Starting phenix.real_space_refine on Mon Feb 19 16:44:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9w_35286/02_2024/8i9w_35286_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9w_35286/02_2024/8i9w_35286.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9w_35286/02_2024/8i9w_35286.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9w_35286/02_2024/8i9w_35286.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9w_35286/02_2024/8i9w_35286_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9w_35286/02_2024/8i9w_35286_updated.pdb" } resolution = 3.1 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= 0.011 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 2 6.06 5 P 2424 5.49 5 S 274 5.16 5 C 76964 2.51 5 N 25186 2.21 5 O 31990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "CA ARG 63": "NH1" <-> "NH2" Residue "CA PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA GLU 198": "OE1" <-> "OE2" Residue "CA PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CB TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CB GLU 219": "OE1" <-> "OE2" Residue "CC GLU 153": "OE1" <-> "OE2" Residue "CC ASP 162": "OD1" <-> "OD2" Residue "CC ASP 164": "OD1" <-> "OD2" Residue "CC TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CC TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CC ASP 202": "OD1" <-> "OD2" Residue "CC GLU 260": "OE1" <-> "OE2" Residue "CC PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CC ASP 377": "OD1" <-> "OD2" Residue "CC TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CC TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE ASP 267": "OD1" <-> "OD2" Residue "CE PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE ASP 433": "OD1" <-> "OD2" Residue "CE GLU 498": "OE1" <-> "OE2" Residue "CE TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE TYR 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CF PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CF GLU 152": "OE1" <-> "OE2" Residue "CF PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CG TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CG TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CG TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CG PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH ASP 6": "OD1" <-> "OD2" Residue "CH ASP 18": "OD1" <-> "OD2" Residue "CH ASP 86": "OD1" <-> "OD2" Residue "CH ASP 88": "OD1" <-> "OD2" Residue "CH ASP 144": "OD1" <-> "OD2" Residue "CH TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH ASP 225": "OD1" <-> "OD2" Residue "CH PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH ASP 298": "OD1" <-> "OD2" Residue "CH PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH ASP 394": "OD1" <-> "OD2" Residue "CH PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH ASP 455": "OD1" <-> "OD2" Residue "CH GLU 466": "OE1" <-> "OE2" Residue "CI TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CI PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CI PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CI GLU 294": "OE1" <-> "OE2" Residue "CJ TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CJ PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CJ GLU 169": "OE1" <-> "OE2" Residue "CJ TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CJ PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CJ PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CK TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CK GLU 131": "OE1" <-> "OE2" Residue "CM ASP 189": "OD1" <-> "OD2" Residue "CM GLU 193": "OE1" <-> "OE2" Residue "CM PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CN TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CN PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CN PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CN PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CO PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CP GLU 255": "OE1" <-> "OE2" Residue "CP PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CP GLU 356": "OE1" <-> "OE2" Residue "CP PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CP GLU 382": "OE1" <-> "OE2" Residue "CP PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CP ASP 451": "OD1" <-> "OD2" Residue "CP TYR 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CP GLU 518": "OE1" <-> "OE2" Residue "CP TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CP PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CP TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CP ASP 574": "OD1" <-> "OD2" Residue "CP PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CQ ASP 66": "OD1" <-> "OD2" Residue "CQ TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CQ PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CR TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CR GLU 191": "OE1" <-> "OE2" Residue "CS PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CT PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CT PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CT PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CU PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CU PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CU GLU 353": "OE1" <-> "OE2" Residue "CV GLU 11": "OE1" <-> "OE2" Residue "CV PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CV TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CV GLU 128": "OE1" <-> "OE2" Residue "CY ASP 456": "OD1" <-> "OD2" Residue "CY TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CY GLU 624": "OE1" <-> "OE2" Residue "Cb GLU 14": "OE1" <-> "OE2" Residue "Cb PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cb GLU 298": "OE1" <-> "OE2" Residue "Cb TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cb PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB ASP 61": "OD1" <-> "OD2" Residue "LB GLU 74": "OE1" <-> "OE2" Residue "LB TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB ASP 290": "OD1" <-> "OD2" Residue "LB TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB GLU 353": "OE1" <-> "OE2" Residue "LC PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC ASP 266": "OD1" <-> "OD2" Residue "LE TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LE ASP 120": "OD1" <-> "OD2" Residue "LE GLU 121": "OE1" <-> "OE2" Residue "LE TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LE PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LE ASP 193": "OD1" <-> "OD2" Residue "LF PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LF TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG GLU 147": "OE1" <-> "OE2" Residue "LG ASP 161": "OD1" <-> "OD2" Residue "LH GLU 93": "OE1" <-> "OE2" Residue "LH PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LH PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LK ASP 164": "OD1" <-> "OD2" Residue "LL ASP 27": "OD1" <-> "OD2" Residue "LL PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LL GLU 79": "OE1" <-> "OE2" Residue "LM PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN ASP 124": "OD1" <-> "OD2" Residue "LN ASP 136": "OD1" <-> "OD2" Residue "LO TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO GLU 108": "OE1" <-> "OE2" Residue "LO GLU 159": "OE1" <-> "OE2" Residue "LQ TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS ASP 82": "OD1" <-> "OD2" Residue "LV PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LX TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LY PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ld TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lf TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lf PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lh ASP 101": "OD1" <-> "OD2" Residue "Li GLU 63": "OE1" <-> "OE2" Residue "Lj ARG 87": "NH1" <-> "NH2" Residue "Lq PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lq PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lq TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 136840 Number of models: 1 Model: "" Number of chains: 55 Chain: "C1" Number of atoms: 46266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2163, 46266 Classifications: {'RNA': 2163} Modifications used: {'rna2p_pur': 208, 'rna2p_pyr': 147, 'rna3p_pur': 978, 'rna3p_pyr': 830} Link IDs: {'rna2p': 354, 'rna3p': 1808} Chain breaks: 17 Chain: "C2" Number of atoms: 5456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 5456 Classifications: {'RNA': 256} Modifications used: {'rna2p_pur': 30, 'rna2p_pyr': 25, 'rna3p_pur': 101, 'rna3p_pyr': 100} Link IDs: {'rna2p': 55, 'rna3p': 200} Chain breaks: 1 Chain: "CA" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2069 Classifications: {'peptide': 251} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 239} Chain breaks: 1 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: 2413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2413 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 38, 'TRANS': 252} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 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: 4085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 4085 Classifications: {'peptide': 503} Link IDs: {'PTRANS': 23, 'TRANS': 479} Chain breaks: 1 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: 3092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3092 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 353} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "CK" Number of atoms: 1908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1908 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 11, 'TRANS': 226} Chain breaks: 1 Chain: "CL" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 2239 Classifications: {'peptide': 397} Incomplete info: {'truncation_to_alanine': 255} Link IDs: {'CIS': 1, 'PTRANS': 33, 'TRANS': 362} Chain breaks: 1 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: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1820 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 11, 'TRANS': 211} 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: 2798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2798 Classifications: {'peptide': 356} Link IDs: {'PTRANS': 19, 'TRANS': 336} Chain: "CQ" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1056 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} 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: 1891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1891 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain breaks: 6 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "CT" Number of atoms: 3911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3911 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 18, 'TRANS': 469} Chain breaks: 4 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: "CV" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1073 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 6, 'TRANS': 132} 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: "CY" Number of atoms: 2919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2919 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 346} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Cb" Number of atoms: 5005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 5005 Classifications: {'peptide': 634} Link IDs: {'PTRANS': 34, 'TRANS': 599} Chain breaks: 5 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: "LB" Number of atoms: 2696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2696 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 12, 'TRANS': 326} 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: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1403 Classifications: {'peptide': 179} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 165} Chain breaks: 1 Chain: "LF" Number of atoms: 2017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2017 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 13, 'TRANS': 233} Chain: "LG" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1644 Classifications: {'peptide': 204} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 195} 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: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1200 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 5, 'TRANS': 147} Chain breaks: 2 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: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 354 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 4, 'TRANS': 42} Chain breaks: 1 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: "Ld" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 890 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "Le" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1025 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} 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: {'PTRANS': 8, 'TRANS': 198} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 85006 SG CYSCQ 32 142.619 48.725 204.837 1.00 72.30 S ATOM 85038 SG CYSCQ 36 141.802 48.635 200.619 1.00 69.91 S ATOM A0QQN SG CYSLj 19 169.100 120.657 135.473 1.00 53.69 S ATOM A0QRF SG CYSLj 22 170.476 122.065 138.653 1.00 45.42 S ATOM A0QU5 SG CYSLj 34 166.753 122.128 138.139 1.00 47.61 S ATOM A0QUM SG CYSLj 37 168.859 124.362 135.943 1.00 45.50 S Time building chain proxies: 51.34, per 1000 atoms: 0.38 Number of scatterers: 136840 At special positions: 0 Unit cell: (257.07, 261.25, 314.545, 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 2 29.99 S 274 16.00 P 2424 15.00 O 31990 8.00 N 25186 7.00 C 76964 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 50.19 Conformation dependent library (CDL) restraints added in 11.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNCQ1000 " pdb="ZN ZNCQ1000 " - pdb=" SG CYSCQ 36 " pdb="ZN ZNCQ1000 " - pdb=" SG CYSCQ 32 " pdb=" ZNLj1001 " pdb="ZN ZNLj1001 " - pdb=" SG CYSLj 34 " pdb="ZN ZNLj1001 " - pdb=" SG CYSLj 19 " pdb="ZN ZNLj1001 " - pdb=" SG CYSLj 22 " pdb="ZN ZNLj1001 " - pdb=" SG CYSLj 37 " Number of angles added : 6 21136 Ramachandran restraints generated. 10568 Oldfield, 0 Emsley, 10568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 20246 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: 410 helices and 85 sheets defined 50.9% alpha, 11.8% beta 807 base pairs and 1220 stacking pairs defined. Time for finding SS restraints: 76.21 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 removed outlier: 4.050A pdb=" N CYSCA 78 " --> pdb=" O LEUCA 74 " (cutoff:3.500A) Processing helix chain 'CA' and resid 143 through 150 Proline residue: CA 150 - end of helix Processing helix chain 'CA' and resid 151 through 164 Processing helix chain 'CA' and resid 263 through 295 Processing helix chain 'CB' and resid 19 through 40 Processing helix chain 'CB' and resid 52 through 60 Processing helix chain 'CB' and resid 104 through 114 Processing helix chain 'CB' and resid 117 through 125 removed outlier: 5.028A pdb=" N GLYCB 125 " --> pdb=" O ARGCB 121 " (cutoff:3.500A) Processing helix chain 'CB' and resid 129 through 137 Processing helix chain 'CB' and resid 139 through 151 removed outlier: 5.364A pdb=" N ASPCB 151 " --> pdb=" O PHECB 147 " (cutoff:3.500A) Processing helix chain 'CB' and resid 156 through 167 removed outlier: 4.285A pdb=" N ASNCB 161 " --> pdb=" O THRCB 157 " (cutoff:3.500A) removed outlier: 5.141A 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 175 removed outlier: 4.619A pdb=" N THRCB 174 " --> pdb=" O THRCB 170 " (cutoff:3.500A) Processing helix chain 'CB' and resid 216 through 230 Processing helix chain 'CB' and resid 251 through 269 Processing helix chain 'CC' and resid 177 through 182 removed outlier: 4.358A pdb=" N ASPCC 181 " --> pdb=" O LEUCC 177 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N SERCC 182 " --> pdb=" O SERCC 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'CC' and resid 177 through 182' 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: 4.381A 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: 4.007A 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: 5.797A 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: 5.313A 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 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 286 Proline residue: CE 286 - end of helix 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 421 Processing helix chain 'CE' and resid 437 through 451 removed outlier: 3.714A pdb=" N ARGCE 450 " --> pdb=" O GLYCE 446 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLYCE 451 " --> pdb=" O ARGCE 447 " (cutoff:3.500A) Processing helix chain 'CE' and resid 466 through 477 removed outlier: 4.371A pdb=" N LEUCE 470 " --> pdb=" O GLUCE 466 " (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: 4.205A pdb=" N LEUCE 536 " --> pdb=" O ASPCE 532 " (cutoff:3.500A) removed outlier: 5.757A 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 37 Proline residue: CF 35 - end of helix Processing helix chain 'CF' and resid 52 through 61 Processing helix chain 'CF' and resid 69 through 78 Processing helix chain 'CF' and resid 88 through 97 removed outlier: 3.573A pdb=" N TYRCF 95 " --> pdb=" O ARGCF 91 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N THRCF 97 " --> pdb=" O THRCF 93 " (cutoff:3.500A) Processing helix chain 'CF' and resid 108 through 120 removed outlier: 5.958A pdb=" N SERCF 120 " --> pdb=" O PHECF 116 " (cutoff:3.500A) Processing helix chain 'CF' and resid 150 through 155 removed outlier: 3.752A pdb=" N ASPCF 154 " --> pdb=" O PROCF 150 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N VALCF 155 " --> pdb=" O PROCF 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'CF' and resid 150 through 155' Processing helix chain 'CF' and resid 159 through 169 Proline residue: CF 163 - end of helix Processing helix chain 'CF' and resid 202 through 213 Processing helix chain 'CG' and resid 5 through 20 Processing helix chain 'CG' and resid 22 through 28 removed outlier: 4.640A pdb=" N LEUCG 26 " --> pdb=" O ASPCG 22 " (cutoff:3.500A) Processing helix chain 'CG' and resid 49 through 58 removed outlier: 5.127A pdb=" N CYSCG 58 " --> pdb=" O ASNCG 54 " (cutoff:3.500A) Processing helix chain 'CG' and resid 60 through 65 removed outlier: 5.750A 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 115 through 120 removed outlier: 5.590A pdb=" N GLYCG 120 " --> pdb=" O LYSCG 116 " (cutoff:3.500A) Processing helix chain 'CG' and resid 150 through 157 Processing helix chain 'CG' and resid 170 through 177 removed outlier: 4.429A pdb=" N LEUCG 174 " --> pdb=" O CYSCG 170 " (cutoff:3.500A) removed outlier: 4.114A 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 66 Processing helix chain 'CH' and resid 69 through 74 removed outlier: 3.809A pdb=" N GLNCH 73 " --> pdb=" O VALCH 69 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N HISCH 74 " --> pdb=" O LEUCH 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'CH' and resid 69 through 74' Processing helix chain 'CH' and resid 75 through 85 Processing helix chain 'CH' and resid 86 through 118 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 removed outlier: 3.671A pdb=" N LEUCH 245 " --> pdb=" O ALACH 241 " (cutoff:3.500A) Processing helix chain 'CH' and resid 262 through 278 Proline residue: CH 275 - end of helix Processing helix chain 'CH' and resid 288 through 293 removed outlier: 4.044A pdb=" N LYSCH 292 " --> pdb=" O LYSCH 288 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYSCH 293 " --> pdb=" O METCH 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'CH' and resid 288 through 293' Processing helix chain 'CH' and resid 298 through 311 removed outlier: 4.155A pdb=" N SERCH 311 " --> pdb=" O ASPCH 307 " (cutoff:3.500A) Processing helix chain 'CH' and resid 326 through 352 removed outlier: 4.484A pdb=" N HISCH 352 " --> pdb=" O LYSCH 348 " (cutoff:3.500A) Processing helix chain 'CH' and resid 358 through 369 Processing helix chain 'CH' and resid 384 through 390 removed outlier: 4.164A pdb=" N LYSCH 388 " --> pdb=" O PROCH 384 " (cutoff:3.500A) Processing helix chain 'CH' and resid 403 through 412 Processing helix chain 'CH' and resid 421 through 426 removed outlier: 4.901A pdb=" N TRPCH 425 " --> pdb=" O LEUCH 421 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ILECH 426 " --> pdb=" O ARGCH 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'CH' and resid 421 through 426' Processing helix chain 'CH' and resid 445 through 450 Processing helix chain 'CH' and resid 453 through 472 removed outlier: 4.743A pdb=" N LYSCH 457 " --> pdb=" O ASPCH 453 " (cutoff:3.500A) Processing helix chain 'CH' and resid 483 through 509 Processing helix chain 'CI' and resid 199 through 211 Processing helix chain 'CI' and resid 237 through 249 Processing helix chain 'CI' and resid 264 through 269 removed outlier: 3.772A pdb=" N VALCI 268 " --> pdb=" O PROCI 264 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N HISCI 269 " --> pdb=" O PROCI 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'CI' and resid 264 through 269' Processing helix chain 'CI' and resid 284 through 296 Proline residue: CI 296 - end of helix Processing helix chain 'CI' and resid 300 through 321 Processing helix chain 'CJ' and resid 11 through 16 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 54 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 Processing helix chain 'CJ' and resid 123 through 131 Processing helix chain 'CJ' and resid 133 through 154 removed outlier: 4.387A pdb=" N ASPCJ 142 " --> pdb=" O LEUCJ 138 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ASPCJ 143 " --> pdb=" O ARGCJ 139 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 161 through 183 Processing helix chain 'CJ' and resid 225 through 250 Processing helix chain 'CJ' and resid 258 through 265 Processing helix chain 'CJ' and resid 379 through 391 Processing helix chain 'CJ' and resid 457 through 468 removed outlier: 3.905A pdb=" N VALCJ 461 " --> pdb=" O GLNCJ 457 " (cutoff:3.500A) 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 41 removed outlier: 4.621A pdb=" N GLYCK 32 " --> pdb=" O ALACK 28 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N HISCK 33 " --> pdb=" O ALACK 29 " (cutoff:3.500A) Processing helix chain 'CK' and resid 44 through 75 removed outlier: 5.904A pdb=" N LYSCK 48 " --> pdb=" O GLYCK 44 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLYCK 75 " --> pdb=" O ARGCK 71 " (cutoff:3.500A) Processing helix chain 'CK' and resid 98 through 117 Processing helix chain 'CK' and resid 128 through 141 removed outlier: 4.190A pdb=" N LYSCK 141 " --> pdb=" O LYSCK 137 " (cutoff:3.500A) Processing helix chain 'CK' and resid 174 through 179 removed outlier: 5.572A pdb=" N TYRCK 179 " --> pdb=" O METCK 175 " (cutoff:3.500A) Processing helix chain 'CK' and resid 206 through 213 Processing helix chain 'CK' and resid 248 through 253 removed outlier: 4.089A pdb=" N GLYCK 253 " --> pdb=" O PROCK 249 " (cutoff:3.500A) Processing helix chain 'CL' and resid 17 through 42 Processing helix chain 'CL' and resid 61 through 80 Processing helix chain 'CL' and resid 190 through 205 removed outlier: 4.951A pdb=" N LYSCL 196 " --> pdb=" O LYSCL 192 " (cutoff:3.500A) removed outlier: 4.945A 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 233 removed outlier: 5.510A pdb=" N GLNCL 227 " --> pdb=" O HISCL 223 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ALACL 228 " --> pdb=" O ASPCL 224 " (cutoff:3.500A) Processing helix chain 'CL' and resid 245 through 250 removed outlier: 4.795A 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: 4.460A 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 402 Processing helix chain 'CL' and resid 413 through 428 removed outlier: 4.948A 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: 4.395A 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 25 through 47 Processing helix chain 'CM' and resid 53 through 78 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 156 Processing helix chain 'CM' and resid 171 through 179 Processing helix chain 'CM' and resid 186 through 197 Processing helix chain 'CM' and resid 200 through 209 removed outlier: 4.701A pdb=" N TRPCM 209 " --> pdb=" O ALACM 205 " (cutoff:3.500A) Processing helix chain 'CM' and resid 238 through 249 removed outlier: 4.644A pdb=" N ASNCM 242 " --> pdb=" O GLUCM 238 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALACM 243 " --> pdb=" O GLUCM 239 " (cutoff:3.500A) Processing helix chain 'CN' and resid 12 through 17 removed outlier: 4.259A pdb=" N PHECN 16 " --> pdb=" O GLUCN 12 " (cutoff:3.500A) 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: 6.895A pdb=" N ASNCN 234 " --> pdb=" O PROCN 230 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYSCN 238 " --> pdb=" O ASNCN 234 " (cutoff:3.500A) Processing helix chain 'CN' and resid 239 through 245 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 231 through 249 Processing helix chain 'CP' and resid 258 through 275 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 Processing helix chain 'CP' and resid 392 through 403 Processing helix chain 'CP' and resid 414 through 429 removed outlier: 3.848A pdb=" N GLYCP 420 " --> pdb=" O SERCP 416 " (cutoff:3.500A) Processing helix chain 'CP' and resid 442 through 447 Processing helix chain 'CP' and resid 464 through 469 Proline residue: CP 469 - end of helix Processing helix chain 'CP' and resid 476 through 498 Proline residue: CP 484 - end of helix Processing helix chain 'CP' and resid 520 through 531 removed outlier: 4.044A pdb=" N VALCP 524 " --> pdb=" O ASNCP 520 " (cutoff:3.500A) Processing helix chain 'CQ' and resid 33 through 43 Processing helix chain 'CQ' and resid 45 through 50 removed outlier: 5.353A pdb=" N LYSCQ 50 " --> pdb=" O PROCQ 46 " (cutoff:3.500A) Processing helix chain 'CQ' and resid 52 through 60 Processing helix chain 'CQ' and resid 66 through 72 removed outlier: 4.880A pdb=" N ALACQ 72 " --> pdb=" O THRCQ 68 " (cutoff:3.500A) Processing helix chain 'CQ' and resid 82 through 125 removed outlier: 6.205A pdb=" N GLYCQ 114 " --> pdb=" O LYSCQ 110 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LYSCQ 115 " --> pdb=" O ARGCQ 111 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ARGCQ 116 " --> pdb=" O METCQ 112 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ALACQ 117 " --> pdb=" O ALACQ 113 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ARGCQ 118 " --> pdb=" O GLYCQ 114 " (cutoff:3.500A) 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 166 through 178 Processing helix chain 'CR' and resid 188 through 202 Processing helix chain 'CR' and resid 205 through 212 Processing helix chain 'CR' and resid 221 through 233 Processing helix chain 'CS' and resid 465 through 488 removed outlier: 5.320A pdb=" N ASPCS 487 " --> pdb=" O LYSCS 483 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ALACS 488 " --> pdb=" O ALACS 484 " (cutoff:3.500A) Processing helix chain 'CS' and resid 489 through 497 Processing helix chain 'CS' and resid 500 through 505 removed outlier: 4.674A pdb=" N TRPCS 504 " --> pdb=" O ASPCS 500 " (cutoff:3.500A) Processing helix chain 'CS' and resid 563 through 572 removed outlier: 3.979A pdb=" N SERCS 571 " --> pdb=" O ARGCS 567 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLNCS 572 " --> pdb=" O GLYCS 568 " (cutoff:3.500A) Processing helix chain 'CS' and resid 573 through 579 Proline residue: CS 579 - end of helix Processing helix chain 'CS' and resid 656 through 669 removed outlier: 4.867A pdb=" N GLYCS 669 " --> pdb=" O GLNCS 665 " (cutoff:3.500A) Processing helix chain 'CS' and resid 672 through 682 removed outlier: 4.873A pdb=" N ASNCS 682 " --> pdb=" O ASPCS 678 " (cutoff:3.500A) Processing helix chain 'CS' and resid 693 through 704 Processing helix chain 'CS' and resid 711 through 723 Processing helix chain 'CS' and resid 729 through 752 Processing helix chain 'CS' and resid 816 through 834 Processing helix chain 'CT' and resid 122 through 141 Processing helix chain 'CT' and resid 147 through 158 removed outlier: 4.432A pdb=" N THRCT 158 " --> pdb=" O ARGCT 154 " (cutoff:3.500A) Processing helix chain 'CT' and resid 160 through 179 Processing helix chain 'CT' and resid 198 through 228 removed outlier: 5.393A pdb=" N SERCT 228 " --> pdb=" O TYRCT 224 " (cutoff:3.500A) Processing helix chain 'CT' and resid 237 through 253 Processing helix chain 'CT' and resid 258 through 272 removed outlier: 4.667A pdb=" N THRCT 272 " --> pdb=" O LYSCT 268 " (cutoff:3.500A) Processing helix chain 'CT' and resid 276 through 293 Processing helix chain 'CT' and resid 296 through 314 Processing helix chain 'CT' and resid 319 through 329 removed outlier: 3.745A pdb=" N PHECT 325 " --> pdb=" O VALCT 321 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEUCT 326 " --> pdb=" O LEUCT 322 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ARGCT 329 " --> pdb=" O PHECT 325 " (cutoff:3.500A) Processing helix chain 'CT' and resid 368 through 415 Processing helix chain 'CT' and resid 416 through 435 removed outlier: 3.608A pdb=" N METCT 420 " --> pdb=" O VALCT 416 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLYCT 421 " --> pdb=" O PROCT 417 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ALACT 422 " --> pdb=" O HISCT 418 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N HISCT 432 " --> pdb=" O ALACT 428 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N LEUCT 433 " --> pdb=" O LYSCT 429 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ASNCT 435 " --> pdb=" O ALACT 431 " (cutoff:3.500A) Processing helix chain 'CT' and resid 436 through 455 Processing helix chain 'CT' and resid 477 through 495 Processing helix chain 'CT' and resid 496 through 502 Processing helix chain 'CT' and resid 509 through 526 removed outlier: 5.099A pdb=" N LEUCT 521 " --> pdb=" O TYRCT 517 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N SERCT 522 " --> pdb=" O ARGCT 518 " (cutoff:3.500A) Processing helix chain 'CT' and resid 562 through 576 Processing helix chain 'CT' and resid 585 through 603 Processing helix chain 'CT' and resid 604 through 622 Processing helix chain 'CT' and resid 623 through 632 removed outlier: 4.771A pdb=" N ALACT 628 " --> pdb=" O ARGCT 624 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEUCT 629 " --> pdb=" O LYSCT 625 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TRPCT 630 " --> pdb=" O VALCT 626 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N THRCT 632 " --> pdb=" O ALACT 628 " (cutoff:3.500A) Processing helix chain 'CT' and resid 647 through 652 removed outlier: 4.826A pdb=" N ASNCT 652 " --> pdb=" O VALCT 648 " (cutoff:3.500A) Processing helix chain 'CT' and resid 660 through 667 removed outlier: 4.674A pdb=" N LYSCT 666 " --> pdb=" O GLUCT 662 " (cutoff:3.500A) Processing helix chain 'CT' and resid 669 through 686 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: 3.883A 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: 5.848A pdb=" N VALCU 362 " --> pdb=" O PHECU 358 " (cutoff:3.500A) Processing helix chain 'CV' and resid 5 through 14 Processing helix chain 'CV' and resid 86 through 99 Processing helix chain 'CV' and resid 104 through 124 removed outlier: 4.718A pdb=" N GLNCV 109 " --> pdb=" O ALACV 105 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ALACV 110 " --> pdb=" O ASPCV 106 " (cutoff:3.500A) Proline residue: CV 124 - end of helix Processing helix chain 'CV' and resid 135 through 140 Processing helix chain 'CX' and resid 65 through 70 removed outlier: 4.917A 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 'CY' and resid 371 through 389 Processing helix chain 'CY' and resid 393 through 411 Processing helix chain 'CY' and resid 413 through 434 removed outlier: 4.820A pdb=" N THRCY 434 " --> pdb=" O GLYCY 430 " (cutoff:3.500A) Processing helix chain 'CY' and resid 438 through 457 removed outlier: 4.414A pdb=" N GLUCY 451 " --> pdb=" O ASNCY 447 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEUCY 452 " --> pdb=" O SERCY 448 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TRPCY 453 " --> pdb=" O ALACY 449 " (cutoff:3.500A) Processing helix chain 'CY' and resid 458 through 482 Processing helix chain 'CY' and resid 485 through 492 removed outlier: 4.486A pdb=" N ASNCY 492 " --> pdb=" O ARGCY 488 " (cutoff:3.500A) Processing helix chain 'CY' and resid 493 through 510 Processing helix chain 'CY' and resid 527 through 543 removed outlier: 3.634A pdb=" N LEUCY 531 " --> pdb=" O LEUCY 527 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ILECY 542 " --> pdb=" O ALACY 538 " (cutoff:3.500A) Proline residue: CY 543 - end of helix Processing helix chain 'CY' and resid 547 through 565 removed outlier: 3.856A pdb=" N ARGCY 551 " --> pdb=" O TYRCY 547 " (cutoff:3.500A) Processing helix chain 'CY' and resid 571 through 581 Processing helix chain 'CY' and resid 611 through 634 Processing helix chain 'CY' and resid 638 through 659 Proline residue: CY 645 - end of helix Processing helix chain 'CY' and resid 666 through 692 Processing helix chain 'CY' and resid 701 through 707 Processing helix chain 'CY' and resid 716 through 748 Processing helix chain 'Cb' and resid 16 through 21 removed outlier: 4.561A pdb=" N SERCb 20 " --> pdb=" O ASPCb 16 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEUCb 21 " --> pdb=" O ILECb 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'Cb' and resid 16 through 21' 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 295 through 301 removed outlier: 5.740A pdb=" N THRCb 299 " --> pdb=" O LEUCb 295 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYSCb 300 " --> pdb=" O ASPCb 296 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VALCb 301 " --> pdb=" O ALACb 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'Cb' and resid 295 through 301' 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 431 removed outlier: 5.976A pdb=" N ALACb 427 " --> pdb=" O THRCb 423 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ASPCb 431 " --> pdb=" O ALACb 427 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 446 through 459 removed outlier: 4.947A pdb=" N THRCb 457 " --> pdb=" O ARGCb 453 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ALACb 458 " --> pdb=" O VALCb 454 " (cutoff:3.500A) removed outlier: 5.838A 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: 4.798A pdb=" N LYSCb 567 " --> pdb=" O VALCb 563 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 573 through 578 removed outlier: 4.650A pdb=" N GLYCb 577 " --> pdb=" O HISCb 573 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N GLUCb 578 " --> pdb=" O ALACb 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'Cb' and resid 573 through 578' Processing helix chain 'Cb' and resid 579 through 588 removed outlier: 3.876A pdb=" N ARGCb 587 " --> pdb=" O GLUCb 583 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 589 through 597 removed outlier: 4.405A 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 811 through 821 Processing helix chain 'Cb' and resid 833 through 841 Processing helix chain 'Cb' and resid 865 through 880 Processing helix chain 'Cz' and resid 47 through 92 Processing helix chain 'LB' and resid 111 through 120 removed outlier: 4.710A pdb=" N LYSLB 120 " --> pdb=" O ARGLB 116 " (cutoff:3.500A) Processing helix chain 'LB' and resid 130 through 139 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: 4.012A 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 30 removed outlier: 4.733A pdb=" N SERLC 28 " --> pdb=" O PROLC 24 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALALC 29 " --> pdb=" O LYSLC 25 " (cutoff:3.500A) Proline residue: LC 30 - end of helix No H-bonds generated for 'chain 'LC' and resid 24 through 30' Processing helix chain 'LC' and resid 32 through 48 removed outlier: 4.300A pdb=" N LYSLC 47 " --> pdb=" O METLC 43 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ARGLC 48 " --> pdb=" O ALALC 44 " (cutoff:3.500A) Processing helix chain 'LC' and resid 115 through 133 removed outlier: 5.061A 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 Processing helix chain 'LC' and resid 166 through 177 Processing helix chain 'LC' and resid 178 through 189 Processing helix chain 'LC' and resid 194 through 200 removed outlier: 4.667A pdb=" N METLC 198 " --> pdb=" O GLYLC 194 " (cutoff:3.500A) Processing helix chain 'LC' and resid 220 through 227 removed outlier: 4.448A pdb=" N LYSLC 224 " --> pdb=" O LYSLC 220 " (cutoff:3.500A) 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: 3.994A pdb=" N ASPLC 266 " --> pdb=" O ILELC 262 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALALC 267 " --> pdb=" O LYSLC 263 " (cutoff:3.500A) Processing helix chain 'LC' and resid 286 through 293 Processing helix chain 'LC' and resid 294 through 300 Processing helix chain 'LC' and resid 318 through 323 removed outlier: 4.574A pdb=" N LYSLC 323 " --> pdb=" O PROLC 319 " (cutoff:3.500A) Processing helix chain 'LC' and resid 324 through 330 Processing helix chain 'LC' and resid 332 through 340 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: 5.179A pdb=" N ILELE 103 " --> pdb=" O ALALE 99 " (cutoff:3.500A) Processing helix chain 'LE' and resid 115 through 124 removed outlier: 4.158A pdb=" N GLNLE 124 " --> pdb=" O ASPLE 120 " (cutoff:3.500A) Processing helix chain 'LE' and resid 131 through 140 removed outlier: 3.683A pdb=" N GLULE 140 " --> pdb=" O LYSLE 136 " (cutoff:3.500A) Processing helix chain 'LE' and resid 155 through 174 removed outlier: 3.789A pdb=" N LYSLE 163 " --> pdb=" O ALALE 159 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALALE 164 " --> pdb=" O ALALE 160 " (cutoff:3.500A) Processing helix chain 'LE' and resid 178 through 186 removed outlier: 5.273A pdb=" N SERLE 186 " --> pdb=" O TYRLE 182 " (cutoff:3.500A) Processing helix chain 'LF' and resid 8 through 14 Processing helix chain 'LF' and resid 15 through 34 removed outlier: 5.271A pdb=" N GLULF 31 " --> pdb=" O LYSLF 27 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ARGLF 32 " --> pdb=" O ALALF 28 " (cutoff:3.500A) Processing helix chain 'LF' and resid 40 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 removed outlier: 3.987A pdb=" N VALLF 197 " --> pdb=" O GLULF 193 " (cutoff:3.500A) Processing helix chain 'LF' and resid 200 through 209 removed outlier: 4.946A pdb=" N TRPLF 209 " --> pdb=" O ALALF 205 " (cutoff:3.500A) Processing helix chain 'LF' and resid 239 through 249 removed outlier: 4.545A 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: 4.275A pdb=" N PHELG 81 " --> pdb=" O ALALG 77 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N THRLG 84 " --> pdb=" O GLNLG 80 " (cutoff:3.500A) Processing helix chain 'LG' and resid 86 through 99 removed outlier: 3.621A pdb=" N LYSLG 99 " --> pdb=" O LYSLG 95 " (cutoff:3.500A) Processing helix chain 'LG' and resid 104 through 121 Processing helix chain 'LG' and resid 138 through 149 Processing helix chain 'LG' and resid 168 through 177 Processing helix chain 'LG' and resid 185 through 194 removed outlier: 3.566A pdb=" N VALLG 193 " --> pdb=" O LEULG 189 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N HISLG 194 " --> pdb=" O GLYLG 190 " (cutoff:3.500A) Processing helix chain 'LG' and resid 207 through 233 removed outlier: 4.999A pdb=" N ASNLG 212 " --> pdb=" O SERLG 208 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLULG 213 " --> pdb=" O GLULG 209 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N LYSLG 228 " --> pdb=" O GLYLG 224 " (cutoff:3.500A) Processing helix chain 'LG' and resid 242 through 257 Processing helix chain 'LH' and resid 98 through 121 Processing helix chain 'LH' and resid 189 through 205 removed outlier: 4.342A pdb=" N LYSLH 205 " --> pdb=" O GLNLH 201 " (cutoff:3.500A) Processing helix chain 'LH' and resid 210 through 215 removed outlier: 5.135A pdb=" N LEULH 215 " --> pdb=" O ILELH 211 " (cutoff:3.500A) Processing helix chain 'LK' and resid 31 through 36 removed outlier: 5.338A pdb=" N LEULK 35 " --> pdb=" O LYSLK 31 " (cutoff:3.500A) 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 117 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: 4.912A 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 98 removed outlier: 5.314A pdb=" N ASNLM 98 " --> pdb=" O TRPLM 94 " (cutoff:3.500A) Processing helix chain 'LM' and resid 99 through 112 Processing helix chain 'LM' and resid 114 through 136 Processing helix chain 'LN' and resid 2 through 14 removed outlier: 4.393A pdb=" N LYSLN 14 " --> pdb=" O LEULN 10 " (cutoff:3.500A) Processing helix chain 'LN' and resid 16 through 34 removed outlier: 4.506A 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: 5.948A 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: 5.741A pdb=" N ASNLO 43 " --> pdb=" O CYSLO 39 " (cutoff:3.500A) Processing helix chain 'LO' and resid 47 through 62 removed outlier: 5.206A 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: 5.153A pdb=" N LYSLO 105 " --> pdb=" O LEULO 101 " (cutoff:3.500A) Processing helix chain 'LO' and resid 111 through 118 removed outlier: 4.308A pdb=" N LYSLO 116 " --> pdb=" O PROLO 112 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LYSLO 117 " --> pdb=" O PROLO 113 " (cutoff:3.500A) removed outlier: 5.343A 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 152 through 189 removed outlier: 4.048A pdb=" N ALALO 189 " --> pdb=" O LYSLO 185 " (cutoff:3.500A) Processing helix chain 'LO' and resid 192 through 203 Processing helix chain 'LP' and resid 25 through 37 Processing helix chain 'LP' and resid 40 through 54 Processing helix chain 'LP' and resid 70 through 77 removed outlier: 4.620A pdb=" N LYSLP 74 " --> pdb=" O THRLP 70 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLNLP 75 " --> pdb=" O ALALP 71 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TRPLP 76 " --> pdb=" O GLNLP 72 " (cutoff:3.500A) Processing helix chain 'LP' and resid 84 through 106 Processing helix chain 'LP' and resid 172 through 185 Processing helix chain 'LQ' and resid 51 through 68 Processing helix chain 'LQ' and resid 70 through 83 removed outlier: 5.321A pdb=" N SERLQ 83 " --> pdb=" O ARGLQ 79 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 91 through 101 removed outlier: 4.973A 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: 5.171A pdb=" N HISLS 122 " --> pdb=" O PHELS 118 " (cutoff:3.500A) Processing helix chain 'LS' and resid 137 through 145 Processing helix chain 'LT' and resid 54 through 59 removed outlier: 5.497A pdb=" N GLYLT 59 " --> pdb=" O LYSLT 55 " (cutoff:3.500A) Processing helix chain 'LT' and resid 100 through 123 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 'Ld' and resid 23 through 29 Processing helix chain 'Ld' and resid 35 through 53 Processing helix chain 'Ld' and resid 60 through 69 Processing helix chain 'Le' and resid 22 through 27 removed outlier: 4.804A 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 79 through 88 removed outlier: 5.131A 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 removed outlier: 3.695A pdb=" N TYRLf 46 " --> pdb=" O ALALf 42 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 8 through 15 removed outlier: 3.857A pdb=" N SERLh 14 " --> pdb=" O GLYLh 10 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LYSLh 15 " --> pdb=" O GLNLh 11 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 16 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 34 through 39 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: 4.728A 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: 4.628A pdb=" N ASPLq 18 " --> pdb=" O ALALq 14 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N TYRLq 19 " --> pdb=" O GLULq 15 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SERLq 20 " --> pdb=" O LEULq 16 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASNLq 21 " --> pdb=" O LEULq 17 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 73 through 81 Processing helix chain 'Lq' and resid 86 through 97 removed outlier: 4.676A pdb=" N LYSLq 97 " --> pdb=" O LEULq 93 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 98 through 108 Processing helix chain 'Lq' and resid 113 through 121 Proline residue: Lq 121 - end of helix Processing helix chain 'Lq' and resid 123 through 129 removed outlier: 3.908A pdb=" N GLYLq 127 " --> pdb=" O LEULq 123 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEULq 128 " --> pdb=" O LEULq 124 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 146 through 152 Processing helix chain 'Lq' and resid 175 through 195 removed outlier: 5.200A pdb=" N LYSLq 195 " --> pdb=" O VALLq 191 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 197 through 202 removed outlier: 5.005A pdb=" N GLYLq 202 " --> pdb=" O GLNLq 199 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'CA' and resid 61 through 66 removed outlier: 6.314A pdb=" N ALACA 94 " --> pdb=" O SERCA 41 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LYSCA 114 " --> pdb=" O ILECA 243 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N GLYCA 235 " --> pdb=" O METCA 123 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N METCA 123 " --> pdb=" O GLYCA 235 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VALCA 239 " --> pdb=" O ASNCA 119 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ASNCA 119 " --> pdb=" O VALCA 239 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'CA' and resid 136 through 142 removed outlier: 7.670A pdb=" N ARGCA 137 " --> pdb=" O ILECA 176 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N HISCA 178 " --> pdb=" O ARGCA 137 " (cutoff:3.500A) removed outlier: 6.263A 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 removed outlier: 3.626A pdb=" N ILECA 244 " --> pdb=" O LYSCA 114 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'CA' and resid 193 through 200 removed outlier: 7.423A pdb=" N ASNCA 193 " --> pdb=" O ILECA 234 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'CB' and resid 80 through 83 Processing sheet with id= 6, first strand: chain 'CB' and resid 97 through 100 Processing sheet with id= 7, first strand: chain 'CB' and resid 240 through 246 removed outlier: 6.997A pdb=" N ILECB 62 " --> pdb=" O VALCB 245 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ARGCB 279 " --> pdb=" O GLNCB 295 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N GLNCB 295 " --> pdb=" O ARGCB 279 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'CC' and resid 137 through 141 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 384 through 387 removed outlier: 5.102A pdb=" N SERCE 458 " --> pdb=" O GLUCE 333 " (cutoff:3.500A) removed outlier: 4.759A 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: 6.710A pdb=" N VALCF 42 " --> pdb=" O LEUCF 224 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'CF' and resid 135 through 139 removed outlier: 6.640A pdb=" N VALCF 135 " --> pdb=" O ILECF 194 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYRCF 192 " --> pdb=" O VALCF 137 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N THRCF 139 " --> pdb=" O GLUCF 190 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N GLUCF 190 " --> pdb=" O THRCF 139 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'CF' and resid 172 through 175 Processing sheet with id= 14, first strand: chain 'CF' and resid 232 through 236 Processing sheet with id= 15, first strand: chain 'CF' and resid 38 through 42 removed outlier: 8.507A pdb=" N GLNCF 38 " --> pdb=" O SERCF 229 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'CG' and resid 37 through 40 removed outlier: 6.395A pdb=" N VALCG 45 " --> pdb=" O LEUCG 71 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'CG' and resid 96 through 100 Processing sheet with id= 18, first strand: chain 'CH' and resid 202 through 209 removed outlier: 7.236A pdb=" N SERCH 202 " --> pdb=" O PROCH 221 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ARGCH 167 " --> pdb=" O ARGCH 214 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLYCH 173 " --> pdb=" O THRCH 220 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALACH 319 " --> pdb=" O LEUCH 286 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'CI' and resid 214 through 218 removed outlier: 4.689A pdb=" N VALCI 188 " --> pdb=" O VALCI 263 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'CJ' and resid 186 through 191 Processing sheet with id= 21, first strand: chain 'CJ' and resid 394 through 397 Processing sheet with id= 22, first strand: chain 'CK' and resid 190 through 195 removed outlier: 5.396A pdb=" N TYRCK 242 " --> pdb=" O LEUCK 260 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ILECK 220 " --> pdb=" O LYSCK 201 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'CL' and resid 267 through 270 removed outlier: 6.035A pdb=" N ILECL 208 " --> pdb=" O ARGCL 238 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N GLYCL 319 " --> pdb=" O SERCL 373 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'CM' and resid 119 through 124 Processing sheet with id= 25, first strand: chain 'CN' and resid 1 through 4 Processing sheet with id= 26, first strand: chain 'CN' and resid 23 through 27 Processing sheet with id= 27, first strand: chain 'CN' and resid 69 through 73 Processing sheet with id= 28, first strand: chain 'CN' and resid 114 through 117 Processing sheet with id= 29, first strand: chain 'CN' and resid 158 through 161 Processing sheet with id= 30, first strand: chain 'CP' and resid 330 through 333 removed outlier: 6.867A pdb=" N THRCP 330 " --> pdb=" O PHECP 345 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VALCP 340 " --> pdb=" O THRCP 310 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N HISCP 361 " --> pdb=" O ASNCP 311 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'CP' and resid 432 through 438 removed outlier: 5.362A pdb=" N ASNCP 432 " --> pdb=" O GLYCP 406 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASPCP 412 " --> pdb=" O CYSCP 436 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N TYRCP 438 " --> pdb=" O ASPCP 412 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASPCP 456 " --> pdb=" O METCP 387 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N CYSCP 513 " --> pdb=" O ALACP 457 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N GLYCP 506 " --> pdb=" O LYSCP 583 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LYSCP 580 " --> pdb=" O VALCP 537 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ASNCP 533 " --> pdb=" O ILECP 584 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'CP' and resid 563 through 568 removed outlier: 6.414A pdb=" N ASPCP 574 " --> pdb=" O PROCP 568 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'CQ' and resid 3 through 6 removed outlier: 4.752A pdb=" N ARGCQ 11 " --> pdb=" O CYSCQ 6 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'CQ' and resid 18 through 22 Processing sheet with id= 35, first strand: chain 'CS' and resid 789 through 793 Processing sheet with id= 36, first strand: chain 'CV' and resid 51 through 56 removed outlier: 4.776A pdb=" N ALACV 51 " --> pdb=" O LYSCV 66 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N SERCV 77 " --> pdb=" O LYSCV 67 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'Cb' and resid 190 through 194 removed outlier: 4.321A pdb=" N VALCb 131 " --> pdb=" O VALCb 291 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N METCb 133 " --> pdb=" O VALCb 293 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'Cb' and resid 392 through 396 removed outlier: 7.305A pdb=" N ASPCb 503 " --> pdb=" O LEUCb 305 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N SERCb 307 " --> pdb=" O ASPCb 503 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N VALCb 505 " --> pdb=" O SERCb 307 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'LB' and resid 53 through 58 removed outlier: 6.759A pdb=" N ILELB 78 " --> pdb=" O ALALB 51 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ARGLB 335 " --> pdb=" O LYSLB 50 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILELB 336 " --> pdb=" O VALLB 221 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N VALLB 221 " --> pdb=" O ILELB 336 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N HISLB 274 " --> pdb=" O THRLB 222 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'LB' and resid 84 through 87 removed outlier: 6.166A pdb=" N LEULB 162 " --> pdb=" O VALLB 87 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VALLB 158 " --> pdb=" O TYRLB 92 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLYLB 91 " --> pdb=" O LEULB 102 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'LB' and resid 285 through 288 Processing sheet with id= 42, first strand: chain 'LB' and resid 77 through 80 Processing sheet with id= 43, first strand: chain 'LB' and resid 88 through 91 Processing sheet with id= 44, first strand: chain 'LB' and resid 159 through 165 removed outlier: 4.856A pdb=" N VALLB 159 " --> pdb=" O ILELB 184 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THRLB 165 " --> pdb=" O HISLB 178 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N HISLB 178 " --> pdb=" O THRLB 165 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'LB' and resid 213 through 217 removed outlier: 3.804A pdb=" N GLULB 214 " --> pdb=" O ILELB 283 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'LC' and resid 6 through 9 removed outlier: 4.824A pdb=" N ALALC 19 " --> pdb=" O VALLC 9 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'LC' and resid 76 through 79 removed outlier: 4.471A pdb=" N GLNLC 88 " --> pdb=" O VALLC 78 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'LC' and resid 231 through 236 removed outlier: 5.416A pdb=" N PHELC 254 " --> pdb=" O GLYLC 208 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'LE' and resid 55 through 61 removed outlier: 3.638A pdb=" N LEULE 60 " --> pdb=" O LYSLE 68 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LYSLE 68 " --> pdb=" O LEULE 60 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'LE' and resid 81 through 84 Processing sheet with id= 51, first strand: chain 'LF' and resid 118 through 124 removed outlier: 3.568A pdb=" N ASNLF 119 " --> pdb=" O ARGLF 94 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'LF' and resid 159 through 162 Processing sheet with id= 53, first strand: chain 'LG' and resid 179 through 184 Processing sheet with id= 54, first strand: chain 'LH' and resid 5 through 12 removed outlier: 6.076A pdb=" N GLYLH 88 " --> pdb=" O VALLH 12 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'LH' and resid 54 through 57 removed outlier: 6.329A pdb=" N ARGLH 60 " --> pdb=" O LEULH 75 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'LH' and resid 137 through 142 removed outlier: 4.935A pdb=" N TYRLH 149 " --> pdb=" O METLH 167 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'LH' and resid 171 through 175 removed outlier: 5.555A pdb=" N ASPLH 181 " --> pdb=" O TYRLH 129 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'LK' and resid 12 through 16 Processing sheet with id= 59, first strand: chain 'LL' and resid 56 through 59 Processing sheet with id= 60, first strand: chain 'LM' and resid 18 through 22 removed outlier: 4.677A pdb=" N ARGLM 18 " --> pdb=" O ILELM 30 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEULM 40 " --> pdb=" O VALLM 31 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'LN' and resid 35 through 39 removed outlier: 6.637A pdb=" N VALLN 35 " --> pdb=" O ARGLN 65 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILELN 133 " --> pdb=" O LEULN 116 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'LN' and resid 117 through 121 removed outlier: 6.679A pdb=" N TYRLN 129 " --> pdb=" O VALLN 121 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'LO' and resid 7 through 11 Processing sheet with id= 64, first strand: chain 'LP' and resid 14 through 20 removed outlier: 6.494A pdb=" N ILELP 149 " --> pdb=" O LYSLP 115 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'LP' and resid 57 through 60 removed outlier: 5.390A pdb=" N ARGLP 80 " --> pdb=" O METLP 60 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'LP' and resid 116 through 122 Processing sheet with id= 67, first strand: chain 'LQ' and resid 146 through 149 Processing sheet with id= 68, first strand: chain 'LS' and resid 24 through 30 removed outlier: 6.552A pdb=" N ILELS 10 " --> pdb=" O VALLS 59 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'LS' and resid 86 through 96 removed outlier: 5.210A pdb=" N ASNLS 74 " --> pdb=" O LEULS 129 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'LS' and resid 6 through 10 Processing sheet with id= 71, first strand: chain 'LT' and resid 40 through 43 removed outlier: 7.687A pdb=" N HISLT 95 " --> pdb=" O LYSLT 43 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'LT' and resid 73 through 79 Processing sheet with id= 73, first strand: chain 'LV' and resid 35 through 39 removed outlier: 6.060A pdb=" N ASNLV 100 " --> pdb=" O ILELV 24 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILELV 104 " --> pdb=" O ALALV 28 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'LV' and resid 86 through 89 Processing sheet with id= 75, first strand: chain 'LV' and resid 81 through 84 removed outlier: 6.592A pdb=" N ASPLV 99 " --> pdb=" O ALALV 84 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'LY' and resid 55 through 58 Processing sheet with id= 77, first strand: chain 'LY' and resid 85 through 88 removed outlier: 4.747A pdb=" N GLNLY 92 " --> pdb=" O LYSLY 88 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'Ld' and resid 56 through 59 removed outlier: 4.908A pdb=" N ASPLd 56 " --> pdb=" O LEULd 97 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ALALd 17 " --> pdb=" O VALLd 117 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'Le' and resid 72 through 78 Processing sheet with id= 80, first strand: chain 'Lf' and resid 12 through 16 removed outlier: 5.767A pdb=" N LYSLf 12 " --> pdb=" O GLULf 35 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEULf 31 " --> pdb=" O LEULf 16 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ARGLf 84 " --> pdb=" O THRLf 74 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LYSLf 65 " --> pdb=" O ALALf 57 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LYSLf 49 " --> pdb=" O ILELf 73 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'Lf' and resid 10 through 16 Processing sheet with id= 82, first strand: chain 'Lj' and resid 15 through 18 removed outlier: 7.616A pdb=" N THRLj 15 " --> pdb=" O HISLj 28 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N GLYLj 17 " --> pdb=" O SERLj 26 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'Lq' and resid 30 through 37 removed outlier: 7.818A pdb=" N GLULq 30 " --> pdb=" O ASNLq 171 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASNLq 171 " --> pdb=" O GLULq 30 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VALLq 32 " --> pdb=" O VALLq 169 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'Lq' and resid 50 through 54 removed outlier: 4.012A pdb=" N GLYLq 51 " --> pdb=" O PHELq 157 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VALLq 53 " --> pdb=" O VALLq 155 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VALLq 155 " --> pdb=" O VALLq 53 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'Lq' and resid 65 through 68 4346 hydrogen bonds defined for protein. 12918 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2031 hydrogen bonds 3360 hydrogen bond angles 0 basepair planarities 807 basepair parallelities 1220 stacking parallelities Total time for adding SS restraints: 119.53 Time building geometry restraints manager: 54.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 17346 1.31 - 1.44: 51541 1.44 - 1.56: 70304 1.56 - 1.69: 4827 1.69 - 1.82: 458 Bond restraints: 144476 Sorted by residual: bond pdb=" OG1 TPOCC 163 " pdb=" P TPOCC 163 " ideal model delta sigma weight residual 1.717 1.601 0.116 2.00e-02 2.50e+03 3.39e+01 bond pdb=" O3P SEPCC 160 " pdb=" P SEPCC 160 " ideal model delta sigma weight residual 1.610 1.510 0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" O2P SEPCC 160 " pdb=" P SEPCC 160 " ideal model delta sigma weight residual 1.610 1.511 0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" O1P SEPCC 160 " pdb=" P SEPCC 160 " ideal model delta sigma weight residual 1.610 1.513 0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" N GLNCb 571 " pdb=" CA GLNCb 571 " ideal model delta sigma weight residual 1.452 1.504 -0.052 1.25e-02 6.40e+03 1.71e+01 ... (remaining 144471 not shown) Histogram of bond angle deviations from ideal: 96.00 - 103.97: 8810 103.97 - 111.95: 77682 111.95 - 119.93: 60483 119.93 - 127.90: 55292 127.90 - 135.88: 4424 Bond angle restraints: 206691 Sorted by residual: angle pdb=" C4' GC11134 " pdb=" C3' GC11134 " pdb=" O3' GC11134 " ideal model delta sigma weight residual 109.40 120.76 -11.36 1.50e+00 4.44e-01 5.74e+01 angle pdb=" C ALALN 39 " pdb=" N SERLN 40 " pdb=" CA SERLN 40 " ideal model delta sigma weight residual 121.54 135.88 -14.34 1.91e+00 2.74e-01 5.64e+01 angle pdb=" CB ARGCI 313 " pdb=" CG ARGCI 313 " pdb=" CD ARGCI 313 " ideal model delta sigma weight residual 111.30 127.52 -16.22 2.30e+00 1.89e-01 4.98e+01 angle pdb=" CA ASPLN 124 " pdb=" CB ASPLN 124 " pdb=" CG ASPLN 124 " ideal model delta sigma weight residual 112.60 119.51 -6.91 1.00e+00 1.00e+00 4.77e+01 angle pdb=" C4' GC13267 " pdb=" C3' GC13267 " pdb=" C2' GC13267 " ideal model delta sigma weight residual 102.60 96.00 6.60 1.00e+00 1.00e+00 4.36e+01 ... (remaining 206686 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 84297 35.97 - 71.93: 6313 71.93 - 107.90: 728 107.90 - 143.86: 20 143.86 - 179.83: 21 Dihedral angle restraints: 91379 sinusoidal: 60161 harmonic: 31218 Sorted by residual: dihedral pdb=" CA LEULB 17 " pdb=" C LEULB 17 " pdb=" N PROLB 18 " pdb=" CA PROLB 18 " ideal model delta harmonic sigma weight residual -180.00 -63.72 -116.28 0 5.00e+00 4.00e-02 5.41e+02 dihedral pdb=" CA ALALN 39 " pdb=" C ALALN 39 " pdb=" N SERLN 40 " pdb=" CA SERLN 40 " ideal model delta harmonic sigma weight residual 180.00 119.49 60.51 0 5.00e+00 4.00e-02 1.46e+02 dihedral pdb=" C5' GC11134 " pdb=" C4' GC11134 " pdb=" C3' GC11134 " pdb=" O3' GC11134 " ideal model delta sinusoidal sigma weight residual 147.00 80.38 66.62 1 8.00e+00 1.56e-02 9.05e+01 ... (remaining 91376 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 22320 0.074 - 0.148: 2194 0.148 - 0.221: 431 0.221 - 0.295: 53 0.295 - 0.369: 12 Chirality restraints: 25010 Sorted by residual: chirality pdb=" CB VALLH 108 " pdb=" CA VALLH 108 " pdb=" CG1 VALLH 108 " pdb=" CG2 VALLH 108 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CA PHECP 576 " pdb=" N PHECP 576 " pdb=" C PHECP 576 " pdb=" CB PHECP 576 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" C3' GC11134 " pdb=" C4' GC11134 " pdb=" O3' GC11134 " pdb=" C2' GC11134 " both_signs ideal model delta sigma weight residual False -2.74 -2.40 -0.35 2.00e-01 2.50e+01 3.03e+00 ... (remaining 25007 not shown) Planarity restraints: 17391 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALACP 281 " -0.026 2.00e-02 2.50e+03 5.44e-02 2.96e+01 pdb=" C ALACP 281 " 0.094 2.00e-02 2.50e+03 pdb=" O ALACP 281 " -0.036 2.00e-02 2.50e+03 pdb=" N GLUCP 282 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALACG 56 " -0.027 2.00e-02 2.50e+03 5.32e-02 2.83e+01 pdb=" C ALACG 56 " 0.092 2.00e-02 2.50e+03 pdb=" O ALACG 56 " -0.034 2.00e-02 2.50e+03 pdb=" N THRCG 57 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALALN 39 " -0.025 2.00e-02 2.50e+03 5.30e-02 2.80e+01 pdb=" C ALALN 39 " 0.091 2.00e-02 2.50e+03 pdb=" O ALALN 39 " -0.036 2.00e-02 2.50e+03 pdb=" N SERLN 40 " -0.030 2.00e-02 2.50e+03 ... (remaining 17388 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 871 2.54 - 3.13: 101089 3.13 - 3.72: 244001 3.72 - 4.31: 336127 4.31 - 4.90: 494731 Nonbonded interactions: 1176819 Sorted by model distance: nonbonded pdb=" O4 UC1 670 " pdb=" O6 GC1 684 " model vdw 1.953 3.040 nonbonded pdb=" O2 UC12433 " pdb=" O6 GC12436 " model vdw 2.022 2.432 nonbonded pdb=" O6 GC1 974 " pdb=" O4 UC11038 " model vdw 2.043 2.432 nonbonded pdb=" OE1 GLUCF 21 " pdb=" NH1 ARGCF 25 " model vdw 2.072 2.520 nonbonded pdb=" OG SERCP 470 " pdb=" ND2 ASNCP 474 " model vdw 2.082 2.520 ... (remaining 1176814 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'CM' selection = (chain 'LF' and (resid 12 through 219 or resid 235 through 249)) } 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 individual isotropic 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: 3.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.140 Extract box with map and model: 19.130 Check model and map are aligned: 1.510 Set scattering table: 0.960 Process input model: 421.020 Find NCS groups from input model: 4.190 Set up NCS constraints: 0.460 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: 0.030 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 453.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 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 : 0.004 0.117 144476 Z= 0.261 Angle : 0.759 16.224 206691 Z= 0.458 Chirality : 0.048 0.369 25010 Planarity : 0.006 0.107 17391 Dihedral : 20.732 179.826 71133 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.91 % Favored : 94.84 % Rotamer: Outliers : 0.63 % Allowed : 1.07 % Favored : 98.30 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.01 % Twisted Proline : 0.37 % Twisted General : 0.01 % 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: 10568 helix: 0.81 (0.07), residues: 4891 sheet: -0.30 (0.14), residues: 1251 loop : -1.08 (0.09), residues: 4426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRPLS 78 HIS 0.009 0.001 HISCJ 177 PHE 0.041 0.002 PHECT 243 TYR 0.033 0.002 TYRCT 315 ARG 0.018 0.001 ARGCQ 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21136 Ramachandran restraints generated. 10568 Oldfield, 0 Emsley, 10568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21136 Ramachandran restraints generated. 10568 Oldfield, 0 Emsley, 10568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2321 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 2265 time to evaluate : 8.591 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: CA 159 PHE cc_start: 0.8069 (m-10) cc_final: 0.7778 (m-80) REVERT: CA 273 LYS cc_start: 0.7702 (mttm) cc_final: 0.7459 (mmtt) REVERT: CC 161 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.8079 (p0) REVERT: CC 287 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7621 (tt0) REVERT: CE 415 ASP cc_start: 0.7490 (m-30) cc_final: 0.7265 (m-30) REVERT: CF 4 SER cc_start: 0.5676 (t) cc_final: 0.5381 (p) REVERT: CF 39 HIS cc_start: 0.7240 (m-70) cc_final: 0.6693 (m90) REVERT: CG 32 ASP cc_start: 0.7469 (p0) cc_final: 0.6554 (t0) REVERT: CG 110 TYR cc_start: 0.7661 (m-10) cc_final: 0.7302 (m-10) REVERT: CH 23 ARG cc_start: 0.7724 (ttm-80) cc_final: 0.7508 (mmt90) REVERT: CH 140 LYS cc_start: 0.7745 (mmmm) cc_final: 0.7425 (mtmt) REVERT: CH 508 MET cc_start: 0.3233 (tpt) cc_final: 0.3005 (tpt) REVERT: CI 261 LYS cc_start: 0.8336 (mtmm) cc_final: 0.8047 (mttm) REVERT: CI 294 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7501 (mm-30) REVERT: CN 117 ILE cc_start: 0.9001 (pt) cc_final: 0.8788 (pt) REVERT: CR 189 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7239 (mm-30) REVERT: CR 196 GLN cc_start: 0.8540 (tp40) cc_final: 0.8119 (tp40) REVERT: CS 476 TYR cc_start: 0.8417 (t80) cc_final: 0.7940 (t80) REVERT: CS 802 LYS cc_start: 0.5934 (tptm) cc_final: 0.5710 (tptm) REVERT: CS 816 ASP cc_start: 0.6962 (m-30) cc_final: 0.6079 (t70) REVERT: CT 310 MET cc_start: 0.8530 (mtt) cc_final: 0.7967 (mtt) REVERT: CV 11 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7245 (mm-30) REVERT: CX 95 VAL cc_start: 0.8570 (p) cc_final: 0.8283 (p) REVERT: CX 129 ILE cc_start: 0.8764 (mt) cc_final: 0.8469 (mt) REVERT: Cb 1 MET cc_start: 0.5342 (tpp) cc_final: 0.5103 (tpt) REVERT: Cb 514 LEU cc_start: 0.7938 (tp) cc_final: 0.7633 (tp) REVERT: Cb 522 ASN cc_start: 0.7535 (m-40) cc_final: 0.7154 (m-40) REVERT: Cb 531 ILE cc_start: 0.6967 (mm) cc_final: 0.6450 (mm) REVERT: Cb 586 VAL cc_start: 0.8131 (OUTLIER) cc_final: 0.7894 (t) REVERT: Cb 816 TRP cc_start: 0.8042 (t60) cc_final: 0.7696 (t60) REVERT: Cz 47 SER cc_start: 0.8154 (t) cc_final: 0.7673 (p) REVERT: LB 84 MET cc_start: 0.8803 (mtm) cc_final: 0.8294 (mtm) REVERT: LB 135 LYS cc_start: 0.8523 (mtpt) cc_final: 0.8182 (mttt) REVERT: LB 283 ILE cc_start: 0.8556 (tt) cc_final: 0.8335 (mt) REVERT: LC 137 MET cc_start: 0.8359 (mtt) cc_final: 0.8141 (mtp) REVERT: LC 183 GLU cc_start: 0.6820 (mm-30) cc_final: 0.6608 (tp30) REVERT: LC 284 GLN cc_start: 0.8460 (tp-100) cc_final: 0.8074 (tp40) REVERT: LC 321 ARG cc_start: 0.7731 (mtp85) cc_final: 0.7398 (mtm180) REVERT: LC 340 LYS cc_start: 0.8141 (mttm) cc_final: 0.7888 (mmtm) REVERT: LE 127 TYR cc_start: 0.7889 (t80) cc_final: 0.7532 (t80) REVERT: LG 133 TYR cc_start: 0.8744 (m-80) cc_final: 0.8447 (m-80) REVERT: LH 65 GLU cc_start: 0.7433 (mp0) cc_final: 0.7155 (tp30) REVERT: LH 109 ARG cc_start: 0.8059 (ttt-90) cc_final: 0.7628 (ttp-170) REVERT: LL 20 ARG cc_start: 0.7217 (ptp-170) cc_final: 0.6767 (ptm160) REVERT: LL 57 ILE cc_start: 0.8524 (pt) cc_final: 0.8246 (mm) REVERT: LL 106 GLU cc_start: 0.6749 (mm-30) cc_final: 0.6500 (mm-30) REVERT: LM 61 ARG cc_start: 0.7331 (ttm-80) cc_final: 0.7107 (mmt-90) REVERT: LN 41 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7899 (ptp-110) REVERT: LN 49 ARG cc_start: 0.7694 (ttt90) cc_final: 0.7476 (ttt90) REVERT: LN 67 ARG cc_start: 0.7548 (mtt-85) cc_final: 0.7325 (mmm160) REVERT: LN 108 ARG cc_start: 0.7582 (mtm-85) cc_final: 0.7178 (mtt-85) REVERT: LN 127 TYR cc_start: 0.8397 (m-80) cc_final: 0.8045 (m-80) REVERT: LO 147 VAL cc_start: 0.8766 (p) cc_final: 0.8504 (m) REVERT: LO 161 ARG cc_start: 0.7496 (ttm170) cc_final: 0.7268 (mtp180) REVERT: LP 178 VAL cc_start: 0.8618 (m) cc_final: 0.8304 (t) REVERT: LS 117 ARG cc_start: 0.7733 (mtt180) cc_final: 0.7476 (mtt90) REVERT: LV 26 ASN cc_start: 0.8294 (m-40) cc_final: 0.7899 (m-40) REVERT: LV 58 ASP cc_start: 0.7465 (m-30) cc_final: 0.7222 (m-30) REVERT: LV 59 MET cc_start: 0.8095 (ttm) cc_final: 0.7772 (ttp) REVERT: LV 108 LYS cc_start: 0.8082 (mttp) cc_final: 0.7583 (mmtt) REVERT: LY 4 ARG cc_start: 0.7217 (mtm110) cc_final: 0.6814 (mmt180) REVERT: LY 6 THR cc_start: 0.8230 (m) cc_final: 0.7926 (p) REVERT: LY 110 LEU cc_start: 0.7657 (mt) cc_final: 0.7075 (mt) REVERT: Ld 45 LYS cc_start: 0.8285 (mttt) cc_final: 0.7897 (mtmt) REVERT: Ld 68 TRP cc_start: 0.6478 (m100) cc_final: 0.6114 (m100) REVERT: Le 83 VAL cc_start: 0.7970 (m) cc_final: 0.7745 (m) REVERT: Le 90 ASN cc_start: 0.7470 (m-40) cc_final: 0.7240 (m110) REVERT: Lh 47 ASN cc_start: 0.7375 (t0) cc_final: 0.6773 (t0) REVERT: Lh 48 LYS cc_start: 0.8476 (tttp) cc_final: 0.8160 (tptt) REVERT: Lh 49 ILE cc_start: 0.7612 (mt) cc_final: 0.7117 (mt) outliers start: 56 outliers final: 6 residues processed: 2304 average time/residue: 1.3209 time to fit residues: 5072.4774 Evaluate side-chains 1204 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1195 time to evaluate : 8.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CC residue 161 ASP Chi-restraints excluded: chain CH residue 286 LEU Chi-restraints excluded: chain CL residue 19 ARG Chi-restraints excluded: chain Cb residue 512 VAL Chi-restraints excluded: chain Cb residue 586 VAL Chi-restraints excluded: chain LE residue 154 VAL Chi-restraints excluded: chain LF residue 94 ARG Chi-restraints excluded: chain LN residue 27 CYS Chi-restraints excluded: chain LN residue 41 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1291 random chunks: chunk 1090 optimal weight: 3.9990 chunk 978 optimal weight: 1.9990 chunk 542 optimal weight: 50.0000 chunk 334 optimal weight: 0.9980 chunk 660 optimal weight: 10.0000 chunk 522 optimal weight: 0.6980 chunk 1011 optimal weight: 1.9990 chunk 391 optimal weight: 7.9990 chunk 615 optimal weight: 7.9990 chunk 753 optimal weight: 30.0000 chunk 1172 optimal weight: 10.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 109 ASN CA 119 ASN CA 246 GLN CA 285 GLN ** CB 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CB 234 HIS CC 243 GLN CE 299 GLN CF 14 GLN CF 16 ASN CG 106 GLN CH 89 HIS CH 176 ASN CH 226 HIS ** CH 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CH 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CH 324 GLN ** CH 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 102 ASN CJ 109 ASN CJ 153 ASN CJ 176 GLN CJ 183 HIS CJ 242 ASN CJ 381 GLN ** CK 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CK 40 GLN CK 57 GLN CK 72 ASN ** CM 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CN 95 GLN ** CN 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CP 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CP 437 ASN CQ 24 ASN CR 133 GLN ** CR 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CR 202 HIS CS 467 GLN CS 478 HIS CS 726 ASN ** CS 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CT 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CT 506 HIS ** CV 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CV 122 GLN CX 113 GLN ** CY 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CY 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CY 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CY 509 HIS ** Cb 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 121 ASN LB 281 HIS LC 217 HIS LE 162 GLN LE 172 ASN LF 78 GLN LF 119 ASN ** LF 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LH 195 GLN LL 114 GLN ** LN 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 118 GLN LQ 98 ASN LS 13 HIS LT 95 HIS ** LV 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LY 127 GLN Lh 37 GLN Lh 50 HIS Lh 118 GLN Li 47 GLN ** Lq 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 144476 Z= 0.223 Angle : 0.604 12.891 206691 Z= 0.311 Chirality : 0.038 0.277 25010 Planarity : 0.005 0.088 17391 Dihedral : 21.826 179.787 49544 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.46 % Favored : 95.40 % Rotamer: Outliers : 1.47 % Allowed : 9.80 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.01 % Twisted Proline : 0.37 % Twisted General : 0.00 % 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: 0.11 (0.08), residues: 10568 helix: 1.11 (0.07), residues: 4903 sheet: -0.28 (0.14), residues: 1266 loop : -0.95 (0.09), residues: 4399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRPCY 387 HIS 0.007 0.001 HISCP 316 PHE 0.046 0.002 PHECK 133 TYR 0.027 0.002 TYRCT 315 ARG 0.008 0.001 ARGLQ 138 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21136 Ramachandran restraints generated. 10568 Oldfield, 0 Emsley, 10568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21136 Ramachandran restraints generated. 10568 Oldfield, 0 Emsley, 10568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1321 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 1190 time to evaluate : 8.702 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: CA 273 LYS cc_start: 0.7796 (mttm) cc_final: 0.7454 (mmtt) REVERT: CB 288 THR cc_start: 0.8270 (OUTLIER) cc_final: 0.8068 (t) REVERT: CC 233 ARG cc_start: 0.6652 (tpp-160) cc_final: 0.6363 (tpt170) REVERT: CC 287 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7571 (tt0) REVERT: CC 292 MET cc_start: 0.8964 (mmm) cc_final: 0.8643 (mmm) REVERT: CC 324 TYR cc_start: 0.5769 (p90) cc_final: 0.5450 (p90) REVERT: CE 134 MET cc_start: 0.6904 (mtp) cc_final: 0.6657 (mtp) REVERT: CE 308 ARG cc_start: 0.8098 (mtm110) cc_final: 0.7876 (mtm-85) REVERT: CE 415 ASP cc_start: 0.7543 (m-30) cc_final: 0.7307 (m-30) REVERT: CF 39 HIS cc_start: 0.7386 (m-70) cc_final: 0.7005 (m90) REVERT: CF 95 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.6632 (t80) REVERT: CG 106 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7713 (tp40) REVERT: CH 140 LYS cc_start: 0.7821 (mmmm) cc_final: 0.7403 (mtmt) REVERT: CH 236 MET cc_start: 0.7096 (tpp) cc_final: 0.6894 (tpp) REVERT: CH 508 MET cc_start: 0.3291 (tpt) cc_final: 0.3042 (tpt) REVERT: CI 210 PHE cc_start: 0.8652 (OUTLIER) cc_final: 0.8180 (t80) REVERT: CI 261 LYS cc_start: 0.8403 (mtmm) cc_final: 0.8045 (mttm) REVERT: CN 173 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8400 (tt) REVERT: CP 246 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7727 (mm) REVERT: CP 487 GLN cc_start: 0.7985 (mt0) cc_final: 0.7673 (mt0) REVERT: CQ 1 MET cc_start: 0.7010 (ptm) cc_final: 0.6621 (ttt) REVERT: CQ 93 MET cc_start: 0.8385 (mmm) cc_final: 0.7776 (mtp) REVERT: CQ 104 GLU cc_start: 0.8750 (tp30) cc_final: 0.8548 (tp30) REVERT: CU 217 HIS cc_start: 0.7578 (p90) cc_final: 0.7329 (p90) REVERT: Cb 331 MET cc_start: 0.8497 (tpp) cc_final: 0.8203 (tpt) REVERT: Cb 522 ASN cc_start: 0.7590 (m-40) cc_final: 0.7243 (m-40) REVERT: Cb 531 ILE cc_start: 0.6993 (mm) cc_final: 0.6439 (mm) REVERT: Cb 588 ASP cc_start: 0.6998 (m-30) cc_final: 0.6780 (m-30) REVERT: Cb 842 LEU cc_start: 0.7430 (tp) cc_final: 0.7215 (tt) REVERT: LB 84 MET cc_start: 0.8787 (mtm) cc_final: 0.8357 (mtm) REVERT: LB 271 MET cc_start: 0.6545 (tpt) cc_final: 0.6270 (tpt) REVERT: LB 350 LYS cc_start: 0.8221 (ttmm) cc_final: 0.7963 (tttp) REVERT: LC 137 MET cc_start: 0.8345 (mtt) cc_final: 0.8144 (mtp) REVERT: LC 176 ILE cc_start: 0.8454 (tt) cc_final: 0.8123 (pt) REVERT: LC 183 GLU cc_start: 0.6904 (mm-30) cc_final: 0.6672 (tp30) REVERT: LC 321 ARG cc_start: 0.7972 (mtp85) cc_final: 0.7510 (mtm180) REVERT: LC 340 LYS cc_start: 0.8142 (mttm) cc_final: 0.7884 (mmtm) REVERT: LG 78 ILE cc_start: 0.7892 (mt) cc_final: 0.7691 (mp) REVERT: LG 101 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.7697 (ttm170) REVERT: LH 65 GLU cc_start: 0.7518 (mp0) cc_final: 0.7127 (tp30) REVERT: LH 109 ARG cc_start: 0.8231 (ttt-90) cc_final: 0.7729 (tmm160) REVERT: LK 133 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8771 (mm) REVERT: LL 20 ARG cc_start: 0.7186 (ptp-170) cc_final: 0.6915 (ptm160) REVERT: LM 61 ARG cc_start: 0.7496 (ttm-80) cc_final: 0.7117 (mmt-90) REVERT: LN 27 CYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8224 (t) REVERT: LN 41 ARG cc_start: 0.8207 (ptp-110) cc_final: 0.7816 (ptp-110) REVERT: LN 67 ARG cc_start: 0.7626 (mtt-85) cc_final: 0.7315 (mmm160) REVERT: LN 108 ARG cc_start: 0.7682 (mtm-85) cc_final: 0.7140 (mtt-85) REVERT: LN 127 TYR cc_start: 0.8343 (m-80) cc_final: 0.8132 (m-80) REVERT: LO 147 VAL cc_start: 0.8801 (p) cc_final: 0.8500 (m) REVERT: LP 152 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7343 (mt-10) REVERT: LP 178 VAL cc_start: 0.8769 (m) cc_final: 0.8492 (t) REVERT: LQ 105 LYS cc_start: 0.7621 (mtmm) cc_final: 0.7291 (mtmm) REVERT: LS 45 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8447 (mp) REVERT: LS 117 ARG cc_start: 0.7820 (mtt180) cc_final: 0.7375 (mtm180) REVERT: LV 59 MET cc_start: 0.8152 (ttm) cc_final: 0.7834 (ttp) REVERT: LV 108 LYS cc_start: 0.8132 (mttp) cc_final: 0.7583 (mmtt) REVERT: LY 4 ARG cc_start: 0.7381 (mtm110) cc_final: 0.6974 (mmt180) REVERT: LY 110 LEU cc_start: 0.7701 (mt) cc_final: 0.7313 (mt) REVERT: Ld 79 ILE cc_start: 0.7563 (tt) cc_final: 0.7156 (pt) REVERT: Le 90 ASN cc_start: 0.7855 (m-40) cc_final: 0.7648 (m-40) REVERT: Lh 48 LYS cc_start: 0.8466 (tttp) cc_final: 0.8228 (tptt) REVERT: Lq 184 MET cc_start: 0.8124 (mmm) cc_final: 0.7836 (mmp) outliers start: 131 outliers final: 80 residues processed: 1266 average time/residue: 1.2541 time to fit residues: 2736.5088 Evaluate side-chains 1125 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1035 time to evaluate : 8.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CB residue 101 THR Chi-restraints excluded: chain CB residue 232 LEU Chi-restraints excluded: chain CB residue 288 THR Chi-restraints excluded: chain CC residue 122 VAL Chi-restraints excluded: chain CC residue 238 LEU Chi-restraints excluded: chain CE residue 366 SER Chi-restraints excluded: chain CF residue 9 VAL Chi-restraints excluded: chain CF residue 95 TYR Chi-restraints excluded: chain CF residue 137 VAL Chi-restraints excluded: chain CG residue 5 THR Chi-restraints excluded: chain CG residue 6 ASP Chi-restraints excluded: chain CG residue 21 THR Chi-restraints excluded: chain CG residue 93 ASN Chi-restraints excluded: chain CG residue 106 GLN Chi-restraints excluded: chain CG residue 139 ASP Chi-restraints excluded: chain CH residue 285 VAL Chi-restraints excluded: chain CH residue 403 LEU Chi-restraints excluded: chain CI residue 210 PHE Chi-restraints excluded: chain CI residue 218 VAL Chi-restraints excluded: chain CJ residue 37 CYS Chi-restraints excluded: chain CJ residue 171 LEU Chi-restraints excluded: chain CK residue 121 ILE Chi-restraints excluded: chain CK residue 239 TRP Chi-restraints excluded: chain CL residue 35 GLU Chi-restraints excluded: chain CN residue 10 SER Chi-restraints excluded: chain CN residue 39 GLU Chi-restraints excluded: chain CN residue 91 ASP Chi-restraints excluded: chain CN residue 114 THR Chi-restraints excluded: chain CN residue 173 LEU Chi-restraints excluded: chain CP residue 246 LEU Chi-restraints excluded: chain CP residue 466 CYS Chi-restraints excluded: chain CP residue 552 MET Chi-restraints excluded: chain CP residue 571 TYR Chi-restraints excluded: chain CR residue 128 SER Chi-restraints excluded: chain CS residue 487 ASP Chi-restraints excluded: chain CS residue 705 LYS Chi-restraints excluded: chain CS residue 795 THR Chi-restraints excluded: chain CT residue 504 ASP Chi-restraints excluded: chain CU residue 220 VAL Chi-restraints excluded: chain CU residue 256 SER Chi-restraints excluded: chain CV residue 33 LEU Chi-restraints excluded: chain CV residue 36 THR Chi-restraints excluded: chain CX residue 80 VAL Chi-restraints excluded: chain CX residue 93 VAL Chi-restraints excluded: chain CY residue 628 GLU Chi-restraints excluded: chain Cb residue 481 LEU Chi-restraints excluded: chain Cb residue 512 VAL Chi-restraints excluded: chain Cb residue 583 GLU Chi-restraints excluded: chain Cb residue 873 VAL Chi-restraints excluded: chain LB residue 112 ASP Chi-restraints excluded: chain LB residue 157 THR Chi-restraints excluded: chain LB residue 320 ASN Chi-restraints excluded: chain LB residue 357 LEU Chi-restraints excluded: chain LC residue 211 ILE Chi-restraints excluded: chain LC residue 223 VAL Chi-restraints excluded: chain LC residue 283 SER Chi-restraints excluded: chain LE residue 52 LEU Chi-restraints excluded: chain LE residue 73 LEU Chi-restraints excluded: chain LE residue 154 VAL Chi-restraints excluded: chain LE residue 156 SER Chi-restraints excluded: chain LE residue 157 THR Chi-restraints excluded: chain LF residue 48 GLN Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 94 ARG Chi-restraints excluded: chain LF residue 174 ILE Chi-restraints excluded: chain LG residue 70 MET Chi-restraints excluded: chain LG residue 101 ARG Chi-restraints excluded: chain LH residue 89 VAL Chi-restraints excluded: chain LH residue 105 LEU Chi-restraints excluded: chain LH residue 145 GLU Chi-restraints excluded: chain LH residue 175 ILE Chi-restraints excluded: chain LH residue 185 LEU Chi-restraints excluded: chain LK residue 133 LEU Chi-restraints excluded: chain LL residue 46 LEU Chi-restraints excluded: chain LL residue 76 THR Chi-restraints excluded: chain LM residue 111 SER Chi-restraints excluded: chain LN residue 10 LEU Chi-restraints excluded: chain LN residue 27 CYS Chi-restraints excluded: chain LN residue 149 ASN Chi-restraints excluded: chain LO residue 68 THR Chi-restraints excluded: chain LO residue 131 LEU Chi-restraints excluded: chain LQ residue 108 VAL Chi-restraints excluded: chain LQ residue 148 THR Chi-restraints excluded: chain LS residue 45 LEU Chi-restraints excluded: chain LV residue 80 ILE Chi-restraints excluded: chain LY residue 46 SER Chi-restraints excluded: chain LY residue 90 THR Chi-restraints excluded: chain LY residue 128 VAL Chi-restraints excluded: chain Lh residue 84 ASP Chi-restraints excluded: chain Lq residue 206 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1291 random chunks: chunk 651 optimal weight: 1.9990 chunk 363 optimal weight: 10.0000 chunk 975 optimal weight: 6.9990 chunk 798 optimal weight: 40.0000 chunk 323 optimal weight: 6.9990 chunk 1174 optimal weight: 30.0000 chunk 1268 optimal weight: 2.9990 chunk 1045 optimal weight: 7.9990 chunk 1164 optimal weight: 3.9990 chunk 400 optimal weight: 20.0000 chunk 942 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CB 73 HIS ** CB 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CF 14 GLN CH 226 HIS ** CH 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CH 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CH 333 HIS ** CI 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CK 10 HIS CK 203 ASN CM 206 ASN CN 95 GLN ** CN 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CP 300 ASN ** CP 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CP 361 HIS ** CP 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CQ 24 ASN CR 148 GLN CR 202 HIS CS 744 GLN ** CT 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CV 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CV 122 GLN ** CY 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CY 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CY 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CY 497 HIS ** Cb 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cb 820 HIS LB 320 ASN LB 379 GLN LC 142 GLN LE 116 GLN LF 9 GLN LF 178 ASN LF 200 ASN LH 201 GLN LO 43 ASN LP 75 GLN LP 118 GLN ** LV 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ld 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lf 44 ASN Lh 115 HIS Li 47 GLN ** Lq 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 144476 Z= 0.320 Angle : 0.658 12.510 206691 Z= 0.338 Chirality : 0.041 0.293 25010 Planarity : 0.006 0.078 17391 Dihedral : 21.780 179.994 49531 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.49 % Favored : 95.38 % Rotamer: Outliers : 2.19 % Allowed : 12.05 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.01 % Twisted Proline : 0.37 % Twisted General : 0.00 % 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: 0.16 (0.08), residues: 10568 helix: 1.17 (0.07), residues: 4902 sheet: -0.31 (0.14), residues: 1257 loop : -0.95 (0.09), residues: 4409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRPCM 209 HIS 0.010 0.001 HISCB 73 PHE 0.027 0.002 PHECU 358 TYR 0.029 0.002 TYRCC 149 ARG 0.013 0.001 ARGCQ 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21136 Ramachandran restraints generated. 10568 Oldfield, 0 Emsley, 10568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21136 Ramachandran restraints generated. 10568 Oldfield, 0 Emsley, 10568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1270 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 1075 time to evaluate : 8.900 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: CB 161 ASN cc_start: 0.7715 (p0) cc_final: 0.7374 (p0) REVERT: CC 233 ARG cc_start: 0.6602 (tpp-160) cc_final: 0.6084 (tpt170) REVERT: CC 292 MET cc_start: 0.8974 (mmm) cc_final: 0.8623 (mmm) REVERT: CC 324 TYR cc_start: 0.5863 (p90) cc_final: 0.5607 (p90) REVERT: CC 373 MET cc_start: -0.0632 (ptt) cc_final: -0.1428 (ptt) REVERT: CF 95 TYR cc_start: 0.7997 (OUTLIER) cc_final: 0.6693 (t80) REVERT: CH 140 LYS cc_start: 0.8023 (mmmm) cc_final: 0.7785 (mtmt) REVERT: CH 236 MET cc_start: 0.7338 (tpp) cc_final: 0.7047 (tpp) REVERT: CH 469 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7628 (pp20) REVERT: CH 508 MET cc_start: 0.3682 (tpt) cc_final: 0.3280 (tpt) REVERT: CI 210 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.8337 (t80) REVERT: CI 261 LYS cc_start: 0.8535 (mtmm) cc_final: 0.8198 (mttm) REVERT: CJ 147 MET cc_start: 0.7002 (mmp) cc_final: 0.6784 (mmp) REVERT: CJ 227 MET cc_start: 0.8026 (pmm) cc_final: 0.7419 (ptp) REVERT: CK 137 LYS cc_start: 0.6407 (OUTLIER) cc_final: 0.5640 (tttp) REVERT: CN 241 ILE cc_start: 0.8914 (mp) cc_final: 0.8631 (mt) REVERT: CO 89 LYS cc_start: 0.8625 (mmmt) cc_final: 0.8299 (mmtt) REVERT: CQ 96 ILE cc_start: 0.9312 (mp) cc_final: 0.9108 (mp) REVERT: CQ 112 MET cc_start: 0.5491 (mmt) cc_final: 0.4972 (mmt) REVERT: CR 178 ARG cc_start: 0.7349 (ttm170) cc_final: 0.7051 (ttm170) REVERT: CS 479 TYR cc_start: 0.8284 (t80) cc_final: 0.8042 (t80) REVERT: CU 217 HIS cc_start: 0.7728 (p90) cc_final: 0.7430 (p90) REVERT: Cb 331 MET cc_start: 0.8272 (tpp) cc_final: 0.8029 (tpt) REVERT: Cb 522 ASN cc_start: 0.7616 (m-40) cc_final: 0.7291 (m-40) REVERT: Cb 531 ILE cc_start: 0.7020 (mm) cc_final: 0.6470 (mm) REVERT: Cb 588 ASP cc_start: 0.6891 (m-30) cc_final: 0.6666 (m-30) REVERT: LB 84 MET cc_start: 0.8758 (mtm) cc_final: 0.8540 (mtp) REVERT: LB 166 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7096 (mp10) REVERT: LB 167 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7926 (tp) REVERT: LB 350 LYS cc_start: 0.8410 (ttmm) cc_final: 0.8075 (ttmt) REVERT: LC 176 ILE cc_start: 0.8526 (tt) cc_final: 0.8281 (pt) REVERT: LC 183 GLU cc_start: 0.6955 (mm-30) cc_final: 0.6731 (tp30) REVERT: LC 301 ARG cc_start: 0.7405 (ttm170) cc_final: 0.7161 (ttm110) REVERT: LC 321 ARG cc_start: 0.8232 (mtp85) cc_final: 0.7695 (mtm180) REVERT: LE 25 GLN cc_start: 0.7100 (mt0) cc_final: 0.6787 (mt0) REVERT: LE 127 TYR cc_start: 0.8302 (t80) cc_final: 0.7997 (t80) REVERT: LG 101 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.7840 (ttm170) REVERT: LH 65 GLU cc_start: 0.7623 (mp0) cc_final: 0.7273 (tp30) REVERT: LK 133 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8871 (mm) REVERT: LM 61 ARG cc_start: 0.7533 (ttm-80) cc_final: 0.7195 (mmm-85) REVERT: LN 41 ARG cc_start: 0.8373 (ptp-110) cc_final: 0.8085 (ptp-110) REVERT: LN 67 ARG cc_start: 0.7700 (mtt-85) cc_final: 0.7393 (mmm160) REVERT: LO 147 VAL cc_start: 0.8851 (p) cc_final: 0.8609 (m) REVERT: LQ 105 LYS cc_start: 0.7685 (mtmm) cc_final: 0.7395 (mtmm) REVERT: LS 45 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8447 (mp) REVERT: LS 117 ARG cc_start: 0.7890 (mtt180) cc_final: 0.7349 (mtm180) REVERT: LV 59 MET cc_start: 0.8226 (ttm) cc_final: 0.7909 (ttp) REVERT: LV 108 LYS cc_start: 0.8304 (mttp) cc_final: 0.7756 (mmtt) REVERT: LY 4 ARG cc_start: 0.7540 (mtm110) cc_final: 0.6986 (mmt180) REVERT: LY 110 LEU cc_start: 0.8338 (mt) cc_final: 0.8092 (mt) REVERT: Le 90 ASN cc_start: 0.8090 (m-40) cc_final: 0.7883 (m-40) REVERT: Lf 24 ASN cc_start: 0.8508 (OUTLIER) cc_final: 0.8222 (m110) REVERT: Lh 48 LYS cc_start: 0.8391 (tttp) cc_final: 0.8128 (tptt) REVERT: Li 32 LYS cc_start: 0.7541 (mmtt) cc_final: 0.7097 (ttpt) REVERT: Lj 25 ARG cc_start: 0.7740 (mtp-110) cc_final: 0.7512 (mtp85) REVERT: Lq 63 MET cc_start: 0.5903 (mmm) cc_final: 0.5430 (mmm) REVERT: Lq 103 LEU cc_start: 0.8733 (tp) cc_final: 0.8150 (pp) REVERT: Lq 184 MET cc_start: 0.8261 (mmm) cc_final: 0.7881 (mmp) outliers start: 195 outliers final: 110 residues processed: 1209 average time/residue: 1.1958 time to fit residues: 2492.9798 Evaluate side-chains 1079 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 959 time to evaluate : 8.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 122 THR Chi-restraints excluded: chain CA residue 241 THR Chi-restraints excluded: chain CB residue 74 ASP Chi-restraints excluded: chain CB residue 101 THR Chi-restraints excluded: chain CB residue 232 LEU Chi-restraints excluded: chain CC residue 204 LEU Chi-restraints excluded: chain CC residue 221 THR Chi-restraints excluded: chain CC residue 338 MET Chi-restraints excluded: chain CC residue 351 ASP Chi-restraints excluded: chain CE residue 188 VAL Chi-restraints excluded: chain CE residue 234 VAL Chi-restraints excluded: chain CE residue 366 SER Chi-restraints excluded: chain CF residue 9 VAL Chi-restraints excluded: chain CF residue 21 GLU Chi-restraints excluded: chain CF residue 72 LEU Chi-restraints excluded: chain CF residue 95 TYR Chi-restraints excluded: chain CF residue 137 VAL Chi-restraints excluded: chain CG residue 5 THR Chi-restraints excluded: chain CG residue 6 ASP Chi-restraints excluded: chain CH residue 235 GLU Chi-restraints excluded: chain CH residue 285 VAL Chi-restraints excluded: chain CH residue 403 LEU Chi-restraints excluded: chain CH residue 406 ASP Chi-restraints excluded: chain CH residue 469 GLU Chi-restraints excluded: chain CI residue 210 PHE Chi-restraints excluded: chain CJ residue 37 CYS Chi-restraints excluded: chain CK residue 121 ILE Chi-restraints excluded: chain CK residue 137 LYS Chi-restraints excluded: chain CK residue 234 SER Chi-restraints excluded: chain CK residue 239 TRP Chi-restraints excluded: chain CL residue 35 GLU Chi-restraints excluded: chain CN residue 39 GLU Chi-restraints excluded: chain CN residue 91 ASP Chi-restraints excluded: chain CN residue 114 THR Chi-restraints excluded: chain CN residue 148 VAL Chi-restraints excluded: chain CN residue 173 LEU Chi-restraints excluded: chain CN residue 206 THR Chi-restraints excluded: chain CN residue 209 ASP Chi-restraints excluded: chain CP residue 436 CYS Chi-restraints excluded: chain CP residue 466 CYS Chi-restraints excluded: chain CP residue 524 VAL Chi-restraints excluded: chain CP residue 552 MET Chi-restraints excluded: chain CP residue 571 TYR Chi-restraints excluded: chain CS residue 705 LYS Chi-restraints excluded: chain CS residue 718 ILE Chi-restraints excluded: chain CS residue 795 THR Chi-restraints excluded: chain CT residue 244 THR Chi-restraints excluded: chain CT residue 504 ASP Chi-restraints excluded: chain CU residue 220 VAL Chi-restraints excluded: chain CU residue 256 SER Chi-restraints excluded: chain CV residue 36 THR Chi-restraints excluded: chain CV residue 86 THR Chi-restraints excluded: chain CX residue 80 VAL Chi-restraints excluded: chain CX residue 82 VAL Chi-restraints excluded: chain CX residue 93 VAL Chi-restraints excluded: chain Cb residue 481 LEU Chi-restraints excluded: chain Cb residue 512 VAL Chi-restraints excluded: chain Cb residue 582 ASN Chi-restraints excluded: chain Cb residue 583 GLU Chi-restraints excluded: chain Cb residue 873 VAL Chi-restraints excluded: chain Cz residue 47 SER Chi-restraints excluded: chain LB residue 112 ASP Chi-restraints excluded: chain LB residue 157 THR Chi-restraints excluded: chain LB residue 158 VAL Chi-restraints excluded: chain LB residue 166 GLN Chi-restraints excluded: chain LB residue 167 ILE Chi-restraints excluded: chain LB residue 189 VAL Chi-restraints excluded: chain LB residue 320 ASN Chi-restraints excluded: chain LB residue 357 LEU Chi-restraints excluded: chain LB residue 359 TRP Chi-restraints excluded: chain LC residue 146 VAL Chi-restraints excluded: chain LC residue 158 VAL Chi-restraints excluded: chain LC residue 188 SER Chi-restraints excluded: chain LC residue 211 ILE Chi-restraints excluded: chain LC residue 223 VAL Chi-restraints excluded: chain LE residue 52 LEU Chi-restraints excluded: chain LE residue 71 VAL Chi-restraints excluded: chain LE residue 74 LYS Chi-restraints excluded: chain LE residue 156 SER Chi-restraints excluded: chain LE residue 157 THR Chi-restraints excluded: chain LE residue 166 ASP Chi-restraints excluded: chain LE residue 177 ASP Chi-restraints excluded: chain LF residue 13 LEU Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LF residue 94 ARG Chi-restraints excluded: chain LF residue 174 ILE Chi-restraints excluded: chain LG residue 70 MET Chi-restraints excluded: chain LG residue 101 ARG Chi-restraints excluded: chain LH residue 89 VAL Chi-restraints excluded: chain LH residue 185 LEU Chi-restraints excluded: chain LK residue 133 LEU Chi-restraints excluded: chain LL residue 46 LEU Chi-restraints excluded: chain LL residue 51 VAL Chi-restraints excluded: chain LL residue 76 THR Chi-restraints excluded: chain LL residue 92 THR Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LM residue 52 THR Chi-restraints excluded: chain LM residue 111 SER Chi-restraints excluded: chain LM residue 112 LEU Chi-restraints excluded: chain LN residue 10 LEU Chi-restraints excluded: chain LN residue 149 ASN Chi-restraints excluded: chain LO residue 8 VAL Chi-restraints excluded: chain LO residue 131 LEU Chi-restraints excluded: chain LO residue 181 SER Chi-restraints excluded: chain LP residue 14 SER Chi-restraints excluded: chain LQ residue 108 VAL Chi-restraints excluded: chain LQ residue 148 THR Chi-restraints excluded: chain LS residue 45 LEU Chi-restraints excluded: chain LT residue 156 TYR Chi-restraints excluded: chain LV residue 80 ILE Chi-restraints excluded: chain LY residue 6 THR Chi-restraints excluded: chain LY residue 46 SER Chi-restraints excluded: chain LY residue 64 ASP Chi-restraints excluded: chain LY residue 90 THR Chi-restraints excluded: chain LY residue 128 VAL Chi-restraints excluded: chain Lf residue 24 ASN Chi-restraints excluded: chain Lh residue 21 THR Chi-restraints excluded: chain Lh residue 84 ASP Chi-restraints excluded: chain Lq residue 206 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1291 random chunks: chunk 1160 optimal weight: 5.9990 chunk 883 optimal weight: 8.9990 chunk 609 optimal weight: 7.9990 chunk 130 optimal weight: 40.0000 chunk 560 optimal weight: 40.0000 chunk 788 optimal weight: 3.9990 chunk 1178 optimal weight: 8.9990 chunk 1247 optimal weight: 8.9990 chunk 615 optimal weight: 7.9990 chunk 1117 optimal weight: 5.9990 chunk 336 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 148 GLN CB 73 HIS ** CB 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CE 299 GLN CF 58 HIS CG 106 GLN CH 14 GLN ** CH 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CH 226 HIS ** CH 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CH 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CI 277 ASN CJ 27 GLN CJ 153 ASN CJ 459 GLN CK 244 GLN CM 119 ASN CO 15 GLN CQ 24 ASN CR 21 ASN ** CT 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CU 232 GLN ** CV 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CV 37 ASN ** CY 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CY 474 HIS ** CY 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LB 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LB 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 346 HIS LC 264 GLN ** LE 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 10 ASN LK 97 ASN LL 19 GLN LP 118 GLN LP 170 HIS LS 13 HIS ** LV 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 64 ASN Li 47 GLN ** Lq 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.158 144476 Z= 0.509 Angle : 0.789 14.821 206691 Z= 0.399 Chirality : 0.048 0.350 25010 Planarity : 0.007 0.113 17391 Dihedral : 21.902 179.258 49529 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.82 % Favored : 95.02 % Rotamer: Outliers : 3.03 % Allowed : 13.94 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.01 % Twisted Proline : 0.37 % Twisted General : 0.00 % 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: -0.10 (0.08), residues: 10568 helix: 0.94 (0.07), residues: 4906 sheet: -0.48 (0.14), residues: 1271 loop : -1.05 (0.09), residues: 4391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRPCb 816 HIS 0.011 0.002 HISLf 7 PHE 0.033 0.002 PHECB 281 TYR 0.037 0.003 TYRCC 149 ARG 0.011 0.001 ARGLP 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21136 Ramachandran restraints generated. 10568 Oldfield, 0 Emsley, 10568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21136 Ramachandran restraints generated. 10568 Oldfield, 0 Emsley, 10568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1265 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 995 time to evaluate : 8.747 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: CC 233 ARG cc_start: 0.6665 (tpp-160) cc_final: 0.6157 (tpm170) REVERT: CC 324 TYR cc_start: 0.6019 (p90) cc_final: 0.5692 (p90) REVERT: CC 373 MET cc_start: -0.0669 (ptt) cc_final: -0.1591 (ptt) REVERT: CF 95 TYR cc_start: 0.8077 (OUTLIER) cc_final: 0.6757 (t80) REVERT: CF 211 LEU cc_start: 0.8736 (mm) cc_final: 0.8512 (mm) REVERT: CH 236 MET cc_start: 0.7550 (tpp) cc_final: 0.7290 (tpp) REVERT: CH 508 MET cc_start: 0.3772 (tpt) cc_final: 0.3258 (tpt) REVERT: CI 210 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.8439 (t80) REVERT: CI 213 ILE cc_start: 0.8597 (mp) cc_final: 0.8388 (mt) REVERT: CI 261 LYS cc_start: 0.8651 (mtmm) cc_final: 0.8276 (mttm) REVERT: CJ 227 MET cc_start: 0.8130 (pmm) cc_final: 0.7780 (pmm) REVERT: CK 137 LYS cc_start: 0.6452 (OUTLIER) cc_final: 0.5399 (tttp) REVERT: CM 209 TRP cc_start: 0.7945 (t-100) cc_final: 0.7730 (t60) REVERT: CN 140 GLN cc_start: 0.7327 (tm-30) cc_final: 0.6965 (tm-30) REVERT: CN 173 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8451 (tt) REVERT: CO 29 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7615 (ptp-110) REVERT: CQ 42 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7413 (mtp) REVERT: CQ 104 GLU cc_start: 0.8841 (tp30) cc_final: 0.8540 (tp30) REVERT: CQ 112 MET cc_start: 0.5703 (mmt) cc_final: 0.5478 (mmm) REVERT: CT 137 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7945 (mp10) REVERT: CU 217 HIS cc_start: 0.7998 (p90) cc_final: 0.7527 (p90) REVERT: CY 378 MET cc_start: 0.7946 (mpp) cc_final: 0.7744 (mpp) REVERT: Cb 305 LEU cc_start: 0.6457 (tt) cc_final: 0.6182 (tp) REVERT: Cb 522 ASN cc_start: 0.7582 (m-40) cc_final: 0.7101 (m-40) REVERT: LB 137 TYR cc_start: 0.7079 (t80) cc_final: 0.6640 (t80) REVERT: LB 166 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.6957 (mp10) REVERT: LB 283 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8290 (mt) REVERT: LE 25 GLN cc_start: 0.7096 (mt0) cc_final: 0.6845 (mt0) REVERT: LE 127 TYR cc_start: 0.8341 (t80) cc_final: 0.8116 (t80) REVERT: LG 101 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8339 (ttm170) REVERT: LG 246 GLN cc_start: 0.8021 (tp40) cc_final: 0.7798 (tp-100) REVERT: LL 20 ARG cc_start: 0.7360 (ptp-170) cc_final: 0.6990 (ptm160) REVERT: LM 61 ARG cc_start: 0.7605 (ttm-80) cc_final: 0.7196 (mpt180) REVERT: LN 41 ARG cc_start: 0.8523 (ptp-110) cc_final: 0.8141 (ptp-110) REVERT: LN 67 ARG cc_start: 0.7779 (mtt-85) cc_final: 0.7486 (mmm160) REVERT: LO 1 MET cc_start: 0.5147 (pmm) cc_final: 0.4850 (mtt) REVERT: LO 182 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6718 (mt-10) REVERT: LS 45 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8446 (mp) REVERT: LS 117 ARG cc_start: 0.8020 (mtt180) cc_final: 0.7398 (mtm180) REVERT: LT 104 ASP cc_start: 0.8193 (t70) cc_final: 0.7943 (t0) REVERT: LV 59 MET cc_start: 0.8283 (ttm) cc_final: 0.7932 (ttp) REVERT: LY 4 ARG cc_start: 0.7661 (mtm180) cc_final: 0.7014 (mmt180) REVERT: Le 30 ASP cc_start: 0.6473 (OUTLIER) cc_final: 0.5992 (t70) REVERT: Lf 58 GLN cc_start: 0.7264 (mm110) cc_final: 0.7043 (mm-40) REVERT: Lh 49 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8227 (pt) REVERT: Li 38 ARG cc_start: 0.6474 (mmm-85) cc_final: 0.6227 (tpt170) REVERT: Lj 25 ARG cc_start: 0.7801 (mtp-110) cc_final: 0.7542 (mtp85) REVERT: Lj 64 MET cc_start: 0.7730 (mmm) cc_final: 0.7366 (mmm) REVERT: Lj 84 LYS cc_start: 0.8353 (mtpp) cc_final: 0.8147 (mtpt) REVERT: Lq 63 MET cc_start: 0.6321 (mmm) cc_final: 0.5985 (mmm) REVERT: Lq 103 LEU cc_start: 0.8708 (tp) cc_final: 0.8225 (pp) outliers start: 270 outliers final: 171 residues processed: 1180 average time/residue: 1.2292 time to fit residues: 2524.0321 Evaluate side-chains 1119 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 935 time to evaluate : 8.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 122 THR Chi-restraints excluded: chain CA residue 241 THR Chi-restraints excluded: chain CB residue 74 ASP Chi-restraints excluded: chain CB residue 101 THR Chi-restraints excluded: chain CB residue 174 THR Chi-restraints excluded: chain CC residue 147 ILE Chi-restraints excluded: chain CC residue 204 LEU Chi-restraints excluded: chain CC residue 218 THR Chi-restraints excluded: chain CC residue 221 THR Chi-restraints excluded: chain CC residue 238 LEU Chi-restraints excluded: chain CC residue 338 MET Chi-restraints excluded: chain CC residue 351 ASP Chi-restraints excluded: chain CE residue 188 VAL Chi-restraints excluded: chain CE residue 234 VAL Chi-restraints excluded: chain CE residue 284 ILE Chi-restraints excluded: chain CE residue 366 SER Chi-restraints excluded: chain CE residue 367 CYS Chi-restraints excluded: chain CE residue 478 VAL Chi-restraints excluded: chain CE residue 490 ILE Chi-restraints excluded: chain CF residue 9 VAL Chi-restraints excluded: chain CF residue 95 TYR Chi-restraints excluded: chain CF residue 141 ILE Chi-restraints excluded: chain CG residue 5 THR Chi-restraints excluded: chain CG residue 6 ASP Chi-restraints excluded: chain CG residue 93 ASN Chi-restraints excluded: chain CH residue 54 GLU Chi-restraints excluded: chain CH residue 121 LEU Chi-restraints excluded: chain CH residue 235 GLU Chi-restraints excluded: chain CH residue 285 VAL Chi-restraints excluded: chain CH residue 403 LEU Chi-restraints excluded: chain CH residue 406 ASP Chi-restraints excluded: chain CI residue 191 ILE Chi-restraints excluded: chain CI residue 210 PHE Chi-restraints excluded: chain CJ residue 37 CYS Chi-restraints excluded: chain CJ residue 100 VAL Chi-restraints excluded: chain CK residue 60 GLN Chi-restraints excluded: chain CK residue 121 ILE Chi-restraints excluded: chain CK residue 137 LYS Chi-restraints excluded: chain CK residue 234 SER Chi-restraints excluded: chain CK residue 252 ASP Chi-restraints excluded: chain CL residue 35 GLU Chi-restraints excluded: chain CN residue 39 GLU Chi-restraints excluded: chain CN residue 91 ASP Chi-restraints excluded: chain CN residue 114 THR Chi-restraints excluded: chain CN residue 148 VAL Chi-restraints excluded: chain CN residue 173 LEU Chi-restraints excluded: chain CN residue 206 THR Chi-restraints excluded: chain CN residue 209 ASP Chi-restraints excluded: chain CO residue 29 ARG Chi-restraints excluded: chain CO residue 105 SER Chi-restraints excluded: chain CP residue 436 CYS Chi-restraints excluded: chain CP residue 466 CYS Chi-restraints excluded: chain CP residue 516 CYS Chi-restraints excluded: chain CP residue 524 VAL Chi-restraints excluded: chain CP residue 552 MET Chi-restraints excluded: chain CP residue 571 TYR Chi-restraints excluded: chain CP residue 576 PHE Chi-restraints excluded: chain CQ residue 42 MET Chi-restraints excluded: chain CQ residue 79 VAL Chi-restraints excluded: chain CR residue 131 VAL Chi-restraints excluded: chain CR residue 167 GLU Chi-restraints excluded: chain CS residue 656 THR Chi-restraints excluded: chain CS residue 672 THR Chi-restraints excluded: chain CS residue 705 LYS Chi-restraints excluded: chain CS residue 718 ILE Chi-restraints excluded: chain CS residue 795 THR Chi-restraints excluded: chain CS residue 819 MET Chi-restraints excluded: chain CT residue 137 GLN Chi-restraints excluded: chain CT residue 244 THR Chi-restraints excluded: chain CT residue 411 ILE Chi-restraints excluded: chain CT residue 504 ASP Chi-restraints excluded: chain CT residue 603 VAL Chi-restraints excluded: chain CT residue 626 VAL Chi-restraints excluded: chain CU residue 248 LEU Chi-restraints excluded: chain CU residue 256 SER Chi-restraints excluded: chain CU residue 266 THR Chi-restraints excluded: chain CV residue 20 LEU Chi-restraints excluded: chain CV residue 36 THR Chi-restraints excluded: chain CV residue 80 THR Chi-restraints excluded: chain CV residue 86 THR Chi-restraints excluded: chain CV residue 96 SER Chi-restraints excluded: chain CX residue 80 VAL Chi-restraints excluded: chain CX residue 82 VAL Chi-restraints excluded: chain CX residue 93 VAL Chi-restraints excluded: chain CY residue 474 HIS Chi-restraints excluded: chain CY residue 495 TYR Chi-restraints excluded: chain CY residue 742 GLU Chi-restraints excluded: chain Cb residue 473 SER Chi-restraints excluded: chain Cb residue 481 LEU Chi-restraints excluded: chain Cb residue 503 ASP Chi-restraints excluded: chain Cb residue 512 VAL Chi-restraints excluded: chain Cb residue 582 ASN Chi-restraints excluded: chain Cb residue 583 GLU Chi-restraints excluded: chain Cb residue 873 VAL Chi-restraints excluded: chain Cz residue 28 ASN Chi-restraints excluded: chain Cz residue 47 SER Chi-restraints excluded: chain LB residue 103 THR Chi-restraints excluded: chain LB residue 112 ASP Chi-restraints excluded: chain LB residue 157 THR Chi-restraints excluded: chain LB residue 158 VAL Chi-restraints excluded: chain LB residue 166 GLN Chi-restraints excluded: chain LB residue 189 VAL Chi-restraints excluded: chain LB residue 205 THR Chi-restraints excluded: chain LB residue 211 GLU Chi-restraints excluded: chain LB residue 283 ILE Chi-restraints excluded: chain LB residue 320 ASN Chi-restraints excluded: chain LB residue 329 VAL Chi-restraints excluded: chain LB residue 357 LEU Chi-restraints excluded: chain LB residue 359 TRP Chi-restraints excluded: chain LC residue 6 THR Chi-restraints excluded: chain LC residue 20 THR Chi-restraints excluded: chain LC residue 146 VAL Chi-restraints excluded: chain LC residue 158 VAL Chi-restraints excluded: chain LC residue 188 SER Chi-restraints excluded: chain LC residue 211 ILE Chi-restraints excluded: chain LC residue 222 LEU Chi-restraints excluded: chain LC residue 223 VAL Chi-restraints excluded: chain LC residue 256 VAL Chi-restraints excluded: chain LC residue 268 VAL Chi-restraints excluded: chain LE residue 32 ASP Chi-restraints excluded: chain LE residue 71 VAL Chi-restraints excluded: chain LE residue 112 THR Chi-restraints excluded: chain LE residue 156 SER Chi-restraints excluded: chain LE residue 166 ASP Chi-restraints excluded: chain LE residue 177 ASP Chi-restraints excluded: chain LF residue 13 LEU Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LF residue 92 VAL Chi-restraints excluded: chain LF residue 94 ARG Chi-restraints excluded: chain LF residue 98 ILE Chi-restraints excluded: chain LF residue 174 ILE Chi-restraints excluded: chain LF residue 196 THR Chi-restraints excluded: chain LG residue 101 ARG Chi-restraints excluded: chain LG residue 167 VAL Chi-restraints excluded: chain LG residue 203 ILE Chi-restraints excluded: chain LH residue 55 VAL Chi-restraints excluded: chain LH residue 89 VAL Chi-restraints excluded: chain LH residue 175 ILE Chi-restraints excluded: chain LH residue 185 LEU Chi-restraints excluded: chain LH residue 216 ASP Chi-restraints excluded: chain LL residue 51 VAL Chi-restraints excluded: chain LL residue 76 THR Chi-restraints excluded: chain LL residue 92 THR Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LM residue 24 ASN Chi-restraints excluded: chain LM residue 52 THR Chi-restraints excluded: chain LM residue 111 SER Chi-restraints excluded: chain LM residue 138 ILE Chi-restraints excluded: chain LN residue 10 LEU Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LN residue 149 ASN Chi-restraints excluded: chain LO residue 8 VAL Chi-restraints excluded: chain LO residue 121 VAL Chi-restraints excluded: chain LO residue 131 LEU Chi-restraints excluded: chain LO residue 160 GLU Chi-restraints excluded: chain LP residue 14 SER Chi-restraints excluded: chain LP residue 118 GLN Chi-restraints excluded: chain LQ residue 108 VAL Chi-restraints excluded: chain LS residue 8 GLN Chi-restraints excluded: chain LS residue 45 LEU Chi-restraints excluded: chain LS residue 57 GLU Chi-restraints excluded: chain LS residue 79 LEU Chi-restraints excluded: chain LT residue 83 ARG Chi-restraints excluded: chain LT residue 156 TYR Chi-restraints excluded: chain LV residue 21 VAL Chi-restraints excluded: chain LV residue 79 VAL Chi-restraints excluded: chain LV residue 80 ILE Chi-restraints excluded: chain LY residue 6 THR Chi-restraints excluded: chain LY residue 25 VAL Chi-restraints excluded: chain LY residue 46 SER Chi-restraints excluded: chain LY residue 64 ASP Chi-restraints excluded: chain LY residue 90 THR Chi-restraints excluded: chain LY residue 128 VAL Chi-restraints excluded: chain Ld residue 116 VAL Chi-restraints excluded: chain Le residue 30 ASP Chi-restraints excluded: chain Le residue 68 MET Chi-restraints excluded: chain Lf residue 60 GLU Chi-restraints excluded: chain Lh residue 7 VAL Chi-restraints excluded: chain Lh residue 49 ILE Chi-restraints excluded: chain Lh residue 84 ASP Chi-restraints excluded: chain Lh residue 105 VAL Chi-restraints excluded: chain Li residue 30 VAL Chi-restraints excluded: chain Lq residue 206 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1291 random chunks: chunk 1039 optimal weight: 0.9980 chunk 708 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 929 optimal weight: 0.7980 chunk 514 optimal weight: 5.9990 chunk 1064 optimal weight: 0.5980 chunk 862 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 637 optimal weight: 5.9990 chunk 1120 optimal weight: 0.9990 chunk 314 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CB 33 HIS ** CB 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CF 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CG 18 ASN CG 106 GLN CH 226 HIS ** CH 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CH 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CI 286 ASN CJ 153 ASN CK 203 ASN CN 82 GLN ** CN 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CP 474 ASN CQ 24 ASN CS 665 GLN CT 506 HIS ** CV 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CX 113 GLN ** CY 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CY 474 HIS CY 481 ASN ** Cb 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 38 HIS LC 264 GLN LC 297 GLN LF 178 ASN LH 202 GLN LL 114 GLN LM 106 GLN LN 156 HIS LS 13 HIS LT 146 ASN ** LV 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LV 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LY 56 GLN LY 62 HIS ** Ld 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 67 GLN ** Lj 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lq 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.094 144476 Z= 0.153 Angle : 0.566 14.280 206691 Z= 0.290 Chirality : 0.036 0.288 25010 Planarity : 0.005 0.085 17391 Dihedral : 21.777 178.499 49529 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.13 % Favored : 95.74 % Rotamer: Outliers : 1.99 % Allowed : 15.78 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.01 % Twisted Proline : 0.37 % Twisted General : 0.00 % 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: 0.36 (0.08), residues: 10568 helix: 1.39 (0.07), residues: 4931 sheet: -0.33 (0.14), residues: 1245 loop : -0.89 (0.09), residues: 4392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRPCb 816 HIS 0.018 0.001 HISCY 474 PHE 0.025 0.001 PHECE 165 TYR 0.025 0.001 TYRLV 37 ARG 0.010 0.000 ARGCC 312 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21136 Ramachandran restraints generated. 10568 Oldfield, 0 Emsley, 10568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21136 Ramachandran restraints generated. 10568 Oldfield, 0 Emsley, 10568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1192 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 1015 time to evaluate : 8.719 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: CC 205 GLN cc_start: 0.8344 (tp-100) cc_final: 0.8126 (tp40) REVERT: CC 233 ARG cc_start: 0.6534 (tpp-160) cc_final: 0.6050 (tpm170) REVERT: CC 324 TYR cc_start: 0.5959 (p90) cc_final: 0.5656 (p90) REVERT: CC 373 MET cc_start: -0.0625 (ptt) cc_final: -0.1186 (ptt) REVERT: CF 95 TYR cc_start: 0.8020 (OUTLIER) cc_final: 0.7031 (t80) REVERT: CF 211 LEU cc_start: 0.8586 (mm) cc_final: 0.8233 (mm) REVERT: CG 106 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7802 (mm-40) REVERT: CH 236 MET cc_start: 0.7301 (tpp) cc_final: 0.7076 (tpp) REVERT: CH 246 ARG cc_start: 0.7135 (mtp85) cc_final: 0.6459 (mtt90) REVERT: CH 508 MET cc_start: 0.4269 (tpt) cc_final: 0.3643 (tpt) REVERT: CI 213 ILE cc_start: 0.8553 (mp) cc_final: 0.8346 (mt) REVERT: CI 261 LYS cc_start: 0.8580 (mtmm) cc_final: 0.8247 (mttm) REVERT: CJ 227 MET cc_start: 0.8007 (pmm) cc_final: 0.7272 (ptp) REVERT: CK 42 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8364 (pp) REVERT: CK 117 PHE cc_start: 0.8065 (m-10) cc_final: 0.7803 (m-10) REVERT: CK 137 LYS cc_start: 0.6556 (OUTLIER) cc_final: 0.5396 (tttp) REVERT: CL 45 TRP cc_start: 0.6795 (m-10) cc_final: 0.6548 (m-10) REVERT: CN 1 MET cc_start: 0.5659 (ptp) cc_final: 0.5245 (mtt) REVERT: CN 140 GLN cc_start: 0.7221 (tm-30) cc_final: 0.6929 (tm-30) REVERT: CP 521 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7021 (mp0) REVERT: CQ 93 MET cc_start: 0.7957 (mtp) cc_final: 0.7696 (mtp) REVERT: CR 70 LYS cc_start: 0.7168 (mtpp) cc_final: 0.6808 (mmtm) REVERT: CU 336 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7679 (mp10) REVERT: CV 106 ASP cc_start: 0.7025 (p0) cc_final: 0.6721 (p0) REVERT: CV 120 ARG cc_start: 0.7918 (tpp80) cc_final: 0.7614 (tpt-90) REVERT: CY 539 MET cc_start: 0.5972 (mmm) cc_final: 0.5720 (mmm) REVERT: Cb 305 LEU cc_start: 0.6376 (tt) cc_final: 0.6157 (tp) REVERT: Cb 395 TYR cc_start: 0.8094 (p90) cc_final: 0.7638 (p90) REVERT: Cb 522 ASN cc_start: 0.7687 (m-40) cc_final: 0.7192 (m-40) REVERT: Cb 531 ILE cc_start: 0.6944 (mm) cc_final: 0.6603 (mm) REVERT: Cb 588 ASP cc_start: 0.6635 (m-30) cc_final: 0.6106 (m-30) REVERT: LB 84 MET cc_start: 0.8782 (mtm) cc_final: 0.8567 (mtp) REVERT: LB 137 TYR cc_start: 0.7063 (t80) cc_final: 0.6453 (t80) REVERT: LB 166 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7302 (mp10) REVERT: LC 43 MET cc_start: 0.9052 (ttm) cc_final: 0.8663 (mtt) REVERT: LC 301 ARG cc_start: 0.7493 (ttm170) cc_final: 0.7275 (ttm110) REVERT: LC 321 ARG cc_start: 0.8289 (mtp85) cc_final: 0.7569 (mtm180) REVERT: LE 25 GLN cc_start: 0.6952 (mt0) cc_final: 0.6723 (mt0) REVERT: LE 127 TYR cc_start: 0.8372 (t80) cc_final: 0.8160 (t80) REVERT: LG 54 LYS cc_start: 0.6853 (ttmt) cc_final: 0.5618 (ptpp) REVERT: LG 246 GLN cc_start: 0.7999 (tp40) cc_final: 0.7537 (mm-40) REVERT: LM 61 ARG cc_start: 0.7565 (ttm-80) cc_final: 0.7250 (mpt180) REVERT: LN 67 ARG cc_start: 0.7754 (mtt-85) cc_final: 0.7402 (mmm160) REVERT: LO 1 MET cc_start: 0.4739 (pmm) cc_final: 0.4469 (mtt) REVERT: LO 147 VAL cc_start: 0.8765 (p) cc_final: 0.8449 (m) REVERT: LS 117 ARG cc_start: 0.7914 (mtt180) cc_final: 0.7253 (mtm180) REVERT: LT 134 MET cc_start: 0.8521 (mmp) cc_final: 0.8060 (mmt) REVERT: LT 136 ARG cc_start: 0.7162 (mtt180) cc_final: 0.6962 (mtm-85) REVERT: LV 59 MET cc_start: 0.8191 (ttm) cc_final: 0.7872 (ttp) REVERT: LY 4 ARG cc_start: 0.7545 (mtm180) cc_final: 0.6951 (mmt180) REVERT: Ld 79 ILE cc_start: 0.7540 (mt) cc_final: 0.7050 (pt) REVERT: Lh 49 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8163 (pt) REVERT: Lj 25 ARG cc_start: 0.7566 (mtp-110) cc_final: 0.7336 (mtp85) REVERT: Lq 63 MET cc_start: 0.5915 (mmm) cc_final: 0.5617 (mmm) REVERT: Lq 103 LEU cc_start: 0.8706 (tp) cc_final: 0.8137 (pp) REVERT: Lq 184 MET cc_start: 0.8331 (mmm) cc_final: 0.7901 (mmp) outliers start: 177 outliers final: 105 residues processed: 1134 average time/residue: 1.2264 time to fit residues: 2416.6793 Evaluate side-chains 1055 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 942 time to evaluate : 8.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 122 THR Chi-restraints excluded: chain CB residue 74 ASP Chi-restraints excluded: chain CB residue 101 THR Chi-restraints excluded: chain CB residue 254 LYS Chi-restraints excluded: chain CC residue 204 LEU Chi-restraints excluded: chain CC residue 338 MET Chi-restraints excluded: chain CC residue 351 ASP Chi-restraints excluded: chain CE residue 188 VAL Chi-restraints excluded: chain CE residue 366 SER Chi-restraints excluded: chain CE residue 367 CYS Chi-restraints excluded: chain CE residue 478 VAL Chi-restraints excluded: chain CE residue 490 ILE Chi-restraints excluded: chain CF residue 9 VAL Chi-restraints excluded: chain CF residue 16 ASN Chi-restraints excluded: chain CF residue 72 LEU Chi-restraints excluded: chain CF residue 95 TYR Chi-restraints excluded: chain CG residue 5 THR Chi-restraints excluded: chain CG residue 6 ASP Chi-restraints excluded: chain CG residue 93 ASN Chi-restraints excluded: chain CG residue 106 GLN Chi-restraints excluded: chain CH residue 54 GLU Chi-restraints excluded: chain CH residue 285 VAL Chi-restraints excluded: chain CI residue 320 LEU Chi-restraints excluded: chain CJ residue 37 CYS Chi-restraints excluded: chain CK residue 42 LEU Chi-restraints excluded: chain CK residue 121 ILE Chi-restraints excluded: chain CK residue 135 VAL Chi-restraints excluded: chain CK residue 137 LYS Chi-restraints excluded: chain CK residue 150 ILE Chi-restraints excluded: chain CK residue 252 ASP Chi-restraints excluded: chain CL residue 19 ARG Chi-restraints excluded: chain CL residue 35 GLU Chi-restraints excluded: chain CN residue 39 GLU Chi-restraints excluded: chain CN residue 91 ASP Chi-restraints excluded: chain CN residue 114 THR Chi-restraints excluded: chain CN residue 206 THR Chi-restraints excluded: chain CP residue 516 CYS Chi-restraints excluded: chain CP residue 521 GLU Chi-restraints excluded: chain CP residue 524 VAL Chi-restraints excluded: chain CP residue 552 MET Chi-restraints excluded: chain CP residue 571 TYR Chi-restraints excluded: chain CP residue 576 PHE Chi-restraints excluded: chain CQ residue 68 THR Chi-restraints excluded: chain CS residue 718 ILE Chi-restraints excluded: chain CS residue 795 THR Chi-restraints excluded: chain CT residue 244 THR Chi-restraints excluded: chain CT residue 504 ASP Chi-restraints excluded: chain CT residue 603 VAL Chi-restraints excluded: chain CU residue 336 GLN Chi-restraints excluded: chain CV residue 36 THR Chi-restraints excluded: chain CV residue 86 THR Chi-restraints excluded: chain CV residue 96 SER Chi-restraints excluded: chain CX residue 80 VAL Chi-restraints excluded: chain CX residue 93 VAL Chi-restraints excluded: chain CY residue 474 HIS Chi-restraints excluded: chain CY residue 742 GLU Chi-restraints excluded: chain Cb residue 481 LEU Chi-restraints excluded: chain Cb residue 512 VAL Chi-restraints excluded: chain Cb residue 582 ASN Chi-restraints excluded: chain Cb residue 583 GLU Chi-restraints excluded: chain Cb residue 603 ILE Chi-restraints excluded: chain LB residue 112 ASP Chi-restraints excluded: chain LB residue 158 VAL Chi-restraints excluded: chain LB residue 166 GLN Chi-restraints excluded: chain LB residue 189 VAL Chi-restraints excluded: chain LB residue 205 THR Chi-restraints excluded: chain LB residue 211 GLU Chi-restraints excluded: chain LB residue 359 TRP Chi-restraints excluded: chain LC residue 6 THR Chi-restraints excluded: chain LC residue 20 THR Chi-restraints excluded: chain LC residue 146 VAL Chi-restraints excluded: chain LC residue 158 VAL Chi-restraints excluded: chain LC residue 181 ASP Chi-restraints excluded: chain LC residue 211 ILE Chi-restraints excluded: chain LC residue 223 VAL Chi-restraints excluded: chain LE residue 52 LEU Chi-restraints excluded: chain LE residue 74 LYS Chi-restraints excluded: chain LE residue 156 SER Chi-restraints excluded: chain LE residue 177 ASP Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 94 ARG Chi-restraints excluded: chain LF residue 174 ILE Chi-restraints excluded: chain LG residue 70 MET Chi-restraints excluded: chain LH residue 105 LEU Chi-restraints excluded: chain LH residue 127 MET Chi-restraints excluded: chain LH residue 185 LEU Chi-restraints excluded: chain LK residue 121 PHE Chi-restraints excluded: chain LL residue 76 THR Chi-restraints excluded: chain LL residue 92 THR Chi-restraints excluded: chain LM residue 24 ASN Chi-restraints excluded: chain LN residue 149 ASN Chi-restraints excluded: chain LO residue 8 VAL Chi-restraints excluded: chain LO residue 131 LEU Chi-restraints excluded: chain LO residue 181 SER Chi-restraints excluded: chain LQ residue 108 VAL Chi-restraints excluded: chain LS residue 8 GLN Chi-restraints excluded: chain LS residue 24 LEU Chi-restraints excluded: chain LS residue 88 HIS Chi-restraints excluded: chain LT residue 74 VAL Chi-restraints excluded: chain LT residue 156 TYR Chi-restraints excluded: chain LV residue 79 VAL Chi-restraints excluded: chain LV residue 80 ILE Chi-restraints excluded: chain LY residue 46 SER Chi-restraints excluded: chain LY residue 64 ASP Chi-restraints excluded: chain LY residue 90 THR Chi-restraints excluded: chain LY residue 128 VAL Chi-restraints excluded: chain Ld residue 44 ILE Chi-restraints excluded: chain Ld residue 116 VAL Chi-restraints excluded: chain Lh residue 49 ILE Chi-restraints excluded: chain Lh residue 67 GLN Chi-restraints excluded: chain Lh residue 84 ASP Chi-restraints excluded: chain Lh residue 105 VAL Chi-restraints excluded: chain Lq residue 206 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1291 random chunks: chunk 419 optimal weight: 1.9990 chunk 1123 optimal weight: 7.9990 chunk 246 optimal weight: 0.5980 chunk 732 optimal weight: 50.0000 chunk 308 optimal weight: 2.9990 chunk 1249 optimal weight: 10.0000 chunk 1036 optimal weight: 8.9990 chunk 578 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 413 optimal weight: 5.9990 chunk 655 optimal weight: 10.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 148 GLN CB 33 HIS ** CB 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CG 18 ASN CG 106 GLN ** CH 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CH 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CH 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CI 286 ASN CJ 153 ASN CK 72 ASN CK 203 ASN CM 206 ASN CN 82 GLN CP 316 HIS CP 474 ASN CQ 24 ASN CR 137 GLN CS 665 GLN CT 171 GLN ** CV 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CY 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CY 474 HIS ** Cb 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 294 ASN LB 320 ASN LS 13 HIS LS 21 ASN ** LV 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LV 100 ASN ** LV 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Le 90 ASN Li 47 GLN ** Lq 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 144476 Z= 0.242 Angle : 0.592 12.567 206691 Z= 0.304 Chirality : 0.038 0.291 25010 Planarity : 0.005 0.083 17391 Dihedral : 21.690 178.844 49529 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.67 % Favored : 95.19 % Rotamer: Outliers : 2.36 % Allowed : 16.03 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.01 % Twisted Proline : 0.37 % Twisted General : 0.00 % 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: 0.41 (0.08), residues: 10568 helix: 1.43 (0.07), residues: 4931 sheet: -0.30 (0.14), residues: 1224 loop : -0.86 (0.09), residues: 4413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRPCb 816 HIS 0.010 0.001 HISCY 474 PHE 0.025 0.001 PHECQ 107 TYR 0.018 0.002 TYRLC 269 ARG 0.011 0.000 ARGCY 405 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21136 Ramachandran restraints generated. 10568 Oldfield, 0 Emsley, 10568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21136 Ramachandran restraints generated. 10568 Oldfield, 0 Emsley, 10568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1176 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 966 time to evaluate : 8.788 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: CA 202 VAL cc_start: 0.9146 (OUTLIER) cc_final: 0.8939 (m) REVERT: CC 205 GLN cc_start: 0.8407 (tp-100) cc_final: 0.8155 (tp40) REVERT: CC 233 ARG cc_start: 0.6591 (tpp-160) cc_final: 0.6066 (tpm170) REVERT: CC 324 TYR cc_start: 0.5997 (p90) cc_final: 0.5681 (p90) REVERT: CC 373 MET cc_start: -0.0622 (ptt) cc_final: -0.0986 (ptt) REVERT: CF 95 TYR cc_start: 0.7939 (OUTLIER) cc_final: 0.7135 (t80) REVERT: CF 211 LEU cc_start: 0.8605 (mm) cc_final: 0.8205 (mm) REVERT: CH 246 ARG cc_start: 0.7145 (OUTLIER) cc_final: 0.6513 (mtt90) REVERT: CH 508 MET cc_start: 0.4352 (tpt) cc_final: 0.3784 (tpt) REVERT: CI 213 ILE cc_start: 0.8582 (mp) cc_final: 0.8376 (mt) REVERT: CI 261 LYS cc_start: 0.8610 (mtmm) cc_final: 0.8281 (mttm) REVERT: CK 42 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8456 (pp) REVERT: CK 137 LYS cc_start: 0.6683 (OUTLIER) cc_final: 0.5435 (tttp) REVERT: CK 164 ARG cc_start: 0.7179 (OUTLIER) cc_final: 0.6769 (mtm180) REVERT: CL 45 TRP cc_start: 0.6885 (m-10) cc_final: 0.6635 (m-10) REVERT: CN 1 MET cc_start: 0.5678 (ptp) cc_final: 0.5269 (mtt) REVERT: CO 29 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7449 (ptp-110) REVERT: CP 521 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: CQ 93 MET cc_start: 0.8001 (mtp) cc_final: 0.7714 (mtp) REVERT: CR 70 LYS cc_start: 0.7192 (mtpp) cc_final: 0.6817 (mmtm) REVERT: CU 336 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7658 (mp10) REVERT: CV 106 ASP cc_start: 0.7099 (p0) cc_final: 0.6767 (p0) REVERT: CY 539 MET cc_start: 0.6226 (mmm) cc_final: 0.6001 (mmm) REVERT: Cb 530 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7641 (t0) REVERT: Cb 584 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7656 (tt0) REVERT: LB 84 MET cc_start: 0.8790 (mtm) cc_final: 0.8369 (mtm) REVERT: LB 137 TYR cc_start: 0.7196 (t80) cc_final: 0.6517 (t80) REVERT: LB 166 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7318 (mp10) REVERT: LC 43 MET cc_start: 0.9142 (ttm) cc_final: 0.8850 (mtt) REVERT: LC 221 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6375 (pm20) REVERT: LC 321 ARG cc_start: 0.8271 (mtp85) cc_final: 0.7549 (mtm180) REVERT: LE 25 GLN cc_start: 0.7011 (mt0) cc_final: 0.6782 (mt0) REVERT: LF 239 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7586 (mm-30) REVERT: LG 101 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8080 (ttm170) REVERT: LG 246 GLN cc_start: 0.8015 (tp40) cc_final: 0.7549 (mm-40) REVERT: LH 57 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.7992 (mt) REVERT: LM 61 ARG cc_start: 0.7582 (ttm-80) cc_final: 0.7190 (mpt180) REVERT: LM 112 LEU cc_start: 0.8934 (tt) cc_final: 0.8637 (tt) REVERT: LN 67 ARG cc_start: 0.7756 (mtt-85) cc_final: 0.7364 (mmm160) REVERT: LO 1 MET cc_start: 0.4912 (pmm) cc_final: 0.4659 (mtt) REVERT: LS 45 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8333 (mp) REVERT: LS 117 ARG cc_start: 0.7943 (mtt180) cc_final: 0.7275 (mtm180) REVERT: LT 134 MET cc_start: 0.8481 (mmp) cc_final: 0.8024 (mmt) REVERT: LT 136 ARG cc_start: 0.7261 (mtt180) cc_final: 0.7017 (mtm-85) REVERT: LV 59 MET cc_start: 0.8203 (ttm) cc_final: 0.7952 (ttp) REVERT: LY 4 ARG cc_start: 0.7613 (mtm180) cc_final: 0.6973 (mmt90) REVERT: Ld 79 ILE cc_start: 0.7558 (mt) cc_final: 0.7008 (pt) REVERT: Le 90 ASN cc_start: 0.8322 (m-40) cc_final: 0.8092 (m110) REVERT: Lf 4 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7503 (mt-10) REVERT: Lf 58 GLN cc_start: 0.7173 (mm-40) cc_final: 0.6946 (tm-30) REVERT: Lh 49 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8138 (pt) REVERT: Lj 25 ARG cc_start: 0.7665 (mtp-110) cc_final: 0.7414 (mtp85) REVERT: Lq 63 MET cc_start: 0.5561 (mmm) cc_final: 0.5299 (mmm) REVERT: Lq 103 LEU cc_start: 0.8747 (tp) cc_final: 0.8183 (pp) REVERT: Lq 184 MET cc_start: 0.8321 (mmm) cc_final: 0.7937 (mmp) outliers start: 210 outliers final: 153 residues processed: 1114 average time/residue: 1.2216 time to fit residues: 2379.2903 Evaluate side-chains 1105 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 934 time to evaluate : 8.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 82 GLU Chi-restraints excluded: chain CA residue 122 THR Chi-restraints excluded: chain CA residue 202 VAL Chi-restraints excluded: chain CA residue 241 THR Chi-restraints excluded: chain CB residue 74 ASP Chi-restraints excluded: chain CB residue 91 THR Chi-restraints excluded: chain CB residue 101 THR Chi-restraints excluded: chain CB residue 254 LYS Chi-restraints excluded: chain CC residue 204 LEU Chi-restraints excluded: chain CC residue 338 MET Chi-restraints excluded: chain CC residue 351 ASP Chi-restraints excluded: chain CC residue 411 TYR Chi-restraints excluded: chain CE residue 188 VAL Chi-restraints excluded: chain CE residue 234 VAL Chi-restraints excluded: chain CE residue 366 SER Chi-restraints excluded: chain CE residue 367 CYS Chi-restraints excluded: chain CE residue 478 VAL Chi-restraints excluded: chain CE residue 490 ILE Chi-restraints excluded: chain CF residue 9 VAL Chi-restraints excluded: chain CF residue 15 VAL Chi-restraints excluded: chain CF residue 72 LEU Chi-restraints excluded: chain CF residue 95 TYR Chi-restraints excluded: chain CF residue 137 VAL Chi-restraints excluded: chain CF residue 141 ILE Chi-restraints excluded: chain CF residue 170 MET Chi-restraints excluded: chain CG residue 5 THR Chi-restraints excluded: chain CG residue 6 ASP Chi-restraints excluded: chain CH residue 54 GLU Chi-restraints excluded: chain CH residue 246 ARG Chi-restraints excluded: chain CH residue 285 VAL Chi-restraints excluded: chain CJ residue 37 CYS Chi-restraints excluded: chain CK residue 42 LEU Chi-restraints excluded: chain CK residue 60 GLN Chi-restraints excluded: chain CK residue 73 VAL Chi-restraints excluded: chain CK residue 121 ILE Chi-restraints excluded: chain CK residue 124 VAL Chi-restraints excluded: chain CK residue 135 VAL Chi-restraints excluded: chain CK residue 137 LYS Chi-restraints excluded: chain CK residue 150 ILE Chi-restraints excluded: chain CK residue 164 ARG Chi-restraints excluded: chain CK residue 252 ASP Chi-restraints excluded: chain CL residue 19 ARG Chi-restraints excluded: chain CL residue 35 GLU Chi-restraints excluded: chain CN residue 39 GLU Chi-restraints excluded: chain CN residue 91 ASP Chi-restraints excluded: chain CN residue 114 THR Chi-restraints excluded: chain CN residue 197 MET Chi-restraints excluded: chain CN residue 199 VAL Chi-restraints excluded: chain CN residue 206 THR Chi-restraints excluded: chain CO residue 29 ARG Chi-restraints excluded: chain CP residue 436 CYS Chi-restraints excluded: chain CP residue 516 CYS Chi-restraints excluded: chain CP residue 521 GLU Chi-restraints excluded: chain CP residue 524 VAL Chi-restraints excluded: chain CP residue 546 GLU Chi-restraints excluded: chain CP residue 552 MET Chi-restraints excluded: chain CP residue 571 TYR Chi-restraints excluded: chain CP residue 576 PHE Chi-restraints excluded: chain CQ residue 79 VAL Chi-restraints excluded: chain CR residue 131 VAL Chi-restraints excluded: chain CS residue 672 THR Chi-restraints excluded: chain CS residue 705 LYS Chi-restraints excluded: chain CS residue 718 ILE Chi-restraints excluded: chain CS residue 795 THR Chi-restraints excluded: chain CT residue 137 GLN Chi-restraints excluded: chain CT residue 244 THR Chi-restraints excluded: chain CT residue 504 ASP Chi-restraints excluded: chain CT residue 626 VAL Chi-restraints excluded: chain CU residue 256 SER Chi-restraints excluded: chain CU residue 286 LYS Chi-restraints excluded: chain CU residue 336 GLN Chi-restraints excluded: chain CV residue 20 LEU Chi-restraints excluded: chain CV residue 36 THR Chi-restraints excluded: chain CV residue 61 VAL Chi-restraints excluded: chain CV residue 86 THR Chi-restraints excluded: chain CV residue 96 SER Chi-restraints excluded: chain CX residue 80 VAL Chi-restraints excluded: chain CX residue 82 VAL Chi-restraints excluded: chain CX residue 93 VAL Chi-restraints excluded: chain CY residue 415 VAL Chi-restraints excluded: chain CY residue 474 HIS Chi-restraints excluded: chain CY residue 495 TYR Chi-restraints excluded: chain CY residue 742 GLU Chi-restraints excluded: chain Cb residue 177 LEU Chi-restraints excluded: chain Cb residue 302 SER Chi-restraints excluded: chain Cb residue 481 LEU Chi-restraints excluded: chain Cb residue 512 VAL Chi-restraints excluded: chain Cb residue 530 ASP Chi-restraints excluded: chain Cb residue 573 HIS Chi-restraints excluded: chain Cb residue 582 ASN Chi-restraints excluded: chain Cb residue 583 GLU Chi-restraints excluded: chain Cb residue 584 GLU Chi-restraints excluded: chain Cb residue 603 ILE Chi-restraints excluded: chain LB residue 103 THR Chi-restraints excluded: chain LB residue 112 ASP Chi-restraints excluded: chain LB residue 157 THR Chi-restraints excluded: chain LB residue 158 VAL Chi-restraints excluded: chain LB residue 166 GLN Chi-restraints excluded: chain LB residue 189 VAL Chi-restraints excluded: chain LB residue 205 THR Chi-restraints excluded: chain LB residue 211 GLU Chi-restraints excluded: chain LB residue 320 ASN Chi-restraints excluded: chain LB residue 329 VAL Chi-restraints excluded: chain LB residue 357 LEU Chi-restraints excluded: chain LB residue 359 TRP Chi-restraints excluded: chain LC residue 6 THR Chi-restraints excluded: chain LC residue 20 THR Chi-restraints excluded: chain LC residue 146 VAL Chi-restraints excluded: chain LC residue 158 VAL Chi-restraints excluded: chain LC residue 211 ILE Chi-restraints excluded: chain LC residue 221 GLU Chi-restraints excluded: chain LC residue 222 LEU Chi-restraints excluded: chain LC residue 223 VAL Chi-restraints excluded: chain LE residue 32 ASP Chi-restraints excluded: chain LE residue 52 LEU Chi-restraints excluded: chain LE residue 156 SER Chi-restraints excluded: chain LE residue 157 THR Chi-restraints excluded: chain LE residue 166 ASP Chi-restraints excluded: chain LE residue 177 ASP Chi-restraints excluded: chain LF residue 13 LEU Chi-restraints excluded: chain LF residue 14 VAL Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 94 ARG Chi-restraints excluded: chain LF residue 110 GLN Chi-restraints excluded: chain LF residue 174 ILE Chi-restraints excluded: chain LF residue 239 GLU Chi-restraints excluded: chain LG residue 101 ARG Chi-restraints excluded: chain LH residue 55 VAL Chi-restraints excluded: chain LH residue 57 ILE Chi-restraints excluded: chain LH residue 61 LEU Chi-restraints excluded: chain LH residue 80 VAL Chi-restraints excluded: chain LH residue 89 VAL Chi-restraints excluded: chain LH residue 105 LEU Chi-restraints excluded: chain LH residue 127 MET Chi-restraints excluded: chain LH residue 185 LEU Chi-restraints excluded: chain LK residue 121 PHE Chi-restraints excluded: chain LL residue 46 LEU Chi-restraints excluded: chain LL residue 76 THR Chi-restraints excluded: chain LL residue 92 THR Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LM residue 24 ASN Chi-restraints excluded: chain LM residue 111 SER Chi-restraints excluded: chain LM residue 138 ILE Chi-restraints excluded: chain LN residue 149 ASN Chi-restraints excluded: chain LO residue 8 VAL Chi-restraints excluded: chain LO residue 90 ILE Chi-restraints excluded: chain LO residue 131 LEU Chi-restraints excluded: chain LO residue 181 SER Chi-restraints excluded: chain LP residue 13 LYS Chi-restraints excluded: chain LQ residue 108 VAL Chi-restraints excluded: chain LQ residue 160 THR Chi-restraints excluded: chain LS residue 8 GLN Chi-restraints excluded: chain LS residue 24 LEU Chi-restraints excluded: chain LS residue 45 LEU Chi-restraints excluded: chain LS residue 88 HIS Chi-restraints excluded: chain LT residue 156 TYR Chi-restraints excluded: chain LV residue 21 VAL Chi-restraints excluded: chain LV residue 79 VAL Chi-restraints excluded: chain LV residue 80 ILE Chi-restraints excluded: chain LY residue 6 THR Chi-restraints excluded: chain LY residue 46 SER Chi-restraints excluded: chain LY residue 64 ASP Chi-restraints excluded: chain LY residue 90 THR Chi-restraints excluded: chain LY residue 128 VAL Chi-restraints excluded: chain Ld residue 44 ILE Chi-restraints excluded: chain Ld residue 116 VAL Chi-restraints excluded: chain Le residue 1 MET Chi-restraints excluded: chain Lh residue 49 ILE Chi-restraints excluded: chain Lh residue 84 ASP Chi-restraints excluded: chain Lh residue 105 VAL Chi-restraints excluded: chain Lq residue 206 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1291 random chunks: chunk 1204 optimal weight: 0.6980 chunk 140 optimal weight: 6.9990 chunk 711 optimal weight: 40.0000 chunk 912 optimal weight: 7.9990 chunk 706 optimal weight: 4.9990 chunk 1051 optimal weight: 9.9990 chunk 697 optimal weight: 4.9990 chunk 1244 optimal weight: 0.2980 chunk 778 optimal weight: 3.9990 chunk 758 optimal weight: 3.9990 chunk 574 optimal weight: 6.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CB 33 HIS ** CB 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CB 105 GLN ** CB 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CE 299 GLN ** CF 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CF 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CH 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CH 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CH 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 153 ASN CK 203 ASN CN 82 GLN CQ 24 ASN CS 665 GLN CT 506 HIS ** CV 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CY 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CY 474 HIS ** Cb 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 294 ASN LS 13 HIS ** LS 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LV 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LV 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 47 ASN Lh 67 GLN Li 47 GLN ** Lq 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 144476 Z= 0.256 Angle : 0.599 12.627 206691 Z= 0.307 Chirality : 0.039 0.293 25010 Planarity : 0.005 0.081 17391 Dihedral : 21.684 178.505 49529 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.55 % Favored : 95.33 % Rotamer: Outliers : 2.50 % Allowed : 16.38 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.01 % Twisted Proline : 0.37 % Twisted General : 0.00 % 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: 0.44 (0.08), residues: 10568 helix: 1.45 (0.07), residues: 4926 sheet: -0.27 (0.14), residues: 1233 loop : -0.85 (0.09), residues: 4409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRPCb 816 HIS 0.026 0.001 HISCY 474 PHE 0.026 0.002 PHECQ 107 TYR 0.023 0.002 TYRCM 142 ARG 0.008 0.000 ARGCE 571 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21136 Ramachandran restraints generated. 10568 Oldfield, 0 Emsley, 10568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21136 Ramachandran restraints generated. 10568 Oldfield, 0 Emsley, 10568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1175 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 952 time to evaluate : 8.705 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: CA 202 VAL cc_start: 0.9157 (OUTLIER) cc_final: 0.8937 (m) REVERT: CC 205 GLN cc_start: 0.8455 (tp-100) cc_final: 0.8185 (tp40) REVERT: CC 233 ARG cc_start: 0.6584 (tpp-160) cc_final: 0.6132 (tpm170) REVERT: CC 324 TYR cc_start: 0.6001 (p90) cc_final: 0.5681 (p90) REVERT: CC 373 MET cc_start: -0.0565 (ptt) cc_final: -0.0876 (ptt) REVERT: CF 95 TYR cc_start: 0.7935 (OUTLIER) cc_final: 0.7212 (t80) REVERT: CF 211 LEU cc_start: 0.8618 (mm) cc_final: 0.8208 (mm) REVERT: CG 106 GLN cc_start: 0.8157 (mm-40) cc_final: 0.7858 (tp40) REVERT: CG 140 ILE cc_start: 0.8917 (mt) cc_final: 0.8687 (mt) REVERT: CH 246 ARG cc_start: 0.7172 (OUTLIER) cc_final: 0.6530 (mtt90) REVERT: CH 508 MET cc_start: 0.4277 (tpt) cc_final: 0.3865 (tpt) REVERT: CI 213 ILE cc_start: 0.8580 (mp) cc_final: 0.8379 (mt) REVERT: CI 261 LYS cc_start: 0.8631 (mtmm) cc_final: 0.8303 (mttm) REVERT: CJ 227 MET cc_start: 0.7920 (pmm) cc_final: 0.7117 (ptp) REVERT: CK 42 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8460 (pp) REVERT: CK 137 LYS cc_start: 0.6500 (OUTLIER) cc_final: 0.5235 (tttp) REVERT: CK 147 TRP cc_start: 0.7119 (t60) cc_final: 0.6751 (t-100) REVERT: CK 164 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.6738 (mtm-85) REVERT: CL 45 TRP cc_start: 0.6878 (m-10) cc_final: 0.6634 (m-10) REVERT: CN 1 MET cc_start: 0.5682 (ptp) cc_final: 0.5276 (mtt) REVERT: CO 29 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7453 (ptp-110) REVERT: CP 509 VAL cc_start: 0.7919 (OUTLIER) cc_final: 0.7649 (p) REVERT: CP 521 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7075 (mp0) REVERT: CQ 93 MET cc_start: 0.7978 (mtp) cc_final: 0.7666 (mtp) REVERT: CQ 100 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7413 (mtp-110) REVERT: CR 178 ARG cc_start: 0.7301 (ttm170) cc_final: 0.7098 (ttm170) REVERT: CU 336 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7646 (mp10) REVERT: CX 122 ARG cc_start: 0.7450 (mtt90) cc_final: 0.7198 (mtt90) REVERT: Cb 530 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7620 (t0) REVERT: LB 84 MET cc_start: 0.8788 (mtm) cc_final: 0.8427 (mtm) REVERT: LB 137 TYR cc_start: 0.7286 (t80) cc_final: 0.6654 (t80) REVERT: LB 166 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7189 (mp10) REVERT: LC 221 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6490 (pm20) REVERT: LC 321 ARG cc_start: 0.8280 (mtp85) cc_final: 0.7548 (mtm180) REVERT: LE 25 GLN cc_start: 0.7021 (mt0) cc_final: 0.6792 (mt0) REVERT: LE 161 ASP cc_start: 0.7292 (m-30) cc_final: 0.7007 (m-30) REVERT: LG 101 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.7858 (ttm170) REVERT: LG 246 GLN cc_start: 0.8030 (tp40) cc_final: 0.7556 (mm-40) REVERT: LH 57 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.7937 (mt) REVERT: LM 61 ARG cc_start: 0.7575 (ttm-80) cc_final: 0.7177 (mpt180) REVERT: LM 112 LEU cc_start: 0.8936 (tt) cc_final: 0.8637 (tt) REVERT: LN 67 ARG cc_start: 0.7776 (mtt-85) cc_final: 0.7402 (mmm160) REVERT: LO 1 MET cc_start: 0.4953 (pmm) cc_final: 0.4679 (mtt) REVERT: LS 45 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8362 (mp) REVERT: LS 117 ARG cc_start: 0.7957 (mtt180) cc_final: 0.7373 (mtm180) REVERT: LT 134 MET cc_start: 0.8450 (mmp) cc_final: 0.8012 (mmt) REVERT: LT 136 ARG cc_start: 0.7254 (mtt180) cc_final: 0.6987 (mtm-85) REVERT: LV 59 MET cc_start: 0.8211 (ttm) cc_final: 0.7945 (ttp) REVERT: LY 4 ARG cc_start: 0.7632 (mtm180) cc_final: 0.6993 (mmt90) REVERT: Lf 4 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7541 (mt-10) REVERT: Lf 58 GLN cc_start: 0.7173 (mm-40) cc_final: 0.6965 (tm-30) REVERT: Lh 49 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8072 (pt) REVERT: Lj 25 ARG cc_start: 0.7714 (mtp-110) cc_final: 0.7497 (mtp85) REVERT: Lq 63 MET cc_start: 0.5123 (mmm) cc_final: 0.4892 (mmm) REVERT: Lq 103 LEU cc_start: 0.8737 (tp) cc_final: 0.8185 (pp) REVERT: Lq 184 MET cc_start: 0.8398 (mmm) cc_final: 0.7964 (mmp) outliers start: 223 outliers final: 160 residues processed: 1111 average time/residue: 1.2411 time to fit residues: 2404.0248 Evaluate side-chains 1108 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 930 time to evaluate : 8.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 82 GLU Chi-restraints excluded: chain CA residue 122 THR Chi-restraints excluded: chain CA residue 202 VAL Chi-restraints excluded: chain CA residue 241 THR Chi-restraints excluded: chain CB residue 74 ASP Chi-restraints excluded: chain CB residue 91 THR Chi-restraints excluded: chain CB residue 101 THR Chi-restraints excluded: chain CB residue 254 LYS Chi-restraints excluded: chain CC residue 204 LEU Chi-restraints excluded: chain CC residue 218 THR Chi-restraints excluded: chain CC residue 338 MET Chi-restraints excluded: chain CC residue 351 ASP Chi-restraints excluded: chain CC residue 411 TYR Chi-restraints excluded: chain CE residue 134 MET Chi-restraints excluded: chain CE residue 188 VAL Chi-restraints excluded: chain CE residue 234 VAL Chi-restraints excluded: chain CE residue 337 VAL Chi-restraints excluded: chain CE residue 366 SER Chi-restraints excluded: chain CE residue 367 CYS Chi-restraints excluded: chain CE residue 478 VAL Chi-restraints excluded: chain CE residue 555 ILE Chi-restraints excluded: chain CF residue 9 VAL Chi-restraints excluded: chain CF residue 15 VAL Chi-restraints excluded: chain CF residue 72 LEU Chi-restraints excluded: chain CF residue 95 TYR Chi-restraints excluded: chain CF residue 137 VAL Chi-restraints excluded: chain CF residue 141 ILE Chi-restraints excluded: chain CF residue 170 MET Chi-restraints excluded: chain CG residue 5 THR Chi-restraints excluded: chain CG residue 6 ASP Chi-restraints excluded: chain CH residue 54 GLU Chi-restraints excluded: chain CH residue 246 ARG Chi-restraints excluded: chain CH residue 285 VAL Chi-restraints excluded: chain CI residue 320 LEU Chi-restraints excluded: chain CJ residue 37 CYS Chi-restraints excluded: chain CK residue 42 LEU Chi-restraints excluded: chain CK residue 60 GLN Chi-restraints excluded: chain CK residue 73 VAL Chi-restraints excluded: chain CK residue 121 ILE Chi-restraints excluded: chain CK residue 124 VAL Chi-restraints excluded: chain CK residue 135 VAL Chi-restraints excluded: chain CK residue 137 LYS Chi-restraints excluded: chain CK residue 150 ILE Chi-restraints excluded: chain CK residue 164 ARG Chi-restraints excluded: chain CK residue 252 ASP Chi-restraints excluded: chain CL residue 19 ARG Chi-restraints excluded: chain CL residue 20 LEU Chi-restraints excluded: chain CL residue 35 GLU Chi-restraints excluded: chain CM residue 55 GLU Chi-restraints excluded: chain CN residue 39 GLU Chi-restraints excluded: chain CN residue 109 VAL Chi-restraints excluded: chain CN residue 114 THR Chi-restraints excluded: chain CN residue 197 MET Chi-restraints excluded: chain CN residue 206 THR Chi-restraints excluded: chain CO residue 29 ARG Chi-restraints excluded: chain CP residue 436 CYS Chi-restraints excluded: chain CP residue 509 VAL Chi-restraints excluded: chain CP residue 516 CYS Chi-restraints excluded: chain CP residue 521 GLU Chi-restraints excluded: chain CP residue 524 VAL Chi-restraints excluded: chain CP residue 546 GLU Chi-restraints excluded: chain CP residue 549 THR Chi-restraints excluded: chain CP residue 552 MET Chi-restraints excluded: chain CP residue 571 TYR Chi-restraints excluded: chain CP residue 576 PHE Chi-restraints excluded: chain CQ residue 68 THR Chi-restraints excluded: chain CQ residue 79 VAL Chi-restraints excluded: chain CQ residue 100 ARG Chi-restraints excluded: chain CR residue 131 VAL Chi-restraints excluded: chain CS residue 656 THR Chi-restraints excluded: chain CS residue 672 THR Chi-restraints excluded: chain CS residue 705 LYS Chi-restraints excluded: chain CS residue 718 ILE Chi-restraints excluded: chain CS residue 795 THR Chi-restraints excluded: chain CT residue 137 GLN Chi-restraints excluded: chain CT residue 244 THR Chi-restraints excluded: chain CT residue 504 ASP Chi-restraints excluded: chain CT residue 603 VAL Chi-restraints excluded: chain CT residue 626 VAL Chi-restraints excluded: chain CT residue 663 LEU Chi-restraints excluded: chain CU residue 256 SER Chi-restraints excluded: chain CU residue 286 LYS Chi-restraints excluded: chain CU residue 336 GLN Chi-restraints excluded: chain CV residue 20 LEU Chi-restraints excluded: chain CV residue 36 THR Chi-restraints excluded: chain CV residue 61 VAL Chi-restraints excluded: chain CV residue 80 THR Chi-restraints excluded: chain CV residue 86 THR Chi-restraints excluded: chain CV residue 96 SER Chi-restraints excluded: chain CX residue 80 VAL Chi-restraints excluded: chain CX residue 82 VAL Chi-restraints excluded: chain CX residue 93 VAL Chi-restraints excluded: chain CY residue 742 GLU Chi-restraints excluded: chain Cb residue 177 LEU Chi-restraints excluded: chain Cb residue 302 SER Chi-restraints excluded: chain Cb residue 473 SER Chi-restraints excluded: chain Cb residue 481 LEU Chi-restraints excluded: chain Cb residue 503 ASP Chi-restraints excluded: chain Cb residue 512 VAL Chi-restraints excluded: chain Cb residue 530 ASP Chi-restraints excluded: chain Cb residue 573 HIS Chi-restraints excluded: chain Cb residue 603 ILE Chi-restraints excluded: chain Cb residue 873 VAL Chi-restraints excluded: chain LB residue 103 THR Chi-restraints excluded: chain LB residue 112 ASP Chi-restraints excluded: chain LB residue 157 THR Chi-restraints excluded: chain LB residue 158 VAL Chi-restraints excluded: chain LB residue 166 GLN Chi-restraints excluded: chain LB residue 189 VAL Chi-restraints excluded: chain LB residue 205 THR Chi-restraints excluded: chain LB residue 211 GLU Chi-restraints excluded: chain LB residue 320 ASN Chi-restraints excluded: chain LB residue 329 VAL Chi-restraints excluded: chain LB residue 359 TRP Chi-restraints excluded: chain LC residue 6 THR Chi-restraints excluded: chain LC residue 20 THR Chi-restraints excluded: chain LC residue 146 VAL Chi-restraints excluded: chain LC residue 158 VAL Chi-restraints excluded: chain LC residue 211 ILE Chi-restraints excluded: chain LC residue 221 GLU Chi-restraints excluded: chain LC residue 222 LEU Chi-restraints excluded: chain LC residue 223 VAL Chi-restraints excluded: chain LE residue 32 ASP Chi-restraints excluded: chain LE residue 52 LEU Chi-restraints excluded: chain LE residue 156 SER Chi-restraints excluded: chain LE residue 177 ASP Chi-restraints excluded: chain LF residue 13 LEU Chi-restraints excluded: chain LF residue 14 VAL Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 94 ARG Chi-restraints excluded: chain LF residue 98 ILE Chi-restraints excluded: chain LF residue 174 ILE Chi-restraints excluded: chain LF residue 196 THR Chi-restraints excluded: chain LG residue 101 ARG Chi-restraints excluded: chain LG residue 203 ILE Chi-restraints excluded: chain LH residue 55 VAL Chi-restraints excluded: chain LH residue 57 ILE Chi-restraints excluded: chain LH residue 61 LEU Chi-restraints excluded: chain LH residue 80 VAL Chi-restraints excluded: chain LH residue 185 LEU Chi-restraints excluded: chain LK residue 111 GLU Chi-restraints excluded: chain LK residue 120 SER Chi-restraints excluded: chain LK residue 121 PHE Chi-restraints excluded: chain LL residue 46 LEU Chi-restraints excluded: chain LL residue 76 THR Chi-restraints excluded: chain LL residue 92 THR Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LM residue 24 ASN Chi-restraints excluded: chain LM residue 57 VAL Chi-restraints excluded: chain LM residue 138 ILE Chi-restraints excluded: chain LN residue 149 ASN Chi-restraints excluded: chain LO residue 8 VAL Chi-restraints excluded: chain LO residue 90 ILE Chi-restraints excluded: chain LO residue 131 LEU Chi-restraints excluded: chain LO residue 181 SER Chi-restraints excluded: chain LQ residue 108 VAL Chi-restraints excluded: chain LQ residue 160 THR Chi-restraints excluded: chain LS residue 8 GLN Chi-restraints excluded: chain LS residue 24 LEU Chi-restraints excluded: chain LS residue 45 LEU Chi-restraints excluded: chain LS residue 88 HIS Chi-restraints excluded: chain LT residue 156 TYR Chi-restraints excluded: chain LV residue 21 VAL Chi-restraints excluded: chain LV residue 79 VAL Chi-restraints excluded: chain LV residue 80 ILE Chi-restraints excluded: chain LY residue 6 THR Chi-restraints excluded: chain LY residue 36 LYS Chi-restraints excluded: chain LY residue 46 SER Chi-restraints excluded: chain LY residue 64 ASP Chi-restraints excluded: chain LY residue 90 THR Chi-restraints excluded: chain LY residue 128 VAL Chi-restraints excluded: chain Ld residue 116 VAL Chi-restraints excluded: chain Lh residue 46 LEU Chi-restraints excluded: chain Lh residue 49 ILE Chi-restraints excluded: chain Lh residue 67 GLN Chi-restraints excluded: chain Lh residue 84 ASP Chi-restraints excluded: chain Lh residue 105 VAL Chi-restraints excluded: chain Lq residue 206 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1291 random chunks: chunk 769 optimal weight: 9.9990 chunk 496 optimal weight: 30.0000 chunk 743 optimal weight: 5.9990 chunk 374 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 241 optimal weight: 3.9990 chunk 791 optimal weight: 3.9990 chunk 847 optimal weight: 0.5980 chunk 615 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 978 optimal weight: 3.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CB 33 HIS ** CB 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CF 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CF 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CH 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CH 266 GLN ** CH 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CH 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 153 ASN CK 203 ASN CQ 24 ASN ** CR 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CS 665 GLN ** CV 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CY 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CY 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 294 ASN LB 320 ASN LE 78 GLN LO 66 ASN LS 13 HIS ** LS 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LV 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Le 90 ASN Lh 47 ASN Li 47 GLN ** Lq 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 144476 Z= 0.267 Angle : 0.603 12.554 206691 Z= 0.309 Chirality : 0.039 0.296 25010 Planarity : 0.005 0.080 17391 Dihedral : 21.677 178.899 49529 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.60 % Favored : 95.28 % Rotamer: Outliers : 2.63 % Allowed : 16.67 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.01 % Twisted Proline : 0.37 % Twisted General : 0.00 % 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: 0.45 (0.08), residues: 10568 helix: 1.46 (0.07), residues: 4923 sheet: -0.34 (0.14), residues: 1231 loop : -0.81 (0.09), residues: 4414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRPCY 387 HIS 0.010 0.001 HISCN 118 PHE 0.026 0.002 PHECQ 107 TYR 0.020 0.002 TYRLE 127 ARG 0.010 0.001 ARGCV 139 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21136 Ramachandran restraints generated. 10568 Oldfield, 0 Emsley, 10568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21136 Ramachandran restraints generated. 10568 Oldfield, 0 Emsley, 10568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1187 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 953 time to evaluate : 8.761 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: CC 233 ARG cc_start: 0.6673 (tpp-160) cc_final: 0.6129 (tpm170) REVERT: CC 324 TYR cc_start: 0.6024 (p90) cc_final: 0.5692 (p90) REVERT: CC 373 MET cc_start: -0.0641 (ptt) cc_final: -0.0895 (ptt) REVERT: CF 211 LEU cc_start: 0.8625 (mm) cc_final: 0.8200 (mm) REVERT: CG 41 GLN cc_start: 0.8272 (tp40) cc_final: 0.8055 (tp40) REVERT: CG 106 GLN cc_start: 0.8318 (mm-40) cc_final: 0.8089 (tp40) REVERT: CG 140 ILE cc_start: 0.8933 (mt) cc_final: 0.8708 (mt) REVERT: CI 261 LYS cc_start: 0.8675 (mtmm) cc_final: 0.8336 (mttm) REVERT: CJ 227 MET cc_start: 0.7929 (pmm) cc_final: 0.7033 (ptp) REVERT: CJ 371 THR cc_start: 0.2096 (OUTLIER) cc_final: 0.1721 (t) REVERT: CK 42 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8472 (pp) REVERT: CK 137 LYS cc_start: 0.6630 (OUTLIER) cc_final: 0.5337 (tttp) REVERT: CK 147 TRP cc_start: 0.7180 (t60) cc_final: 0.6760 (t-100) REVERT: CK 164 ARG cc_start: 0.7151 (OUTLIER) cc_final: 0.6800 (mtm-85) REVERT: CL 45 TRP cc_start: 0.6933 (m-10) cc_final: 0.6678 (m-10) REVERT: CM 17 THR cc_start: 0.2145 (OUTLIER) cc_final: 0.1462 (p) REVERT: CN 1 MET cc_start: 0.5701 (ptp) cc_final: 0.5259 (mtt) REVERT: CO 29 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7443 (ptp-110) REVERT: CP 509 VAL cc_start: 0.7924 (OUTLIER) cc_final: 0.7636 (p) REVERT: CP 521 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7084 (mp0) REVERT: CQ 42 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7248 (mtp) REVERT: CQ 100 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7449 (mtp-110) REVERT: CT 410 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7733 (mtt-85) REVERT: CU 336 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7661 (mp10) REVERT: CX 122 ARG cc_start: 0.7496 (mtt90) cc_final: 0.7271 (mtt90) REVERT: Cb 530 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7625 (t0) REVERT: LB 84 MET cc_start: 0.8838 (mtm) cc_final: 0.8487 (mtm) REVERT: LB 137 TYR cc_start: 0.7297 (t80) cc_final: 0.6688 (t80) REVERT: LB 166 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7346 (mp10) REVERT: LB 283 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8145 (mt) REVERT: LC 221 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6197 (pm20) REVERT: LC 289 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7225 (mtt90) REVERT: LC 321 ARG cc_start: 0.8281 (mtp85) cc_final: 0.7503 (mtm180) REVERT: LE 25 GLN cc_start: 0.7045 (mt0) cc_final: 0.6837 (mt0) REVERT: LF 239 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7633 (mm-30) REVERT: LG 101 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.7864 (ttm170) REVERT: LG 246 GLN cc_start: 0.8030 (tp40) cc_final: 0.7569 (mm-40) REVERT: LH 57 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.7997 (mt) REVERT: LM 61 ARG cc_start: 0.7578 (ttm-80) cc_final: 0.7187 (mpt180) REVERT: LM 112 LEU cc_start: 0.8936 (tt) cc_final: 0.8653 (tt) REVERT: LN 67 ARG cc_start: 0.7781 (mtt-85) cc_final: 0.7400 (mmm160) REVERT: LO 1 MET cc_start: 0.4977 (pmm) cc_final: 0.4712 (mtt) REVERT: LO 147 VAL cc_start: 0.8786 (p) cc_final: 0.8517 (m) REVERT: LS 45 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8362 (mp) REVERT: LS 117 ARG cc_start: 0.7955 (mtt180) cc_final: 0.7368 (mtm180) REVERT: LT 134 MET cc_start: 0.8430 (mmp) cc_final: 0.7988 (mmt) REVERT: LT 136 ARG cc_start: 0.7273 (mtt180) cc_final: 0.7000 (mtm-85) REVERT: LV 59 MET cc_start: 0.8198 (ttm) cc_final: 0.7924 (ttp) REVERT: LY 4 ARG cc_start: 0.7635 (mtm180) cc_final: 0.6993 (mmt90) REVERT: Ld 79 ILE cc_start: 0.7496 (mt) cc_final: 0.6906 (pt) REVERT: Le 90 ASN cc_start: 0.8391 (m-40) cc_final: 0.8130 (m110) REVERT: Lf 4 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7647 (mt-10) REVERT: Lh 49 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8062 (pt) REVERT: Lj 25 ARG cc_start: 0.7705 (mtp-110) cc_final: 0.7497 (mtp85) REVERT: Lq 63 MET cc_start: 0.5221 (mmm) cc_final: 0.4858 (mmm) REVERT: Lq 103 LEU cc_start: 0.8735 (tp) cc_final: 0.8176 (pp) REVERT: Lq 108 ASP cc_start: 0.7356 (p0) cc_final: 0.7152 (p0) REVERT: Lq 184 MET cc_start: 0.8386 (mmm) cc_final: 0.7959 (mmp) outliers start: 234 outliers final: 182 residues processed: 1118 average time/residue: 1.2055 time to fit residues: 2350.7188 Evaluate side-chains 1134 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 930 time to evaluate : 8.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 82 GLU Chi-restraints excluded: chain CA residue 122 THR Chi-restraints excluded: chain CA residue 241 THR Chi-restraints excluded: chain CB residue 74 ASP Chi-restraints excluded: chain CB residue 91 THR Chi-restraints excluded: chain CB residue 101 THR Chi-restraints excluded: chain CB residue 129 ASP Chi-restraints excluded: chain CB residue 180 ILE Chi-restraints excluded: chain CB residue 254 LYS Chi-restraints excluded: chain CB residue 262 VAL Chi-restraints excluded: chain CC residue 204 LEU Chi-restraints excluded: chain CC residue 218 THR Chi-restraints excluded: chain CC residue 221 THR Chi-restraints excluded: chain CC residue 338 MET Chi-restraints excluded: chain CC residue 351 ASP Chi-restraints excluded: chain CC residue 411 TYR Chi-restraints excluded: chain CE residue 188 VAL Chi-restraints excluded: chain CE residue 218 ILE Chi-restraints excluded: chain CE residue 234 VAL Chi-restraints excluded: chain CE residue 337 VAL Chi-restraints excluded: chain CE residue 366 SER Chi-restraints excluded: chain CE residue 367 CYS Chi-restraints excluded: chain CE residue 478 VAL Chi-restraints excluded: chain CE residue 490 ILE Chi-restraints excluded: chain CE residue 555 ILE Chi-restraints excluded: chain CF residue 9 VAL Chi-restraints excluded: chain CF residue 15 VAL Chi-restraints excluded: chain CF residue 72 LEU Chi-restraints excluded: chain CF residue 95 TYR Chi-restraints excluded: chain CF residue 137 VAL Chi-restraints excluded: chain CF residue 141 ILE Chi-restraints excluded: chain CF residue 170 MET Chi-restraints excluded: chain CG residue 5 THR Chi-restraints excluded: chain CG residue 6 ASP Chi-restraints excluded: chain CH residue 54 GLU Chi-restraints excluded: chain CH residue 208 LEU Chi-restraints excluded: chain CH residue 285 VAL Chi-restraints excluded: chain CH residue 406 ASP Chi-restraints excluded: chain CJ residue 37 CYS Chi-restraints excluded: chain CJ residue 100 VAL Chi-restraints excluded: chain CJ residue 371 THR Chi-restraints excluded: chain CK residue 42 LEU Chi-restraints excluded: chain CK residue 60 GLN Chi-restraints excluded: chain CK residue 73 VAL Chi-restraints excluded: chain CK residue 121 ILE Chi-restraints excluded: chain CK residue 124 VAL Chi-restraints excluded: chain CK residue 135 VAL Chi-restraints excluded: chain CK residue 137 LYS Chi-restraints excluded: chain CK residue 150 ILE Chi-restraints excluded: chain CK residue 164 ARG Chi-restraints excluded: chain CK residue 252 ASP Chi-restraints excluded: chain CL residue 19 ARG Chi-restraints excluded: chain CL residue 20 LEU Chi-restraints excluded: chain CL residue 35 GLU Chi-restraints excluded: chain CM residue 17 THR Chi-restraints excluded: chain CM residue 55 GLU Chi-restraints excluded: chain CN residue 39 GLU Chi-restraints excluded: chain CN residue 81 LEU Chi-restraints excluded: chain CN residue 109 VAL Chi-restraints excluded: chain CN residue 114 THR Chi-restraints excluded: chain CN residue 197 MET Chi-restraints excluded: chain CN residue 199 VAL Chi-restraints excluded: chain CN residue 206 THR Chi-restraints excluded: chain CN residue 209 ASP Chi-restraints excluded: chain CO residue 29 ARG Chi-restraints excluded: chain CP residue 316 HIS Chi-restraints excluded: chain CP residue 436 CYS Chi-restraints excluded: chain CP residue 466 CYS Chi-restraints excluded: chain CP residue 509 VAL Chi-restraints excluded: chain CP residue 516 CYS Chi-restraints excluded: chain CP residue 521 GLU Chi-restraints excluded: chain CP residue 524 VAL Chi-restraints excluded: chain CP residue 546 GLU Chi-restraints excluded: chain CP residue 549 THR Chi-restraints excluded: chain CP residue 552 MET Chi-restraints excluded: chain CP residue 571 TYR Chi-restraints excluded: chain CP residue 576 PHE Chi-restraints excluded: chain CQ residue 42 MET Chi-restraints excluded: chain CQ residue 68 THR Chi-restraints excluded: chain CQ residue 79 VAL Chi-restraints excluded: chain CQ residue 100 ARG Chi-restraints excluded: chain CR residue 131 VAL Chi-restraints excluded: chain CS residue 656 THR Chi-restraints excluded: chain CS residue 672 THR Chi-restraints excluded: chain CS residue 705 LYS Chi-restraints excluded: chain CS residue 718 ILE Chi-restraints excluded: chain CS residue 795 THR Chi-restraints excluded: chain CS residue 819 MET Chi-restraints excluded: chain CT residue 137 GLN Chi-restraints excluded: chain CT residue 244 THR Chi-restraints excluded: chain CT residue 410 ARG Chi-restraints excluded: chain CT residue 504 ASP Chi-restraints excluded: chain CT residue 603 VAL Chi-restraints excluded: chain CT residue 626 VAL Chi-restraints excluded: chain CT residue 663 LEU Chi-restraints excluded: chain CU residue 220 VAL Chi-restraints excluded: chain CU residue 256 SER Chi-restraints excluded: chain CU residue 286 LYS Chi-restraints excluded: chain CU residue 336 GLN Chi-restraints excluded: chain CV residue 20 LEU Chi-restraints excluded: chain CV residue 36 THR Chi-restraints excluded: chain CV residue 61 VAL Chi-restraints excluded: chain CV residue 80 THR Chi-restraints excluded: chain CV residue 86 THR Chi-restraints excluded: chain CV residue 96 SER Chi-restraints excluded: chain CX residue 80 VAL Chi-restraints excluded: chain CX residue 82 VAL Chi-restraints excluded: chain CX residue 93 VAL Chi-restraints excluded: chain CY residue 415 VAL Chi-restraints excluded: chain CY residue 474 HIS Chi-restraints excluded: chain CY residue 742 GLU Chi-restraints excluded: chain Cb residue 177 LEU Chi-restraints excluded: chain Cb residue 302 SER Chi-restraints excluded: chain Cb residue 473 SER Chi-restraints excluded: chain Cb residue 481 LEU Chi-restraints excluded: chain Cb residue 503 ASP Chi-restraints excluded: chain Cb residue 512 VAL Chi-restraints excluded: chain Cb residue 530 ASP Chi-restraints excluded: chain Cb residue 603 ILE Chi-restraints excluded: chain Cb residue 873 VAL Chi-restraints excluded: chain LB residue 103 THR Chi-restraints excluded: chain LB residue 112 ASP Chi-restraints excluded: chain LB residue 157 THR Chi-restraints excluded: chain LB residue 158 VAL Chi-restraints excluded: chain LB residue 166 GLN Chi-restraints excluded: chain LB residue 189 VAL Chi-restraints excluded: chain LB residue 205 THR Chi-restraints excluded: chain LB residue 211 GLU Chi-restraints excluded: chain LB residue 283 ILE Chi-restraints excluded: chain LB residue 329 VAL Chi-restraints excluded: chain LB residue 357 LEU Chi-restraints excluded: chain LB residue 359 TRP Chi-restraints excluded: chain LC residue 6 THR Chi-restraints excluded: chain LC residue 20 THR Chi-restraints excluded: chain LC residue 146 VAL Chi-restraints excluded: chain LC residue 158 VAL Chi-restraints excluded: chain LC residue 211 ILE Chi-restraints excluded: chain LC residue 221 GLU Chi-restraints excluded: chain LC residue 222 LEU Chi-restraints excluded: chain LC residue 223 VAL Chi-restraints excluded: chain LC residue 289 ARG Chi-restraints excluded: chain LE residue 32 ASP Chi-restraints excluded: chain LE residue 52 LEU Chi-restraints excluded: chain LE residue 156 SER Chi-restraints excluded: chain LE residue 177 ASP Chi-restraints excluded: chain LF residue 13 LEU Chi-restraints excluded: chain LF residue 14 VAL Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LF residue 94 ARG Chi-restraints excluded: chain LF residue 174 ILE Chi-restraints excluded: chain LF residue 196 THR Chi-restraints excluded: chain LF residue 239 GLU Chi-restraints excluded: chain LG residue 70 MET Chi-restraints excluded: chain LG residue 101 ARG Chi-restraints excluded: chain LG residue 203 ILE Chi-restraints excluded: chain LH residue 55 VAL Chi-restraints excluded: chain LH residue 57 ILE Chi-restraints excluded: chain LH residue 61 LEU Chi-restraints excluded: chain LH residue 80 VAL Chi-restraints excluded: chain LH residue 89 VAL Chi-restraints excluded: chain LH residue 127 MET Chi-restraints excluded: chain LH residue 185 LEU Chi-restraints excluded: chain LK residue 120 SER Chi-restraints excluded: chain LK residue 125 LEU Chi-restraints excluded: chain LL residue 46 LEU Chi-restraints excluded: chain LL residue 76 THR Chi-restraints excluded: chain LL residue 92 THR Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LM residue 24 ASN Chi-restraints excluded: chain LM residue 57 VAL Chi-restraints excluded: chain LM residue 138 ILE Chi-restraints excluded: chain LN residue 10 LEU Chi-restraints excluded: chain LN residue 149 ASN Chi-restraints excluded: chain LO residue 8 VAL Chi-restraints excluded: chain LO residue 90 ILE Chi-restraints excluded: chain LO residue 121 VAL Chi-restraints excluded: chain LO residue 131 LEU Chi-restraints excluded: chain LO residue 181 SER Chi-restraints excluded: chain LQ residue 98 ASN Chi-restraints excluded: chain LQ residue 108 VAL Chi-restraints excluded: chain LQ residue 160 THR Chi-restraints excluded: chain LS residue 8 GLN Chi-restraints excluded: chain LS residue 24 LEU Chi-restraints excluded: chain LS residue 45 LEU Chi-restraints excluded: chain LS residue 79 LEU Chi-restraints excluded: chain LS residue 88 HIS Chi-restraints excluded: chain LT residue 156 TYR Chi-restraints excluded: chain LV residue 21 VAL Chi-restraints excluded: chain LV residue 79 VAL Chi-restraints excluded: chain LV residue 80 ILE Chi-restraints excluded: chain LY residue 6 THR Chi-restraints excluded: chain LY residue 46 SER Chi-restraints excluded: chain LY residue 64 ASP Chi-restraints excluded: chain LY residue 90 THR Chi-restraints excluded: chain LY residue 128 VAL Chi-restraints excluded: chain Ld residue 44 ILE Chi-restraints excluded: chain Ld residue 116 VAL Chi-restraints excluded: chain Lf residue 29 THR Chi-restraints excluded: chain Lh residue 46 LEU Chi-restraints excluded: chain Lh residue 49 ILE Chi-restraints excluded: chain Lh residue 84 ASP Chi-restraints excluded: chain Lh residue 105 VAL Chi-restraints excluded: chain Lq residue 206 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1291 random chunks: chunk 1131 optimal weight: 8.9990 chunk 1192 optimal weight: 0.9990 chunk 1087 optimal weight: 6.9990 chunk 1159 optimal weight: 0.8980 chunk 1191 optimal weight: 6.9990 chunk 697 optimal weight: 3.9990 chunk 505 optimal weight: 50.0000 chunk 910 optimal weight: 0.2980 chunk 355 optimal weight: 5.9990 chunk 1047 optimal weight: 1.9990 chunk 1096 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 148 GLN CB 33 HIS ** CB 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CF 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CF 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CH 237 GLN ** CH 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CH 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CH 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 153 ASN CK 203 ASN CN 82 GLN CQ 24 ASN CS 665 GLN ** CV 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CY 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CY 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CY 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 320 ASN LC 49 GLN LE 78 GLN ** LE 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LO 66 ASN LS 13 HIS ** LS 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LV 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LV 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 47 ASN ** Lj 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lq 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.078 144476 Z= 0.157 Angle : 0.547 11.845 206691 Z= 0.281 Chirality : 0.036 0.272 25010 Planarity : 0.005 0.074 17391 Dihedral : 21.625 179.576 49529 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.15 % Favored : 95.72 % Rotamer: Outliers : 2.03 % Allowed : 17.65 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.01 % Twisted Proline : 0.37 % Twisted General : 0.00 % 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: 0.59 (0.08), residues: 10568 helix: 1.59 (0.07), residues: 4936 sheet: -0.29 (0.14), residues: 1248 loop : -0.77 (0.09), residues: 4384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRPCb 816 HIS 0.008 0.001 HISCN 118 PHE 0.025 0.001 PHECQ 107 TYR 0.022 0.001 TYRCM 142 ARG 0.018 0.000 ARGLq 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21136 Ramachandran restraints generated. 10568 Oldfield, 0 Emsley, 10568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21136 Ramachandran restraints generated. 10568 Oldfield, 0 Emsley, 10568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1153 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 972 time to evaluate : 8.727 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: CC 205 GLN cc_start: 0.8475 (tp40) cc_final: 0.8172 (tp40) REVERT: CC 233 ARG cc_start: 0.6596 (tpp-160) cc_final: 0.6104 (tpm170) REVERT: CC 324 TYR cc_start: 0.5956 (p90) cc_final: 0.5634 (p90) REVERT: CC 373 MET cc_start: -0.0629 (ptt) cc_final: -0.0847 (ptt) REVERT: CF 211 LEU cc_start: 0.8582 (mm) cc_final: 0.8214 (mm) REVERT: CG 41 GLN cc_start: 0.8325 (tp40) cc_final: 0.8117 (tp40) REVERT: CG 140 ILE cc_start: 0.8874 (mt) cc_final: 0.8664 (mt) REVERT: CI 261 LYS cc_start: 0.8665 (mtmm) cc_final: 0.8343 (mttm) REVERT: CJ 227 MET cc_start: 0.7946 (pmm) cc_final: 0.6975 (ptp) REVERT: CJ 371 THR cc_start: 0.2095 (OUTLIER) cc_final: 0.1721 (t) REVERT: CK 42 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8322 (pp) REVERT: CK 137 LYS cc_start: 0.6594 (OUTLIER) cc_final: 0.5199 (tttp) REVERT: CK 147 TRP cc_start: 0.7156 (t60) cc_final: 0.6712 (t-100) REVERT: CL 45 TRP cc_start: 0.6930 (m-10) cc_final: 0.6685 (m-10) REVERT: CN 1 MET cc_start: 0.5448 (ptp) cc_final: 0.5135 (mtt) REVERT: CP 509 VAL cc_start: 0.7911 (OUTLIER) cc_final: 0.7672 (p) REVERT: CP 521 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.6937 (mp0) REVERT: CP 552 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.8024 (ptm) REVERT: CQ 42 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7246 (mtp) REVERT: CR 70 LYS cc_start: 0.7168 (mtpp) cc_final: 0.6792 (mmtm) REVERT: CT 410 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7725 (mtt-85) REVERT: CU 336 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7640 (mp10) REVERT: CV 120 ARG cc_start: 0.7847 (tpp80) cc_final: 0.7509 (tpt-90) REVERT: CX 122 ARG cc_start: 0.7520 (mtt90) cc_final: 0.7299 (mtt90) REVERT: CY 732 ARG cc_start: 0.8894 (ptt-90) cc_final: 0.8480 (ptp-170) REVERT: Cb 331 MET cc_start: 0.8182 (tpp) cc_final: 0.7904 (tpt) REVERT: LB 84 MET cc_start: 0.8838 (mtm) cc_final: 0.8085 (mtm) REVERT: LB 137 TYR cc_start: 0.7250 (t80) cc_final: 0.6665 (t80) REVERT: LB 166 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7394 (mp10) REVERT: LB 283 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8119 (mt) REVERT: LC 43 MET cc_start: 0.9031 (ttm) cc_final: 0.8457 (mtt) REVERT: LC 321 ARG cc_start: 0.8275 (mtp85) cc_final: 0.7576 (mtm180) REVERT: LC 334 SER cc_start: 0.8464 (m) cc_final: 0.8190 (p) REVERT: LE 25 GLN cc_start: 0.6981 (mt0) cc_final: 0.6777 (mt0) REVERT: LG 101 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8194 (ttm170) REVERT: LG 246 GLN cc_start: 0.8008 (tp40) cc_final: 0.7587 (mm-40) REVERT: LM 61 ARG cc_start: 0.7527 (ttm-80) cc_final: 0.7183 (mpt180) REVERT: LM 112 LEU cc_start: 0.8882 (tt) cc_final: 0.8536 (tt) REVERT: LN 67 ARG cc_start: 0.7809 (mtt-85) cc_final: 0.7424 (mmm160) REVERT: LS 117 ARG cc_start: 0.7944 (mtt180) cc_final: 0.7384 (mtm180) REVERT: LT 134 MET cc_start: 0.8365 (mmp) cc_final: 0.7935 (mmt) REVERT: LV 59 MET cc_start: 0.8131 (ttm) cc_final: 0.7893 (ttp) REVERT: LY 4 ARG cc_start: 0.7571 (mtm180) cc_final: 0.6949 (mmt90) REVERT: Ld 24 LEU cc_start: 0.7902 (mt) cc_final: 0.7669 (mt) REVERT: Ld 79 ILE cc_start: 0.7472 (mt) cc_final: 0.6817 (pt) REVERT: Le 90 ASN cc_start: 0.8173 (m-40) cc_final: 0.7965 (m-40) REVERT: Lf 4 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7645 (mt-10) REVERT: Lh 49 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8048 (pt) REVERT: Lj 25 ARG cc_start: 0.7614 (mtp-110) cc_final: 0.7404 (mtp85) REVERT: Lq 63 MET cc_start: 0.5486 (mmm) cc_final: 0.4885 (mmm) REVERT: Lq 103 LEU cc_start: 0.8707 (tp) cc_final: 0.8155 (pp) REVERT: Lq 184 MET cc_start: 0.8373 (mmm) cc_final: 0.7946 (mmp) outliers start: 181 outliers final: 146 residues processed: 1095 average time/residue: 1.2132 time to fit residues: 2317.7128 Evaluate side-chains 1093 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 934 time to evaluate : 8.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 82 GLU Chi-restraints excluded: chain CA residue 122 THR Chi-restraints excluded: chain CB residue 74 ASP Chi-restraints excluded: chain CB residue 91 THR Chi-restraints excluded: chain CB residue 101 THR Chi-restraints excluded: chain CB residue 129 ASP Chi-restraints excluded: chain CB residue 254 LYS Chi-restraints excluded: chain CB residue 262 VAL Chi-restraints excluded: chain CC residue 338 MET Chi-restraints excluded: chain CC residue 411 TYR Chi-restraints excluded: chain CE residue 188 VAL Chi-restraints excluded: chain CE residue 218 ILE Chi-restraints excluded: chain CE residue 337 VAL Chi-restraints excluded: chain CE residue 366 SER Chi-restraints excluded: chain CE residue 367 CYS Chi-restraints excluded: chain CE residue 478 VAL Chi-restraints excluded: chain CE residue 490 ILE Chi-restraints excluded: chain CE residue 555 ILE Chi-restraints excluded: chain CF residue 9 VAL Chi-restraints excluded: chain CF residue 15 VAL Chi-restraints excluded: chain CF residue 72 LEU Chi-restraints excluded: chain CF residue 95 TYR Chi-restraints excluded: chain CF residue 137 VAL Chi-restraints excluded: chain CF residue 141 ILE Chi-restraints excluded: chain CG residue 5 THR Chi-restraints excluded: chain CG residue 6 ASP Chi-restraints excluded: chain CG residue 27 ILE Chi-restraints excluded: chain CH residue 54 GLU Chi-restraints excluded: chain CH residue 208 LEU Chi-restraints excluded: chain CH residue 285 VAL Chi-restraints excluded: chain CH residue 403 LEU Chi-restraints excluded: chain CH residue 469 GLU Chi-restraints excluded: chain CJ residue 37 CYS Chi-restraints excluded: chain CJ residue 371 THR Chi-restraints excluded: chain CK residue 42 LEU Chi-restraints excluded: chain CK residue 60 GLN Chi-restraints excluded: chain CK residue 121 ILE Chi-restraints excluded: chain CK residue 124 VAL Chi-restraints excluded: chain CK residue 137 LYS Chi-restraints excluded: chain CK residue 150 ILE Chi-restraints excluded: chain CK residue 252 ASP Chi-restraints excluded: chain CL residue 19 ARG Chi-restraints excluded: chain CL residue 35 GLU Chi-restraints excluded: chain CM residue 55 GLU Chi-restraints excluded: chain CN residue 39 GLU Chi-restraints excluded: chain CN residue 81 LEU Chi-restraints excluded: chain CN residue 109 VAL Chi-restraints excluded: chain CN residue 114 THR Chi-restraints excluded: chain CN residue 197 MET Chi-restraints excluded: chain CN residue 206 THR Chi-restraints excluded: chain CP residue 509 VAL Chi-restraints excluded: chain CP residue 516 CYS Chi-restraints excluded: chain CP residue 521 GLU Chi-restraints excluded: chain CP residue 524 VAL Chi-restraints excluded: chain CP residue 546 GLU Chi-restraints excluded: chain CP residue 549 THR Chi-restraints excluded: chain CP residue 552 MET Chi-restraints excluded: chain CP residue 571 TYR Chi-restraints excluded: chain CP residue 576 PHE Chi-restraints excluded: chain CQ residue 3 ILE Chi-restraints excluded: chain CQ residue 42 MET Chi-restraints excluded: chain CQ residue 68 THR Chi-restraints excluded: chain CQ residue 112 MET Chi-restraints excluded: chain CR residue 131 VAL Chi-restraints excluded: chain CS residue 718 ILE Chi-restraints excluded: chain CS residue 795 THR Chi-restraints excluded: chain CT residue 137 GLN Chi-restraints excluded: chain CT residue 244 THR Chi-restraints excluded: chain CT residue 410 ARG Chi-restraints excluded: chain CT residue 504 ASP Chi-restraints excluded: chain CT residue 603 VAL Chi-restraints excluded: chain CT residue 626 VAL Chi-restraints excluded: chain CT residue 663 LEU Chi-restraints excluded: chain CU residue 286 LYS Chi-restraints excluded: chain CU residue 336 GLN Chi-restraints excluded: chain CV residue 36 THR Chi-restraints excluded: chain CV residue 61 VAL Chi-restraints excluded: chain CV residue 86 THR Chi-restraints excluded: chain CV residue 96 SER Chi-restraints excluded: chain CX residue 80 VAL Chi-restraints excluded: chain CX residue 93 VAL Chi-restraints excluded: chain CY residue 415 VAL Chi-restraints excluded: chain CY residue 742 GLU Chi-restraints excluded: chain Cb residue 177 LEU Chi-restraints excluded: chain Cb residue 302 SER Chi-restraints excluded: chain Cb residue 481 LEU Chi-restraints excluded: chain Cb residue 503 ASP Chi-restraints excluded: chain Cb residue 512 VAL Chi-restraints excluded: chain Cb residue 603 ILE Chi-restraints excluded: chain LB residue 103 THR Chi-restraints excluded: chain LB residue 112 ASP Chi-restraints excluded: chain LB residue 158 VAL Chi-restraints excluded: chain LB residue 166 GLN Chi-restraints excluded: chain LB residue 189 VAL Chi-restraints excluded: chain LB residue 205 THR Chi-restraints excluded: chain LB residue 283 ILE Chi-restraints excluded: chain LB residue 329 VAL Chi-restraints excluded: chain LB residue 357 LEU Chi-restraints excluded: chain LB residue 359 TRP Chi-restraints excluded: chain LC residue 6 THR Chi-restraints excluded: chain LC residue 20 THR Chi-restraints excluded: chain LC residue 146 VAL Chi-restraints excluded: chain LC residue 158 VAL Chi-restraints excluded: chain LC residue 181 ASP Chi-restraints excluded: chain LC residue 211 ILE Chi-restraints excluded: chain LC residue 222 LEU Chi-restraints excluded: chain LE residue 52 LEU Chi-restraints excluded: chain LE residue 156 SER Chi-restraints excluded: chain LE residue 157 THR Chi-restraints excluded: chain LF residue 13 LEU Chi-restraints excluded: chain LF residue 14 VAL Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LF residue 94 ARG Chi-restraints excluded: chain LF residue 110 GLN Chi-restraints excluded: chain LF residue 174 ILE Chi-restraints excluded: chain LG residue 101 ARG Chi-restraints excluded: chain LH residue 55 VAL Chi-restraints excluded: chain LH residue 80 VAL Chi-restraints excluded: chain LH residue 89 VAL Chi-restraints excluded: chain LH residue 105 LEU Chi-restraints excluded: chain LH residue 127 MET Chi-restraints excluded: chain LH residue 185 LEU Chi-restraints excluded: chain LK residue 121 PHE Chi-restraints excluded: chain LK residue 125 LEU Chi-restraints excluded: chain LL residue 76 THR Chi-restraints excluded: chain LL residue 92 THR Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LM residue 57 VAL Chi-restraints excluded: chain LN residue 10 LEU Chi-restraints excluded: chain LN residue 149 ASN Chi-restraints excluded: chain LO residue 8 VAL Chi-restraints excluded: chain LO residue 66 ASN Chi-restraints excluded: chain LO residue 90 ILE Chi-restraints excluded: chain LO residue 131 LEU Chi-restraints excluded: chain LO residue 181 SER Chi-restraints excluded: chain LQ residue 108 VAL Chi-restraints excluded: chain LQ residue 160 THR Chi-restraints excluded: chain LS residue 8 GLN Chi-restraints excluded: chain LS residue 24 LEU Chi-restraints excluded: chain LS residue 79 LEU Chi-restraints excluded: chain LS residue 88 HIS Chi-restraints excluded: chain LT residue 156 TYR Chi-restraints excluded: chain LV residue 21 VAL Chi-restraints excluded: chain LV residue 79 VAL Chi-restraints excluded: chain LY residue 6 THR Chi-restraints excluded: chain LY residue 46 SER Chi-restraints excluded: chain LY residue 64 ASP Chi-restraints excluded: chain LY residue 90 THR Chi-restraints excluded: chain LY residue 128 VAL Chi-restraints excluded: chain Ld residue 44 ILE Chi-restraints excluded: chain Ld residue 116 VAL Chi-restraints excluded: chain Lf residue 29 THR Chi-restraints excluded: chain Lf residue 47 LEU Chi-restraints excluded: chain Lh residue 46 LEU Chi-restraints excluded: chain Lh residue 49 ILE Chi-restraints excluded: chain Lh residue 84 ASP Chi-restraints excluded: chain Lh residue 105 VAL Chi-restraints excluded: chain Lq residue 206 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1291 random chunks: chunk 1155 optimal weight: 1.9990 chunk 761 optimal weight: 0.8980 chunk 1226 optimal weight: 0.8980 chunk 748 optimal weight: 6.9990 chunk 581 optimal weight: 20.0000 chunk 852 optimal weight: 30.0000 chunk 1286 optimal weight: 9.9990 chunk 1183 optimal weight: 6.9990 chunk 1024 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 791 optimal weight: 6.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 148 GLN CB 33 HIS ** CB 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CF 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CF 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CH 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CH 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CH 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 153 ASN CK 203 ASN CN 82 GLN CS 665 GLN ** CV 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CY 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CY 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CY 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LC 264 GLN LE 78 GLN ** LE 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LO 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 13 HIS ** LS 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LV 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 47 ASN Li 47 GLN ** Lq 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 144476 Z= 0.298 Angle : 0.626 12.527 206691 Z= 0.320 Chirality : 0.040 0.371 25010 Planarity : 0.005 0.078 17391 Dihedral : 21.633 179.178 49529 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.59 % Favored : 95.29 % Rotamer: Outliers : 2.08 % Allowed : 17.67 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.01 % Twisted Proline : 0.37 % Twisted General : 0.00 % 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: 0.50 (0.08), residues: 10568 helix: 1.50 (0.07), residues: 4926 sheet: -0.31 (0.14), residues: 1235 loop : -0.80 (0.09), residues: 4407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRPCb 816 HIS 0.009 0.001 HISCN 118 PHE 0.028 0.002 PHECQ 107 TYR 0.048 0.002 TYRLO 65 ARG 0.011 0.001 ARGLO 64 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21136 Ramachandran restraints generated. 10568 Oldfield, 0 Emsley, 10568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21136 Ramachandran restraints generated. 10568 Oldfield, 0 Emsley, 10568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1124 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 939 time to evaluate : 10.438 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: CC 205 GLN cc_start: 0.8558 (tp40) cc_final: 0.8222 (tp40) REVERT: CC 233 ARG cc_start: 0.6656 (tpp-160) cc_final: 0.6166 (tpm170) REVERT: CC 324 TYR cc_start: 0.5933 (p90) cc_final: 0.5585 (p90) REVERT: CF 211 LEU cc_start: 0.8651 (mm) cc_final: 0.8235 (mm) REVERT: CG 106 GLN cc_start: 0.8301 (mm-40) cc_final: 0.7727 (tm-30) REVERT: CG 140 ILE cc_start: 0.8902 (mt) cc_final: 0.8687 (mt) REVERT: CH 54 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: CI 261 LYS cc_start: 0.8705 (mtmm) cc_final: 0.8323 (mttm) REVERT: CJ 227 MET cc_start: 0.7987 (pmm) cc_final: 0.7041 (ptp) REVERT: CJ 371 THR cc_start: 0.2177 (OUTLIER) cc_final: 0.1805 (t) REVERT: CK 42 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8440 (pp) REVERT: CK 137 LYS cc_start: 0.6595 (OUTLIER) cc_final: 0.5122 (tttp) REVERT: CK 147 TRP cc_start: 0.7265 (t60) cc_final: 0.6858 (t-100) REVERT: CL 45 TRP cc_start: 0.6870 (m-10) cc_final: 0.6648 (m-10) REVERT: CN 1 MET cc_start: 0.5622 (ptp) cc_final: 0.5249 (mtt) REVERT: CP 509 VAL cc_start: 0.7938 (OUTLIER) cc_final: 0.7667 (p) REVERT: CP 521 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: CQ 42 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7450 (mtp) REVERT: CT 410 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7880 (mtt-85) REVERT: CU 336 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7584 (mp10) REVERT: CV 106 ASP cc_start: 0.7105 (p0) cc_final: 0.6802 (p0) REVERT: CX 98 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.6933 (ttt-90) REVERT: CX 122 ARG cc_start: 0.7571 (mtt90) cc_final: 0.7336 (mtt90) REVERT: Cb 331 MET cc_start: 0.8208 (tpp) cc_final: 0.7907 (tpt) REVERT: LB 84 MET cc_start: 0.8842 (mtm) cc_final: 0.8520 (mtm) REVERT: LB 137 TYR cc_start: 0.7326 (t80) cc_final: 0.6690 (t80) REVERT: LB 166 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7248 (mp10) REVERT: LB 227 PHE cc_start: 0.7549 (OUTLIER) cc_final: 0.7215 (t80) REVERT: LB 283 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8157 (mt) REVERT: LC 43 MET cc_start: 0.9202 (ttm) cc_final: 0.8726 (mtt) REVERT: LE 25 GLN cc_start: 0.7016 (mt0) cc_final: 0.6793 (mt0) REVERT: LF 239 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7621 (mm-30) REVERT: LG 101 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.7790 (ttm170) REVERT: LG 246 GLN cc_start: 0.8101 (tp40) cc_final: 0.7717 (mm-40) REVERT: LM 61 ARG cc_start: 0.7576 (ttm-80) cc_final: 0.7170 (mpt180) REVERT: LM 112 LEU cc_start: 0.8950 (tt) cc_final: 0.8676 (tt) REVERT: LN 67 ARG cc_start: 0.7814 (mtt-85) cc_final: 0.7417 (mmm160) REVERT: LO 147 VAL cc_start: 0.8865 (p) cc_final: 0.8570 (m) REVERT: LS 117 ARG cc_start: 0.7938 (mtt180) cc_final: 0.7333 (mtm180) REVERT: LT 134 MET cc_start: 0.8426 (mmp) cc_final: 0.7975 (mmt) REVERT: LV 59 MET cc_start: 0.8160 (ttm) cc_final: 0.7891 (ttp) REVERT: LY 4 ARG cc_start: 0.7626 (mtm180) cc_final: 0.6989 (mmt90) REVERT: Ld 24 LEU cc_start: 0.7943 (mt) cc_final: 0.7705 (mt) REVERT: Ld 79 ILE cc_start: 0.7475 (mt) cc_final: 0.6781 (pt) REVERT: Lf 4 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7659 (mt-10) REVERT: Lh 49 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.8049 (pt) REVERT: Lj 25 ARG cc_start: 0.7747 (mtp-110) cc_final: 0.7544 (mtp85) REVERT: Lq 63 MET cc_start: 0.5558 (mmm) cc_final: 0.4835 (mmm) REVERT: Lq 103 LEU cc_start: 0.8755 (tp) cc_final: 0.8205 (pp) REVERT: Lq 184 MET cc_start: 0.8391 (mmm) cc_final: 0.7965 (mmp) outliers start: 185 outliers final: 151 residues processed: 1071 average time/residue: 1.1782 time to fit residues: 2202.1584 Evaluate side-chains 1095 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 928 time to evaluate : 8.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 82 GLU Chi-restraints excluded: chain CA residue 102 MET Chi-restraints excluded: chain CA residue 122 THR Chi-restraints excluded: chain CA residue 241 THR Chi-restraints excluded: chain CB residue 74 ASP Chi-restraints excluded: chain CB residue 101 THR Chi-restraints excluded: chain CB residue 262 VAL Chi-restraints excluded: chain CC residue 221 THR Chi-restraints excluded: chain CC residue 338 MET Chi-restraints excluded: chain CC residue 411 TYR Chi-restraints excluded: chain CE residue 188 VAL Chi-restraints excluded: chain CE residue 218 ILE Chi-restraints excluded: chain CE residue 234 VAL Chi-restraints excluded: chain CE residue 337 VAL Chi-restraints excluded: chain CE residue 366 SER Chi-restraints excluded: chain CE residue 367 CYS Chi-restraints excluded: chain CE residue 478 VAL Chi-restraints excluded: chain CE residue 490 ILE Chi-restraints excluded: chain CF residue 9 VAL Chi-restraints excluded: chain CF residue 15 VAL Chi-restraints excluded: chain CF residue 72 LEU Chi-restraints excluded: chain CF residue 95 TYR Chi-restraints excluded: chain CF residue 141 ILE Chi-restraints excluded: chain CG residue 5 THR Chi-restraints excluded: chain CG residue 6 ASP Chi-restraints excluded: chain CG residue 27 ILE Chi-restraints excluded: chain CH residue 54 GLU Chi-restraints excluded: chain CH residue 208 LEU Chi-restraints excluded: chain CH residue 285 VAL Chi-restraints excluded: chain CH residue 469 GLU Chi-restraints excluded: chain CJ residue 37 CYS Chi-restraints excluded: chain CJ residue 371 THR Chi-restraints excluded: chain CK residue 42 LEU Chi-restraints excluded: chain CK residue 60 GLN Chi-restraints excluded: chain CK residue 121 ILE Chi-restraints excluded: chain CK residue 124 VAL Chi-restraints excluded: chain CK residue 135 VAL Chi-restraints excluded: chain CK residue 137 LYS Chi-restraints excluded: chain CK residue 150 ILE Chi-restraints excluded: chain CK residue 252 ASP Chi-restraints excluded: chain CL residue 19 ARG Chi-restraints excluded: chain CL residue 35 GLU Chi-restraints excluded: chain CM residue 55 GLU Chi-restraints excluded: chain CN residue 39 GLU Chi-restraints excluded: chain CN residue 81 LEU Chi-restraints excluded: chain CN residue 109 VAL Chi-restraints excluded: chain CN residue 114 THR Chi-restraints excluded: chain CN residue 197 MET Chi-restraints excluded: chain CN residue 206 THR Chi-restraints excluded: chain CP residue 466 CYS Chi-restraints excluded: chain CP residue 509 VAL Chi-restraints excluded: chain CP residue 521 GLU Chi-restraints excluded: chain CP residue 524 VAL Chi-restraints excluded: chain CP residue 546 GLU Chi-restraints excluded: chain CP residue 549 THR Chi-restraints excluded: chain CP residue 571 TYR Chi-restraints excluded: chain CP residue 576 PHE Chi-restraints excluded: chain CQ residue 42 MET Chi-restraints excluded: chain CQ residue 68 THR Chi-restraints excluded: chain CQ residue 79 VAL Chi-restraints excluded: chain CR residue 131 VAL Chi-restraints excluded: chain CS residue 656 THR Chi-restraints excluded: chain CS residue 718 ILE Chi-restraints excluded: chain CS residue 795 THR Chi-restraints excluded: chain CT residue 137 GLN Chi-restraints excluded: chain CT residue 244 THR Chi-restraints excluded: chain CT residue 410 ARG Chi-restraints excluded: chain CT residue 504 ASP Chi-restraints excluded: chain CT residue 603 VAL Chi-restraints excluded: chain CT residue 626 VAL Chi-restraints excluded: chain CT residue 663 LEU Chi-restraints excluded: chain CU residue 220 VAL Chi-restraints excluded: chain CU residue 256 SER Chi-restraints excluded: chain CU residue 286 LYS Chi-restraints excluded: chain CU residue 336 GLN Chi-restraints excluded: chain CV residue 20 LEU Chi-restraints excluded: chain CV residue 36 THR Chi-restraints excluded: chain CV residue 61 VAL Chi-restraints excluded: chain CV residue 80 THR Chi-restraints excluded: chain CV residue 86 THR Chi-restraints excluded: chain CV residue 96 SER Chi-restraints excluded: chain CX residue 80 VAL Chi-restraints excluded: chain CX residue 93 VAL Chi-restraints excluded: chain CX residue 98 ARG Chi-restraints excluded: chain CY residue 415 VAL Chi-restraints excluded: chain CY residue 742 GLU Chi-restraints excluded: chain Cb residue 177 LEU Chi-restraints excluded: chain Cb residue 302 SER Chi-restraints excluded: chain Cb residue 481 LEU Chi-restraints excluded: chain Cb residue 503 ASP Chi-restraints excluded: chain Cb residue 512 VAL Chi-restraints excluded: chain Cb residue 603 ILE Chi-restraints excluded: chain Cb residue 873 VAL Chi-restraints excluded: chain LB residue 103 THR Chi-restraints excluded: chain LB residue 112 ASP Chi-restraints excluded: chain LB residue 158 VAL Chi-restraints excluded: chain LB residue 166 GLN Chi-restraints excluded: chain LB residue 189 VAL Chi-restraints excluded: chain LB residue 205 THR Chi-restraints excluded: chain LB residue 211 GLU Chi-restraints excluded: chain LB residue 227 PHE Chi-restraints excluded: chain LB residue 283 ILE Chi-restraints excluded: chain LB residue 329 VAL Chi-restraints excluded: chain LB residue 357 LEU Chi-restraints excluded: chain LB residue 359 TRP Chi-restraints excluded: chain LC residue 6 THR Chi-restraints excluded: chain LC residue 20 THR Chi-restraints excluded: chain LC residue 146 VAL Chi-restraints excluded: chain LC residue 158 VAL Chi-restraints excluded: chain LC residue 211 ILE Chi-restraints excluded: chain LC residue 222 LEU Chi-restraints excluded: chain LC residue 223 VAL Chi-restraints excluded: chain LE residue 32 ASP Chi-restraints excluded: chain LE residue 52 LEU Chi-restraints excluded: chain LE residue 115 ASP Chi-restraints excluded: chain LE residue 156 SER Chi-restraints excluded: chain LF residue 13 LEU Chi-restraints excluded: chain LF residue 14 VAL Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LF residue 94 ARG Chi-restraints excluded: chain LF residue 110 GLN Chi-restraints excluded: chain LF residue 174 ILE Chi-restraints excluded: chain LF residue 239 GLU Chi-restraints excluded: chain LG residue 101 ARG Chi-restraints excluded: chain LH residue 55 VAL Chi-restraints excluded: chain LH residue 80 VAL Chi-restraints excluded: chain LH residue 89 VAL Chi-restraints excluded: chain LH residue 127 MET Chi-restraints excluded: chain LH residue 185 LEU Chi-restraints excluded: chain LK residue 125 LEU Chi-restraints excluded: chain LL residue 76 THR Chi-restraints excluded: chain LL residue 92 THR Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LM residue 24 ASN Chi-restraints excluded: chain LM residue 57 VAL Chi-restraints excluded: chain LN residue 10 LEU Chi-restraints excluded: chain LN residue 149 ASN Chi-restraints excluded: chain LO residue 8 VAL Chi-restraints excluded: chain LO residue 121 VAL Chi-restraints excluded: chain LO residue 131 LEU Chi-restraints excluded: chain LO residue 181 SER Chi-restraints excluded: chain LQ residue 108 VAL Chi-restraints excluded: chain LQ residue 160 THR Chi-restraints excluded: chain LS residue 8 GLN Chi-restraints excluded: chain LS residue 24 LEU Chi-restraints excluded: chain LS residue 27 MET Chi-restraints excluded: chain LS residue 79 LEU Chi-restraints excluded: chain LS residue 88 HIS Chi-restraints excluded: chain LT residue 74 VAL Chi-restraints excluded: chain LT residue 156 TYR Chi-restraints excluded: chain LV residue 21 VAL Chi-restraints excluded: chain LV residue 79 VAL Chi-restraints excluded: chain LV residue 80 ILE Chi-restraints excluded: chain LY residue 6 THR Chi-restraints excluded: chain LY residue 46 SER Chi-restraints excluded: chain LY residue 64 ASP Chi-restraints excluded: chain LY residue 90 THR Chi-restraints excluded: chain LY residue 128 VAL Chi-restraints excluded: chain Ld residue 44 ILE Chi-restraints excluded: chain Ld residue 116 VAL Chi-restraints excluded: chain Lf residue 29 THR Chi-restraints excluded: chain Lh residue 46 LEU Chi-restraints excluded: chain Lh residue 49 ILE Chi-restraints excluded: chain Lh residue 84 ASP Chi-restraints excluded: chain Lh residue 105 VAL Chi-restraints excluded: chain Lq residue 206 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1291 random chunks: chunk 627 optimal weight: 9.9990 chunk 813 optimal weight: 8.9990 chunk 1090 optimal weight: 0.9980 chunk 313 optimal weight: 0.0980 chunk 944 optimal weight: 0.8980 chunk 151 optimal weight: 50.0000 chunk 284 optimal weight: 4.9990 chunk 1025 optimal weight: 9.9990 chunk 429 optimal weight: 5.9990 chunk 1053 optimal weight: 7.9990 chunk 129 optimal weight: 30.0000 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 148 GLN CB 33 HIS ** CB 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CF 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CF 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CH 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CH 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CH 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 153 ASN CK 203 ASN CN 82 GLN CQ 24 ASN CS 665 GLN ** CV 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CY 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CY 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CY 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LC 264 GLN LE 78 GLN ** LE 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LO 66 ASN LS 13 HIS ** LS 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LV 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LV 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Le 90 ASN Lh 47 ASN Li 47 GLN ** Lq 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.158944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.144064 restraints weight = 207641.758| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 0.91 r_work: 0.3617 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 144476 Z= 0.245 Angle : 0.594 15.890 206691 Z= 0.303 Chirality : 0.038 0.381 25010 Planarity : 0.005 0.077 17391 Dihedral : 21.636 179.615 49529 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.48 % Favored : 95.42 % Rotamer: Outliers : 2.20 % Allowed : 17.56 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.01 % Twisted Proline : 0.37 % Twisted General : 0.00 % 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: 0.52 (0.08), residues: 10568 helix: 1.52 (0.07), residues: 4931 sheet: -0.32 (0.14), residues: 1222 loop : -0.78 (0.09), residues: 4415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRPCb 816 HIS 0.009 0.001 HISCN 118 PHE 0.027 0.001 PHECQ 107 TYR 0.041 0.002 TYRCP 279 ARG 0.009 0.000 ARGCV 139 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 38072.75 seconds wall clock time: 665 minutes 34.96 seconds (39934.96 seconds total)