 0.9499 (tp) cc_final: 0.9102 (pp) REVERT: Lq 174 MET cc_start: 0.5245 (ppp) cc_final: 0.4998 (ppp) REVERT: Lq 184 MET cc_start: 0.6497 (mmm) cc_final: 0.5946 (mmm) REVERT: Lq 188 ASN cc_start: 0.8570 (m-40) cc_final: 0.8289 (m-40) REVERT: Lq 206 ILE cc_start: 0.4570 (OUTLIER) cc_final: 0.3931 (tt) REVERT: Cc 37 GLN cc_start: 0.7661 (mm110) cc_final: 0.7110 (tm-30) REVERT: Cc 105 ASP cc_start: 0.6936 (OUTLIER) cc_final: 0.6280 (m-30) REVERT: Cd 26 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7653 (mm-40) REVERT: Cd 37 ARG cc_start: 0.8176 (ttm110) cc_final: 0.7716 (mtt90) REVERT: Cd 224 ASN cc_start: 0.7676 (t0) cc_final: 0.7283 (t0) REVERT: Cd 338 LEU cc_start: 0.9094 (mm) cc_final: 0.8778 (mm) REVERT: Ce 149 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.6748 (mp0) REVERT: Cf 510 LYS cc_start: 0.7240 (mttp) cc_final: 0.6932 (ptpp) REVERT: Cf 513 ILE cc_start: 0.8741 (mm) cc_final: 0.8501 (mt) REVERT: Cf 524 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7271 (mt0) REVERT: Cf 529 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7050 (mm-30) REVERT: Cg 116 PHE cc_start: 0.8750 (m-80) cc_final: 0.8311 (m-80) REVERT: Cg 337 MET cc_start: 0.7615 (mpp) cc_final: 0.7167 (pmm) outliers start: 421 outliers final: 293 residues processed: 1901 average time/residue: 1.1595 time to fit residues: 3833.3325 Evaluate side-chains 1875 residues out of total 8922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 318 poor density : 1557 time to evaluate : 8.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 47 ARG Chi-restraints excluded: chain CA residue 65 ASP Chi-restraints excluded: chain CA residue 70 THR Chi-restraints excluded: chain CA residue 72 SER Chi-restraints excluded: chain CA residue 109 ASN Chi-restraints excluded: chain CA residue 113 VAL Chi-restraints excluded: chain CA residue 118 GLN Chi-restraints excluded: chain CA residue 132 CYS Chi-restraints excluded: chain CA residue 148 GLN Chi-restraints excluded: chain CA residue 184 VAL Chi-restraints excluded: chain CA residue 186 ASP Chi-restraints excluded: chain CA residue 199 VAL Chi-restraints excluded: chain CB residue 44 ASP Chi-restraints excluded: chain CB residue 91 THR Chi-restraints excluded: chain CB residue 131 SER Chi-restraints excluded: chain CB residue 151 ASP Chi-restraints excluded: chain CB residue 170 THR Chi-restraints excluded: chain CB residue 283 VAL Chi-restraints excluded: chain CC residue 118 LEU Chi-restraints excluded: chain CC residue 182 SER Chi-restraints excluded: chain CC residue 246 LEU Chi-restraints excluded: chain CC residue 258 THR Chi-restraints excluded: chain CC residue 265 VAL Chi-restraints excluded: chain CC residue 405 GLU Chi-restraints excluded: chain CE residue 142 ILE Chi-restraints excluded: chain CE residue 184 THR Chi-restraints excluded: chain CE residue 237 LEU Chi-restraints excluded: chain CE residue 301 THR Chi-restraints excluded: chain CE residue 382 LEU Chi-restraints excluded: chain CE residue 412 ILE Chi-restraints excluded: chain CE residue 442 ILE Chi-restraints excluded: chain CE residue 485 PHE Chi-restraints excluded: chain CE residue 496 GLN Chi-restraints excluded: chain CE residue 503 THR Chi-restraints excluded: chain CE residue 555 ILE Chi-restraints excluded: chain CF residue 12 LEU Chi-restraints excluded: chain CF residue 139 THR Chi-restraints excluded: chain CF residue 142 VAL Chi-restraints excluded: chain CF residue 174 MET Chi-restraints excluded: chain CF residue 175 ILE Chi-restraints excluded: chain CF residue 179 VAL Chi-restraints excluded: chain CF residue 194 ILE Chi-restraints excluded: chain CF residue 215 CYS Chi-restraints excluded: chain CF residue 226 TYR Chi-restraints excluded: chain CG residue 59 VAL Chi-restraints excluded: chain CG residue 65 LEU Chi-restraints excluded: chain CG residue 67 LEU Chi-restraints excluded: chain CG residue 71 LEU Chi-restraints excluded: chain CH residue 55 THR Chi-restraints excluded: chain CH residue 56 CYS Chi-restraints excluded: chain CH residue 165 THR Chi-restraints excluded: chain CH residue 203 LEU Chi-restraints excluded: chain CH residue 223 ILE Chi-restraints excluded: chain CH residue 226 HIS Chi-restraints excluded: chain CH residue 264 LYS Chi-restraints excluded: chain CH residue 309 THR Chi-restraints excluded: chain CH residue 314 VAL Chi-restraints excluded: chain CH residue 338 LEU Chi-restraints excluded: chain CH residue 359 THR Chi-restraints excluded: chain CH residue 387 VAL Chi-restraints excluded: chain CH residue 425 TRP Chi-restraints excluded: chain CH residue 473 PHE Chi-restraints excluded: chain CI residue 210 PHE Chi-restraints excluded: chain CI residue 224 THR Chi-restraints excluded: chain CI residue 260 CYS Chi-restraints excluded: chain CI residue 282 VAL Chi-restraints excluded: chain CI residue 293 LEU Chi-restraints excluded: chain CJ residue 17 MET Chi-restraints excluded: chain CJ residue 158 THR Chi-restraints excluded: chain CJ residue 190 LEU Chi-restraints excluded: chain CJ residue 374 LEU Chi-restraints excluded: chain CJ residue 456 VAL Chi-restraints excluded: chain CK residue 36 SER Chi-restraints excluded: chain CK residue 130 GLU Chi-restraints excluded: chain CK residue 152 THR Chi-restraints excluded: chain CK residue 155 THR Chi-restraints excluded: chain CK residue 193 VAL Chi-restraints excluded: chain CK residue 212 LEU Chi-restraints excluded: chain CK residue 216 THR Chi-restraints excluded: chain CK residue 227 ASP Chi-restraints excluded: chain CK residue 258 VAL Chi-restraints excluded: chain CL residue 18 THR Chi-restraints excluded: chain CL residue 38 LEU Chi-restraints excluded: chain CM residue 147 LEU Chi-restraints excluded: chain CM residue 148 LYS Chi-restraints excluded: chain CM residue 244 LEU Chi-restraints excluded: chain CN residue 3 VAL Chi-restraints excluded: chain CN residue 147 LEU Chi-restraints excluded: chain CN residue 154 LEU Chi-restraints excluded: chain CN residue 166 SER Chi-restraints excluded: chain CN residue 198 VAL Chi-restraints excluded: chain CN residue 208 LEU Chi-restraints excluded: chain CN residue 215 LEU Chi-restraints excluded: chain CO residue 19 LYS Chi-restraints excluded: chain CO residue 34 SER Chi-restraints excluded: chain CO residue 37 LEU Chi-restraints excluded: chain CO residue 40 ILE Chi-restraints excluded: chain CO residue 94 LYS Chi-restraints excluded: chain CP residue 267 LEU Chi-restraints excluded: chain CP residue 277 ASN Chi-restraints excluded: chain CP residue 280 LEU Chi-restraints excluded: chain CP residue 306 VAL Chi-restraints excluded: chain CP residue 319 ASP Chi-restraints excluded: chain CP residue 349 VAL Chi-restraints excluded: chain CP residue 425 ILE Chi-restraints excluded: chain CP residue 454 LEU Chi-restraints excluded: chain CP residue 465 ILE Chi-restraints excluded: chain CP residue 487 GLN Chi-restraints excluded: chain CP residue 524 VAL Chi-restraints excluded: chain CP residue 560 LEU Chi-restraints excluded: chain CQ residue 1 MET Chi-restraints excluded: chain CQ residue 6 CYS Chi-restraints excluded: chain CQ residue 34 SER Chi-restraints excluded: chain CQ residue 70 GLN Chi-restraints excluded: chain CQ residue 89 THR Chi-restraints excluded: chain CR residue 33 ASN Chi-restraints excluded: chain CR residue 128 SER Chi-restraints excluded: chain CR residue 177 THR Chi-restraints excluded: chain CR residue 221 THR Chi-restraints excluded: chain CS residue 673 LYS Chi-restraints excluded: chain CS residue 692 LEU Chi-restraints excluded: chain CU residue 219 SER Chi-restraints excluded: chain CU residue 228 ASP Chi-restraints excluded: chain CU residue 320 GLN Chi-restraints excluded: chain CU residue 335 ASN Chi-restraints excluded: chain CU residue 360 VAL Chi-restraints excluded: chain CU residue 366 LEU Chi-restraints excluded: chain CX residue 76 THR Chi-restraints excluded: chain CX residue 105 LEU Chi-restraints excluded: chain CX residue 133 ARG Chi-restraints excluded: chain Cb residue 237 TYR Chi-restraints excluded: chain Cb residue 255 LEU Chi-restraints excluded: chain Cb residue 301 VAL Chi-restraints excluded: chain Cb residue 395 TYR Chi-restraints excluded: chain Cb residue 439 ILE Chi-restraints excluded: chain Cb residue 440 ASN Chi-restraints excluded: chain Cb residue 474 ASP Chi-restraints excluded: chain Cb residue 506 VAL Chi-restraints excluded: chain LB residue 24 ARG Chi-restraints excluded: chain LB residue 109 HIS Chi-restraints excluded: chain LB residue 217 ASP Chi-restraints excluded: chain LB residue 225 HIS Chi-restraints excluded: chain LB residue 227 PHE Chi-restraints excluded: chain LB residue 277 THR Chi-restraints excluded: chain LB residue 284 TYR Chi-restraints excluded: chain LB residue 294 ASN Chi-restraints excluded: chain LB residue 297 THR Chi-restraints excluded: chain LB residue 318 VAL Chi-restraints excluded: chain LB residue 320 ASN Chi-restraints excluded: chain LB residue 364 SER Chi-restraints excluded: chain LC residue 35 ILE Chi-restraints excluded: chain LC residue 61 THR Chi-restraints excluded: chain LC residue 79 SER Chi-restraints excluded: chain LC residue 181 ASP Chi-restraints excluded: chain LC residue 185 VAL Chi-restraints excluded: chain LC residue 270 GLU Chi-restraints excluded: chain LC residue 277 LEU Chi-restraints excluded: chain LC residue 294 THR Chi-restraints excluded: chain LC residue 300 LEU Chi-restraints excluded: chain LC residue 323 LYS Chi-restraints excluded: chain LE residue 103 ILE Chi-restraints excluded: chain LE residue 129 THR Chi-restraints excluded: chain LE residue 138 SER Chi-restraints excluded: chain LE residue 186 SER Chi-restraints excluded: chain LF residue 10 ASN Chi-restraints excluded: chain LF residue 14 VAL Chi-restraints excluded: chain LF residue 67 GLU Chi-restraints excluded: chain LF residue 89 LEU Chi-restraints excluded: chain LF residue 98 ILE Chi-restraints excluded: chain LF residue 100 LYS Chi-restraints excluded: chain LF residue 101 ILE Chi-restraints excluded: chain LF residue 126 THR Chi-restraints excluded: chain LF residue 170 THR Chi-restraints excluded: chain LF residue 178 ASN Chi-restraints excluded: chain LF residue 189 ASP Chi-restraints excluded: chain LG residue 85 LEU Chi-restraints excluded: chain LG residue 89 LEU Chi-restraints excluded: chain LG residue 113 LEU Chi-restraints excluded: chain LG residue 117 THR Chi-restraints excluded: chain LG residue 129 SER Chi-restraints excluded: chain LG residue 139 LEU Chi-restraints excluded: chain LG residue 191 THR Chi-restraints excluded: chain LG residue 197 THR Chi-restraints excluded: chain LG residue 203 ILE Chi-restraints excluded: chain LG residue 204 THR Chi-restraints excluded: chain LG residue 218 ILE Chi-restraints excluded: chain LG residue 229 VAL Chi-restraints excluded: chain LH residue 16 LEU Chi-restraints excluded: chain LH residue 38 LEU Chi-restraints excluded: chain LH residue 47 VAL Chi-restraints excluded: chain LH residue 56 GLU Chi-restraints excluded: chain LH residue 101 VAL Chi-restraints excluded: chain LH residue 128 VAL Chi-restraints excluded: chain LH residue 134 VAL Chi-restraints excluded: chain LH residue 137 GLU Chi-restraints excluded: chain LH residue 149 SER Chi-restraints excluded: chain LH residue 165 GLN Chi-restraints excluded: chain LH residue 167 CYS Chi-restraints excluded: chain LH residue 171 ASN Chi-restraints excluded: chain LK residue 54 LYS Chi-restraints excluded: chain LK residue 60 VAL Chi-restraints excluded: chain LK residue 121 PHE Chi-restraints excluded: chain LK residue 129 VAL Chi-restraints excluded: chain LK residue 132 ILE Chi-restraints excluded: chain LK residue 147 SER Chi-restraints excluded: chain LL residue 17 HIS Chi-restraints excluded: chain LL residue 46 LEU Chi-restraints excluded: chain LL residue 62 THR Chi-restraints excluded: chain LL residue 66 ASN Chi-restraints excluded: chain LL residue 78 GLU Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LM residue 98 ASN Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LN residue 97 SER Chi-restraints excluded: chain LN residue 101 THR Chi-restraints excluded: chain LN residue 110 CYS Chi-restraints excluded: chain LN residue 125 SER Chi-restraints excluded: chain LN residue 178 HIS Chi-restraints excluded: chain LN residue 181 ASN Chi-restraints excluded: chain LO residue 34 ILE Chi-restraints excluded: chain LO residue 106 VAL Chi-restraints excluded: chain LO residue 128 VAL Chi-restraints excluded: chain LO residue 146 GLU Chi-restraints excluded: chain LO residue 147 VAL Chi-restraints excluded: chain LO residue 196 SER Chi-restraints excluded: chain LP residue 12 THR Chi-restraints excluded: chain LP residue 20 SER Chi-restraints excluded: chain LP residue 29 THR Chi-restraints excluded: chain LP residue 52 ILE Chi-restraints excluded: chain LP residue 116 HIS Chi-restraints excluded: chain LQ residue 52 VAL Chi-restraints excluded: chain LQ residue 69 GLU Chi-restraints excluded: chain LQ residue 85 ILE Chi-restraints excluded: chain LQ residue 108 VAL Chi-restraints excluded: chain LQ residue 148 THR Chi-restraints excluded: chain LS residue 13 HIS Chi-restraints excluded: chain LS residue 59 VAL Chi-restraints excluded: chain LS residue 65 SER Chi-restraints excluded: chain LS residue 72 VAL Chi-restraints excluded: chain LS residue 79 LEU Chi-restraints excluded: chain LS residue 87 THR Chi-restraints excluded: chain LS residue 117 ARG Chi-restraints excluded: chain LS residue 120 SER Chi-restraints excluded: chain LS residue 133 GLU Chi-restraints excluded: chain LS residue 171 SER Chi-restraints excluded: chain LT residue 42 ILE Chi-restraints excluded: chain LT residue 66 ASN Chi-restraints excluded: chain LT residue 72 VAL Chi-restraints excluded: chain LT residue 97 LYS Chi-restraints excluded: chain LT residue 143 ILE Chi-restraints excluded: chain LT residue 146 ASN Chi-restraints excluded: chain LV residue 21 VAL Chi-restraints excluded: chain LV residue 59 MET Chi-restraints excluded: chain LV residue 65 LYS Chi-restraints excluded: chain LV residue 88 LYS Chi-restraints excluded: chain LY residue 1 MET Chi-restraints excluded: chain LY residue 6 THR Chi-restraints excluded: chain LY residue 55 VAL Chi-restraints excluded: chain LY residue 70 THR Chi-restraints excluded: chain LY residue 71 SER Chi-restraints excluded: chain LY residue 85 THR Chi-restraints excluded: chain LY residue 86 ARG Chi-restraints excluded: chain LY residue 128 VAL Chi-restraints excluded: chain Le residue 8 VAL Chi-restraints excluded: chain Le residue 24 ASP Chi-restraints excluded: chain Le residue 31 SER Chi-restraints excluded: chain Le residue 96 GLU Chi-restraints excluded: chain Le residue 121 THR Chi-restraints excluded: chain Le residue 129 THR Chi-restraints excluded: chain Lf residue 32 ILE Chi-restraints excluded: chain Lf residue 37 VAL Chi-restraints excluded: chain Lf residue 99 SER Chi-restraints excluded: chain Lf residue 108 SER Chi-restraints excluded: chain Lh residue 36 ILE Chi-restraints excluded: chain Lh residue 61 THR Chi-restraints excluded: chain Lh residue 108 LYS Chi-restraints excluded: chain Li residue 27 THR Chi-restraints excluded: chain Li residue 66 VAL Chi-restraints excluded: chain Li residue 70 LEU Chi-restraints excluded: chain Li residue 97 GLU Chi-restraints excluded: chain Li residue 106 SER Chi-restraints excluded: chain Lj residue 26 SER Chi-restraints excluded: chain Lj residue 59 THR Chi-restraints excluded: chain Lj residue 61 THR Chi-restraints excluded: chain Lj residue 68 SER Chi-restraints excluded: chain Lj residue 69 THR Chi-restraints excluded: chain Lj residue 82 VAL Chi-restraints excluded: chain Lq residue 107 TYR Chi-restraints excluded: chain Lq residue 206 ILE Chi-restraints excluded: chain Cc residue 17 SER Chi-restraints excluded: chain Cc residue 90 LEU Chi-restraints excluded: chain Cc residue 96 THR Chi-restraints excluded: chain Cc residue 102 THR Chi-restraints excluded: chain Cc residue 105 ASP Chi-restraints excluded: chain Cc residue 106 VAL Chi-restraints excluded: chain Cc residue 236 THR Chi-restraints excluded: chain Cd residue 70 ASP Chi-restraints excluded: chain Cd residue 77 ASP Chi-restraints excluded: chain Cd residue 86 VAL Chi-restraints excluded: chain Cd residue 220 SER Chi-restraints excluded: chain Cd residue 231 THR Chi-restraints excluded: chain Cd residue 286 THR Chi-restraints excluded: chain Cd residue 290 ARG Chi-restraints excluded: chain Cd residue 310 GLU Chi-restraints excluded: chain Cd residue 311 LEU Chi-restraints excluded: chain Cd residue 404 VAL Chi-restraints excluded: chain Cd residue 436 LEU Chi-restraints excluded: chain Ce residue 10 ILE Chi-restraints excluded: chain Ce residue 39 ASN Chi-restraints excluded: chain Ce residue 149 GLU Chi-restraints excluded: chain Ce residue 165 THR Chi-restraints excluded: chain Cf residue 463 ARG Chi-restraints excluded: chain Cf residue 484 VAL Chi-restraints excluded: chain Cf residue 524 GLN Chi-restraints excluded: chain Cg residue 67 LEU Chi-restraints excluded: chain Cg residue 91 LEU Chi-restraints excluded: chain Cg residue 213 ASN Chi-restraints excluded: chain Cg residue 352 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1262 random chunks: chunk 410 optimal weight: 0.9980 chunk 1098 optimal weight: 3.9990 chunk 241 optimal weight: 7.9990 chunk 716 optimal weight: 50.0000 chunk 301 optimal weight: 10.0000 chunk 1221 optimal weight: 0.9980 chunk 1013 optimal weight: 5.9990 chunk 565 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 403 optimal weight: 30.0000 chunk 641 optimal weight: 10.0000 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** CA 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 150 HIS ** CB 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 174 ASN ** CC 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CE 280 GLN CE 405 ASN ** CE 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CE 576 GLN CI 256 HIS ** CI 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 15 ASN ** CJ 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 124 ASN CJ 242 ASN ** CJ 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CP 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CP 424 ASN ** CP 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CP 474 ASN CQ 70 GLN ** CR 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CS 664 HIS ** CU 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cb 13 ASN ** Cb 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 121 ASN ** LB 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 59 HIS LC 60 GLN LC 228 ASN ** LE 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LH 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LH 165 GLN LK 65 GLN ** LK 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LK 100 HIS LL 17 HIS LM 110 GLN ** LQ 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 98 ASN LS 122 HIS ** LT 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LV 30 ASN ** LV 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LV 100 ASN LY 116 ASN Li 72 ASN ** Cc 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cd 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 141322 Z= 0.287 Angle : 0.669 27.899 202294 Z= 0.336 Chirality : 0.042 1.912 24461 Planarity : 0.005 0.098 16966 Dihedral : 21.995 176.245 48692 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.06 % Favored : 94.74 % Rotamer: Outliers : 4.83 % Allowed : 20.65 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.02 % Twisted Proline : 0.38 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.08), residues: 10278 helix: 1.21 (0.08), residues: 4628 sheet: -0.15 (0.14), residues: 1331 loop : -0.93 (0.09), residues: 4319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRPCJ 460 HIS 0.010 0.001 HISLN 178 PHE 0.039 0.002 PHECh 334 TYR 0.029 0.002 TYRCP 279 ARG 0.016 0.001 ARGCP 318 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20556 Ramachandran restraints generated. 10278 Oldfield, 0 Emsley, 10278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20556 Ramachandran restraints generated. 10278 Oldfield, 0 Emsley, 10278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2044 residues out of total 8922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 419 poor density : 1625 time to evaluate : 8.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CA 76 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7278 (tp30) REVERT: CB 147 PHE cc_start: 0.8836 (t80) cc_final: 0.8383 (t80) REVERT: CC 137 TYR cc_start: 0.8247 (p90) cc_final: 0.7581 (p90) REVERT: CC 194 LYS cc_start: 0.8528 (ptpp) cc_final: 0.8081 (mttp) REVERT: CC 246 LEU cc_start: 0.5157 (OUTLIER) cc_final: 0.4684 (mp) REVERT: CC 381 ASP cc_start: 0.9066 (m-30) cc_final: 0.8355 (p0) REVERT: CE 226 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7947 (mt-10) REVERT: CE 277 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8189 (mp0) REVERT: CE 540 LYS cc_start: 0.8448 (mmmt) cc_final: 0.8221 (mmmt) REVERT: CF 41 PHE cc_start: 0.7510 (m-80) cc_final: 0.7243 (m-80) REVERT: CF 194 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8275 (mt) REVERT: CH 33 ARG cc_start: 0.4082 (mmt180) cc_final: 0.3262 (mtm180) REVERT: CH 150 ASP cc_start: 0.8661 (t0) cc_final: 0.8407 (t0) REVERT: CH 220 THR cc_start: 0.8494 (m) cc_final: 0.7970 (p) REVERT: CH 231 MET cc_start: 0.8307 (mmt) cc_final: 0.7864 (mmt) REVERT: CH 236 MET cc_start: 0.8601 (mmm) cc_final: 0.7918 (tpp) REVERT: CH 253 MET cc_start: 0.7850 (pmm) cc_final: 0.7374 (pmm) REVERT: CH 333 HIS cc_start: 0.8364 (t70) cc_final: 0.8117 (t-170) REVERT: CH 437 ILE cc_start: 0.8567 (mt) cc_final: 0.8199 (mt) REVERT: CI 250 LYS cc_start: 0.8399 (mptt) cc_final: 0.8182 (mmtm) REVERT: CI 274 LYS cc_start: 0.8243 (ptmm) cc_final: 0.7964 (ptmm) REVERT: CI 320 LEU cc_start: 0.8910 (pp) cc_final: 0.8630 (tp) REVERT: CJ 190 LEU cc_start: 0.3442 (OUTLIER) cc_final: 0.3235 (pp) REVERT: CJ 196 TYR cc_start: 0.8766 (m-80) cc_final: 0.8369 (m-80) REVERT: CJ 230 PHE cc_start: 0.9156 (m-80) cc_final: 0.8692 (m-80) REVERT: CK 67 GLN cc_start: 0.8182 (mt0) cc_final: 0.7691 (tm-30) REVERT: CK 110 ARG cc_start: 0.8860 (mtp85) cc_final: 0.8629 (mtp85) REVERT: CK 132 MET cc_start: 0.6830 (tpp) cc_final: 0.6597 (tpp) REVERT: CK 163 ARG cc_start: 0.7075 (ptt180) cc_final: 0.6456 (ptt180) REVERT: CK 179 TYR cc_start: 0.9152 (m-80) cc_final: 0.8832 (m-10) REVERT: CK 201 LYS cc_start: 0.8959 (mmpt) cc_final: 0.8645 (mmtm) REVERT: CK 212 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9282 (mm) REVERT: CL 23 LYS cc_start: 0.7609 (ttmm) cc_final: 0.7081 (tptt) REVERT: CL 63 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8950 (mm-30) REVERT: CL 73 ARG cc_start: 0.9097 (tmm-80) cc_final: 0.8581 (ttp80) REVERT: CM 139 TRP cc_start: 0.7535 (m-90) cc_final: 0.7166 (m-90) REVERT: CM 190 LEU cc_start: 0.9080 (mt) cc_final: 0.8801 (mt) REVERT: CM 209 TRP cc_start: 0.7934 (m100) cc_final: 0.7485 (m100) REVERT: CN 57 ARG cc_start: 0.8173 (ttm-80) cc_final: 0.7793 (mtp85) REVERT: CN 245 PHE cc_start: 0.9036 (m-80) cc_final: 0.8655 (m-10) REVERT: CO 3 LYS cc_start: 0.7581 (mmmt) cc_final: 0.7236 (mttt) REVERT: CP 374 MET cc_start: 0.8174 (mtp) cc_final: 0.7849 (mtp) REVERT: CP 398 MET cc_start: 0.8112 (ppp) cc_final: 0.7771 (ppp) REVERT: CP 402 MET cc_start: 0.6755 (ptp) cc_final: 0.6541 (ptp) REVERT: CP 409 PHE cc_start: 0.8344 (m-10) cc_final: 0.8083 (m-10) REVERT: CP 524 VAL cc_start: 0.9125 (OUTLIER) cc_final: 0.8890 (p) REVERT: CP 552 MET cc_start: 0.8450 (mmm) cc_final: 0.8145 (mmm) REVERT: CP 581 PHE cc_start: 0.7879 (m-10) cc_final: 0.7592 (m-10) REVERT: CQ 8 PHE cc_start: 0.8749 (t80) cc_final: 0.7787 (t80) REVERT: CQ 45 ASN cc_start: 0.8464 (t0) cc_final: 0.7833 (t0) REVERT: CQ 51 TRP cc_start: 0.8599 (p-90) cc_final: 0.8043 (p-90) REVERT: CQ 55 TYR cc_start: 0.8888 (t80) cc_final: 0.8421 (t80) REVERT: CQ 93 MET cc_start: 0.7521 (mmt) cc_final: 0.7287 (mmt) REVERT: CR 73 LEU cc_start: 0.6034 (tp) cc_final: 0.5758 (tp) REVERT: CR 135 GLN cc_start: 0.7671 (tm-30) cc_final: 0.7395 (tm-30) REVERT: CS 475 MET cc_start: 0.7972 (mtt) cc_final: 0.7530 (mtp) REVERT: CU 320 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.7328 (mp10) REVERT: CU 364 ASN cc_start: 0.8847 (p0) cc_final: 0.8575 (p0) REVERT: Cz 26 ARG cc_start: 0.7657 (ttm-80) cc_final: 0.7025 (ttt-90) REVERT: Cz 51 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.6576 (ttt90) REVERT: Cb 110 PHE cc_start: 0.7740 (m-80) cc_final: 0.7465 (t80) REVERT: Cb 249 MET cc_start: 0.8796 (mmp) cc_final: 0.8002 (ttm) REVERT: Cb 380 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8274 (mm-30) REVERT: Ch 295 ASN cc_start: 0.8530 (p0) cc_final: 0.8255 (m-40) REVERT: Ch 331 ARG cc_start: 0.8292 (mmt180) cc_final: 0.7493 (ptt180) REVERT: LB 227 PHE cc_start: 0.6038 (OUTLIER) cc_final: 0.4920 (m-10) REVERT: LB 284 TYR cc_start: 0.8192 (OUTLIER) cc_final: 0.7782 (m-10) REVERT: LC 304 LYS cc_start: 0.8010 (mttp) cc_final: 0.7771 (tttt) REVERT: LC 350 LYS cc_start: 0.8911 (ttpt) cc_final: 0.8639 (ttpp) REVERT: LE 33 GLU cc_start: 0.6873 (tm-30) cc_final: 0.5946 (tp30) REVERT: LE 53 GLN cc_start: 0.8399 (mm-40) cc_final: 0.7681 (mp10) REVERT: LE 56 THR cc_start: 0.9493 (m) cc_final: 0.9239 (m) REVERT: LE 177 ASP cc_start: 0.8839 (OUTLIER) cc_final: 0.8432 (p0) REVERT: LF 45 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8374 (mp0) REVERT: LF 66 ARG cc_start: 0.7967 (mmm-85) cc_final: 0.7569 (mmm160) REVERT: LF 98 ILE cc_start: 0.5532 (OUTLIER) cc_final: 0.5271 (pt) REVERT: LF 134 LYS cc_start: 0.8829 (tttt) cc_final: 0.8373 (tptt) REVERT: LF 172 ASN cc_start: 0.8452 (m-40) cc_final: 0.7991 (p0) REVERT: LF 230 GLU cc_start: 0.7187 (tt0) cc_final: 0.6927 (tp30) REVERT: LG 55 TRP cc_start: 0.7300 (m100) cc_final: 0.6815 (m100) REVERT: LG 64 GLN cc_start: 0.8691 (mt0) cc_final: 0.8406 (mt0) REVERT: LG 158 ASN cc_start: 0.9071 (p0) cc_final: 0.8759 (p0) REVERT: LG 159 ASP cc_start: 0.8670 (p0) cc_final: 0.7935 (p0) REVERT: LH 55 LEU cc_start: 0.8796 (pt) cc_final: 0.8537 (pt) REVERT: LH 100 ASN cc_start: 0.8483 (t0) cc_final: 0.8212 (t0) REVERT: LH 137 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7719 (mt-10) REVERT: LH 170 ARG cc_start: 0.7915 (mtp180) cc_final: 0.7600 (ttp80) REVERT: LH 173 ASP cc_start: 0.8481 (t0) cc_final: 0.8130 (t70) REVERT: LK 35 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.7014 (tt) REVERT: LK 54 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7565 (ptmm) REVERT: LK 74 VAL cc_start: 0.7865 (OUTLIER) cc_final: 0.7575 (p) REVERT: LK 83 ARG cc_start: 0.8421 (mmm160) cc_final: 0.8171 (mmm160) REVERT: LK 121 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.8040 (t80) REVERT: LK 132 ILE cc_start: 0.9298 (OUTLIER) cc_final: 0.9019 (tp) REVERT: LL 78 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7154 (tt0) REVERT: LL 114 GLN cc_start: 0.7880 (tp40) cc_final: 0.7370 (tp40) REVERT: LM 42 ASP cc_start: 0.8625 (t0) cc_final: 0.7940 (t0) REVERT: LO 146 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: LP 40 LYS cc_start: 0.8876 (mmmt) cc_final: 0.8579 (mmmt) REVERT: LP 75 GLN cc_start: 0.6896 (pt0) cc_final: 0.6223 (mm110) REVERT: LP 155 GLU cc_start: 0.7715 (tp30) cc_final: 0.7263 (tp30) REVERT: LS 21 ASN cc_start: 0.8131 (t0) cc_final: 0.7553 (t0) REVERT: LS 55 THR cc_start: 0.8771 (p) cc_final: 0.8253 (t) REVERT: LS 60 SER cc_start: 0.9119 (t) cc_final: 0.8795 (m) REVERT: LS 75 PHE cc_start: 0.9155 (m-80) cc_final: 0.8594 (m-80) REVERT: LS 79 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7745 (mp) REVERT: LS 81 TYR cc_start: 0.8666 (p90) cc_final: 0.8235 (p90) REVERT: LS 117 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.7181 (mtt180) REVERT: LT 52 MET cc_start: 0.4901 (ptm) cc_final: 0.3912 (mtt) REVERT: LT 103 GLU cc_start: 0.9165 (pt0) cc_final: 0.8948 (pm20) REVERT: LT 146 ASN cc_start: 0.8585 (m-40) cc_final: 0.8009 (m-40) REVERT: LV 65 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8213 (tmtt) REVERT: LV 72 ARG cc_start: 0.8268 (ttm110) cc_final: 0.8014 (mtt-85) REVERT: LY 51 LYS cc_start: 0.8814 (ttpp) cc_final: 0.8499 (ttpt) REVERT: LY 54 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7938 (tp30) REVERT: LY 92 GLN cc_start: 0.8241 (tm-30) cc_final: 0.7655 (tm-30) REVERT: LY 126 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7978 (mt-10) REVERT: Le 6 LYS cc_start: 0.8031 (ttmm) cc_final: 0.7080 (tptt) REVERT: Le 30 ASP cc_start: 0.7678 (t70) cc_final: 0.7290 (t0) REVERT: Le 96 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6148 (tp30) REVERT: Le 114 LYS cc_start: 0.8845 (tptt) cc_final: 0.8502 (tttt) REVERT: Lh 16 ASN cc_start: 0.7718 (p0) cc_final: 0.7496 (p0) REVERT: Lh 47 ASN cc_start: 0.7946 (t0) cc_final: 0.7594 (t0) REVERT: Lh 108 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7641 (ptpt) REVERT: Lj 30 GLN cc_start: 0.8390 (mm-40) cc_final: 0.8168 (mm-40) REVERT: Lq 63 MET cc_start: 0.7292 (mpp) cc_final: 0.6235 (mpp) REVERT: Lq 66 CYS cc_start: 0.9173 (p) cc_final: 0.8811 (p) REVERT: Lq 103 LEU cc_start: 0.9487 (tp) cc_final: 0.9109 (pp) REVERT: Lq 174 MET cc_start: 0.5266 (ppp) cc_final: 0.4953 (ppp) REVERT: Lq 184 MET cc_start: 0.6482 (mmm) cc_final: 0.5915 (mmm) REVERT: Lq 188 ASN cc_start: 0.8581 (m-40) cc_final: 0.8311 (m-40) REVERT: Lq 206 ILE cc_start: 0.4503 (OUTLIER) cc_final: 0.3850 (tt) REVERT: Cc 37 GLN cc_start: 0.7614 (mm110) cc_final: 0.7070 (tm-30) REVERT: Cc 105 ASP cc_start: 0.7027 (OUTLIER) cc_final: 0.6356 (m-30) REVERT: Cc 189 ILE cc_start: 0.9143 (mm) cc_final: 0.8929 (mm) REVERT: Cd 26 GLN cc_start: 0.7884 (mm-40) cc_final: 0.7649 (mm-40) REVERT: Cd 37 ARG cc_start: 0.8173 (ttm110) cc_final: 0.7759 (mtt90) REVERT: Cd 224 ASN cc_start: 0.7693 (t0) cc_final: 0.7283 (t0) REVERT: Cd 308 TYR cc_start: 0.8880 (m-10) cc_final: 0.8492 (m-10) REVERT: Cd 338 LEU cc_start: 0.9122 (mm) cc_final: 0.8810 (mm) REVERT: Cd 349 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7719 (mt0) REVERT: Ce 149 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.6771 (mp0) REVERT: Cf 513 ILE cc_start: 0.8632 (mm) cc_final: 0.8431 (mt) REVERT: Cf 529 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7174 (mm-30) REVERT: Cg 116 PHE cc_start: 0.8740 (m-80) cc_final: 0.8254 (m-80) REVERT: Cg 149 MET cc_start: 0.6489 (ppp) cc_final: 0.6166 (tmm) REVERT: Cg 337 MET cc_start: 0.7475 (mpp) cc_final: 0.6992 (pmm) outliers start: 419 outliers final: 317 residues processed: 1879 average time/residue: 1.2641 time to fit residues: 4123.6116 Evaluate side-chains 1897 residues out of total 8922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 347 poor density : 1550 time to evaluate : 8.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 47 ARG Chi-restraints excluded: chain CA residue 65 ASP Chi-restraints excluded: chain CA residue 70 THR Chi-restraints excluded: chain CA residue 72 SER Chi-restraints excluded: chain CA residue 109 ASN Chi-restraints excluded: chain CA residue 113 VAL Chi-restraints excluded: chain CA residue 118 GLN Chi-restraints excluded: chain CA residue 148 GLN Chi-restraints excluded: chain CA residue 184 VAL Chi-restraints excluded: chain CA residue 186 ASP Chi-restraints excluded: chain CA residue 199 VAL Chi-restraints excluded: chain CA residue 229 ILE Chi-restraints excluded: chain CA residue 294 ARG Chi-restraints excluded: chain CA residue 295 GLN Chi-restraints excluded: chain CB residue 44 ASP Chi-restraints excluded: chain CB residue 131 SER Chi-restraints excluded: chain CB residue 151 ASP Chi-restraints excluded: chain CB residue 170 THR Chi-restraints excluded: chain CB residue 185 MET Chi-restraints excluded: chain CB residue 283 VAL Chi-restraints excluded: chain CC residue 118 LEU Chi-restraints excluded: chain CC residue 122 VAL Chi-restraints excluded: chain CC residue 182 SER Chi-restraints excluded: chain CC residue 246 LEU Chi-restraints excluded: chain CC residue 258 THR Chi-restraints excluded: chain CC residue 265 VAL Chi-restraints excluded: chain CC residue 268 LYS Chi-restraints excluded: chain CE residue 142 ILE Chi-restraints excluded: chain CE residue 184 THR Chi-restraints excluded: chain CE residue 237 LEU Chi-restraints excluded: chain CE residue 277 GLU Chi-restraints excluded: chain CE residue 301 THR Chi-restraints excluded: chain CE residue 382 LEU Chi-restraints excluded: chain CE residue 410 THR Chi-restraints excluded: chain CE residue 411 LEU Chi-restraints excluded: chain CE residue 412 ILE Chi-restraints excluded: chain CE residue 421 LEU Chi-restraints excluded: chain CE residue 442 ILE Chi-restraints excluded: chain CE residue 463 GLN Chi-restraints excluded: chain CE residue 485 PHE Chi-restraints excluded: chain CE residue 496 GLN Chi-restraints excluded: chain CE residue 503 THR Chi-restraints excluded: chain CE residue 555 ILE Chi-restraints excluded: chain CF residue 8 ARG Chi-restraints excluded: chain CF residue 12 LEU Chi-restraints excluded: chain CF residue 139 THR Chi-restraints excluded: chain CF residue 142 VAL Chi-restraints excluded: chain CF residue 174 MET Chi-restraints excluded: chain CF residue 175 ILE Chi-restraints excluded: chain CF residue 179 VAL Chi-restraints excluded: chain CF residue 183 ASP Chi-restraints excluded: chain CF residue 194 ILE Chi-restraints excluded: chain CF residue 215 CYS Chi-restraints excluded: chain CF residue 226 TYR Chi-restraints excluded: chain CG residue 59 VAL Chi-restraints excluded: chain CG residue 65 LEU Chi-restraints excluded: chain CG residue 67 LEU Chi-restraints excluded: chain CG residue 71 LEU Chi-restraints excluded: chain CG residue 166 ARG Chi-restraints excluded: chain CH residue 55 THR Chi-restraints excluded: chain CH residue 56 CYS Chi-restraints excluded: chain CH residue 165 THR Chi-restraints excluded: chain CH residue 203 LEU Chi-restraints excluded: chain CH residue 223 ILE Chi-restraints excluded: chain CH residue 226 HIS Chi-restraints excluded: chain CH residue 264 LYS Chi-restraints excluded: chain CH residue 314 VAL Chi-restraints excluded: chain CH residue 338 LEU Chi-restraints excluded: chain CH residue 359 THR Chi-restraints excluded: chain CH residue 387 VAL Chi-restraints excluded: chain CH residue 473 PHE Chi-restraints excluded: chain CI residue 210 PHE Chi-restraints excluded: chain CI residue 224 THR Chi-restraints excluded: chain CI residue 258 LEU Chi-restraints excluded: chain CI residue 259 THR Chi-restraints excluded: chain CI residue 268 VAL Chi-restraints excluded: chain CI residue 282 VAL Chi-restraints excluded: chain CI residue 293 LEU Chi-restraints excluded: chain CJ residue 17 MET Chi-restraints excluded: chain CJ residue 124 ASN Chi-restraints excluded: chain CJ residue 158 THR Chi-restraints excluded: chain CJ residue 190 LEU Chi-restraints excluded: chain CJ residue 374 LEU Chi-restraints excluded: chain CJ residue 456 VAL Chi-restraints excluded: chain CK residue 36 SER Chi-restraints excluded: chain CK residue 130 GLU Chi-restraints excluded: chain CK residue 152 THR Chi-restraints excluded: chain CK residue 155 THR Chi-restraints excluded: chain CK residue 193 VAL Chi-restraints excluded: chain CK residue 212 LEU Chi-restraints excluded: chain CK residue 216 THR Chi-restraints excluded: chain CK residue 227 ASP Chi-restraints excluded: chain CK residue 258 VAL Chi-restraints excluded: chain CL residue 18 THR Chi-restraints excluded: chain CL residue 38 LEU Chi-restraints excluded: chain CL residue 65 LEU Chi-restraints excluded: chain CM residue 147 LEU Chi-restraints excluded: chain CM residue 148 LYS Chi-restraints excluded: chain CM residue 244 LEU Chi-restraints excluded: chain CM residue 246 ARG Chi-restraints excluded: chain CN residue 3 VAL Chi-restraints excluded: chain CN residue 147 LEU Chi-restraints excluded: chain CN residue 154 LEU Chi-restraints excluded: chain CN residue 198 VAL Chi-restraints excluded: chain CN residue 205 VAL Chi-restraints excluded: chain CN residue 208 LEU Chi-restraints excluded: chain CN residue 215 LEU Chi-restraints excluded: chain CO residue 19 LYS Chi-restraints excluded: chain CO residue 34 SER Chi-restraints excluded: chain CO residue 37 LEU Chi-restraints excluded: chain CO residue 40 ILE Chi-restraints excluded: chain CO residue 94 LYS Chi-restraints excluded: chain CP residue 267 LEU Chi-restraints excluded: chain CP residue 277 ASN Chi-restraints excluded: chain CP residue 306 VAL Chi-restraints excluded: chain CP residue 319 ASP Chi-restraints excluded: chain CP residue 349 VAL Chi-restraints excluded: chain CP residue 454 LEU Chi-restraints excluded: chain CP residue 465 ILE Chi-restraints excluded: chain CP residue 524 VAL Chi-restraints excluded: chain CP residue 560 LEU Chi-restraints excluded: chain CQ residue 1 MET Chi-restraints excluded: chain CQ residue 6 CYS Chi-restraints excluded: chain CQ residue 34 SER Chi-restraints excluded: chain CQ residue 89 THR Chi-restraints excluded: chain CR residue 5 LEU Chi-restraints excluded: chain CR residue 33 ASN Chi-restraints excluded: chain CR residue 128 SER Chi-restraints excluded: chain CR residue 177 THR Chi-restraints excluded: chain CR residue 221 THR Chi-restraints excluded: chain CS residue 673 LYS Chi-restraints excluded: chain CS residue 692 LEU Chi-restraints excluded: chain CU residue 219 SER Chi-restraints excluded: chain CU residue 228 ASP Chi-restraints excluded: chain CU residue 320 GLN Chi-restraints excluded: chain CU residue 335 ASN Chi-restraints excluded: chain CU residue 360 VAL Chi-restraints excluded: chain CU residue 366 LEU Chi-restraints excluded: chain CX residue 76 THR Chi-restraints excluded: chain CX residue 133 ARG Chi-restraints excluded: chain Cz residue 50 LEU Chi-restraints excluded: chain Cz residue 51 ARG Chi-restraints excluded: chain Cb residue 237 TYR Chi-restraints excluded: chain Cb residue 255 LEU Chi-restraints excluded: chain Cb residue 301 VAL Chi-restraints excluded: chain Cb residue 312 VAL Chi-restraints excluded: chain Cb residue 439 ILE Chi-restraints excluded: chain Cb residue 440 ASN Chi-restraints excluded: chain Cb residue 474 ASP Chi-restraints excluded: chain Cb residue 506 VAL Chi-restraints excluded: chain LB residue 24 ARG Chi-restraints excluded: chain LB residue 217 ASP Chi-restraints excluded: chain LB residue 225 HIS Chi-restraints excluded: chain LB residue 227 PHE Chi-restraints excluded: chain LB residue 277 THR Chi-restraints excluded: chain LB residue 284 TYR Chi-restraints excluded: chain LB residue 294 ASN Chi-restraints excluded: chain LB residue 297 THR Chi-restraints excluded: chain LB residue 313 VAL Chi-restraints excluded: chain LB residue 318 VAL Chi-restraints excluded: chain LB residue 320 ASN Chi-restraints excluded: chain LB residue 364 SER Chi-restraints excluded: chain LB residue 388 LEU Chi-restraints excluded: chain LC residue 35 ILE Chi-restraints excluded: chain LC residue 61 THR Chi-restraints excluded: chain LC residue 79 SER Chi-restraints excluded: chain LC residue 181 ASP Chi-restraints excluded: chain LC residue 185 VAL Chi-restraints excluded: chain LC residue 270 GLU Chi-restraints excluded: chain LC residue 277 LEU Chi-restraints excluded: chain LC residue 294 THR Chi-restraints excluded: chain LC residue 300 LEU Chi-restraints excluded: chain LC residue 323 LYS Chi-restraints excluded: chain LE residue 71 VAL Chi-restraints excluded: chain LE residue 103 ILE Chi-restraints excluded: chain LE residue 129 THR Chi-restraints excluded: chain LE residue 138 SER Chi-restraints excluded: chain LE residue 177 ASP Chi-restraints excluded: chain LE residue 186 SER Chi-restraints excluded: chain LE residue 198 MET Chi-restraints excluded: chain LF residue 10 ASN Chi-restraints excluded: chain LF residue 14 VAL Chi-restraints excluded: chain LF residue 24 SER Chi-restraints excluded: chain LF residue 45 GLU Chi-restraints excluded: chain LF residue 89 LEU Chi-restraints excluded: chain LF residue 98 ILE Chi-restraints excluded: chain LF residue 100 LYS Chi-restraints excluded: chain LF residue 101 ILE Chi-restraints excluded: chain LF residue 126 THR Chi-restraints excluded: chain LF residue 170 THR Chi-restraints excluded: chain LF residue 189 ASP Chi-restraints excluded: chain LG residue 85 LEU Chi-restraints excluded: chain LG residue 89 LEU Chi-restraints excluded: chain LG residue 113 LEU Chi-restraints excluded: chain LG residue 117 THR Chi-restraints excluded: chain LG residue 129 SER Chi-restraints excluded: chain LG residue 139 LEU Chi-restraints excluded: chain LG residue 191 THR Chi-restraints excluded: chain LG residue 197 THR Chi-restraints excluded: chain LG residue 201 VAL Chi-restraints excluded: chain LG residue 203 ILE Chi-restraints excluded: chain LG residue 204 THR Chi-restraints excluded: chain LG residue 218 ILE Chi-restraints excluded: chain LG residue 229 VAL Chi-restraints excluded: chain LH residue 16 LEU Chi-restraints excluded: chain LH residue 38 LEU Chi-restraints excluded: chain LH residue 47 VAL Chi-restraints excluded: chain LH residue 56 GLU Chi-restraints excluded: chain LH residue 101 VAL Chi-restraints excluded: chain LH residue 103 VAL Chi-restraints excluded: chain LH residue 128 VAL Chi-restraints excluded: chain LH residue 134 VAL Chi-restraints excluded: chain LH residue 137 GLU Chi-restraints excluded: chain LH residue 149 SER Chi-restraints excluded: chain LH residue 167 CYS Chi-restraints excluded: chain LH residue 171 ASN Chi-restraints excluded: chain LK residue 35 LEU Chi-restraints excluded: chain LK residue 54 LYS Chi-restraints excluded: chain LK residue 60 VAL Chi-restraints excluded: chain LK residue 71 VAL Chi-restraints excluded: chain LK residue 74 VAL Chi-restraints excluded: chain LK residue 100 HIS Chi-restraints excluded: chain LK residue 121 PHE Chi-restraints excluded: chain LK residue 129 VAL Chi-restraints excluded: chain LK residue 132 ILE Chi-restraints excluded: chain LK residue 147 SER Chi-restraints excluded: chain LL residue 17 HIS Chi-restraints excluded: chain LL residue 46 LEU Chi-restraints excluded: chain LL residue 62 THR Chi-restraints excluded: chain LL residue 78 GLU Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LM residue 98 ASN Chi-restraints excluded: chain LN residue 33 LEU Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LN residue 97 SER Chi-restraints excluded: chain LN residue 101 THR Chi-restraints excluded: chain LN residue 110 CYS Chi-restraints excluded: chain LN residue 125 SER Chi-restraints excluded: chain LN residue 149 ASN Chi-restraints excluded: chain LN residue 178 HIS Chi-restraints excluded: chain LN residue 181 ASN Chi-restraints excluded: chain LO residue 22 SER Chi-restraints excluded: chain LO residue 34 ILE Chi-restraints excluded: chain LO residue 106 VAL Chi-restraints excluded: chain LO residue 128 VAL Chi-restraints excluded: chain LO residue 146 GLU Chi-restraints excluded: chain LO residue 147 VAL Chi-restraints excluded: chain LO residue 196 SER Chi-restraints excluded: chain LP residue 12 THR Chi-restraints excluded: chain LP residue 20 SER Chi-restraints excluded: chain LP residue 29 THR Chi-restraints excluded: chain LP residue 52 ILE Chi-restraints excluded: chain LP residue 116 HIS Chi-restraints excluded: chain LQ residue 52 VAL Chi-restraints excluded: chain LQ residue 69 GLU Chi-restraints excluded: chain LQ residue 85 ILE Chi-restraints excluded: chain LQ residue 108 VAL Chi-restraints excluded: chain LQ residue 148 THR Chi-restraints excluded: chain LS residue 13 HIS Chi-restraints excluded: chain LS residue 59 VAL Chi-restraints excluded: chain LS residue 65 SER Chi-restraints excluded: chain LS residue 72 VAL Chi-restraints excluded: chain LS residue 79 LEU Chi-restraints excluded: chain LS residue 87 THR Chi-restraints excluded: chain LS residue 117 ARG Chi-restraints excluded: chain LS residue 120 SER Chi-restraints excluded: chain LS residue 133 GLU Chi-restraints excluded: chain LS residue 171 SER Chi-restraints excluded: chain LT residue 42 ILE Chi-restraints excluded: chain LT residue 66 ASN Chi-restraints excluded: chain LT residue 72 VAL Chi-restraints excluded: chain LT residue 143 ILE Chi-restraints excluded: chain LT residue 150 THR Chi-restraints excluded: chain LV residue 21 VAL Chi-restraints excluded: chain LV residue 30 ASN Chi-restraints excluded: chain LV residue 59 MET Chi-restraints excluded: chain LV residue 65 LYS Chi-restraints excluded: chain LV residue 88 LYS Chi-restraints excluded: chain LY residue 1 MET Chi-restraints excluded: chain LY residue 6 THR Chi-restraints excluded: chain LY residue 53 ASP Chi-restraints excluded: chain LY residue 55 VAL Chi-restraints excluded: chain LY residue 70 THR Chi-restraints excluded: chain LY residue 71 SER Chi-restraints excluded: chain LY residue 85 THR Chi-restraints excluded: chain LY residue 86 ARG Chi-restraints excluded: chain LY residue 128 VAL Chi-restraints excluded: chain Le residue 8 VAL Chi-restraints excluded: chain Le residue 24 ASP Chi-restraints excluded: chain Le residue 31 SER Chi-restraints excluded: chain Le residue 79 ASN Chi-restraints excluded: chain Le residue 96 GLU Chi-restraints excluded: chain Le residue 121 THR Chi-restraints excluded: chain Le residue 129 THR Chi-restraints excluded: chain Lf residue 32 ILE Chi-restraints excluded: chain Lf residue 37 VAL Chi-restraints excluded: chain Lf residue 99 SER Chi-restraints excluded: chain Lf residue 108 SER Chi-restraints excluded: chain Lh residue 14 SER Chi-restraints excluded: chain Lh residue 36 ILE Chi-restraints excluded: chain Lh residue 61 THR Chi-restraints excluded: chain Lh residue 108 LYS Chi-restraints excluded: chain Li residue 27 THR Chi-restraints excluded: chain Li residue 64 ARG Chi-restraints excluded: chain Li residue 66 VAL Chi-restraints excluded: chain Li residue 70 LEU Chi-restraints excluded: chain Li residue 97 GLU Chi-restraints excluded: chain Li residue 106 SER Chi-restraints excluded: chain Lj residue 26 SER Chi-restraints excluded: chain Lj residue 59 THR Chi-restraints excluded: chain Lj residue 61 THR Chi-restraints excluded: chain Lj residue 68 SER Chi-restraints excluded: chain Lj residue 69 THR Chi-restraints excluded: chain Lj residue 82 VAL Chi-restraints excluded: chain Lq residue 99 LEU Chi-restraints excluded: chain Lq residue 107 TYR Chi-restraints excluded: chain Lq residue 206 ILE Chi-restraints excluded: chain Cc residue 17 SER Chi-restraints excluded: chain Cc residue 90 LEU Chi-restraints excluded: chain Cc residue 96 THR Chi-restraints excluded: chain Cc residue 105 ASP Chi-restraints excluded: chain Cc residue 106 VAL Chi-restraints excluded: chain Cc residue 236 THR Chi-restraints excluded: chain Cd residue 70 ASP Chi-restraints excluded: chain Cd residue 77 ASP Chi-restraints excluded: chain Cd residue 86 VAL Chi-restraints excluded: chain Cd residue 220 SER Chi-restraints excluded: chain Cd residue 231 THR Chi-restraints excluded: chain Cd residue 286 THR Chi-restraints excluded: chain Cd residue 290 ARG Chi-restraints excluded: chain Cd residue 310 GLU Chi-restraints excluded: chain Cd residue 349 GLN Chi-restraints excluded: chain Cd residue 393 ILE Chi-restraints excluded: chain Cd residue 404 VAL Chi-restraints excluded: chain Ce residue 10 ILE Chi-restraints excluded: chain Ce residue 39 ASN Chi-restraints excluded: chain Ce residue 41 GLN Chi-restraints excluded: chain Ce residue 114 THR Chi-restraints excluded: chain Ce residue 149 GLU Chi-restraints excluded: chain Ce residue 165 THR Chi-restraints excluded: chain Cf residue 463 ARG Chi-restraints excluded: chain Cf residue 484 VAL Chi-restraints excluded: chain Cg residue 67 LEU Chi-restraints excluded: chain Cg residue 91 LEU Chi-restraints excluded: chain Cg residue 103 LEU Chi-restraints excluded: chain Cg residue 213 ASN Chi-restraints excluded: chain Cg residue 352 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1262 random chunks: chunk 1177 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 695 optimal weight: 9.9990 chunk 891 optimal weight: 3.9990 chunk 690 optimal weight: 0.9990 chunk 1027 optimal weight: 1.9990 chunk 681 optimal weight: 5.9990 chunk 1216 optimal weight: 0.9990 chunk 761 optimal weight: 20.0000 chunk 741 optimal weight: 6.9990 chunk 561 optimal weight: 20.0000 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** CA 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 22 GLN ** CB 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 105 GLN CB 240 ASN ** CB 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 174 ASN ** CE 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CI 256 HIS ** CI 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CP 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CP 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CU 320 GLN ** Cb 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 121 ASN ** LB 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 203 HIS LC 228 ASN ** LH 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LH 164 GLN LH 165 GLN LL 17 HIS ** LQ 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 98 ASN ** LT 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LV 30 ASN ** LV 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LV 100 ASN LY 116 ASN Li 72 ASN ** Cd 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cf 524 GLN ** Cg 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 141322 Z= 0.212 Angle : 0.640 27.528 202294 Z= 0.321 Chirality : 0.040 1.941 24461 Planarity : 0.005 0.100 16966 Dihedral : 21.959 176.588 48692 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.82 % Favored : 95.00 % Rotamer: Outliers : 4.34 % Allowed : 21.85 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.02 % Twisted Proline : 0.38 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.08), residues: 10278 helix: 1.28 (0.08), residues: 4621 sheet: -0.11 (0.14), residues: 1333 loop : -0.89 (0.09), residues: 4324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRPCf 509 HIS 0.017 0.001 HISLK 100 PHE 0.042 0.002 PHECh 334 TYR 0.039 0.002 TYRCb 397 ARG 0.016 0.001 ARGCE 279 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20556 Ramachandran restraints generated. 10278 Oldfield, 0 Emsley, 10278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20556 Ramachandran restraints generated. 10278 Oldfield, 0 Emsley, 10278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2022 residues out of total 8922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 376 poor density : 1646 time to evaluate : 8.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CA 39 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7151 (tt) REVERT: CA 76 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7426 (tp30) REVERT: CB 147 PHE cc_start: 0.8807 (t80) cc_final: 0.8427 (t80) REVERT: CC 137 TYR cc_start: 0.8235 (p90) cc_final: 0.7526 (p90) REVERT: CC 194 LYS cc_start: 0.8489 (ptpp) cc_final: 0.8065 (mttp) REVERT: CC 246 LEU cc_start: 0.5162 (OUTLIER) cc_final: 0.4724 (mp) REVERT: CC 381 ASP cc_start: 0.9099 (m-30) cc_final: 0.8369 (p0) REVERT: CE 226 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7955 (mt-10) REVERT: CE 277 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8193 (mp0) REVERT: CE 375 GLU cc_start: 0.7993 (tp30) cc_final: 0.7767 (tt0) REVERT: CE 540 LYS cc_start: 0.8404 (mmmt) cc_final: 0.8191 (mmmt) REVERT: CF 41 PHE cc_start: 0.7452 (m-80) cc_final: 0.7217 (m-80) REVERT: CF 194 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8264 (mt) REVERT: CG 137 MET cc_start: 0.7517 (pmm) cc_final: 0.6932 (pmm) REVERT: CH 33 ARG cc_start: 0.4067 (mmt180) cc_final: 0.3191 (mtm180) REVERT: CH 115 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8862 (mm) REVERT: CH 150 ASP cc_start: 0.8616 (t0) cc_final: 0.8374 (t0) REVERT: CH 171 VAL cc_start: 0.8981 (t) cc_final: 0.8695 (t) REVERT: CH 220 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.7934 (p) REVERT: CH 231 MET cc_start: 0.8287 (mmt) cc_final: 0.7963 (mmt) REVERT: CH 236 MET cc_start: 0.8621 (mmm) cc_final: 0.8061 (tpp) REVERT: CH 250 LEU cc_start: 0.8924 (mt) cc_final: 0.8587 (tp) REVERT: CH 253 MET cc_start: 0.7985 (pmm) cc_final: 0.7433 (pmm) REVERT: CH 297 LEU cc_start: 0.7112 (pt) cc_final: 0.6738 (pt) REVERT: CH 333 HIS cc_start: 0.8341 (t70) cc_final: 0.8112 (t-170) REVERT: CH 437 ILE cc_start: 0.8554 (mt) cc_final: 0.8184 (mt) REVERT: CI 246 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8447 (mtm110) REVERT: CI 250 LYS cc_start: 0.8360 (mptt) cc_final: 0.8053 (mmtm) REVERT: CI 274 LYS cc_start: 0.8179 (ptmm) cc_final: 0.7924 (ptmm) REVERT: CI 320 LEU cc_start: 0.8895 (pp) cc_final: 0.8558 (tp) REVERT: CJ 196 TYR cc_start: 0.8761 (m-80) cc_final: 0.8360 (m-80) REVERT: CJ 230 PHE cc_start: 0.9191 (m-80) cc_final: 0.8708 (m-80) REVERT: CK 67 GLN cc_start: 0.8106 (mt0) cc_final: 0.7695 (tm-30) REVERT: CK 110 ARG cc_start: 0.8798 (mtp85) cc_final: 0.8580 (mtp85) REVERT: CK 163 ARG cc_start: 0.7115 (ptt180) cc_final: 0.6523 (ptt180) REVERT: CK 164 ARG cc_start: 0.7209 (mtm110) cc_final: 0.6365 (ptp-170) REVERT: CK 179 TYR cc_start: 0.9133 (m-80) cc_final: 0.8843 (m-10) REVERT: CK 201 LYS cc_start: 0.8947 (mmpt) cc_final: 0.8642 (mmtm) REVERT: CK 212 LEU cc_start: 0.9562 (OUTLIER) cc_final: 0.9262 (mm) REVERT: CL 23 LYS cc_start: 0.7605 (ttmm) cc_final: 0.7075 (tptt) REVERT: CM 190 LEU cc_start: 0.9091 (mt) cc_final: 0.8819 (mt) REVERT: CM 209 TRP cc_start: 0.7965 (m100) cc_final: 0.7505 (m100) REVERT: CN 57 ARG cc_start: 0.8157 (ttm-80) cc_final: 0.7784 (mtp85) REVERT: CN 245 PHE cc_start: 0.9033 (m-80) cc_final: 0.8664 (m-10) REVERT: CO 3 LYS cc_start: 0.7507 (mmmt) cc_final: 0.7154 (mttt) REVERT: CO 89 LYS cc_start: 0.8789 (mmmt) cc_final: 0.8420 (mtmm) REVERT: CP 374 MET cc_start: 0.8174 (mtp) cc_final: 0.7863 (mtp) REVERT: CP 398 MET cc_start: 0.8105 (ppp) cc_final: 0.7740 (ppp) REVERT: CP 402 MET cc_start: 0.6734 (ptp) cc_final: 0.6431 (ptt) REVERT: CP 409 PHE cc_start: 0.8372 (m-10) cc_final: 0.8109 (m-10) REVERT: CP 524 VAL cc_start: 0.9102 (OUTLIER) cc_final: 0.8855 (p) REVERT: CP 552 MET cc_start: 0.8417 (mmm) cc_final: 0.8133 (mmm) REVERT: CP 581 PHE cc_start: 0.7966 (m-10) cc_final: 0.7692 (m-10) REVERT: CQ 8 PHE cc_start: 0.8628 (t80) cc_final: 0.8117 (t80) REVERT: CQ 45 ASN cc_start: 0.8461 (t0) cc_final: 0.7483 (t0) REVERT: CQ 51 TRP cc_start: 0.8720 (p-90) cc_final: 0.7896 (p-90) REVERT: CQ 55 TYR cc_start: 0.8905 (t80) cc_final: 0.8541 (t80) REVERT: CR 73 LEU cc_start: 0.6064 (tp) cc_final: 0.5769 (tp) REVERT: CR 135 GLN cc_start: 0.7681 (tm-30) cc_final: 0.7460 (tm-30) REVERT: CR 183 THR cc_start: 0.8119 (m) cc_final: 0.7906 (m) REVERT: CS 475 MET cc_start: 0.7989 (mtt) cc_final: 0.7495 (mtp) REVERT: CU 277 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.7529 (ptm-80) REVERT: CU 320 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.7371 (mp-120) REVERT: CU 364 ASN cc_start: 0.8827 (p0) cc_final: 0.8554 (p0) REVERT: Cz 26 ARG cc_start: 0.7668 (ttm-80) cc_final: 0.7130 (ttt-90) REVERT: Cb 110 PHE cc_start: 0.7715 (m-80) cc_final: 0.7499 (t80) REVERT: Cb 242 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8200 (mt-10) REVERT: Cb 249 MET cc_start: 0.8797 (mmp) cc_final: 0.8024 (ttm) REVERT: Cb 380 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8218 (mm-30) REVERT: Ch 292 LYS cc_start: 0.7739 (tptt) cc_final: 0.7417 (ptpt) REVERT: Ch 295 ASN cc_start: 0.8641 (p0) cc_final: 0.7849 (m-40) REVERT: Ch 331 ARG cc_start: 0.8268 (mmt180) cc_final: 0.7473 (ptt180) REVERT: LB 227 PHE cc_start: 0.6107 (OUTLIER) cc_final: 0.4906 (m-10) REVERT: LB 284 TYR cc_start: 0.8115 (OUTLIER) cc_final: 0.7725 (m-10) REVERT: LC 304 LYS cc_start: 0.7887 (mttp) cc_final: 0.7680 (tttt) REVERT: LC 350 LYS cc_start: 0.8899 (ttpt) cc_final: 0.8644 (ttpp) REVERT: LE 33 GLU cc_start: 0.6877 (tm-30) cc_final: 0.5817 (tp30) REVERT: LE 53 GLN cc_start: 0.8391 (mm-40) cc_final: 0.7671 (mp10) REVERT: LE 177 ASP cc_start: 0.8864 (OUTLIER) cc_final: 0.8474 (p0) REVERT: LF 45 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8384 (mp0) REVERT: LF 66 ARG cc_start: 0.7938 (mmm-85) cc_final: 0.7566 (mmm160) REVERT: LF 98 ILE cc_start: 0.5549 (OUTLIER) cc_final: 0.5292 (pt) REVERT: LF 134 LYS cc_start: 0.8784 (tttt) cc_final: 0.8262 (tptt) REVERT: LF 172 ASN cc_start: 0.8349 (m-40) cc_final: 0.7904 (p0) REVERT: LF 230 GLU cc_start: 0.7183 (tt0) cc_final: 0.6908 (tp30) REVERT: LG 55 TRP cc_start: 0.7315 (m100) cc_final: 0.6810 (m100) REVERT: LG 64 GLN cc_start: 0.8684 (mt0) cc_final: 0.8357 (mt0) REVERT: LG 158 ASN cc_start: 0.9074 (p0) cc_final: 0.8795 (p0) REVERT: LG 159 ASP cc_start: 0.8617 (p0) cc_final: 0.8049 (p0) REVERT: LH 170 ARG cc_start: 0.8006 (mtp180) cc_final: 0.7778 (ttp80) REVERT: LH 173 ASP cc_start: 0.8476 (t0) cc_final: 0.8113 (t70) REVERT: LK 35 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.7119 (tt) REVERT: LK 74 VAL cc_start: 0.7988 (OUTLIER) cc_final: 0.7727 (p) REVERT: LK 114 ARG cc_start: 0.8662 (mpp80) cc_final: 0.8141 (mtm-85) REVERT: LK 121 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.8099 (t80) REVERT: LK 132 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.9004 (tp) REVERT: LL 17 HIS cc_start: 0.4749 (OUTLIER) cc_final: 0.3988 (m90) REVERT: LL 78 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.7149 (tt0) REVERT: LL 114 GLN cc_start: 0.7881 (tp40) cc_final: 0.7369 (tp40) REVERT: LM 42 ASP cc_start: 0.8531 (t0) cc_final: 0.7872 (t0) REVERT: LO 146 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7264 (mp0) REVERT: LP 40 LYS cc_start: 0.8842 (mmmt) cc_final: 0.8579 (mmmt) REVERT: LP 75 GLN cc_start: 0.6767 (pt0) cc_final: 0.6019 (mm110) REVERT: LQ 45 LYS cc_start: 0.6679 (ttpt) cc_final: 0.6270 (ttpt) REVERT: LQ 142 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7359 (mt-10) REVERT: LS 55 THR cc_start: 0.8756 (p) cc_final: 0.8224 (t) REVERT: LS 60 SER cc_start: 0.9105 (t) cc_final: 0.8773 (m) REVERT: LS 81 TYR cc_start: 0.8599 (p90) cc_final: 0.8150 (p90) REVERT: LT 52 MET cc_start: 0.4574 (ptm) cc_final: 0.3716 (mtt) REVERT: LT 103 GLU cc_start: 0.9165 (pt0) cc_final: 0.8944 (pm20) REVERT: LT 146 ASN cc_start: 0.8540 (m-40) cc_final: 0.8276 (m-40) REVERT: LV 65 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8220 (tmtt) REVERT: LV 72 ARG cc_start: 0.8257 (ttm110) cc_final: 0.8034 (mtt-85) REVERT: LY 51 LYS cc_start: 0.8839 (ttpp) cc_final: 0.8522 (ttpt) REVERT: LY 54 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7918 (tp30) REVERT: LY 92 GLN cc_start: 0.8216 (tm-30) cc_final: 0.7618 (tm-30) REVERT: LY 126 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7978 (mt-10) REVERT: Le 6 LYS cc_start: 0.8018 (ttmm) cc_final: 0.7064 (tptt) REVERT: Le 30 ASP cc_start: 0.7674 (t70) cc_final: 0.7270 (t0) REVERT: Le 96 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6002 (tp30) REVERT: Le 114 LYS cc_start: 0.8777 (tptt) cc_final: 0.8456 (tttt) REVERT: Lh 16 ASN cc_start: 0.7633 (p0) cc_final: 0.7412 (p0) REVERT: Lh 47 ASN cc_start: 0.7928 (t0) cc_final: 0.7543 (t0) REVERT: Lh 108 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7601 (ptpt) REVERT: Li 72 ASN cc_start: 0.8384 (m-40) cc_final: 0.8059 (t0) REVERT: Lj 30 GLN cc_start: 0.8378 (mm-40) cc_final: 0.8141 (mm-40) REVERT: Lq 63 MET cc_start: 0.7476 (mpp) cc_final: 0.6395 (mpp) REVERT: Lq 66 CYS cc_start: 0.9109 (p) cc_final: 0.8687 (p) REVERT: Lq 103 LEU cc_start: 0.9490 (tp) cc_final: 0.9097 (pp) REVERT: Lq 174 MET cc_start: 0.5203 (ppp) cc_final: 0.4863 (ppp) REVERT: Lq 184 MET cc_start: 0.6408 (mmm) cc_final: 0.5844 (mmm) REVERT: Lq 188 ASN cc_start: 0.8573 (m-40) cc_final: 0.8297 (m-40) REVERT: Lq 206 ILE cc_start: 0.4510 (OUTLIER) cc_final: 0.3844 (tt) REVERT: Cc 37 GLN cc_start: 0.7626 (mm110) cc_final: 0.7106 (tm-30) REVERT: Cc 105 ASP cc_start: 0.6879 (OUTLIER) cc_final: 0.6282 (m-30) REVERT: Cc 115 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8521 (tt) REVERT: Cc 189 ILE cc_start: 0.9160 (mm) cc_final: 0.8952 (mm) REVERT: Cd 37 ARG cc_start: 0.8200 (ttm110) cc_final: 0.7784 (mtt90) REVERT: Cd 224 ASN cc_start: 0.7563 (t0) cc_final: 0.7148 (t0) REVERT: Cd 338 LEU cc_start: 0.9129 (mm) cc_final: 0.8822 (mm) REVERT: Cd 349 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7701 (mt0) REVERT: Ce 10 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7674 (pt) REVERT: Ce 149 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.6795 (mp0) REVERT: Cf 524 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7550 (mt0) REVERT: Cg 116 PHE cc_start: 0.8689 (m-80) cc_final: 0.8220 (m-80) REVERT: Cg 149 MET cc_start: 0.6402 (ppp) cc_final: 0.5962 (tmm) REVERT: Cg 337 MET cc_start: 0.7436 (mpp) cc_final: 0.7077 (pmm) outliers start: 376 outliers final: 291 residues processed: 1868 average time/residue: 1.1734 time to fit residues: 3808.9241 Evaluate side-chains 1891 residues out of total 8922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 324 poor density : 1567 time to evaluate : 8.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 39 LEU Chi-restraints excluded: chain CA residue 47 ARG Chi-restraints excluded: chain CA residue 65 ASP Chi-restraints excluded: chain CA residue 70 THR Chi-restraints excluded: chain CA residue 109 ASN Chi-restraints excluded: chain CA residue 113 VAL Chi-restraints excluded: chain CA residue 118 GLN Chi-restraints excluded: chain CA residue 148 GLN Chi-restraints excluded: chain CA residue 184 VAL Chi-restraints excluded: chain CA residue 186 ASP Chi-restraints excluded: chain CA residue 199 VAL Chi-restraints excluded: chain CB residue 21 ASP Chi-restraints excluded: chain CB residue 44 ASP Chi-restraints excluded: chain CB residue 131 SER Chi-restraints excluded: chain CB residue 151 ASP Chi-restraints excluded: chain CB residue 170 THR Chi-restraints excluded: chain CB residue 185 MET Chi-restraints excluded: chain CB residue 283 VAL Chi-restraints excluded: chain CC residue 118 LEU Chi-restraints excluded: chain CC residue 122 VAL Chi-restraints excluded: chain CC residue 182 SER Chi-restraints excluded: chain CC residue 246 LEU Chi-restraints excluded: chain CC residue 258 THR Chi-restraints excluded: chain CC residue 265 VAL Chi-restraints excluded: chain CC residue 268 LYS Chi-restraints excluded: chain CE residue 142 ILE Chi-restraints excluded: chain CE residue 184 THR Chi-restraints excluded: chain CE residue 237 LEU Chi-restraints excluded: chain CE residue 277 GLU Chi-restraints excluded: chain CE residue 284 ILE Chi-restraints excluded: chain CE residue 301 THR Chi-restraints excluded: chain CE residue 367 CYS Chi-restraints excluded: chain CE residue 382 LEU Chi-restraints excluded: chain CE residue 410 THR Chi-restraints excluded: chain CE residue 411 LEU Chi-restraints excluded: chain CE residue 412 ILE Chi-restraints excluded: chain CE residue 421 LEU Chi-restraints excluded: chain CE residue 442 ILE Chi-restraints excluded: chain CE residue 463 GLN Chi-restraints excluded: chain CE residue 485 PHE Chi-restraints excluded: chain CE residue 496 GLN Chi-restraints excluded: chain CE residue 555 ILE Chi-restraints excluded: chain CF residue 8 ARG Chi-restraints excluded: chain CF residue 12 LEU Chi-restraints excluded: chain CF residue 139 THR Chi-restraints excluded: chain CF residue 142 VAL Chi-restraints excluded: chain CF residue 174 MET Chi-restraints excluded: chain CF residue 175 ILE Chi-restraints excluded: chain CF residue 179 VAL Chi-restraints excluded: chain CF residue 194 ILE Chi-restraints excluded: chain CF residue 226 TYR Chi-restraints excluded: chain CF residue 241 LYS Chi-restraints excluded: chain CG residue 59 VAL Chi-restraints excluded: chain CG residue 65 LEU Chi-restraints excluded: chain CG residue 67 LEU Chi-restraints excluded: chain CG residue 71 LEU Chi-restraints excluded: chain CG residue 87 LEU Chi-restraints excluded: chain CG residue 166 ARG Chi-restraints excluded: chain CH residue 55 THR Chi-restraints excluded: chain CH residue 56 CYS Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 115 LEU Chi-restraints excluded: chain CH residue 165 THR Chi-restraints excluded: chain CH residue 203 LEU Chi-restraints excluded: chain CH residue 220 THR Chi-restraints excluded: chain CH residue 226 HIS Chi-restraints excluded: chain CH residue 281 MET Chi-restraints excluded: chain CH residue 314 VAL Chi-restraints excluded: chain CH residue 338 LEU Chi-restraints excluded: chain CH residue 359 THR Chi-restraints excluded: chain CH residue 387 VAL Chi-restraints excluded: chain CH residue 473 PHE Chi-restraints excluded: chain CI residue 210 PHE Chi-restraints excluded: chain CI residue 224 THR Chi-restraints excluded: chain CI residue 246 ARG Chi-restraints excluded: chain CI residue 258 LEU Chi-restraints excluded: chain CI residue 259 THR Chi-restraints excluded: chain CI residue 268 VAL Chi-restraints excluded: chain CI residue 282 VAL Chi-restraints excluded: chain CI residue 293 LEU Chi-restraints excluded: chain CJ residue 17 MET Chi-restraints excluded: chain CJ residue 158 THR Chi-restraints excluded: chain CJ residue 456 VAL Chi-restraints excluded: chain CK residue 36 SER Chi-restraints excluded: chain CK residue 130 GLU Chi-restraints excluded: chain CK residue 152 THR Chi-restraints excluded: chain CK residue 155 THR Chi-restraints excluded: chain CK residue 193 VAL Chi-restraints excluded: chain CK residue 212 LEU Chi-restraints excluded: chain CK residue 216 THR Chi-restraints excluded: chain CK residue 227 ASP Chi-restraints excluded: chain CK residue 258 VAL Chi-restraints excluded: chain CL residue 18 THR Chi-restraints excluded: chain CL residue 38 LEU Chi-restraints excluded: chain CL residue 65 LEU Chi-restraints excluded: chain CM residue 147 LEU Chi-restraints excluded: chain CM residue 148 LYS Chi-restraints excluded: chain CM residue 244 LEU Chi-restraints excluded: chain CM residue 246 ARG Chi-restraints excluded: chain CN residue 3 VAL Chi-restraints excluded: chain CN residue 51 THR Chi-restraints excluded: chain CN residue 109 VAL Chi-restraints excluded: chain CN residue 147 LEU Chi-restraints excluded: chain CN residue 198 VAL Chi-restraints excluded: chain CN residue 205 VAL Chi-restraints excluded: chain CN residue 208 LEU Chi-restraints excluded: chain CN residue 215 LEU Chi-restraints excluded: chain CO residue 34 SER Chi-restraints excluded: chain CO residue 37 LEU Chi-restraints excluded: chain CO residue 40 ILE Chi-restraints excluded: chain CP residue 267 LEU Chi-restraints excluded: chain CP residue 277 ASN Chi-restraints excluded: chain CP residue 306 VAL Chi-restraints excluded: chain CP residue 319 ASP Chi-restraints excluded: chain CP residue 454 LEU Chi-restraints excluded: chain CP residue 524 VAL Chi-restraints excluded: chain CQ residue 6 CYS Chi-restraints excluded: chain CQ residue 34 SER Chi-restraints excluded: chain CQ residue 89 THR Chi-restraints excluded: chain CR residue 33 ASN Chi-restraints excluded: chain CR residue 128 SER Chi-restraints excluded: chain CR residue 153 LEU Chi-restraints excluded: chain CR residue 177 THR Chi-restraints excluded: chain CR residue 221 THR Chi-restraints excluded: chain CS residue 673 LYS Chi-restraints excluded: chain CS residue 692 LEU Chi-restraints excluded: chain CU residue 228 ASP Chi-restraints excluded: chain CU residue 277 ARG Chi-restraints excluded: chain CU residue 315 VAL Chi-restraints excluded: chain CU residue 320 GLN Chi-restraints excluded: chain CU residue 335 ASN Chi-restraints excluded: chain CU residue 366 LEU Chi-restraints excluded: chain CX residue 76 THR Chi-restraints excluded: chain CX residue 105 LEU Chi-restraints excluded: chain CX residue 133 ARG Chi-restraints excluded: chain Cz residue 50 LEU Chi-restraints excluded: chain Cb residue 193 LEU Chi-restraints excluded: chain Cb residue 237 TYR Chi-restraints excluded: chain Cb residue 255 LEU Chi-restraints excluded: chain Cb residue 301 VAL Chi-restraints excluded: chain Cb residue 312 VAL Chi-restraints excluded: chain Cb residue 430 ILE Chi-restraints excluded: chain Cb residue 439 ILE Chi-restraints excluded: chain Cb residue 440 ASN Chi-restraints excluded: chain Cb residue 454 VAL Chi-restraints excluded: chain LB residue 24 ARG Chi-restraints excluded: chain LB residue 217 ASP Chi-restraints excluded: chain LB residue 227 PHE Chi-restraints excluded: chain LB residue 277 THR Chi-restraints excluded: chain LB residue 284 TYR Chi-restraints excluded: chain LB residue 294 ASN Chi-restraints excluded: chain LB residue 297 THR Chi-restraints excluded: chain LB residue 313 VAL Chi-restraints excluded: chain LB residue 318 VAL Chi-restraints excluded: chain LB residue 320 ASN Chi-restraints excluded: chain LB residue 348 SER Chi-restraints excluded: chain LC residue 61 THR Chi-restraints excluded: chain LC residue 181 ASP Chi-restraints excluded: chain LC residue 185 VAL Chi-restraints excluded: chain LC residue 228 ASN Chi-restraints excluded: chain LC residue 270 GLU Chi-restraints excluded: chain LC residue 277 LEU Chi-restraints excluded: chain LC residue 300 LEU Chi-restraints excluded: chain LC residue 323 LYS Chi-restraints excluded: chain LE residue 71 VAL Chi-restraints excluded: chain LE residue 103 ILE Chi-restraints excluded: chain LE residue 107 VAL Chi-restraints excluded: chain LE residue 129 THR Chi-restraints excluded: chain LE residue 138 SER Chi-restraints excluded: chain LE residue 177 ASP Chi-restraints excluded: chain LF residue 10 ASN Chi-restraints excluded: chain LF residue 14 VAL Chi-restraints excluded: chain LF residue 24 SER Chi-restraints excluded: chain LF residue 26 GLU Chi-restraints excluded: chain LF residue 45 GLU Chi-restraints excluded: chain LF residue 89 LEU Chi-restraints excluded: chain LF residue 98 ILE Chi-restraints excluded: chain LF residue 100 LYS Chi-restraints excluded: chain LF residue 126 THR Chi-restraints excluded: chain LF residue 170 THR Chi-restraints excluded: chain LF residue 189 ASP Chi-restraints excluded: chain LF residue 208 LEU Chi-restraints excluded: chain LG residue 85 LEU Chi-restraints excluded: chain LG residue 89 LEU Chi-restraints excluded: chain LG residue 113 LEU Chi-restraints excluded: chain LG residue 117 THR Chi-restraints excluded: chain LG residue 129 SER Chi-restraints excluded: chain LG residue 139 LEU Chi-restraints excluded: chain LG residue 167 VAL Chi-restraints excluded: chain LG residue 191 THR Chi-restraints excluded: chain LG residue 197 THR Chi-restraints excluded: chain LG residue 201 VAL Chi-restraints excluded: chain LG residue 203 ILE Chi-restraints excluded: chain LG residue 204 THR Chi-restraints excluded: chain LG residue 218 ILE Chi-restraints excluded: chain LG residue 229 VAL Chi-restraints excluded: chain LH residue 16 LEU Chi-restraints excluded: chain LH residue 38 LEU Chi-restraints excluded: chain LH residue 47 VAL Chi-restraints excluded: chain LH residue 56 GLU Chi-restraints excluded: chain LH residue 128 VAL Chi-restraints excluded: chain LH residue 134 VAL Chi-restraints excluded: chain LH residue 165 GLN Chi-restraints excluded: chain LH residue 167 CYS Chi-restraints excluded: chain LH residue 171 ASN Chi-restraints excluded: chain LK residue 35 LEU Chi-restraints excluded: chain LK residue 60 VAL Chi-restraints excluded: chain LK residue 71 VAL Chi-restraints excluded: chain LK residue 74 VAL Chi-restraints excluded: chain LK residue 100 HIS Chi-restraints excluded: chain LK residue 121 PHE Chi-restraints excluded: chain LK residue 132 ILE Chi-restraints excluded: chain LK residue 147 SER Chi-restraints excluded: chain LL residue 17 HIS Chi-restraints excluded: chain LL residue 46 LEU Chi-restraints excluded: chain LL residue 78 GLU Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LM residue 98 ASN Chi-restraints excluded: chain LN residue 33 LEU Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LN residue 97 SER Chi-restraints excluded: chain LN residue 101 THR Chi-restraints excluded: chain LN residue 125 SER Chi-restraints excluded: chain LN residue 149 ASN Chi-restraints excluded: chain LN residue 178 HIS Chi-restraints excluded: chain LN residue 181 ASN Chi-restraints excluded: chain LO residue 34 ILE Chi-restraints excluded: chain LO residue 106 VAL Chi-restraints excluded: chain LO residue 128 VAL Chi-restraints excluded: chain LO residue 146 GLU Chi-restraints excluded: chain LO residue 147 VAL Chi-restraints excluded: chain LO residue 196 SER Chi-restraints excluded: chain LO residue 202 TYR Chi-restraints excluded: chain LP residue 12 THR Chi-restraints excluded: chain LP residue 29 THR Chi-restraints excluded: chain LP residue 52 ILE Chi-restraints excluded: chain LP residue 116 HIS Chi-restraints excluded: chain LQ residue 52 VAL Chi-restraints excluded: chain LQ residue 69 GLU Chi-restraints excluded: chain LQ residue 108 VAL Chi-restraints excluded: chain LQ residue 123 VAL Chi-restraints excluded: chain LQ residue 148 THR Chi-restraints excluded: chain LS residue 13 HIS Chi-restraints excluded: chain LS residue 59 VAL Chi-restraints excluded: chain LS residue 65 SER Chi-restraints excluded: chain LS residue 72 VAL Chi-restraints excluded: chain LS residue 87 THR Chi-restraints excluded: chain LS residue 120 SER Chi-restraints excluded: chain LS residue 133 GLU Chi-restraints excluded: chain LS residue 171 SER Chi-restraints excluded: chain LT residue 42 ILE Chi-restraints excluded: chain LT residue 66 ASN Chi-restraints excluded: chain LT residue 72 VAL Chi-restraints excluded: chain LT residue 97 LYS Chi-restraints excluded: chain LT residue 143 ILE Chi-restraints excluded: chain LV residue 21 VAL Chi-restraints excluded: chain LV residue 65 LYS Chi-restraints excluded: chain LV residue 71 LEU Chi-restraints excluded: chain LV residue 88 LYS Chi-restraints excluded: chain LY residue 6 THR Chi-restraints excluded: chain LY residue 53 ASP Chi-restraints excluded: chain LY residue 55 VAL Chi-restraints excluded: chain LY residue 70 THR Chi-restraints excluded: chain LY residue 85 THR Chi-restraints excluded: chain LY residue 86 ARG Chi-restraints excluded: chain LY residue 128 VAL Chi-restraints excluded: chain Le residue 8 VAL Chi-restraints excluded: chain Le residue 24 ASP Chi-restraints excluded: chain Le residue 31 SER Chi-restraints excluded: chain Le residue 79 ASN Chi-restraints excluded: chain Le residue 96 GLU Chi-restraints excluded: chain Le residue 121 THR Chi-restraints excluded: chain Lf residue 9 LEU Chi-restraints excluded: chain Lf residue 32 ILE Chi-restraints excluded: chain Lf residue 99 SER Chi-restraints excluded: chain Lf residue 108 SER Chi-restraints excluded: chain Lh residue 14 SER Chi-restraints excluded: chain Lh residue 36 ILE Chi-restraints excluded: chain Lh residue 108 LYS Chi-restraints excluded: chain Li residue 27 THR Chi-restraints excluded: chain Li residue 66 VAL Chi-restraints excluded: chain Li residue 97 GLU Chi-restraints excluded: chain Li residue 106 SER Chi-restraints excluded: chain Lj residue 26 SER Chi-restraints excluded: chain Lj residue 61 THR Chi-restraints excluded: chain Lj residue 68 SER Chi-restraints excluded: chain Lj residue 69 THR Chi-restraints excluded: chain Lj residue 82 VAL Chi-restraints excluded: chain Lq residue 99 LEU Chi-restraints excluded: chain Lq residue 107 TYR Chi-restraints excluded: chain Lq residue 175 THR Chi-restraints excluded: chain Lq residue 206 ILE Chi-restraints excluded: chain Cc residue 17 SER Chi-restraints excluded: chain Cc residue 90 LEU Chi-restraints excluded: chain Cc residue 96 THR Chi-restraints excluded: chain Cc residue 105 ASP Chi-restraints excluded: chain Cc residue 106 VAL Chi-restraints excluded: chain Cc residue 115 LEU Chi-restraints excluded: chain Cd residue 70 ASP Chi-restraints excluded: chain Cd residue 77 ASP Chi-restraints excluded: chain Cd residue 86 VAL Chi-restraints excluded: chain Cd residue 231 THR Chi-restraints excluded: chain Cd residue 286 THR Chi-restraints excluded: chain Cd residue 290 ARG Chi-restraints excluded: chain Cd residue 310 GLU Chi-restraints excluded: chain Cd residue 311 LEU Chi-restraints excluded: chain Cd residue 349 GLN Chi-restraints excluded: chain Cd residue 404 VAL Chi-restraints excluded: chain Ce residue 10 ILE Chi-restraints excluded: chain Ce residue 41 GLN Chi-restraints excluded: chain Ce residue 73 MET Chi-restraints excluded: chain Ce residue 126 ILE Chi-restraints excluded: chain Ce residue 149 GLU Chi-restraints excluded: chain Cf residue 463 ARG Chi-restraints excluded: chain Cf residue 484 VAL Chi-restraints excluded: chain Cf residue 509 TRP Chi-restraints excluded: chain Cf residue 524 GLN Chi-restraints excluded: chain Cg residue 46 THR Chi-restraints excluded: chain Cg residue 67 LEU Chi-restraints excluded: chain Cg residue 91 LEU Chi-restraints excluded: chain Cg residue 103 LEU Chi-restraints excluded: chain Cg residue 115 HIS Chi-restraints excluded: chain Cg residue 213 ASN Chi-restraints excluded: chain Cg residue 352 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1262 random chunks: chunk 752 optimal weight: 50.0000 chunk 485 optimal weight: 8.9990 chunk 726 optimal weight: 50.0000 chunk 366 optimal weight: 9.9990 chunk 239 optimal weight: 0.9990 chunk 235 optimal weight: 40.0000 chunk 773 optimal weight: 6.9990 chunk 828 optimal weight: 0.5980 chunk 601 optimal weight: 9.9990 chunk 113 optimal weight: 7.9990 chunk 956 optimal weight: 3.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** CA 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 22 GLN ** CB 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 249 ASN ** CB 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 174 ASN ** CC 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CI 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 124 ASN ** CJ 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CP 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CP 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CR 133 GLN ** CR 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CU 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cb 13 ASN ** Cb 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ch 287 GLN LB 121 ASN LC 59 HIS ** LE 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 178 ASN ** LG 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LH 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LH 164 GLN ** LK 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LK 100 HIS LL 17 HIS ** LQ 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 98 ASN ** LT 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LV 30 ASN ** LV 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LV 100 ASN LY 116 ASN Lf 44 ASN ** Lh 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cd 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cf 524 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 141322 Z= 0.370 Angle : 0.725 28.370 202294 Z= 0.363 Chirality : 0.044 1.874 24461 Planarity : 0.006 0.098 16966 Dihedral : 21.973 176.911 48692 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.37 % Favored : 94.44 % Rotamer: Outliers : 4.73 % Allowed : 22.08 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.02 % Twisted Proline : 0.38 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.08), residues: 10278 helix: 1.17 (0.08), residues: 4614 sheet: -0.19 (0.14), residues: 1353 loop : -0.98 (0.09), residues: 4311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRPCf 509 HIS 0.012 0.001 HISLK 100 PHE 0.043 0.002 PHECh 334 TYR 0.038 0.002 TYRCb 397 ARG 0.013 0.001 ARGCd 366 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20556 Ramachandran restraints generated. 10278 Oldfield, 0 Emsley, 10278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20556 Ramachandran restraints generated. 10278 Oldfield, 0 Emsley, 10278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2016 residues out of total 8922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 410 poor density : 1606 time to evaluate : 8.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CA 76 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7506 (tp30) REVERT: CA 128 PHE cc_start: 0.8438 (m-80) cc_final: 0.8186 (m-80) REVERT: CB 147 PHE cc_start: 0.8867 (t80) cc_final: 0.8371 (t80) REVERT: CC 137 TYR cc_start: 0.8247 (p90) cc_final: 0.7285 (p90) REVERT: CC 141 LYS cc_start: 0.8435 (tppt) cc_final: 0.8231 (tptm) REVERT: CC 194 LYS cc_start: 0.8574 (ptpp) cc_final: 0.8106 (mttp) REVERT: CC 246 LEU cc_start: 0.5222 (OUTLIER) cc_final: 0.4753 (mp) REVERT: CC 381 ASP cc_start: 0.9133 (m-30) cc_final: 0.8403 (p0) REVERT: CE 226 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7923 (mt-10) REVERT: CE 277 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8204 (mp0) REVERT: CE 375 GLU cc_start: 0.8081 (tp30) cc_final: 0.7839 (tt0) REVERT: CE 540 LYS cc_start: 0.8414 (mmmt) cc_final: 0.8201 (mmmt) REVERT: CF 194 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8400 (mt) REVERT: CG 15 LYS cc_start: 0.9095 (mmtt) cc_final: 0.8695 (mtmt) REVERT: CG 137 MET cc_start: 0.7730 (pmm) cc_final: 0.7151 (pmm) REVERT: CH 33 ARG cc_start: 0.3992 (mmt180) cc_final: 0.3009 (mtm180) REVERT: CH 150 ASP cc_start: 0.8686 (t0) cc_final: 0.8448 (t0) REVERT: CH 231 MET cc_start: 0.8403 (mmt) cc_final: 0.8067 (mmt) REVERT: CH 236 MET cc_start: 0.8671 (mmm) cc_final: 0.8089 (tpp) REVERT: CH 253 MET cc_start: 0.7993 (pmm) cc_final: 0.7346 (pmm) REVERT: CH 437 ILE cc_start: 0.8624 (mt) cc_final: 0.8230 (mt) REVERT: CI 246 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8450 (mtm110) REVERT: CI 250 LYS cc_start: 0.8528 (mptt) cc_final: 0.8251 (mmtm) REVERT: CI 274 LYS cc_start: 0.8190 (ptmm) cc_final: 0.7936 (ptmm) REVERT: CI 285 TRP cc_start: 0.8402 (m100) cc_final: 0.7967 (m-90) REVERT: CJ 124 ASN cc_start: 0.2783 (OUTLIER) cc_final: 0.2497 (m110) REVERT: CJ 196 TYR cc_start: 0.8769 (m-80) cc_final: 0.8374 (m-80) REVERT: CJ 230 PHE cc_start: 0.9229 (m-80) cc_final: 0.8637 (m-80) REVERT: CK 67 GLN cc_start: 0.8186 (mt0) cc_final: 0.7692 (tm-30) REVERT: CK 164 ARG cc_start: 0.7169 (mtm110) cc_final: 0.6900 (ptp-170) REVERT: CK 179 TYR cc_start: 0.9164 (m-80) cc_final: 0.8856 (m-10) REVERT: CK 201 LYS cc_start: 0.9034 (mmpt) cc_final: 0.8713 (mmtm) REVERT: CL 23 LYS cc_start: 0.7555 (ttmm) cc_final: 0.7042 (tptt) REVERT: CL 40 ARG cc_start: 0.8451 (mtm-85) cc_final: 0.8050 (ttp-170) REVERT: CM 190 LEU cc_start: 0.9095 (mt) cc_final: 0.8825 (mt) REVERT: CM 209 TRP cc_start: 0.7920 (m100) cc_final: 0.7466 (m100) REVERT: CN 57 ARG cc_start: 0.8195 (ttm-80) cc_final: 0.7817 (mtp85) REVERT: CN 79 GLN cc_start: 0.7889 (tp40) cc_final: 0.7665 (tp-100) REVERT: CN 245 PHE cc_start: 0.9071 (m-80) cc_final: 0.8750 (m-10) REVERT: CO 3 LYS cc_start: 0.7632 (mmmt) cc_final: 0.7327 (mttt) REVERT: CO 89 LYS cc_start: 0.8776 (mmmt) cc_final: 0.8393 (mtmm) REVERT: CP 374 MET cc_start: 0.8193 (mtp) cc_final: 0.7862 (mtp) REVERT: CP 398 MET cc_start: 0.8153 (ppp) cc_final: 0.7634 (ppp) REVERT: CP 402 MET cc_start: 0.6663 (ptp) cc_final: 0.6347 (ptt) REVERT: CP 409 PHE cc_start: 0.8460 (m-10) cc_final: 0.8067 (m-10) REVERT: CP 552 MET cc_start: 0.8474 (mmm) cc_final: 0.8214 (mmm) REVERT: CQ 8 PHE cc_start: 0.8627 (t80) cc_final: 0.8393 (t80) REVERT: CQ 45 ASN cc_start: 0.8538 (t0) cc_final: 0.7757 (t0) REVERT: CQ 51 TRP cc_start: 0.8858 (p-90) cc_final: 0.8137 (p-90) REVERT: CQ 55 TYR cc_start: 0.8896 (t80) cc_final: 0.8550 (t80) REVERT: CR 73 LEU cc_start: 0.6058 (tp) cc_final: 0.5792 (tp) REVERT: CS 471 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7025 (mm-30) REVERT: CS 475 MET cc_start: 0.8037 (mtt) cc_final: 0.7692 (mtp) REVERT: CS 689 LYS cc_start: 0.7274 (mmpt) cc_final: 0.7004 (mmpt) REVERT: CS 700 GLU cc_start: 0.6028 (mm-30) cc_final: 0.5565 (mm-30) REVERT: CS 721 LYS cc_start: 0.7223 (mmmt) cc_final: 0.6735 (mmtt) REVERT: CU 270 ASP cc_start: 0.8646 (t0) cc_final: 0.8406 (t0) REVERT: CU 277 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.7393 (ptm-80) REVERT: CU 364 ASN cc_start: 0.8865 (p0) cc_final: 0.8594 (p0) REVERT: Cz 26 ARG cc_start: 0.7817 (ttm-80) cc_final: 0.7259 (ttt-90) REVERT: Cz 51 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.6772 (ttt90) REVERT: Ch 292 LYS cc_start: 0.7900 (tptt) cc_final: 0.7552 (pttm) REVERT: Ch 295 ASN cc_start: 0.8715 (p0) cc_final: 0.7950 (m-40) REVERT: Ch 331 ARG cc_start: 0.8256 (mmt180) cc_final: 0.7439 (ptt180) REVERT: LB 227 PHE cc_start: 0.6224 (OUTLIER) cc_final: 0.5094 (m-10) REVERT: LB 284 TYR cc_start: 0.8221 (OUTLIER) cc_final: 0.7877 (m-10) REVERT: LC 220 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.7693 (mtmt) REVERT: LC 304 LYS cc_start: 0.7978 (mttp) cc_final: 0.7660 (tttt) REVERT: LC 350 LYS cc_start: 0.8930 (ttpt) cc_final: 0.8656 (ttpp) REVERT: LE 53 GLN cc_start: 0.8243 (mm-40) cc_final: 0.7682 (mp10) REVERT: LE 177 ASP cc_start: 0.8873 (OUTLIER) cc_final: 0.8493 (p0) REVERT: LF 45 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8401 (mp0) REVERT: LF 66 ARG cc_start: 0.7966 (mmm-85) cc_final: 0.7621 (mmm160) REVERT: LF 134 LYS cc_start: 0.8773 (tttt) cc_final: 0.8260 (tptt) REVERT: LF 230 GLU cc_start: 0.7189 (tt0) cc_final: 0.6923 (tp30) REVERT: LG 64 GLN cc_start: 0.8703 (mt0) cc_final: 0.8405 (mt0) REVERT: LG 158 ASN cc_start: 0.9053 (p0) cc_final: 0.8837 (p0) REVERT: LG 159 ASP cc_start: 0.8655 (p0) cc_final: 0.8090 (p0) REVERT: LH 55 LEU cc_start: 0.8807 (pt) cc_final: 0.8563 (pt) REVERT: LH 170 ARG cc_start: 0.8006 (mtp180) cc_final: 0.7707 (ttp80) REVERT: LH 173 ASP cc_start: 0.8513 (t0) cc_final: 0.8180 (t70) REVERT: LK 35 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.7149 (tt) REVERT: LK 114 ARG cc_start: 0.8701 (mpp80) cc_final: 0.8073 (mtm180) REVERT: LK 121 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.8045 (t80) REVERT: LK 132 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.9032 (tp) REVERT: LL 78 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7179 (tt0) REVERT: LM 42 ASP cc_start: 0.8666 (t0) cc_final: 0.7980 (t0) REVERT: LO 146 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7150 (mp0) REVERT: LO 178 ARG cc_start: 0.7455 (mmm160) cc_final: 0.7243 (mmm-85) REVERT: LP 75 GLN cc_start: 0.7056 (pt0) cc_final: 0.6233 (mm110) REVERT: LP 89 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8178 (tt0) REVERT: LS 21 ASN cc_start: 0.7961 (t0) cc_final: 0.7411 (t0) REVERT: LS 55 THR cc_start: 0.8803 (p) cc_final: 0.8316 (t) REVERT: LS 60 SER cc_start: 0.9077 (t) cc_final: 0.8710 (m) REVERT: LS 117 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.7188 (mtt180) REVERT: LT 52 MET cc_start: 0.4579 (ptm) cc_final: 0.3743 (mtt) REVERT: LT 103 GLU cc_start: 0.9149 (pt0) cc_final: 0.8934 (pm20) REVERT: LT 112 ASN cc_start: 0.8686 (m-40) cc_final: 0.8413 (p0) REVERT: LT 146 ASN cc_start: 0.8488 (m-40) cc_final: 0.7937 (m-40) REVERT: LV 61 MET cc_start: 0.8491 (mmm) cc_final: 0.8228 (mmp) REVERT: LV 65 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8263 (tmtt) REVERT: LV 138 VAL cc_start: 0.9120 (OUTLIER) cc_final: 0.8839 (m) REVERT: LY 51 LYS cc_start: 0.8802 (ttpp) cc_final: 0.8481 (ttpt) REVERT: LY 54 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7950 (tp30) REVERT: LY 92 GLN cc_start: 0.8284 (tm-30) cc_final: 0.7630 (tm-30) REVERT: LY 126 GLU cc_start: 0.8287 (mt-10) cc_final: 0.8002 (mt-10) REVERT: Le 6 LYS cc_start: 0.8008 (ttmm) cc_final: 0.7076 (tptt) REVERT: Le 30 ASP cc_start: 0.7742 (t70) cc_final: 0.7413 (t0) REVERT: Le 96 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6017 (tp30) REVERT: Le 114 LYS cc_start: 0.8765 (tptt) cc_final: 0.8474 (tttt) REVERT: Lf 46 TYR cc_start: 0.8538 (m-80) cc_final: 0.8196 (m-80) REVERT: Lh 16 ASN cc_start: 0.7768 (p0) cc_final: 0.7558 (p0) REVERT: Lh 47 ASN cc_start: 0.7996 (t0) cc_final: 0.7617 (t0) REVERT: Lh 95 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7195 (mtt-85) REVERT: Lh 108 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7481 (ptmt) REVERT: Li 72 ASN cc_start: 0.8363 (m-40) cc_final: 0.8050 (t0) REVERT: Li 100 GLN cc_start: 0.8273 (tp40) cc_final: 0.7722 (tm-30) REVERT: Lj 30 GLN cc_start: 0.8431 (mm-40) cc_final: 0.8183 (mm-40) REVERT: Lq 63 MET cc_start: 0.7471 (mpp) cc_final: 0.6367 (mpp) REVERT: Lq 66 CYS cc_start: 0.9131 (p) cc_final: 0.8684 (p) REVERT: Lq 83 ASP cc_start: 0.4963 (p0) cc_final: 0.4723 (p0) REVERT: Lq 103 LEU cc_start: 0.9473 (tp) cc_final: 0.9097 (pp) REVERT: Lq 174 MET cc_start: 0.5344 (ppp) cc_final: 0.4980 (ppp) REVERT: Lq 184 MET cc_start: 0.6408 (mmm) cc_final: 0.5862 (mmm) REVERT: Lq 188 ASN cc_start: 0.8577 (m-40) cc_final: 0.8283 (m-40) REVERT: Lq 206 ILE cc_start: 0.4631 (OUTLIER) cc_final: 0.3950 (tt) REVERT: Cc 37 GLN cc_start: 0.7748 (mm110) cc_final: 0.7193 (tm-30) REVERT: Cc 110 GLU cc_start: 0.7853 (pp20) cc_final: 0.7409 (tm-30) REVERT: Cd 37 ARG cc_start: 0.8182 (ttm110) cc_final: 0.7749 (mtt90) REVERT: Cd 224 ASN cc_start: 0.7690 (t0) cc_final: 0.7281 (t0) REVERT: Cd 308 TYR cc_start: 0.8946 (m-10) cc_final: 0.8601 (m-10) REVERT: Cd 338 LEU cc_start: 0.9190 (mm) cc_final: 0.8861 (mm) REVERT: Cd 349 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7725 (mt0) REVERT: Cd 351 ASP cc_start: 0.7730 (t0) cc_final: 0.7523 (t0) REVERT: Cd 373 VAL cc_start: 0.8204 (m) cc_final: 0.7862 (p) REVERT: Ce 149 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.6743 (mp0) REVERT: Cf 510 LYS cc_start: 0.7257 (mttp) cc_final: 0.6753 (mtmm) REVERT: Cf 529 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7084 (mm-30) REVERT: Cg 116 PHE cc_start: 0.8620 (m-80) cc_final: 0.8110 (m-80) REVERT: Cg 149 MET cc_start: 0.6497 (ppp) cc_final: 0.6093 (tmm) outliers start: 410 outliers final: 324 residues processed: 1857 average time/residue: 1.1709 time to fit residues: 3792.3096 Evaluate side-chains 1897 residues out of total 8922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 350 poor density : 1547 time to evaluate : 8.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 65 ASP Chi-restraints excluded: chain CA residue 70 THR Chi-restraints excluded: chain CA residue 80 LEU Chi-restraints excluded: chain CA residue 109 ASN Chi-restraints excluded: chain CA residue 113 VAL Chi-restraints excluded: chain CA residue 148 GLN Chi-restraints excluded: chain CA residue 184 VAL Chi-restraints excluded: chain CA residue 186 ASP Chi-restraints excluded: chain CA residue 199 VAL Chi-restraints excluded: chain CA residue 262 ILE Chi-restraints excluded: chain CB residue 21 ASP Chi-restraints excluded: chain CB residue 22 GLN Chi-restraints excluded: chain CB residue 44 ASP Chi-restraints excluded: chain CB residue 65 THR Chi-restraints excluded: chain CB residue 91 THR Chi-restraints excluded: chain CB residue 98 CYS Chi-restraints excluded: chain CB residue 131 SER Chi-restraints excluded: chain CB residue 151 ASP Chi-restraints excluded: chain CB residue 185 MET Chi-restraints excluded: chain CC residue 118 LEU Chi-restraints excluded: chain CC residue 182 SER Chi-restraints excluded: chain CC residue 246 LEU Chi-restraints excluded: chain CC residue 258 THR Chi-restraints excluded: chain CC residue 265 VAL Chi-restraints excluded: chain CE residue 142 ILE Chi-restraints excluded: chain CE residue 184 THR Chi-restraints excluded: chain CE residue 237 LEU Chi-restraints excluded: chain CE residue 277 GLU Chi-restraints excluded: chain CE residue 296 SER Chi-restraints excluded: chain CE residue 301 THR Chi-restraints excluded: chain CE residue 367 CYS Chi-restraints excluded: chain CE residue 382 LEU Chi-restraints excluded: chain CE residue 410 THR Chi-restraints excluded: chain CE residue 411 LEU Chi-restraints excluded: chain CE residue 412 ILE Chi-restraints excluded: chain CE residue 421 LEU Chi-restraints excluded: chain CE residue 442 ILE Chi-restraints excluded: chain CE residue 463 GLN Chi-restraints excluded: chain CE residue 485 PHE Chi-restraints excluded: chain CE residue 496 GLN Chi-restraints excluded: chain CE residue 503 THR Chi-restraints excluded: chain CE residue 555 ILE Chi-restraints excluded: chain CF residue 8 ARG Chi-restraints excluded: chain CF residue 12 LEU Chi-restraints excluded: chain CF residue 139 THR Chi-restraints excluded: chain CF residue 142 VAL Chi-restraints excluded: chain CF residue 174 MET Chi-restraints excluded: chain CF residue 175 ILE Chi-restraints excluded: chain CF residue 179 VAL Chi-restraints excluded: chain CF residue 194 ILE Chi-restraints excluded: chain CF residue 226 TYR Chi-restraints excluded: chain CF residue 241 LYS Chi-restraints excluded: chain CG residue 59 VAL Chi-restraints excluded: chain CG residue 67 LEU Chi-restraints excluded: chain CG residue 71 LEU Chi-restraints excluded: chain CG residue 87 LEU Chi-restraints excluded: chain CG residue 166 ARG Chi-restraints excluded: chain CH residue 55 THR Chi-restraints excluded: chain CH residue 56 CYS Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 115 LEU Chi-restraints excluded: chain CH residue 165 THR Chi-restraints excluded: chain CH residue 203 LEU Chi-restraints excluded: chain CH residue 223 ILE Chi-restraints excluded: chain CH residue 226 HIS Chi-restraints excluded: chain CH residue 281 MET Chi-restraints excluded: chain CH residue 282 VAL Chi-restraints excluded: chain CH residue 314 VAL Chi-restraints excluded: chain CH residue 338 LEU Chi-restraints excluded: chain CH residue 387 VAL Chi-restraints excluded: chain CH residue 473 PHE Chi-restraints excluded: chain CI residue 210 PHE Chi-restraints excluded: chain CI residue 213 ILE Chi-restraints excluded: chain CI residue 216 LEU Chi-restraints excluded: chain CI residue 224 THR Chi-restraints excluded: chain CI residue 246 ARG Chi-restraints excluded: chain CI residue 258 LEU Chi-restraints excluded: chain CI residue 259 THR Chi-restraints excluded: chain CI residue 268 VAL Chi-restraints excluded: chain CI residue 277 ASN Chi-restraints excluded: chain CI residue 282 VAL Chi-restraints excluded: chain CI residue 293 LEU Chi-restraints excluded: chain CJ residue 17 MET Chi-restraints excluded: chain CJ residue 124 ASN Chi-restraints excluded: chain CJ residue 158 THR Chi-restraints excluded: chain CJ residue 374 LEU Chi-restraints excluded: chain CJ residue 456 VAL Chi-restraints excluded: chain CK residue 36 SER Chi-restraints excluded: chain CK residue 130 GLU Chi-restraints excluded: chain CK residue 152 THR Chi-restraints excluded: chain CK residue 155 THR Chi-restraints excluded: chain CK residue 193 VAL Chi-restraints excluded: chain CK residue 216 THR Chi-restraints excluded: chain CK residue 227 ASP Chi-restraints excluded: chain CK residue 258 VAL Chi-restraints excluded: chain CL residue 18 THR Chi-restraints excluded: chain CL residue 38 LEU Chi-restraints excluded: chain CL residue 65 LEU Chi-restraints excluded: chain CM residue 147 LEU Chi-restraints excluded: chain CM residue 148 LYS Chi-restraints excluded: chain CM residue 244 LEU Chi-restraints excluded: chain CM residue 246 ARG Chi-restraints excluded: chain CN residue 3 VAL Chi-restraints excluded: chain CN residue 51 THR Chi-restraints excluded: chain CN residue 109 VAL Chi-restraints excluded: chain CN residue 147 LEU Chi-restraints excluded: chain CN residue 154 LEU Chi-restraints excluded: chain CN residue 186 VAL Chi-restraints excluded: chain CN residue 197 MET Chi-restraints excluded: chain CN residue 198 VAL Chi-restraints excluded: chain CN residue 205 VAL Chi-restraints excluded: chain CN residue 215 LEU Chi-restraints excluded: chain CO residue 34 SER Chi-restraints excluded: chain CO residue 37 LEU Chi-restraints excluded: chain CO residue 40 ILE Chi-restraints excluded: chain CP residue 267 LEU Chi-restraints excluded: chain CP residue 277 ASN Chi-restraints excluded: chain CP residue 306 VAL Chi-restraints excluded: chain CP residue 319 ASP Chi-restraints excluded: chain CP residue 349 VAL Chi-restraints excluded: chain CP residue 524 VAL Chi-restraints excluded: chain CP residue 560 LEU Chi-restraints excluded: chain CQ residue 1 MET Chi-restraints excluded: chain CQ residue 6 CYS Chi-restraints excluded: chain CQ residue 34 SER Chi-restraints excluded: chain CQ residue 89 THR Chi-restraints excluded: chain CR residue 5 LEU Chi-restraints excluded: chain CR residue 33 ASN Chi-restraints excluded: chain CR residue 128 SER Chi-restraints excluded: chain CR residue 177 THR Chi-restraints excluded: chain CR residue 221 THR Chi-restraints excluded: chain CS residue 673 LYS Chi-restraints excluded: chain CS residue 692 LEU Chi-restraints excluded: chain CU residue 196 LEU Chi-restraints excluded: chain CU residue 203 ILE Chi-restraints excluded: chain CU residue 219 SER Chi-restraints excluded: chain CU residue 228 ASP Chi-restraints excluded: chain CU residue 277 ARG Chi-restraints excluded: chain CU residue 335 ASN Chi-restraints excluded: chain CU residue 366 LEU Chi-restraints excluded: chain CX residue 76 THR Chi-restraints excluded: chain CX residue 105 LEU Chi-restraints excluded: chain CX residue 133 ARG Chi-restraints excluded: chain Cz residue 50 LEU Chi-restraints excluded: chain Cz residue 51 ARG Chi-restraints excluded: chain Cb residue 207 MET Chi-restraints excluded: chain Cb residue 237 TYR Chi-restraints excluded: chain Cb residue 255 LEU Chi-restraints excluded: chain Cb residue 301 VAL Chi-restraints excluded: chain Cb residue 312 VAL Chi-restraints excluded: chain Cb residue 328 ILE Chi-restraints excluded: chain Cb residue 439 ILE Chi-restraints excluded: chain Cb residue 440 ASN Chi-restraints excluded: chain Cb residue 474 ASP Chi-restraints excluded: chain LB residue 24 ARG Chi-restraints excluded: chain LB residue 217 ASP Chi-restraints excluded: chain LB residue 225 HIS Chi-restraints excluded: chain LB residue 227 PHE Chi-restraints excluded: chain LB residue 277 THR Chi-restraints excluded: chain LB residue 284 TYR Chi-restraints excluded: chain LB residue 294 ASN Chi-restraints excluded: chain LB residue 297 THR Chi-restraints excluded: chain LB residue 313 VAL Chi-restraints excluded: chain LB residue 318 VAL Chi-restraints excluded: chain LB residue 320 ASN Chi-restraints excluded: chain LB residue 348 SER Chi-restraints excluded: chain LB residue 364 SER Chi-restraints excluded: chain LB residue 388 LEU Chi-restraints excluded: chain LC residue 35 ILE Chi-restraints excluded: chain LC residue 37 LYS Chi-restraints excluded: chain LC residue 61 THR Chi-restraints excluded: chain LC residue 79 SER Chi-restraints excluded: chain LC residue 181 ASP Chi-restraints excluded: chain LC residue 185 VAL Chi-restraints excluded: chain LC residue 220 LYS Chi-restraints excluded: chain LC residue 270 GLU Chi-restraints excluded: chain LC residue 277 LEU Chi-restraints excluded: chain LC residue 300 LEU Chi-restraints excluded: chain LC residue 323 LYS Chi-restraints excluded: chain LE residue 103 ILE Chi-restraints excluded: chain LE residue 107 VAL Chi-restraints excluded: chain LE residue 129 THR Chi-restraints excluded: chain LE residue 138 SER Chi-restraints excluded: chain LE residue 177 ASP Chi-restraints excluded: chain LE residue 198 MET Chi-restraints excluded: chain LF residue 10 ASN Chi-restraints excluded: chain LF residue 14 VAL Chi-restraints excluded: chain LF residue 24 SER Chi-restraints excluded: chain LF residue 26 GLU Chi-restraints excluded: chain LF residue 45 GLU Chi-restraints excluded: chain LF residue 89 LEU Chi-restraints excluded: chain LF residue 100 LYS Chi-restraints excluded: chain LF residue 101 ILE Chi-restraints excluded: chain LF residue 126 THR Chi-restraints excluded: chain LF residue 170 THR Chi-restraints excluded: chain LF residue 189 ASP Chi-restraints excluded: chain LF residue 208 LEU Chi-restraints excluded: chain LG residue 85 LEU Chi-restraints excluded: chain LG residue 89 LEU Chi-restraints excluded: chain LG residue 113 LEU Chi-restraints excluded: chain LG residue 117 THR Chi-restraints excluded: chain LG residue 129 SER Chi-restraints excluded: chain LG residue 139 LEU Chi-restraints excluded: chain LG residue 167 VAL Chi-restraints excluded: chain LG residue 191 THR Chi-restraints excluded: chain LG residue 201 VAL Chi-restraints excluded: chain LG residue 203 ILE Chi-restraints excluded: chain LG residue 204 THR Chi-restraints excluded: chain LG residue 218 ILE Chi-restraints excluded: chain LH residue 16 LEU Chi-restraints excluded: chain LH residue 38 LEU Chi-restraints excluded: chain LH residue 47 VAL Chi-restraints excluded: chain LH residue 56 GLU Chi-restraints excluded: chain LH residue 101 VAL Chi-restraints excluded: chain LH residue 128 VAL Chi-restraints excluded: chain LH residue 134 VAL Chi-restraints excluded: chain LH residue 149 SER Chi-restraints excluded: chain LH residue 167 CYS Chi-restraints excluded: chain LH residue 171 ASN Chi-restraints excluded: chain LK residue 35 LEU Chi-restraints excluded: chain LK residue 60 VAL Chi-restraints excluded: chain LK residue 71 VAL Chi-restraints excluded: chain LK residue 100 HIS Chi-restraints excluded: chain LK residue 121 PHE Chi-restraints excluded: chain LK residue 132 ILE Chi-restraints excluded: chain LK residue 147 SER Chi-restraints excluded: chain LL residue 17 HIS Chi-restraints excluded: chain LL residue 46 LEU Chi-restraints excluded: chain LL residue 62 THR Chi-restraints excluded: chain LL residue 78 GLU Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LM residue 98 ASN Chi-restraints excluded: chain LN residue 33 LEU Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LN residue 97 SER Chi-restraints excluded: chain LN residue 101 THR Chi-restraints excluded: chain LN residue 110 CYS Chi-restraints excluded: chain LN residue 125 SER Chi-restraints excluded: chain LN residue 178 HIS Chi-restraints excluded: chain LN residue 181 ASN Chi-restraints excluded: chain LO residue 22 SER Chi-restraints excluded: chain LO residue 34 ILE Chi-restraints excluded: chain LO residue 106 VAL Chi-restraints excluded: chain LO residue 128 VAL Chi-restraints excluded: chain LO residue 146 GLU Chi-restraints excluded: chain LO residue 147 VAL Chi-restraints excluded: chain LO residue 196 SER Chi-restraints excluded: chain LP residue 12 THR Chi-restraints excluded: chain LP residue 29 THR Chi-restraints excluded: chain LP residue 52 ILE Chi-restraints excluded: chain LP residue 116 HIS Chi-restraints excluded: chain LQ residue 52 VAL Chi-restraints excluded: chain LQ residue 69 GLU Chi-restraints excluded: chain LQ residue 85 ILE Chi-restraints excluded: chain LQ residue 108 VAL Chi-restraints excluded: chain LQ residue 113 THR Chi-restraints excluded: chain LQ residue 123 VAL Chi-restraints excluded: chain LQ residue 148 THR Chi-restraints excluded: chain LS residue 13 HIS Chi-restraints excluded: chain LS residue 59 VAL Chi-restraints excluded: chain LS residue 65 SER Chi-restraints excluded: chain LS residue 72 VAL Chi-restraints excluded: chain LS residue 87 THR Chi-restraints excluded: chain LS residue 117 ARG Chi-restraints excluded: chain LS residue 120 SER Chi-restraints excluded: chain LS residue 133 GLU Chi-restraints excluded: chain LS residue 171 SER Chi-restraints excluded: chain LT residue 42 ILE Chi-restraints excluded: chain LT residue 66 ASN Chi-restraints excluded: chain LT residue 72 VAL Chi-restraints excluded: chain LT residue 97 LYS Chi-restraints excluded: chain LT residue 143 ILE Chi-restraints excluded: chain LV residue 21 VAL Chi-restraints excluded: chain LV residue 30 ASN Chi-restraints excluded: chain LV residue 59 MET Chi-restraints excluded: chain LV residue 65 LYS Chi-restraints excluded: chain LV residue 88 LYS Chi-restraints excluded: chain LV residue 138 VAL Chi-restraints excluded: chain LY residue 1 MET Chi-restraints excluded: chain LY residue 53 ASP Chi-restraints excluded: chain LY residue 55 VAL Chi-restraints excluded: chain LY residue 70 THR Chi-restraints excluded: chain LY residue 71 SER Chi-restraints excluded: chain LY residue 85 THR Chi-restraints excluded: chain LY residue 86 ARG Chi-restraints excluded: chain LY residue 128 VAL Chi-restraints excluded: chain Le residue 8 VAL Chi-restraints excluded: chain Le residue 24 ASP Chi-restraints excluded: chain Le residue 31 SER Chi-restraints excluded: chain Le residue 79 ASN Chi-restraints excluded: chain Le residue 96 GLU Chi-restraints excluded: chain Le residue 121 THR Chi-restraints excluded: chain Lf residue 108 SER Chi-restraints excluded: chain Lh residue 14 SER Chi-restraints excluded: chain Lh residue 36 ILE Chi-restraints excluded: chain Lh residue 61 THR Chi-restraints excluded: chain Lh residue 95 ARG Chi-restraints excluded: chain Lh residue 108 LYS Chi-restraints excluded: chain Li residue 27 THR Chi-restraints excluded: chain Li residue 66 VAL Chi-restraints excluded: chain Li residue 70 LEU Chi-restraints excluded: chain Li residue 97 GLU Chi-restraints excluded: chain Li residue 106 SER Chi-restraints excluded: chain Lj residue 26 SER Chi-restraints excluded: chain Lj residue 59 THR Chi-restraints excluded: chain Lj residue 61 THR Chi-restraints excluded: chain Lj residue 69 THR Chi-restraints excluded: chain Lj residue 82 VAL Chi-restraints excluded: chain Lq residue 99 LEU Chi-restraints excluded: chain Lq residue 107 TYR Chi-restraints excluded: chain Lq residue 175 THR Chi-restraints excluded: chain Lq residue 206 ILE Chi-restraints excluded: chain Cc residue 17 SER Chi-restraints excluded: chain Cc residue 90 LEU Chi-restraints excluded: chain Cc residue 96 THR Chi-restraints excluded: chain Cc residue 104 ILE Chi-restraints excluded: chain Cc residue 105 ASP Chi-restraints excluded: chain Cc residue 106 VAL Chi-restraints excluded: chain Cc residue 236 THR Chi-restraints excluded: chain Cd residue 70 ASP Chi-restraints excluded: chain Cd residue 77 ASP Chi-restraints excluded: chain Cd residue 86 VAL Chi-restraints excluded: chain Cd residue 220 SER Chi-restraints excluded: chain Cd residue 231 THR Chi-restraints excluded: chain Cd residue 286 THR Chi-restraints excluded: chain Cd residue 290 ARG Chi-restraints excluded: chain Cd residue 310 GLU Chi-restraints excluded: chain Cd residue 311 LEU Chi-restraints excluded: chain Cd residue 349 GLN Chi-restraints excluded: chain Cd residue 404 VAL Chi-restraints excluded: chain Ce residue 10 ILE Chi-restraints excluded: chain Ce residue 41 GLN Chi-restraints excluded: chain Ce residue 48 SER Chi-restraints excluded: chain Ce residue 73 MET Chi-restraints excluded: chain Ce residue 84 SER Chi-restraints excluded: chain Ce residue 126 ILE Chi-restraints excluded: chain Ce residue 149 GLU Chi-restraints excluded: chain Ce residue 165 THR Chi-restraints excluded: chain Ce residue 195 LEU Chi-restraints excluded: chain Cf residue 463 ARG Chi-restraints excluded: chain Cf residue 484 VAL Chi-restraints excluded: chain Cf residue 509 TRP Chi-restraints excluded: chain Cf residue 524 GLN Chi-restraints excluded: chain Cg residue 46 THR Chi-restraints excluded: chain Cg residue 67 LEU Chi-restraints excluded: chain Cg residue 89 HIS Chi-restraints excluded: chain Cg residue 91 LEU Chi-restraints excluded: chain Cg residue 103 LEU Chi-restraints excluded: chain Cg residue 213 ASN Chi-restraints excluded: chain Cg residue 352 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1262 random chunks: chunk 1106 optimal weight: 0.8980 chunk 1165 optimal weight: 0.8980 chunk 1063 optimal weight: 0.2980 chunk 1133 optimal weight: 0.8980 chunk 1164 optimal weight: 1.9990 chunk 682 optimal weight: 0.2980 chunk 493 optimal weight: 5.9990 chunk 890 optimal weight: 0.8980 chunk 347 optimal weight: 1.9990 chunk 1024 optimal weight: 0.8980 chunk 1072 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** CA 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 22 GLN ** CB 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 174 ASN ** CE 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CI 256 HIS ** CJ 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 124 ASN ** CJ 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CK 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CK 203 ASN ** CN 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CP 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CP 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CP 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cb 13 ASN ** Cb 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 121 ASN ** LB 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 178 ASN ** LH 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LK 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LK 100 HIS LL 17 HIS ** LQ 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 98 ASN LT 90 ASN ** LT 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LV 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LV 100 ASN LY 116 ASN Lf 44 ASN Lq 27 ASN Ce 12 GLN Cf 524 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 141322 Z= 0.170 Angle : 0.648 27.228 202294 Z= 0.324 Chirality : 0.039 1.964 24461 Planarity : 0.005 0.099 16966 Dihedral : 21.933 176.780 48692 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.35 % Favored : 95.49 % Rotamer: Outliers : 3.00 % Allowed : 24.11 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.02 % Twisted Proline : 0.38 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.08), residues: 10278 helix: 1.28 (0.08), residues: 4616 sheet: -0.14 (0.14), residues: 1331 loop : -0.89 (0.09), residues: 4331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRPCf 509 HIS 0.049 0.001 HISLK 100 PHE 0.046 0.002 PHECh 334 TYR 0.035 0.002 TYRCK 168 ARG 0.015 0.001 ARGCf 523 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20556 Ramachandran restraints generated. 10278 Oldfield, 0 Emsley, 10278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20556 Ramachandran restraints generated. 10278 Oldfield, 0 Emsley, 10278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1953 residues out of total 8922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 1693 time to evaluate : 7.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CB 147 PHE cc_start: 0.8759 (t80) cc_final: 0.8387 (t80) REVERT: CB 258 ASN cc_start: 0.7368 (m-40) cc_final: 0.6759 (m-40) REVERT: CC 137 TYR cc_start: 0.8188 (p90) cc_final: 0.7343 (p90) REVERT: CC 141 LYS cc_start: 0.8426 (tppt) cc_final: 0.8163 (tptm) REVERT: CC 194 LYS cc_start: 0.8475 (ptpp) cc_final: 0.8048 (mttp) REVERT: CC 246 LEU cc_start: 0.5415 (OUTLIER) cc_final: 0.4869 (mp) REVERT: CC 381 ASP cc_start: 0.9150 (m-30) cc_final: 0.8458 (p0) REVERT: CE 226 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7920 (mt-10) REVERT: CE 246 ASP cc_start: 0.8408 (t70) cc_final: 0.7685 (t0) REVERT: CE 277 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8217 (mp0) REVERT: CE 375 GLU cc_start: 0.7970 (tp30) cc_final: 0.7723 (tt0) REVERT: CF 41 PHE cc_start: 0.7249 (m-80) cc_final: 0.7022 (m-80) REVERT: CF 194 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8265 (mt) REVERT: CG 137 MET cc_start: 0.7774 (pmm) cc_final: 0.7228 (pmm) REVERT: CG 169 ASP cc_start: 0.5383 (p0) cc_final: 0.5137 (m-30) REVERT: CH 33 ARG cc_start: 0.4145 (mmt180) cc_final: 0.2959 (mtm110) REVERT: CH 115 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8914 (mm) REVERT: CH 150 ASP cc_start: 0.8579 (t0) cc_final: 0.8358 (t0) REVERT: CH 231 MET cc_start: 0.8311 (mmt) cc_final: 0.7811 (mmt) REVERT: CH 236 MET cc_start: 0.8588 (mmm) cc_final: 0.7910 (tpp) REVERT: CH 250 LEU cc_start: 0.8934 (mt) cc_final: 0.8614 (tp) REVERT: CH 253 MET cc_start: 0.7999 (pmm) cc_final: 0.7332 (pmm) REVERT: CH 333 HIS cc_start: 0.8406 (t70) cc_final: 0.7538 (t-90) REVERT: CH 437 ILE cc_start: 0.8548 (mt) cc_final: 0.8080 (mt) REVERT: CI 250 LYS cc_start: 0.8323 (mptt) cc_final: 0.8020 (mmtm) REVERT: CI 274 LYS cc_start: 0.8049 (ptmm) cc_final: 0.7803 (ptmm) REVERT: CI 305 LYS cc_start: 0.8745 (pttm) cc_final: 0.8213 (mttt) REVERT: CJ 196 TYR cc_start: 0.8740 (m-80) cc_final: 0.8305 (m-80) REVERT: CJ 230 PHE cc_start: 0.9179 (m-80) cc_final: 0.8667 (m-80) REVERT: CK 67 GLN cc_start: 0.8144 (mt0) cc_final: 0.7654 (tm-30) REVERT: CK 164 ARG cc_start: 0.7121 (mtm110) cc_final: 0.6858 (ptp-170) REVERT: CK 179 TYR cc_start: 0.9138 (m-80) cc_final: 0.8897 (m-10) REVERT: CK 201 LYS cc_start: 0.8969 (mmpt) cc_final: 0.8665 (mmtm) REVERT: CK 212 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9299 (mm) REVERT: CL 23 LYS cc_start: 0.7571 (ttmm) cc_final: 0.7021 (tptt) REVERT: CL 67 GLN cc_start: 0.9102 (tt0) cc_final: 0.8871 (tm-30) REVERT: CM 190 LEU cc_start: 0.9060 (mt) cc_final: 0.8783 (mt) REVERT: CM 209 TRP cc_start: 0.7886 (m100) cc_final: 0.7420 (m100) REVERT: CN 57 ARG cc_start: 0.8273 (ttm-80) cc_final: 0.7823 (mtp85) REVERT: CN 245 PHE cc_start: 0.9011 (m-80) cc_final: 0.8648 (m-10) REVERT: CO 3 LYS cc_start: 0.7413 (mmmt) cc_final: 0.7074 (mttt) REVERT: CO 89 LYS cc_start: 0.8763 (mmmt) cc_final: 0.8411 (mtmm) REVERT: CP 374 MET cc_start: 0.8189 (mtp) cc_final: 0.7840 (mtp) REVERT: CP 398 MET cc_start: 0.8068 (ppp) cc_final: 0.7785 (ppp) REVERT: CP 409 PHE cc_start: 0.8429 (m-10) cc_final: 0.8014 (m-10) REVERT: CP 443 PHE cc_start: 0.7441 (t80) cc_final: 0.7042 (t80) REVERT: CP 552 MET cc_start: 0.8376 (mmm) cc_final: 0.8102 (mmm) REVERT: CQ 8 PHE cc_start: 0.8584 (t80) cc_final: 0.8339 (t80) REVERT: CQ 45 ASN cc_start: 0.8337 (t0) cc_final: 0.7794 (t0) REVERT: CQ 51 TRP cc_start: 0.8781 (p-90) cc_final: 0.8126 (p-90) REVERT: CQ 55 TYR cc_start: 0.8870 (t80) cc_final: 0.8512 (t80) REVERT: CR 73 LEU cc_start: 0.6046 (tp) cc_final: 0.5777 (tp) REVERT: CS 475 MET cc_start: 0.8039 (mtt) cc_final: 0.7718 (mtp) REVERT: CS 700 GLU cc_start: 0.5875 (mm-30) cc_final: 0.5438 (mm-30) REVERT: CS 721 LYS cc_start: 0.7238 (mmmt) cc_final: 0.6733 (mmtt) REVERT: CU 277 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.7619 (ptm-80) REVERT: CU 364 ASN cc_start: 0.8858 (p0) cc_final: 0.8610 (p0) REVERT: Cz 26 ARG cc_start: 0.7652 (ttm-80) cc_final: 0.7166 (ttt-90) REVERT: Cb 110 PHE cc_start: 0.7907 (t80) cc_final: 0.7665 (t80) REVERT: Cb 249 MET cc_start: 0.8754 (mmp) cc_final: 0.8049 (ttm) REVERT: Ch 295 ASN cc_start: 0.8692 (p0) cc_final: 0.8098 (m-40) REVERT: Ch 331 ARG cc_start: 0.8238 (mmt180) cc_final: 0.7451 (ptt180) REVERT: LB 227 PHE cc_start: 0.6236 (OUTLIER) cc_final: 0.5047 (m-10) REVERT: LB 284 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.7512 (m-10) REVERT: LC 304 LYS cc_start: 0.7879 (mttp) cc_final: 0.7633 (tttt) REVERT: LC 341 LEU cc_start: 0.8632 (mp) cc_final: 0.8416 (mp) REVERT: LC 350 LYS cc_start: 0.8919 (ttpt) cc_final: 0.8648 (ttpp) REVERT: LE 33 GLU cc_start: 0.7030 (tm-30) cc_final: 0.6095 (tp30) REVERT: LE 53 GLN cc_start: 0.8230 (mm-40) cc_final: 0.7712 (mp10) REVERT: LF 66 ARG cc_start: 0.7906 (mmm-85) cc_final: 0.7561 (mmm160) REVERT: LF 134 LYS cc_start: 0.8744 (tttt) cc_final: 0.8208 (tptt) REVERT: LF 178 ASN cc_start: 0.8737 (t0) cc_final: 0.7916 (t0) REVERT: LF 230 GLU cc_start: 0.7158 (tt0) cc_final: 0.6897 (tp30) REVERT: LG 64 GLN cc_start: 0.8656 (mt0) cc_final: 0.8320 (mt0) REVERT: LG 159 ASP cc_start: 0.8491 (p0) cc_final: 0.7878 (p0) REVERT: LH 173 ASP cc_start: 0.8460 (t0) cc_final: 0.8090 (t70) REVERT: LK 121 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.8066 (t80) REVERT: LK 132 ILE cc_start: 0.9300 (OUTLIER) cc_final: 0.8932 (tp) REVERT: LL 17 HIS cc_start: 0.4401 (OUTLIER) cc_final: 0.3594 (m90) REVERT: LL 21 ARG cc_start: 0.6962 (mtm110) cc_final: 0.6668 (mtm110) REVERT: LL 42 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7672 (tttm) REVERT: LM 42 ASP cc_start: 0.8494 (t0) cc_final: 0.7846 (t0) REVERT: LN 140 LYS cc_start: 0.7766 (ttpt) cc_final: 0.7342 (tttp) REVERT: LO 146 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7336 (mp0) REVERT: LP 40 LYS cc_start: 0.8728 (mmmt) cc_final: 0.8462 (mmmt) REVERT: LP 75 GLN cc_start: 0.6852 (pt0) cc_final: 0.6079 (mm110) REVERT: LQ 142 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7254 (mm-30) REVERT: LS 5 GLN cc_start: 0.8421 (mm-40) cc_final: 0.7819 (mp10) REVERT: LS 21 ASN cc_start: 0.7982 (t0) cc_final: 0.7418 (t0) REVERT: LS 55 THR cc_start: 0.8732 (p) cc_final: 0.8205 (t) REVERT: LS 60 SER cc_start: 0.9131 (t) cc_final: 0.8752 (m) REVERT: LS 81 TYR cc_start: 0.8596 (p90) cc_final: 0.8219 (p90) REVERT: LT 52 MET cc_start: 0.4620 (ptm) cc_final: 0.3885 (mtt) REVERT: LT 103 GLU cc_start: 0.9097 (pt0) cc_final: 0.8875 (pm20) REVERT: LT 112 ASN cc_start: 0.8672 (m-40) cc_final: 0.8369 (p0) REVERT: LT 146 ASN cc_start: 0.8420 (m-40) cc_final: 0.7861 (m-40) REVERT: LV 61 MET cc_start: 0.8466 (mmm) cc_final: 0.8249 (mmp) REVERT: LV 65 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8195 (tmtt) REVERT: LV 72 ARG cc_start: 0.8213 (ttm110) cc_final: 0.8005 (mtt-85) REVERT: LV 138 VAL cc_start: 0.9127 (OUTLIER) cc_final: 0.8794 (m) REVERT: LY 51 LYS cc_start: 0.8836 (ttpp) cc_final: 0.8512 (ttpt) REVERT: LY 54 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7946 (tp30) REVERT: LY 92 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7634 (tm-30) REVERT: Le 6 LYS cc_start: 0.7977 (ttmm) cc_final: 0.7039 (tptt) REVERT: Le 30 ASP cc_start: 0.7689 (t70) cc_final: 0.7301 (t0) REVERT: Le 114 LYS cc_start: 0.8745 (tptt) cc_final: 0.8461 (tttt) REVERT: Lf 46 TYR cc_start: 0.8221 (m-80) cc_final: 0.7889 (m-80) REVERT: Lh 16 ASN cc_start: 0.7753 (p0) cc_final: 0.7500 (p0) REVERT: Lh 34 LEU cc_start: 0.9253 (tp) cc_final: 0.9005 (tp) REVERT: Lh 47 ASN cc_start: 0.7957 (t0) cc_final: 0.7583 (t0) REVERT: Lh 108 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7304 (ptpt) REVERT: Li 72 ASN cc_start: 0.8344 (m-40) cc_final: 0.8008 (t0) REVERT: Lj 30 GLN cc_start: 0.8342 (mm-40) cc_final: 0.8132 (mm-40) REVERT: Lq 63 MET cc_start: 0.7318 (mpp) cc_final: 0.6238 (mpp) REVERT: Lq 66 CYS cc_start: 0.9050 (p) cc_final: 0.8604 (p) REVERT: Lq 83 ASP cc_start: 0.4495 (p0) cc_final: 0.4240 (p0) REVERT: Lq 103 LEU cc_start: 0.9460 (tp) cc_final: 0.9045 (pp) REVERT: Lq 174 MET cc_start: 0.5177 (ppp) cc_final: 0.4812 (ppp) REVERT: Lq 184 MET cc_start: 0.6497 (mmm) cc_final: 0.5944 (mmm) REVERT: Lq 188 ASN cc_start: 0.8589 (m-40) cc_final: 0.8309 (m-40) REVERT: Lq 206 ILE cc_start: 0.4651 (OUTLIER) cc_final: 0.3965 (tt) REVERT: Cc 37 GLN cc_start: 0.7691 (mm110) cc_final: 0.7225 (tm-30) REVERT: Cc 79 TRP cc_start: 0.7516 (m100) cc_final: 0.7117 (m100) REVERT: Cc 219 ARG cc_start: 0.8123 (ttm-80) cc_final: 0.7884 (ttm-80) REVERT: Cd 37 ARG cc_start: 0.8161 (ttm110) cc_final: 0.7766 (mtt90) REVERT: Cd 224 ASN cc_start: 0.7415 (t0) cc_final: 0.6975 (t0) REVERT: Cd 338 LEU cc_start: 0.9155 (mm) cc_final: 0.8833 (mm) REVERT: Cd 349 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7707 (mt0) REVERT: Ce 10 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7584 (pt) REVERT: Ce 149 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.6817 (mp0) REVERT: Cf 471 GLN cc_start: 0.8677 (mt0) cc_final: 0.8474 (mt0) REVERT: Cf 524 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7530 (mt0) REVERT: Cg 116 PHE cc_start: 0.8576 (m-80) cc_final: 0.8028 (m-80) REVERT: Cg 149 MET cc_start: 0.6532 (ppp) cc_final: 0.6061 (tmm) outliers start: 260 outliers final: 207 residues processed: 1848 average time/residue: 1.1692 time to fit residues: 3759.6018 Evaluate side-chains 1818 residues out of total 8922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 1590 time to evaluate : 8.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 65 ASP Chi-restraints excluded: chain CA residue 109 ASN Chi-restraints excluded: chain CA residue 118 GLN Chi-restraints excluded: chain CA residue 148 GLN Chi-restraints excluded: chain CA residue 184 VAL Chi-restraints excluded: chain CA residue 199 VAL Chi-restraints excluded: chain CA residue 262 ILE Chi-restraints excluded: chain CB residue 22 GLN Chi-restraints excluded: chain CB residue 44 ASP Chi-restraints excluded: chain CB residue 65 THR Chi-restraints excluded: chain CB residue 91 THR Chi-restraints excluded: chain CB residue 98 CYS Chi-restraints excluded: chain CB residue 131 SER Chi-restraints excluded: chain CB residue 151 ASP Chi-restraints excluded: chain CB residue 185 MET Chi-restraints excluded: chain CB residue 283 VAL Chi-restraints excluded: chain CC residue 182 SER Chi-restraints excluded: chain CC residue 246 LEU Chi-restraints excluded: chain CC residue 258 THR Chi-restraints excluded: chain CC residue 265 VAL Chi-restraints excluded: chain CC residue 268 LYS Chi-restraints excluded: chain CE residue 142 ILE Chi-restraints excluded: chain CE residue 237 LEU Chi-restraints excluded: chain CE residue 277 GLU Chi-restraints excluded: chain CE residue 284 ILE Chi-restraints excluded: chain CE residue 296 SER Chi-restraints excluded: chain CE residue 301 THR Chi-restraints excluded: chain CE residue 382 LEU Chi-restraints excluded: chain CE residue 412 ILE Chi-restraints excluded: chain CE residue 421 LEU Chi-restraints excluded: chain CE residue 442 ILE Chi-restraints excluded: chain CE residue 463 GLN Chi-restraints excluded: chain CE residue 485 PHE Chi-restraints excluded: chain CE residue 496 GLN Chi-restraints excluded: chain CE residue 555 ILE Chi-restraints excluded: chain CF residue 8 ARG Chi-restraints excluded: chain CF residue 12 LEU Chi-restraints excluded: chain CF residue 142 VAL Chi-restraints excluded: chain CF residue 174 MET Chi-restraints excluded: chain CF residue 175 ILE Chi-restraints excluded: chain CF residue 179 VAL Chi-restraints excluded: chain CF residue 194 ILE Chi-restraints excluded: chain CF residue 226 TYR Chi-restraints excluded: chain CG residue 59 VAL Chi-restraints excluded: chain CG residue 67 LEU Chi-restraints excluded: chain CG residue 71 LEU Chi-restraints excluded: chain CG residue 87 LEU Chi-restraints excluded: chain CG residue 166 ARG Chi-restraints excluded: chain CH residue 12 THR Chi-restraints excluded: chain CH residue 56 CYS Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 115 LEU Chi-restraints excluded: chain CH residue 203 LEU Chi-restraints excluded: chain CH residue 223 ILE Chi-restraints excluded: chain CH residue 281 MET Chi-restraints excluded: chain CH residue 314 VAL Chi-restraints excluded: chain CH residue 338 LEU Chi-restraints excluded: chain CH residue 387 VAL Chi-restraints excluded: chain CH residue 473 PHE Chi-restraints excluded: chain CI residue 210 PHE Chi-restraints excluded: chain CI residue 224 THR Chi-restraints excluded: chain CI residue 258 LEU Chi-restraints excluded: chain CI residue 259 THR Chi-restraints excluded: chain CI residue 260 CYS Chi-restraints excluded: chain CI residue 268 VAL Chi-restraints excluded: chain CI residue 293 LEU Chi-restraints excluded: chain CJ residue 124 ASN Chi-restraints excluded: chain CJ residue 158 THR Chi-restraints excluded: chain CJ residue 374 LEU Chi-restraints excluded: chain CJ residue 456 VAL Chi-restraints excluded: chain CK residue 36 SER Chi-restraints excluded: chain CK residue 130 GLU Chi-restraints excluded: chain CK residue 152 THR Chi-restraints excluded: chain CK residue 212 LEU Chi-restraints excluded: chain CL residue 38 LEU Chi-restraints excluded: chain CM residue 147 LEU Chi-restraints excluded: chain CM residue 148 LYS Chi-restraints excluded: chain CM residue 244 LEU Chi-restraints excluded: chain CM residue 246 ARG Chi-restraints excluded: chain CN residue 1 MET Chi-restraints excluded: chain CN residue 3 VAL Chi-restraints excluded: chain CN residue 51 THR Chi-restraints excluded: chain CN residue 109 VAL Chi-restraints excluded: chain CN residue 147 LEU Chi-restraints excluded: chain CN residue 205 VAL Chi-restraints excluded: chain CN residue 215 LEU Chi-restraints excluded: chain CO residue 40 ILE Chi-restraints excluded: chain CP residue 267 LEU Chi-restraints excluded: chain CP residue 277 ASN Chi-restraints excluded: chain CP residue 319 ASP Chi-restraints excluded: chain CP residue 524 VAL Chi-restraints excluded: chain CP residue 560 LEU Chi-restraints excluded: chain CQ residue 6 CYS Chi-restraints excluded: chain CQ residue 34 SER Chi-restraints excluded: chain CR residue 33 ASN Chi-restraints excluded: chain CR residue 221 THR Chi-restraints excluded: chain CS residue 673 LYS Chi-restraints excluded: chain CU residue 196 LEU Chi-restraints excluded: chain CU residue 219 SER Chi-restraints excluded: chain CU residue 228 ASP Chi-restraints excluded: chain CU residue 277 ARG Chi-restraints excluded: chain CU residue 335 ASN Chi-restraints excluded: chain CU residue 366 LEU Chi-restraints excluded: chain CX residue 105 LEU Chi-restraints excluded: chain CX residue 133 ARG Chi-restraints excluded: chain Cz residue 50 LEU Chi-restraints excluded: chain Cb residue 207 MET Chi-restraints excluded: chain Cb residue 237 TYR Chi-restraints excluded: chain Cb residue 301 VAL Chi-restraints excluded: chain Cb residue 312 VAL Chi-restraints excluded: chain Cb residue 430 ILE Chi-restraints excluded: chain Cb residue 439 ILE Chi-restraints excluded: chain Cb residue 440 ASN Chi-restraints excluded: chain Cb residue 474 ASP Chi-restraints excluded: chain LB residue 24 ARG Chi-restraints excluded: chain LB residue 227 PHE Chi-restraints excluded: chain LB residue 277 THR Chi-restraints excluded: chain LB residue 284 TYR Chi-restraints excluded: chain LB residue 294 ASN Chi-restraints excluded: chain LB residue 297 THR Chi-restraints excluded: chain LB residue 313 VAL Chi-restraints excluded: chain LB residue 318 VAL Chi-restraints excluded: chain LB residue 320 ASN Chi-restraints excluded: chain LB residue 364 SER Chi-restraints excluded: chain LC residue 185 VAL Chi-restraints excluded: chain LC residue 270 GLU Chi-restraints excluded: chain LC residue 300 LEU Chi-restraints excluded: chain LE residue 71 VAL Chi-restraints excluded: chain LE residue 103 ILE Chi-restraints excluded: chain LE residue 107 VAL Chi-restraints excluded: chain LE residue 138 SER Chi-restraints excluded: chain LF residue 14 VAL Chi-restraints excluded: chain LF residue 24 SER Chi-restraints excluded: chain LF residue 26 GLU Chi-restraints excluded: chain LF residue 89 LEU Chi-restraints excluded: chain LF residue 170 THR Chi-restraints excluded: chain LF residue 189 ASP Chi-restraints excluded: chain LG residue 85 LEU Chi-restraints excluded: chain LG residue 201 VAL Chi-restraints excluded: chain LG residue 203 ILE Chi-restraints excluded: chain LH residue 16 LEU Chi-restraints excluded: chain LH residue 38 LEU Chi-restraints excluded: chain LH residue 47 VAL Chi-restraints excluded: chain LH residue 56 GLU Chi-restraints excluded: chain LH residue 101 VAL Chi-restraints excluded: chain LH residue 134 VAL Chi-restraints excluded: chain LH residue 167 CYS Chi-restraints excluded: chain LK residue 60 VAL Chi-restraints excluded: chain LK residue 71 VAL Chi-restraints excluded: chain LK residue 121 PHE Chi-restraints excluded: chain LK residue 132 ILE Chi-restraints excluded: chain LK residue 147 SER Chi-restraints excluded: chain LL residue 17 HIS Chi-restraints excluded: chain LL residue 42 LYS Chi-restraints excluded: chain LL residue 46 LEU Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LM residue 98 ASN Chi-restraints excluded: chain LN residue 33 LEU Chi-restraints excluded: chain LN residue 97 SER Chi-restraints excluded: chain LN residue 181 ASN Chi-restraints excluded: chain LO residue 146 GLU Chi-restraints excluded: chain LP residue 12 THR Chi-restraints excluded: chain LP residue 29 THR Chi-restraints excluded: chain LP residue 52 ILE Chi-restraints excluded: chain LQ residue 69 GLU Chi-restraints excluded: chain LQ residue 108 VAL Chi-restraints excluded: chain LQ residue 123 VAL Chi-restraints excluded: chain LQ residue 148 THR Chi-restraints excluded: chain LS residue 13 HIS Chi-restraints excluded: chain LS residue 59 VAL Chi-restraints excluded: chain LS residue 65 SER Chi-restraints excluded: chain LS residue 72 VAL Chi-restraints excluded: chain LS residue 87 THR Chi-restraints excluded: chain LS residue 133 GLU Chi-restraints excluded: chain LT residue 42 ILE Chi-restraints excluded: chain LT residue 72 VAL Chi-restraints excluded: chain LT residue 97 LYS Chi-restraints excluded: chain LT residue 143 ILE Chi-restraints excluded: chain LV residue 21 VAL Chi-restraints excluded: chain LV residue 65 LYS Chi-restraints excluded: chain LV residue 88 LYS Chi-restraints excluded: chain LV residue 138 VAL Chi-restraints excluded: chain LY residue 1 MET Chi-restraints excluded: chain LY residue 53 ASP Chi-restraints excluded: chain LY residue 55 VAL Chi-restraints excluded: chain LY residue 85 THR Chi-restraints excluded: chain Le residue 8 VAL Chi-restraints excluded: chain Le residue 24 ASP Chi-restraints excluded: chain Le residue 31 SER Chi-restraints excluded: chain Le residue 79 ASN Chi-restraints excluded: chain Le residue 121 THR Chi-restraints excluded: chain Lf residue 108 SER Chi-restraints excluded: chain Lh residue 14 SER Chi-restraints excluded: chain Lh residue 36 ILE Chi-restraints excluded: chain Lh residue 108 LYS Chi-restraints excluded: chain Lj residue 61 THR Chi-restraints excluded: chain Lj residue 68 SER Chi-restraints excluded: chain Lj residue 82 VAL Chi-restraints excluded: chain Lq residue 107 TYR Chi-restraints excluded: chain Lq residue 175 THR Chi-restraints excluded: chain Lq residue 206 ILE Chi-restraints excluded: chain Cc residue 17 SER Chi-restraints excluded: chain Cc residue 90 LEU Chi-restraints excluded: chain Cd residue 86 VAL Chi-restraints excluded: chain Cd residue 250 ASN Chi-restraints excluded: chain Cd residue 290 ARG Chi-restraints excluded: chain Cd residue 311 LEU Chi-restraints excluded: chain Cd residue 349 GLN Chi-restraints excluded: chain Ce residue 10 ILE Chi-restraints excluded: chain Ce residue 73 MET Chi-restraints excluded: chain Ce residue 84 SER Chi-restraints excluded: chain Ce residue 126 ILE Chi-restraints excluded: chain Ce residue 149 GLU Chi-restraints excluded: chain Ce residue 165 THR Chi-restraints excluded: chain Ce residue 195 LEU Chi-restraints excluded: chain Cf residue 463 ARG Chi-restraints excluded: chain Cf residue 484 VAL Chi-restraints excluded: chain Cf residue 509 TRP Chi-restraints excluded: chain Cf residue 524 GLN Chi-restraints excluded: chain Cg residue 67 LEU Chi-restraints excluded: chain Cg residue 89 HIS Chi-restraints excluded: chain Cg residue 91 LEU Chi-restraints excluded: chain Cg residue 103 LEU Chi-restraints excluded: chain Cg residue 115 HIS Chi-restraints excluded: chain Cg residue 197 LEU Chi-restraints excluded: chain Cg residue 213 ASN Chi-restraints excluded: chain Cg residue 337 MET Chi-restraints excluded: chain Cg residue 352 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1262 random chunks: chunk 1129 optimal weight: 8.9990 chunk 744 optimal weight: 7.9990 chunk 1198 optimal weight: 0.0000 chunk 731 optimal weight: 0.0770 chunk 568 optimal weight: 5.9990 chunk 833 optimal weight: 2.9990 chunk 1257 optimal weight: 9.9990 chunk 1157 optimal weight: 5.9990 chunk 1001 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 773 optimal weight: 7.9990 overall best weight: 3.0148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** CA 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 22 GLN ** CB 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 174 ASN ** CC 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CI 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 183 HIS ** CJ 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CK 203 ASN ** CN 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CP 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CP 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CP 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CR 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 121 ASN ** LB 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LH 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LK 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LK 100 HIS LL 17 HIS LP 101 ASN ** LQ 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 98 ASN ** LT 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LV 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LV 100 ASN LY 116 ASN ** Lh 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ce 12 GLN Ce 41 GLN Cf 524 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 141322 Z= 0.296 Angle : 0.698 27.929 202294 Z= 0.349 Chirality : 0.042 1.900 24461 Planarity : 0.006 0.098 16966 Dihedral : 21.886 176.748 48692 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.18 % Favored : 94.66 % Rotamer: Outliers : 3.18 % Allowed : 24.17 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.02 % Twisted Proline : 0.38 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.08), residues: 10278 helix: 1.23 (0.08), residues: 4615 sheet: -0.17 (0.14), residues: 1364 loop : -0.93 (0.09), residues: 4299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRPCf 509 HIS 0.016 0.001 HISCP 397 PHE 0.047 0.002 PHECI 198 TYR 0.055 0.002 TYRCb 397 ARG 0.013 0.001 ARGCE 279 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20556 Ramachandran restraints generated. 10278 Oldfield, 0 Emsley, 10278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20556 Ramachandran restraints generated. 10278 Oldfield, 0 Emsley, 10278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1855 residues out of total 8922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 1579 time to evaluate : 8.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CA 284 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7856 (mt-10) REVERT: CB 147 PHE cc_start: 0.8839 (t80) cc_final: 0.8391 (t80) REVERT: CC 137 TYR cc_start: 0.8251 (p90) cc_final: 0.7216 (p90) REVERT: CC 246 LEU cc_start: 0.5257 (OUTLIER) cc_final: 0.4810 (mp) REVERT: CC 312 ARG cc_start: 0.7213 (ptt180) cc_final: 0.6966 (ptm160) REVERT: CC 381 ASP cc_start: 0.9149 (m-30) cc_final: 0.8474 (p0) REVERT: CE 226 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7975 (mt-10) REVERT: CE 277 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8449 (mm-30) REVERT: CE 375 GLU cc_start: 0.8048 (tp30) cc_final: 0.7746 (tt0) REVERT: CF 41 PHE cc_start: 0.7234 (m-80) cc_final: 0.6979 (m-80) REVERT: CF 194 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8377 (mt) REVERT: CG 137 MET cc_start: 0.7838 (pmm) cc_final: 0.7307 (pmm) REVERT: CG 156 ARG cc_start: 0.8320 (tpm170) cc_final: 0.7918 (tpm170) REVERT: CG 166 ARG cc_start: 0.7043 (OUTLIER) cc_final: 0.5236 (ttp80) REVERT: CG 169 ASP cc_start: 0.5674 (p0) cc_final: 0.3971 (m-30) REVERT: CH 33 ARG cc_start: 0.4137 (mmt180) cc_final: 0.2868 (mtm110) REVERT: CH 150 ASP cc_start: 0.8685 (t0) cc_final: 0.8430 (t0) REVERT: CH 231 MET cc_start: 0.8396 (mmt) cc_final: 0.8054 (mmt) REVERT: CH 236 MET cc_start: 0.8686 (mmm) cc_final: 0.7940 (tpp) REVERT: CH 250 LEU cc_start: 0.8949 (mt) cc_final: 0.8599 (tp) REVERT: CH 253 MET cc_start: 0.7905 (pmm) cc_final: 0.7031 (pmm) REVERT: CH 333 HIS cc_start: 0.8334 (t70) cc_final: 0.7950 (t-90) REVERT: CH 437 ILE cc_start: 0.8591 (mt) cc_final: 0.8259 (mt) REVERT: CI 250 LYS cc_start: 0.8469 (mptt) cc_final: 0.8203 (mmtm) REVERT: CI 274 LYS cc_start: 0.8049 (ptmm) cc_final: 0.7810 (ptmm) REVERT: CI 285 TRP cc_start: 0.8411 (m100) cc_final: 0.7868 (m-90) REVERT: CJ 196 TYR cc_start: 0.8733 (m-80) cc_final: 0.8302 (m-80) REVERT: CJ 230 PHE cc_start: 0.9174 (m-80) cc_final: 0.8528 (m-80) REVERT: CJ 234 TYR cc_start: 0.8959 (m-10) cc_final: 0.8701 (m-10) REVERT: CK 67 GLN cc_start: 0.8228 (mt0) cc_final: 0.7649 (tm-30) REVERT: CK 179 TYR cc_start: 0.9167 (m-80) cc_final: 0.8906 (m-10) REVERT: CK 201 LYS cc_start: 0.9001 (mmpt) cc_final: 0.8684 (mmtm) REVERT: CK 212 LEU cc_start: 0.9638 (OUTLIER) cc_final: 0.9321 (mm) REVERT: CL 23 LYS cc_start: 0.7618 (ttmm) cc_final: 0.7094 (tptt) REVERT: CL 40 ARG cc_start: 0.8503 (mtm-85) cc_final: 0.8204 (ttp-170) REVERT: CL 69 ARG cc_start: 0.7338 (tmm160) cc_final: 0.7108 (tmm160) REVERT: CL 73 ARG cc_start: 0.9024 (tmm-80) cc_final: 0.8608 (ttp80) REVERT: CM 190 LEU cc_start: 0.9065 (mt) cc_final: 0.8787 (mt) REVERT: CM 209 TRP cc_start: 0.7967 (m100) cc_final: 0.7525 (m100) REVERT: CM 246 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8195 (tpt90) REVERT: CN 57 ARG cc_start: 0.8248 (ttm-80) cc_final: 0.7819 (mtp85) REVERT: CN 245 PHE cc_start: 0.9065 (m-80) cc_final: 0.8734 (m-10) REVERT: CO 3 LYS cc_start: 0.7533 (mmmt) cc_final: 0.7174 (mttt) REVERT: CP 374 MET cc_start: 0.8109 (mtp) cc_final: 0.7701 (mtp) REVERT: CP 398 MET cc_start: 0.8085 (ppp) cc_final: 0.7840 (ppp) REVERT: CP 409 PHE cc_start: 0.8468 (m-10) cc_final: 0.7947 (m-10) REVERT: CP 443 PHE cc_start: 0.7499 (t80) cc_final: 0.7061 (t80) REVERT: CP 552 MET cc_start: 0.8444 (mmm) cc_final: 0.8185 (mmm) REVERT: CQ 45 ASN cc_start: 0.8322 (t0) cc_final: 0.7456 (t0) REVERT: CQ 51 TRP cc_start: 0.8826 (p-90) cc_final: 0.8221 (p-90) REVERT: CR 73 LEU cc_start: 0.5999 (tp) cc_final: 0.5724 (tp) REVERT: CR 136 GLN cc_start: 0.7335 (mm-40) cc_final: 0.7130 (mm-40) REVERT: CR 183 THR cc_start: 0.7984 (m) cc_final: 0.7772 (m) REVERT: CS 471 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7019 (mm-30) REVERT: CS 475 MET cc_start: 0.7950 (mtt) cc_final: 0.7485 (mtp) REVERT: CS 689 LYS cc_start: 0.6947 (mmpt) cc_final: 0.5612 (mmtt) REVERT: CS 700 GLU cc_start: 0.6021 (mm-30) cc_final: 0.5588 (mm-30) REVERT: CS 721 LYS cc_start: 0.7241 (mmmt) cc_final: 0.6772 (mmtt) REVERT: CU 270 ASP cc_start: 0.8652 (t0) cc_final: 0.8388 (t0) REVERT: CU 277 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.7526 (ptm-80) REVERT: CU 364 ASN cc_start: 0.8908 (p0) cc_final: 0.8656 (p0) REVERT: Cz 26 ARG cc_start: 0.7798 (ttm-80) cc_final: 0.7318 (ttt-90) REVERT: Cb 110 PHE cc_start: 0.7924 (t80) cc_final: 0.7709 (t80) REVERT: Ch 292 LYS cc_start: 0.7907 (tptt) cc_final: 0.7568 (pttt) REVERT: Ch 295 ASN cc_start: 0.8720 (p0) cc_final: 0.7987 (m-40) REVERT: Ch 331 ARG cc_start: 0.8285 (mmt180) cc_final: 0.7461 (ptt180) REVERT: LB 227 PHE cc_start: 0.6283 (OUTLIER) cc_final: 0.5185 (m-10) REVERT: LB 284 TYR cc_start: 0.8093 (OUTLIER) cc_final: 0.7709 (m-10) REVERT: LC 304 LYS cc_start: 0.7952 (mttp) cc_final: 0.7682 (tttt) REVERT: LC 341 LEU cc_start: 0.8716 (mp) cc_final: 0.8477 (mp) REVERT: LC 350 LYS cc_start: 0.8934 (ttpt) cc_final: 0.8650 (ttpp) REVERT: LE 53 GLN cc_start: 0.8239 (mm-40) cc_final: 0.7698 (mp10) REVERT: LF 66 ARG cc_start: 0.7909 (mmm-85) cc_final: 0.7579 (mmm160) REVERT: LF 134 LYS cc_start: 0.8765 (tttt) cc_final: 0.8249 (tptt) REVERT: LF 178 ASN cc_start: 0.8697 (t0) cc_final: 0.7900 (t0) REVERT: LF 230 GLU cc_start: 0.7114 (tt0) cc_final: 0.6898 (tp30) REVERT: LG 55 TRP cc_start: 0.7311 (m100) cc_final: 0.6666 (m100) REVERT: LG 64 GLN cc_start: 0.8690 (mt0) cc_final: 0.8356 (mt0) REVERT: LG 159 ASP cc_start: 0.8497 (p0) cc_final: 0.8085 (p0) REVERT: LH 55 LEU cc_start: 0.8792 (pt) cc_final: 0.8516 (pt) REVERT: LH 173 ASP cc_start: 0.8488 (t0) cc_final: 0.8139 (t70) REVERT: LK 121 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.8131 (t80) REVERT: LK 132 ILE cc_start: 0.9328 (OUTLIER) cc_final: 0.8991 (tp) REVERT: LL 21 ARG cc_start: 0.7140 (mtm110) cc_final: 0.6865 (mtt90) REVERT: LL 42 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7766 (ttmt) REVERT: LM 42 ASP cc_start: 0.8608 (t0) cc_final: 0.7995 (t0) REVERT: LO 146 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: LP 40 LYS cc_start: 0.8913 (mmmt) cc_final: 0.8593 (mmmt) REVERT: LP 75 GLN cc_start: 0.7043 (pt0) cc_final: 0.6246 (mm110) REVERT: LP 89 GLN cc_start: 0.8567 (tm-30) cc_final: 0.8154 (tt0) REVERT: LS 21 ASN cc_start: 0.7949 (t0) cc_final: 0.7549 (t0) REVERT: LS 55 THR cc_start: 0.8755 (p) cc_final: 0.8233 (t) REVERT: LS 60 SER cc_start: 0.9077 (t) cc_final: 0.8699 (m) REVERT: LS 81 TYR cc_start: 0.8676 (p90) cc_final: 0.8389 (p90) REVERT: LS 117 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.7166 (mtt180) REVERT: LT 52 MET cc_start: 0.4614 (ptm) cc_final: 0.3809 (mtt) REVERT: LT 103 GLU cc_start: 0.9115 (pt0) cc_final: 0.8875 (pm20) REVERT: LT 146 ASN cc_start: 0.8513 (m-40) cc_final: 0.7968 (m-40) REVERT: LV 61 MET cc_start: 0.8474 (mmm) cc_final: 0.8269 (mmp) REVERT: LV 65 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8250 (tmtt) REVERT: LV 72 ARG cc_start: 0.8249 (ttm110) cc_final: 0.7990 (mtt-85) REVERT: LV 138 VAL cc_start: 0.9126 (OUTLIER) cc_final: 0.8812 (m) REVERT: LY 51 LYS cc_start: 0.8794 (ttpp) cc_final: 0.8473 (ttpt) REVERT: LY 54 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7959 (tp30) REVERT: LY 92 GLN cc_start: 0.8268 (tm-30) cc_final: 0.7632 (tm-30) REVERT: Le 6 LYS cc_start: 0.8019 (ttmm) cc_final: 0.7093 (tptt) REVERT: Le 30 ASP cc_start: 0.7671 (t70) cc_final: 0.7302 (t0) REVERT: Le 62 LYS cc_start: 0.8610 (mtmt) cc_final: 0.8175 (mtmm) REVERT: Le 114 LYS cc_start: 0.8754 (tptt) cc_final: 0.8456 (tttt) REVERT: Lf 23 ARG cc_start: 0.7271 (ptp90) cc_final: 0.6798 (ptp90) REVERT: Lf 46 TYR cc_start: 0.8500 (m-80) cc_final: 0.8124 (m-80) REVERT: Lh 16 ASN cc_start: 0.7794 (p0) cc_final: 0.7551 (p0) REVERT: Lh 47 ASN cc_start: 0.8009 (t0) cc_final: 0.7633 (t0) REVERT: Lh 108 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7473 (ptmt) REVERT: Li 72 ASN cc_start: 0.8338 (m-40) cc_final: 0.7979 (t0) REVERT: Li 100 GLN cc_start: 0.8292 (tp40) cc_final: 0.7766 (tm-30) REVERT: Lj 30 GLN cc_start: 0.8444 (mm-40) cc_final: 0.8198 (mm-40) REVERT: Lq 63 MET cc_start: 0.7404 (mpp) cc_final: 0.6296 (mpp) REVERT: Lq 66 CYS cc_start: 0.8990 (p) cc_final: 0.8622 (p) REVERT: Lq 83 ASP cc_start: 0.4251 (p0) cc_final: 0.3991 (p0) REVERT: Lq 174 MET cc_start: 0.5269 (ppp) cc_final: 0.4820 (ppp) REVERT: Lq 184 MET cc_start: 0.6564 (mmm) cc_final: 0.6024 (mmm) REVERT: Lq 188 ASN cc_start: 0.8546 (m-40) cc_final: 0.8278 (m-40) REVERT: Lq 206 ILE cc_start: 0.4726 (OUTLIER) cc_final: 0.4030 (tt) REVERT: Cc 37 GLN cc_start: 0.7874 (mm110) cc_final: 0.7299 (tm-30) REVERT: Cc 219 ARG cc_start: 0.8072 (ttm-80) cc_final: 0.7845 (ttm-80) REVERT: Cd 37 ARG cc_start: 0.8179 (ttm110) cc_final: 0.7778 (mtt90) REVERT: Cd 224 ASN cc_start: 0.7622 (t0) cc_final: 0.7185 (t0) REVERT: Cd 308 TYR cc_start: 0.8931 (m-10) cc_final: 0.8551 (m-10) REVERT: Cd 338 LEU cc_start: 0.9158 (mm) cc_final: 0.8793 (mm) REVERT: Cd 349 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7702 (mt0) REVERT: Ce 149 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.6783 (mp0) REVERT: Cf 510 LYS cc_start: 0.7235 (mttp) cc_final: 0.6712 (mtmm) REVERT: Cf 524 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7438 (mt0) REVERT: Cf 529 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7203 (mm-30) REVERT: Cg 116 PHE cc_start: 0.8611 (m-80) cc_final: 0.8071 (m-80) REVERT: Cg 149 MET cc_start: 0.6626 (ppp) cc_final: 0.6201 (tmm) outliers start: 276 outliers final: 226 residues processed: 1754 average time/residue: 1.1930 time to fit residues: 3643.2849 Evaluate side-chains 1797 residues out of total 8922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 1550 time to evaluate : 7.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 65 ASP Chi-restraints excluded: chain CA residue 109 ASN Chi-restraints excluded: chain CA residue 118 GLN Chi-restraints excluded: chain CA residue 148 GLN Chi-restraints excluded: chain CA residue 184 VAL Chi-restraints excluded: chain CA residue 199 VAL Chi-restraints excluded: chain CA residue 262 ILE Chi-restraints excluded: chain CB residue 22 GLN Chi-restraints excluded: chain CB residue 44 ASP Chi-restraints excluded: chain CB residue 65 THR Chi-restraints excluded: chain CB residue 91 THR Chi-restraints excluded: chain CB residue 98 CYS Chi-restraints excluded: chain CB residue 131 SER Chi-restraints excluded: chain CB residue 151 ASP Chi-restraints excluded: chain CB residue 185 MET Chi-restraints excluded: chain CC residue 118 LEU Chi-restraints excluded: chain CC residue 172 ILE Chi-restraints excluded: chain CC residue 182 SER Chi-restraints excluded: chain CC residue 246 LEU Chi-restraints excluded: chain CC residue 258 THR Chi-restraints excluded: chain CC residue 265 VAL Chi-restraints excluded: chain CE residue 142 ILE Chi-restraints excluded: chain CE residue 237 LEU Chi-restraints excluded: chain CE residue 277 GLU Chi-restraints excluded: chain CE residue 284 ILE Chi-restraints excluded: chain CE residue 296 SER Chi-restraints excluded: chain CE residue 301 THR Chi-restraints excluded: chain CE residue 367 CYS Chi-restraints excluded: chain CE residue 382 LEU Chi-restraints excluded: chain CE residue 412 ILE Chi-restraints excluded: chain CE residue 421 LEU Chi-restraints excluded: chain CE residue 442 ILE Chi-restraints excluded: chain CE residue 463 GLN Chi-restraints excluded: chain CE residue 485 PHE Chi-restraints excluded: chain CE residue 496 GLN Chi-restraints excluded: chain CE residue 503 THR Chi-restraints excluded: chain CE residue 555 ILE Chi-restraints excluded: chain CF residue 8 ARG Chi-restraints excluded: chain CF residue 12 LEU Chi-restraints excluded: chain CF residue 142 VAL Chi-restraints excluded: chain CF residue 174 MET Chi-restraints excluded: chain CF residue 175 ILE Chi-restraints excluded: chain CF residue 179 VAL Chi-restraints excluded: chain CF residue 194 ILE Chi-restraints excluded: chain CF residue 226 TYR Chi-restraints excluded: chain CG residue 59 VAL Chi-restraints excluded: chain CG residue 67 LEU Chi-restraints excluded: chain CG residue 71 LEU Chi-restraints excluded: chain CG residue 87 LEU Chi-restraints excluded: chain CG residue 106 GLN Chi-restraints excluded: chain CG residue 166 ARG Chi-restraints excluded: chain CH residue 12 THR Chi-restraints excluded: chain CH residue 56 CYS Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 115 LEU Chi-restraints excluded: chain CH residue 203 LEU Chi-restraints excluded: chain CH residue 223 ILE Chi-restraints excluded: chain CH residue 281 MET Chi-restraints excluded: chain CH residue 314 VAL Chi-restraints excluded: chain CH residue 338 LEU Chi-restraints excluded: chain CH residue 387 VAL Chi-restraints excluded: chain CH residue 473 PHE Chi-restraints excluded: chain CI residue 210 PHE Chi-restraints excluded: chain CI residue 224 THR Chi-restraints excluded: chain CI residue 258 LEU Chi-restraints excluded: chain CI residue 259 THR Chi-restraints excluded: chain CI residue 260 CYS Chi-restraints excluded: chain CI residue 268 VAL Chi-restraints excluded: chain CI residue 277 ASN Chi-restraints excluded: chain CI residue 282 VAL Chi-restraints excluded: chain CI residue 293 LEU Chi-restraints excluded: chain CJ residue 158 THR Chi-restraints excluded: chain CJ residue 374 LEU Chi-restraints excluded: chain CJ residue 456 VAL Chi-restraints excluded: chain CK residue 36 SER Chi-restraints excluded: chain CK residue 130 GLU Chi-restraints excluded: chain CK residue 152 THR Chi-restraints excluded: chain CK residue 212 LEU Chi-restraints excluded: chain CL residue 18 THR Chi-restraints excluded: chain CL residue 38 LEU Chi-restraints excluded: chain CM residue 147 LEU Chi-restraints excluded: chain CM residue 148 LYS Chi-restraints excluded: chain CM residue 244 LEU Chi-restraints excluded: chain CM residue 246 ARG Chi-restraints excluded: chain CN residue 1 MET Chi-restraints excluded: chain CN residue 3 VAL Chi-restraints excluded: chain CN residue 51 THR Chi-restraints excluded: chain CN residue 109 VAL Chi-restraints excluded: chain CN residue 147 LEU Chi-restraints excluded: chain CN residue 154 LEU Chi-restraints excluded: chain CN residue 197 MET Chi-restraints excluded: chain CN residue 205 VAL Chi-restraints excluded: chain CN residue 215 LEU Chi-restraints excluded: chain CO residue 40 ILE Chi-restraints excluded: chain CP residue 267 LEU Chi-restraints excluded: chain CP residue 277 ASN Chi-restraints excluded: chain CP residue 387 MET Chi-restraints excluded: chain CP residue 524 VAL Chi-restraints excluded: chain CP residue 560 LEU Chi-restraints excluded: chain CQ residue 6 CYS Chi-restraints excluded: chain CQ residue 34 SER Chi-restraints excluded: chain CR residue 33 ASN Chi-restraints excluded: chain CR residue 221 THR Chi-restraints excluded: chain CS residue 673 LYS Chi-restraints excluded: chain CU residue 196 LEU Chi-restraints excluded: chain CU residue 219 SER Chi-restraints excluded: chain CU residue 228 ASP Chi-restraints excluded: chain CU residue 277 ARG Chi-restraints excluded: chain CU residue 366 LEU Chi-restraints excluded: chain CX residue 105 LEU Chi-restraints excluded: chain CX residue 133 ARG Chi-restraints excluded: chain Cz residue 46 THR Chi-restraints excluded: chain Cz residue 50 LEU Chi-restraints excluded: chain Cb residue 207 MET Chi-restraints excluded: chain Cb residue 237 TYR Chi-restraints excluded: chain Cb residue 301 VAL Chi-restraints excluded: chain Cb residue 312 VAL Chi-restraints excluded: chain Cb residue 430 ILE Chi-restraints excluded: chain Cb residue 439 ILE Chi-restraints excluded: chain Cb residue 440 ASN Chi-restraints excluded: chain Cb residue 474 ASP Chi-restraints excluded: chain LB residue 24 ARG Chi-restraints excluded: chain LB residue 227 PHE Chi-restraints excluded: chain LB residue 277 THR Chi-restraints excluded: chain LB residue 284 TYR Chi-restraints excluded: chain LB residue 294 ASN Chi-restraints excluded: chain LB residue 297 THR Chi-restraints excluded: chain LB residue 313 VAL Chi-restraints excluded: chain LB residue 318 VAL Chi-restraints excluded: chain LB residue 320 ASN Chi-restraints excluded: chain LB residue 348 SER Chi-restraints excluded: chain LB residue 364 SER Chi-restraints excluded: chain LC residue 61 THR Chi-restraints excluded: chain LC residue 181 ASP Chi-restraints excluded: chain LC residue 185 VAL Chi-restraints excluded: chain LC residue 270 GLU Chi-restraints excluded: chain LC residue 300 LEU Chi-restraints excluded: chain LE residue 103 ILE Chi-restraints excluded: chain LE residue 107 VAL Chi-restraints excluded: chain LE residue 138 SER Chi-restraints excluded: chain LF residue 14 VAL Chi-restraints excluded: chain LF residue 24 SER Chi-restraints excluded: chain LF residue 26 GLU Chi-restraints excluded: chain LF residue 89 LEU Chi-restraints excluded: chain LF residue 170 THR Chi-restraints excluded: chain LF residue 172 ASN Chi-restraints excluded: chain LF residue 189 ASP Chi-restraints excluded: chain LF residue 208 LEU Chi-restraints excluded: chain LG residue 85 LEU Chi-restraints excluded: chain LG residue 117 THR Chi-restraints excluded: chain LG residue 139 LEU Chi-restraints excluded: chain LG residue 201 VAL Chi-restraints excluded: chain LG residue 203 ILE Chi-restraints excluded: chain LG residue 204 THR Chi-restraints excluded: chain LH residue 16 LEU Chi-restraints excluded: chain LH residue 38 LEU Chi-restraints excluded: chain LH residue 47 VAL Chi-restraints excluded: chain LH residue 56 GLU Chi-restraints excluded: chain LH residue 128 VAL Chi-restraints excluded: chain LH residue 130 MET Chi-restraints excluded: chain LH residue 134 VAL Chi-restraints excluded: chain LH residue 149 SER Chi-restraints excluded: chain LH residue 167 CYS Chi-restraints excluded: chain LK residue 60 VAL Chi-restraints excluded: chain LK residue 71 VAL Chi-restraints excluded: chain LK residue 100 HIS Chi-restraints excluded: chain LK residue 121 PHE Chi-restraints excluded: chain LK residue 132 ILE Chi-restraints excluded: chain LK residue 147 SER Chi-restraints excluded: chain LL residue 17 HIS Chi-restraints excluded: chain LL residue 42 LYS Chi-restraints excluded: chain LL residue 46 LEU Chi-restraints excluded: chain LL residue 62 THR Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LM residue 98 ASN Chi-restraints excluded: chain LN residue 33 LEU Chi-restraints excluded: chain LN residue 97 SER Chi-restraints excluded: chain LN residue 110 CYS Chi-restraints excluded: chain LN residue 181 ASN Chi-restraints excluded: chain LO residue 146 GLU Chi-restraints excluded: chain LP residue 12 THR Chi-restraints excluded: chain LP residue 29 THR Chi-restraints excluded: chain LP residue 52 ILE Chi-restraints excluded: chain LQ residue 69 GLU Chi-restraints excluded: chain LQ residue 108 VAL Chi-restraints excluded: chain LQ residue 123 VAL Chi-restraints excluded: chain LQ residue 148 THR Chi-restraints excluded: chain LS residue 13 HIS Chi-restraints excluded: chain LS residue 59 VAL Chi-restraints excluded: chain LS residue 65 SER Chi-restraints excluded: chain LS residue 72 VAL Chi-restraints excluded: chain LS residue 87 THR Chi-restraints excluded: chain LS residue 117 ARG Chi-restraints excluded: chain LS residue 133 GLU Chi-restraints excluded: chain LT residue 42 ILE Chi-restraints excluded: chain LT residue 66 ASN Chi-restraints excluded: chain LT residue 72 VAL Chi-restraints excluded: chain LT residue 97 LYS Chi-restraints excluded: chain LT residue 143 ILE Chi-restraints excluded: chain LV residue 21 VAL Chi-restraints excluded: chain LV residue 65 LYS Chi-restraints excluded: chain LV residue 88 LYS Chi-restraints excluded: chain LV residue 138 VAL Chi-restraints excluded: chain LY residue 1 MET Chi-restraints excluded: chain LY residue 53 ASP Chi-restraints excluded: chain LY residue 55 VAL Chi-restraints excluded: chain LY residue 85 THR Chi-restraints excluded: chain LY residue 96 ILE Chi-restraints excluded: chain Le residue 8 VAL Chi-restraints excluded: chain Le residue 24 ASP Chi-restraints excluded: chain Le residue 31 SER Chi-restraints excluded: chain Le residue 79 ASN Chi-restraints excluded: chain Le residue 121 THR Chi-restraints excluded: chain Lf residue 108 SER Chi-restraints excluded: chain Lh residue 14 SER Chi-restraints excluded: chain Lh residue 36 ILE Chi-restraints excluded: chain Lh residue 108 LYS Chi-restraints excluded: chain Lj residue 61 THR Chi-restraints excluded: chain Lj residue 82 VAL Chi-restraints excluded: chain Lq residue 107 TYR Chi-restraints excluded: chain Lq residue 175 THR Chi-restraints excluded: chain Lq residue 206 ILE Chi-restraints excluded: chain Cc residue 17 SER Chi-restraints excluded: chain Cc residue 90 LEU Chi-restraints excluded: chain Cc residue 105 ASP Chi-restraints excluded: chain Cc residue 106 VAL Chi-restraints excluded: chain Cd residue 86 VAL Chi-restraints excluded: chain Cd residue 250 ASN Chi-restraints excluded: chain Cd residue 290 ARG Chi-restraints excluded: chain Cd residue 311 LEU Chi-restraints excluded: chain Cd residue 349 GLN Chi-restraints excluded: chain Ce residue 10 ILE Chi-restraints excluded: chain Ce residue 41 GLN Chi-restraints excluded: chain Ce residue 84 SER Chi-restraints excluded: chain Ce residue 126 ILE Chi-restraints excluded: chain Ce residue 149 GLU Chi-restraints excluded: chain Ce residue 195 LEU Chi-restraints excluded: chain Cf residue 463 ARG Chi-restraints excluded: chain Cf residue 484 VAL Chi-restraints excluded: chain Cf residue 509 TRP Chi-restraints excluded: chain Cf residue 524 GLN Chi-restraints excluded: chain Cg residue 67 LEU Chi-restraints excluded: chain Cg residue 89 HIS Chi-restraints excluded: chain Cg residue 91 LEU Chi-restraints excluded: chain Cg residue 103 LEU Chi-restraints excluded: chain Cg residue 197 LEU Chi-restraints excluded: chain Cg residue 213 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1262 random chunks: chunk 613 optimal weight: 30.0000 chunk 795 optimal weight: 6.9990 chunk 1066 optimal weight: 3.9990 chunk 306 optimal weight: 0.9990 chunk 923 optimal weight: 4.9990 chunk 147 optimal weight: 50.0000 chunk 278 optimal weight: 6.9990 chunk 1002 optimal weight: 5.9990 chunk 419 optimal weight: 0.7980 chunk 1029 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** CA 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 22 GLN ** CB 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 174 ASN ** CC 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 183 HIS ** CJ 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CK 203 ASN ** CN 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CP 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CP 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CP 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CP 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CR 32 ASN ** Cb 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 121 ASN ** LB 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 228 ASN ** LH 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LK 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LQ 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 98 ASN ** LT 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LV 30 ASN ** LV 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LV 100 ASN LY 116 ASN ** Lh 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ce 41 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.156934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.121933 restraints weight = 247731.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.120542 restraints weight = 380262.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.118758 restraints weight = 194669.794| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 141322 Z= 0.294 Angle : 0.705 28.075 202294 Z= 0.352 Chirality : 0.042 1.897 24461 Planarity : 0.006 0.098 16966 Dihedral : 21.892 176.640 48692 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.12 % Favored : 94.72 % Rotamer: Outliers : 3.44 % Allowed : 24.09 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.02 % Twisted Proline : 0.38 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.08), residues: 10278 helix: 1.20 (0.08), residues: 4616 sheet: -0.19 (0.14), residues: 1353 loop : -0.95 (0.09), residues: 4309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRPCf 509 HIS 0.047 0.002 HISLL 17 PHE 0.050 0.002 PHECQ 107 TYR 0.044 0.002 TYRCH 393 ARG 0.012 0.001 ARGLK 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 52941.30 seconds wall clock time: 914 minutes 56.71 seconds (54896.71 seconds total)