Starting phenix.real_space_refine on Fri Mar 15 21:08:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ard_11880/03_2024/7ard_11880_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ard_11880/03_2024/7ard_11880.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ard_11880/03_2024/7ard_11880_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ard_11880/03_2024/7ard_11880_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ard_11880/03_2024/7ard_11880_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ard_11880/03_2024/7ard_11880.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ard_11880/03_2024/7ard_11880.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ard_11880/03_2024/7ard_11880_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ard_11880/03_2024/7ard_11880_updated.pdb" } resolution = 3.11 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= 0.002 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: 7 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 30 5.49 5 S 359 5.16 5 C 45058 2.51 5 N 11534 2.21 5 O 13549 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 38": "OD1" <-> "OD2" Residue "A TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 19": "OD1" <-> "OD2" Residue "B GLU 43": "OE1" <-> "OE2" Residue "C TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C GLU 140": "OE1" <-> "OE2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "C ASP 207": "OD1" <-> "OD2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 138": "OE1" <-> "OE2" Residue "D ASP 175": "OD1" <-> "OD2" Residue "D GLU 192": "OE1" <-> "OE2" Residue "D GLU 202": "OE1" <-> "OE2" Residue "D GLU 268": "OE1" <-> "OE2" Residue "D ASP 378": "OD1" <-> "OD2" Residue "E ASP 174": "OD1" <-> "OD2" Residue "E TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 224": "OE1" <-> "OE2" Residue "E GLU 259": "OE1" <-> "OE2" Residue "F GLU 65": "OE1" <-> "OE2" Residue "F ASP 69": "OD1" <-> "OD2" Residue "F GLU 127": "OE1" <-> "OE2" Residue "F GLU 129": "OE1" <-> "OE2" Residue "F GLU 222": "OE1" <-> "OE2" Residue "G GLU 223": "OE1" <-> "OE2" Residue "G GLU 295": "OE1" <-> "OE2" Residue "G TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 335": "OD1" <-> "OD2" Residue "G ASP 381": "OD1" <-> "OD2" Residue "G ASP 561": "OD1" <-> "OD2" Residue "G TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 202": "OE1" <-> "OE2" Residue "H PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 82": "OD1" <-> "OD2" Residue "I PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 212": "OD1" <-> "OD2" Residue "K TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 119": "OE1" <-> "OE2" Residue "L ASP 176": "OD1" <-> "OD2" Residue "L TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 431": "OD1" <-> "OD2" Residue "L PHE 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 178": "OE1" <-> "OE2" Residue "M GLU 207": "OE1" <-> "OE2" Residue "N TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 156": "OD1" <-> "OD2" Residue "N GLU 179": "OE1" <-> "OE2" Residue "N GLU 255": "OE1" <-> "OE2" Residue "O PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 157": "OE1" <-> "OE2" Residue "O ASP 159": "OD1" <-> "OD2" Residue "P TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 220": "OD1" <-> "OD2" Residue "P GLU 245": "OE1" <-> "OE2" Residue "P PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 39": "OE1" <-> "OE2" Residue "Q GLU 131": "OE1" <-> "OE2" Residue "Q TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 123": "OD1" <-> "OD2" Residue "S ASP 77": "OD1" <-> "OD2" Residue "S GLU 87": "OE1" <-> "OE2" Residue "T GLU 50": "OE1" <-> "OE2" Residue "T ASP 100": "OD1" <-> "OD2" Residue "U GLU 110": "OE1" <-> "OE2" Residue "V ASP 35": "OD1" <-> "OD2" Residue "V ASP 49": "OD1" <-> "OD2" Residue "V ASP 137": "OD1" <-> "OD2" Residue "V TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 10": "OE1" <-> "OE2" Residue "X GLU 25": "OE1" <-> "OE2" Residue "X GLU 45": "OE1" <-> "OE2" Residue "X PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 26": "OE1" <-> "OE2" Residue "Y ASP 47": "OD1" <-> "OD2" Residue "Y TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 172": "OE1" <-> "OE2" Residue "Y TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 36": "OE1" <-> "OE2" Residue "Z PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 41": "OD1" <-> "OD2" Residue "c TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 36": "OE1" <-> "OE2" Residue "c TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 101": "OD1" <-> "OD2" Residue "d ASP 51": "OD1" <-> "OD2" Residue "d ASP 55": "OD1" <-> "OD2" Residue "d GLU 60": "OE1" <-> "OE2" Residue "f TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 102": "OD1" <-> "OD2" Residue "g TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 119": "OD1" <-> "OD2" Residue "h TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 19": "OD1" <-> "OD2" Residue "i GLU 58": "OE1" <-> "OE2" Residue "i TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 38": "OD1" <-> "OD2" Residue "l PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 137": "OE1" <-> "OE2" Residue "m GLU 76": "OE1" <-> "OE2" Residue "m ASP 86": "OD1" <-> "OD2" Residue "m ASP 110": "OD1" <-> "OD2" Residue "m TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 117": "OE1" <-> "OE2" Residue "m TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 67": "OE1" <-> "OE2" Residue "n ASP 99": "OD1" <-> "OD2" Residue "n TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 18": "OD1" <-> "OD2" Residue "p GLU 7": "OE1" <-> "OE2" Residue "p GLU 68": "OE1" <-> "OE2" Residue "r ASP 92": "OD1" <-> "OD2" Residue "s TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 205": "OE1" <-> "OE2" Residue "y GLU 242": "OE1" <-> "OE2" Residue "z TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z GLU 76": "OE1" <-> "OE2" Residue "z ASP 210": "OD1" <-> "OD2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 70559 Number of models: 1 Model: "" Number of chains: 116 Chain: "A" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 999 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "B" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1206 Classifications: {'peptide': 154} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 143} Chain: "C" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1808 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain: "D" Number of atoms: 3178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3178 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain: "E" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1806 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 13, 'TRANS': 221} Chain: "F" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3322 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 19, 'TRANS': 410} Chain: "G" Number of atoms: 5166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 682, 5166 Classifications: {'peptide': 682} Link IDs: {'PTRANS': 27, 'TRANS': 654} Chain: "H" Number of atoms: 2237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2237 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 12, 'TRANS': 280} Chain: "I" Number of atoms: 1602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1602 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 9, 'TRANS': 189} Chain: "J" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1120 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 142} Chain: "K" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 798 Classifications: {'peptide': 104} Link IDs: {'TRANS': 103} Chain: "L" Number of atoms: 4111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4111 Classifications: {'peptide': 536} Link IDs: {'PTRANS': 10, 'TRANS': 525} Chain: "M" Number of atoms: 3425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3425 Classifications: {'peptide': 438} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 423} Chain: "N" Number of atoms: 2967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2967 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 7, 'TRANS': 367} Chain: "O" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1336 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 9, 'TRANS': 151} Chain: "P" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2701 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 16, 'TRANS': 330} Chain: "Q" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1276 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 11, 'TRANS': 150} Chain: "R" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "S" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 716 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "T" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 645 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "U" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 655 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "V" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1052 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "W" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1074 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "X" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "Y" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1583 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 16, 'TRANS': 188} Chain: "Z" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1003 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 11, 'TRANS': 112} Chain: "a" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 515 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "b" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 270 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'TRANS': 53} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'UNK:plan-1': 54} Unresolved non-hydrogen planarities: 54 Chain: "c" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 785 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 11, 'TRANS': 85} Chain: "d" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 650 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "e" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 592 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "f" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 877 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "g" Number of atoms: 1176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1176 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 10, 'TRANS': 136} Chain: "h" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "i" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 922 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "j" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 435 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'TRANS': 86} Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 87 Planarities with less than four sites: {'UNK:plan-1': 87} Unresolved non-hydrogen planarities: 87 Chain: "k" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 367 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain: "l" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1018 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 14, 'TRANS': 112} Chain: "m" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 934 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "n" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1008 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "o" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 704 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "p" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1287 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "q" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 243 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 4, 'TRANS': 23} Chain: "r" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 493 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 5, 'TRANS': 54} Chain: "s" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 933 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 12, 'TRANS': 102} Chain: "t" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 706 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 7, 'TRANS': 74} Chain: "u" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 250 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'TRANS': 49} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'UNK:plan-1': 50} Unresolved non-hydrogen planarities: 50 Chain: "w" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 204 Classifications: {'peptide': 41} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 40} Link IDs: {'TRANS': 40} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 41} Unresolved non-hydrogen planarities: 41 Chain: "x" Number of atoms: 1967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1967 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 11, 'TRANS': 238} Chain: "y" Number of atoms: 2316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2316 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 20, 'TRANS': 287} Chain: "z" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1687 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'PC7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 187 Unusual residues: {'CDL': 1, 'PC7': 1, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "M" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 251 Unusual residues: {'CDL': 1, 'PC7': 2, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "N" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 254 Unusual residues: {'CDL': 1, 'PC7': 2, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 100 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "n" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "t" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PC7': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "F" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "G" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 114 Classifications: {'water': 114} Link IDs: {None: 113} Chain: "H" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "L" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "N" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "O" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "P" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "Q" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "S" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "T" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "W" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "Z" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "a" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "c" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "d" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "e" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "g" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "h" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "i" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "l" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "m" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "n" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "p" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "q" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "r" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "s" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "t" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "x" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "z" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1723 SG CYS B 104 71.973 92.935 107.559 1.00 15.55 S ATOM 1226 SG CYS B 40 72.937 91.574 101.292 1.00 23.10 S ATOM 1951 SG CYS B 134 70.592 87.817 106.027 1.00 18.20 S ATOM 1220 SG CYS B 39 76.978 88.707 105.309 1.00 21.68 S ATOM 8025 SG CYS E 143 35.469 32.592 134.912 1.00 38.70 S ATOM 8056 SG CYS E 148 36.003 29.132 134.614 1.00 38.58 S ATOM 8320 SG CYS E 184 37.879 32.474 139.850 1.00 35.13 S ATOM 8343 SG CYS E 188 38.853 29.221 139.666 1.00 41.60 S ATOM 11720 SG CYS F 390 49.306 52.164 141.422 1.00 18.61 S ATOM 11740 SG CYS F 393 47.521 47.885 138.768 1.00 21.20 S ATOM 11701 SG CYS F 387 42.811 50.735 142.520 1.00 21.51 S ATOM 12072 SG CYS F 433 46.968 47.319 145.249 1.00 21.23 S ATOM 12601 SG CYS G 76 49.898 62.393 144.038 1.00 34.47 S ATOM 12688 SG CYS G 87 52.644 61.653 141.813 1.00 20.77 S ATOM 12713 SG CYS G 90 55.584 60.840 146.267 1.00 24.19 S ATOM 12815 SG CYS G 104 52.691 61.791 148.474 1.00 25.45 S ATOM 13150 SG CYS G 149 52.187 69.847 130.911 1.00 20.71 S ATOM 13089 SG CYS G 140 53.358 68.540 124.605 1.00 15.52 S ATOM 13110 SG CYS G 143 47.772 71.368 127.061 1.00 18.53 S ATOM 13462 SG CYS G 188 42.526 63.571 134.451 1.00 16.47 S ATOM 13486 SG CYS G 191 45.913 65.451 139.155 1.00 15.70 S ATOM 13510 SG CYS G 194 39.763 66.948 139.169 1.00 12.10 S ATOM 13841 SG CYS G 238 44.333 69.738 134.992 1.00 17.66 S ATOM 20880 SG CYS I 175 59.922 80.228 109.229 1.00 18.47 S ATOM 20833 SG CYS I 169 62.628 85.608 106.949 1.00 16.39 S ATOM 20859 SG CYS I 172 65.932 81.229 110.529 1.00 15.11 S ATOM 20603 SG CYS I 140 61.679 85.120 113.186 1.00 14.33 S ATOM 20909 SG CYS I 179 54.085 74.519 111.197 1.00 18.15 S ATOM 20532 SG CYS I 130 49.399 78.838 112.108 1.00 19.48 S ATOM 20575 SG CYS I 136 55.525 80.537 113.635 1.00 14.28 S ATOM 20552 SG CYS I 133 53.212 75.886 116.818 1.00 14.56 S ATOM 39738 SG CYS R 113 42.719 65.571 113.789 1.00 38.16 S Time building chain proxies: 29.38, per 1000 atoms: 0.42 Number of scatterers: 70559 At special positions: 0 Unit cell: (221.805, 262.818, 191.673, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 359 16.00 P 30 15.00 O 13549 8.00 N 11534 7.00 C 45058 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS e 13 " - pdb=" SG CYS e 49 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 22.85 Conformation dependent library (CDL) restraints added in 9.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 500 " pdb="FE1 FES E 500 " - pdb=" SG CYS E 143 " pdb="FE1 FES E 500 " - pdb=" SG CYS E 148 " pdb="FE2 FES E 500 " - pdb=" SG CYS E 184 " pdb="FE2 FES E 500 " - pdb=" SG CYS E 188 " pdb=" FES G 801 " pdb="FE1 FES G 801 " - pdb=" SG CYS G 87 " pdb="FE2 FES G 801 " - pdb=" SG CYS G 90 " pdb="FE1 FES G 801 " - pdb=" SG CYS G 76 " pdb="FE2 FES G 801 " - pdb=" SG CYS G 104 " pdb=" SF4 B 500 " pdb="FE3 SF4 B 500 " - pdb=" SG CYS B 134 " pdb="FE2 SF4 B 500 " - pdb=" SG CYS B 40 " pdb="FE1 SF4 B 500 " - pdb=" SG CYS B 104 " pdb="FE4 SF4 B 500 " - pdb=" SG CYS B 39 " pdb=" SF4 F 501 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 387 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 390 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 433 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 393 " pdb=" SF4 G 802 " pdb="FE2 SF4 G 802 " - pdb=" NE2 HIS G 136 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 140 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 143 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 149 " pdb=" SF4 G 803 " pdb="FE1 SF4 G 803 " - pdb=" SG CYS G 188 " pdb="FE4 SF4 G 803 " - pdb=" SG CYS G 238 " pdb="FE2 SF4 G 803 " - pdb=" SG CYS G 191 " pdb="FE3 SF4 G 803 " - pdb=" SG CYS G 194 " pdb=" SF4 I 500 " pdb="FE4 SF4 I 500 " - pdb=" SG CYS I 140 " pdb="FE2 SF4 I 500 " - pdb=" SG CYS I 169 " pdb="FE1 SF4 I 500 " - pdb=" SG CYS I 175 " pdb="FE3 SF4 I 500 " - pdb=" SG CYS I 172 " pdb=" SF4 I 501 " pdb="FE4 SF4 I 501 " - pdb=" SG CYS I 133 " pdb="FE2 SF4 I 501 " - pdb=" SG CYS I 130 " pdb="FE3 SF4 I 501 " - pdb=" SG CYS I 136 " pdb="FE1 SF4 I 501 " - pdb=" SG CYS I 179 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN R 200 " pdb="ZN ZN R 200 " - pdb=" SG CYS R 113 " 16834 Ramachandran restraints generated. 8417 Oldfield, 0 Emsley, 8417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16312 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 349 helices and 45 sheets defined 52.3% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.61 Creating SS restraints... Processing helix chain 'A' and resid 22 through 28 Processing helix chain 'A' and resid 43 through 65 Proline residue: A 63 - end of helix Processing helix chain 'A' and resid 96 through 118 Proline residue: A 116 - end of helix Processing helix chain 'A' and resid 124 through 146 Processing helix chain 'B' and resid 12 through 28 Processing helix chain 'B' and resid 39 through 47 removed outlier: 3.724A pdb=" N GLU B 43 " --> pdb=" O CYS B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 57 No H-bonds generated for 'chain 'B' and resid 54 through 57' Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 82 through 91 Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'B' and resid 109 through 111 No H-bonds generated for 'chain 'B' and resid 109 through 111' Processing helix chain 'B' and resid 121 through 123 No H-bonds generated for 'chain 'B' and resid 121 through 123' Processing helix chain 'B' and resid 138 through 154 Processing helix chain 'B' and resid 157 through 162 Processing helix chain 'C' and resid 18 through 25 removed outlier: 4.307A pdb=" N GLY C 24 " --> pdb=" O ILE C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 35 Processing helix chain 'C' and resid 63 through 75 removed outlier: 3.522A pdb=" N ILE C 66 " --> pdb=" O PRO C 63 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR C 67 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG C 74 " --> pdb=" O ALA C 71 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP C 75 " --> pdb=" O PHE C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 147 removed outlier: 3.518A pdb=" N ASN C 137 " --> pdb=" O ASN C 134 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TRP C 138 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET C 146 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE C 147 " --> pdb=" O TRP C 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 58 removed outlier: 3.730A pdb=" N GLU D 57 " --> pdb=" O GLU D 53 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 71 removed outlier: 3.613A pdb=" N ILE D 65 " --> pdb=" O ASN D 62 " (cutoff:3.500A) Proline residue: D 66 - end of helix removed outlier: 3.510A pdb=" N ASP D 69 " --> pdb=" O PRO D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 91 removed outlier: 3.566A pdb=" N SER D 82 " --> pdb=" O CYS D 78 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR D 83 " --> pdb=" O MET D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 126 Processing helix chain 'D' and resid 130 through 150 removed outlier: 4.052A pdb=" N GLU D 137 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLU D 138 " --> pdb=" O TRP D 134 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE D 145 " --> pdb=" O LYS D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 194 removed outlier: 4.315A pdb=" N ALA D 184 " --> pdb=" O SER D 180 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N SER D 185 " --> pdb=" O ARG D 181 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU D 193 " --> pdb=" O GLU D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 Processing helix chain 'D' and resid 212 through 218 Processing helix chain 'D' and resid 223 through 226 No H-bonds generated for 'chain 'D' and resid 223 through 226' Processing helix chain 'D' and resid 234 through 237 No H-bonds generated for 'chain 'D' and resid 234 through 237' Processing helix chain 'D' and resid 242 through 244 No H-bonds generated for 'chain 'D' and resid 242 through 244' Processing helix chain 'D' and resid 258 through 282 Processing helix chain 'D' and resid 300 through 305 Processing helix chain 'D' and resid 307 through 318 Processing helix chain 'D' and resid 359 through 370 removed outlier: 3.742A pdb=" N HIS D 363 " --> pdb=" O PRO D 359 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASP D 368 " --> pdb=" O LEU D 364 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N MET D 369 " --> pdb=" O GLN D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 386 removed outlier: 4.394A pdb=" N VAL D 380 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR D 381 " --> pdb=" O ALA D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 393 No H-bonds generated for 'chain 'D' and resid 390 through 393' Processing helix chain 'E' and resid 64 through 76 removed outlier: 3.878A pdb=" N ASN E 76 " --> pdb=" O LYS E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 96 removed outlier: 4.758A pdb=" N ILE E 87 " --> pdb=" O SER E 84 " (cutoff:3.500A) Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 103 through 113 Processing helix chain 'E' and resid 117 through 126 Processing helix chain 'E' and resid 146 through 151 removed outlier: 3.866A pdb=" N GLN E 151 " --> pdb=" O PRO E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 164 Processing helix chain 'E' and resid 216 through 228 Processing helix chain 'F' and resid 45 through 47 No H-bonds generated for 'chain 'F' and resid 45 through 47' Processing helix chain 'F' and resid 61 through 67 Processing helix chain 'F' and resid 73 through 78 Processing helix chain 'F' and resid 81 through 91 Processing helix chain 'F' and resid 103 through 108 Processing helix chain 'F' and resid 134 through 141 removed outlier: 3.658A pdb=" N ILE F 138 " --> pdb=" O LYS F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 157 Processing helix chain 'F' and resid 171 through 186 Processing helix chain 'F' and resid 194 through 196 No H-bonds generated for 'chain 'F' and resid 194 through 196' Processing helix chain 'F' and resid 212 through 215 Processing helix chain 'F' and resid 217 through 225 Processing helix chain 'F' and resid 243 through 245 No H-bonds generated for 'chain 'F' and resid 243 through 245' Processing helix chain 'F' and resid 253 through 265 Proline residue: F 260 - end of helix Processing helix chain 'F' and resid 267 through 273 removed outlier: 4.140A pdb=" N PHE F 273 " --> pdb=" O TRP F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 310 Processing helix chain 'F' and resid 337 through 342 removed outlier: 4.205A pdb=" N ASP F 342 " --> pdb=" O LYS F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 352 Processing helix chain 'F' and resid 371 through 385 Processing helix chain 'F' and resid 391 through 409 removed outlier: 4.444A pdb=" N GLY F 398 " --> pdb=" O ARG F 394 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS F 409 " --> pdb=" O SER F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 427 Processing helix chain 'F' and resid 435 through 449 Proline residue: F 442 - end of helix Processing helix chain 'F' and resid 451 through 463 Processing helix chain 'G' and resid 61 through 67 Processing helix chain 'G' and resid 119 through 134 Processing helix chain 'G' and resid 150 through 158 Processing helix chain 'G' and resid 185 through 187 No H-bonds generated for 'chain 'G' and resid 185 through 187' Processing helix chain 'G' and resid 193 through 200 Processing helix chain 'G' and resid 213 through 215 No H-bonds generated for 'chain 'G' and resid 213 through 215' Processing helix chain 'G' and resid 231 through 237 Processing helix chain 'G' and resid 254 through 256 No H-bonds generated for 'chain 'G' and resid 254 through 256' Processing helix chain 'G' and resid 300 through 309 removed outlier: 4.985A pdb=" N TYR G 306 " --> pdb=" O GLY G 302 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASP G 307 " --> pdb=" O ARG G 303 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N GLY G 308 " --> pdb=" O PHE G 304 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU G 309 " --> pdb=" O GLN G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 343 removed outlier: 3.850A pdb=" N GLY G 343 " --> pdb=" O THR G 339 " (cutoff:3.500A) Processing helix chain 'G' and resid 346 through 348 No H-bonds generated for 'chain 'G' and resid 346 through 348' Processing helix chain 'G' and resid 359 through 372 Processing helix chain 'G' and resid 391 through 393 No H-bonds generated for 'chain 'G' and resid 391 through 393' Processing helix chain 'G' and resid 401 through 405 Processing helix chain 'G' and resid 416 through 419 No H-bonds generated for 'chain 'G' and resid 416 through 419' Processing helix chain 'G' and resid 421 through 433 Processing helix chain 'G' and resid 457 through 465 Processing helix chain 'G' and resid 469 through 476 Processing helix chain 'G' and resid 486 through 489 No H-bonds generated for 'chain 'G' and resid 486 through 489' Processing helix chain 'G' and resid 494 through 508 Processing helix chain 'G' and resid 526 through 533 Processing helix chain 'G' and resid 539 through 543 Processing helix chain 'G' and resid 561 through 563 No H-bonds generated for 'chain 'G' and resid 561 through 563' Processing helix chain 'G' and resid 579 through 582 No H-bonds generated for 'chain 'G' and resid 579 through 582' Processing helix chain 'G' and resid 623 through 634 Processing helix chain 'G' and resid 643 through 653 Processing helix chain 'G' and resid 655 through 658 Processing helix chain 'G' and resid 670 through 676 Processing helix chain 'G' and resid 678 through 683 Processing helix chain 'G' and resid 703 through 707 Processing helix chain 'G' and resid 709 through 718 Processing helix chain 'H' and resid 3 through 30 removed outlier: 5.201A pdb=" N LEU H 10 " --> pdb=" O MET H 7 " (cutoff:3.500A) Proline residue: H 11 - end of helix removed outlier: 3.581A pdb=" N GLU H 23 " --> pdb=" O THR H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 56 removed outlier: 3.676A pdb=" N ASP H 50 " --> pdb=" O GLN H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 89 Proline residue: H 74 - end of helix Processing helix chain 'H' and resid 96 through 105 Processing helix chain 'H' and resid 107 through 118 removed outlier: 4.004A pdb=" N VAL H 111 " --> pdb=" O ALA H 107 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N CYS H 118 " --> pdb=" O ALA H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 151 removed outlier: 3.751A pdb=" N LEU H 125 " --> pdb=" O LYS H 121 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL H 140 " --> pdb=" O SER H 136 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU H 150 " --> pdb=" O LEU H 146 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU H 151 " --> pdb=" O CYS H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 168 Processing helix chain 'H' and resid 174 through 188 removed outlier: 3.758A pdb=" N LEU H 179 " --> pdb=" O PRO H 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 194 No H-bonds generated for 'chain 'H' and resid 192 through 194' Processing helix chain 'H' and resid 196 through 202 removed outlier: 3.606A pdb=" N GLU H 200 " --> pdb=" O LEU H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 210 No H-bonds generated for 'chain 'H' and resid 208 through 210' Processing helix chain 'H' and resid 214 through 238 Processing helix chain 'H' and resid 244 through 259 Processing helix chain 'H' and resid 266 through 275 Processing helix chain 'H' and resid 277 through 289 Processing helix chain 'I' and resid 42 through 50 Processing helix chain 'I' and resid 67 through 78 Processing helix chain 'I' and resid 81 through 95 removed outlier: 3.500A pdb=" N TYR I 89 " --> pdb=" O ARG I 85 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY I 93 " --> pdb=" O TYR I 89 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE I 94 " --> pdb=" O SER I 90 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE I 95 " --> pdb=" O ALA I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 139 Processing helix chain 'I' and resid 174 through 178 Processing helix chain 'I' and resid 197 through 200 Processing helix chain 'I' and resid 204 through 213 Processing helix chain 'I' and resid 215 through 228 removed outlier: 4.130A pdb=" N LEU I 227 " --> pdb=" O ARG I 223 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TYR I 228 " --> pdb=" O THR I 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 20 removed outlier: 4.402A pdb=" N VAL J 12 " --> pdb=" O LEU J 8 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL J 13 " --> pdb=" O SER J 9 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL J 18 " --> pdb=" O LEU J 14 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL J 19 " --> pdb=" O ALA J 15 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 45 Processing helix chain 'J' and resid 49 through 57 Processing helix chain 'J' and resid 62 through 72 Processing helix chain 'J' and resid 85 through 98 Processing helix chain 'J' and resid 114 through 122 Processing helix chain 'J' and resid 126 through 144 Processing helix chain 'K' and resid 26 through 51 removed outlier: 4.687A pdb=" N ALA K 49 " --> pdb=" O GLY K 45 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N VAL K 50 " --> pdb=" O ILE K 46 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 81 Processing helix chain 'K' and resid 85 through 113 Processing helix chain 'L' and resid 2 through 18 removed outlier: 4.119A pdb=" N ALA L 5 " --> pdb=" O PHE L 2 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN L 16 " --> pdb=" O ALA L 13 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE L 18 " --> pdb=" O ALA L 15 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 50 removed outlier: 6.768A pdb=" N VAL L 25 " --> pdb=" O ARG L 21 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N ARG L 26 " --> pdb=" O TYR L 22 " (cutoff:3.500A) Proline residue: L 33 - end of helix Processing helix chain 'L' and resid 81 through 104 removed outlier: 3.730A pdb=" N ASN L 102 " --> pdb=" O HIS L 98 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU L 103 " --> pdb=" O ALA L 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 130 Processing helix chain 'L' and resid 134 through 154 removed outlier: 3.548A pdb=" N GLY L 153 " --> pdb=" O TYR L 149 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TYR L 154 " --> pdb=" O LEU L 150 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 190 Processing helix chain 'L' and resid 205 through 218 removed outlier: 3.844A pdb=" N GLY L 217 " --> pdb=" O LEU L 213 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LYS L 218 " --> pdb=" O GLY L 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 226 through 233 removed outlier: 3.741A pdb=" N ASP L 230 " --> pdb=" O VAL L 226 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N MET L 232 " --> pdb=" O LEU L 228 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N GLU L 233 " --> pdb=" O ALA L 229 " (cutoff:3.500A) Processing helix chain 'L' and resid 236 through 244 Processing helix chain 'L' and resid 248 through 257 removed outlier: 4.495A pdb=" N ILE L 252 " --> pdb=" O VAL L 248 " (cutoff:3.500A) Processing helix chain 'L' and resid 263 through 283 removed outlier: 3.518A pdb=" N ILE L 268 " --> pdb=" O SER L 264 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA L 283 " --> pdb=" O LEU L 279 " (cutoff:3.500A) Processing helix chain 'L' and resid 287 through 308 removed outlier: 3.636A pdb=" N ILE L 291 " --> pdb=" O LEU L 287 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU L 306 " --> pdb=" O MET L 302 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER L 307 " --> pdb=" O MET L 303 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR L 308 " --> pdb=" O ALA L 304 " (cutoff:3.500A) Processing helix chain 'L' and resid 310 through 341 removed outlier: 4.011A pdb=" N ALA L 313 " --> pdb=" O ASP L 310 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA L 324 " --> pdb=" O VAL L 321 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE L 326 " --> pdb=" O HIS L 323 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS L 327 " --> pdb=" O ALA L 324 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER L 333 " --> pdb=" O LEU L 330 " (cutoff:3.500A) Processing helix chain 'L' and resid 346 through 348 No H-bonds generated for 'chain 'L' and resid 346 through 348' Processing helix chain 'L' and resid 356 through 370 Processing helix chain 'L' and resid 376 through 387 removed outlier: 3.803A pdb=" N ILE L 384 " --> pdb=" O SER L 380 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN L 387 " --> pdb=" O SER L 383 " (cutoff:3.500A) Processing helix chain 'L' and resid 392 through 416 Processing helix chain 'L' and resid 434 through 453 removed outlier: 3.552A pdb=" N ILE L 451 " --> pdb=" O MET L 447 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE L 452 " --> pdb=" O LEU L 448 " (cutoff:3.500A) Processing helix chain 'L' and resid 467 through 470 No H-bonds generated for 'chain 'L' and resid 467 through 470' Processing helix chain 'L' and resid 472 through 485 Processing helix chain 'L' and resid 493 through 500 Processing helix chain 'L' and resid 502 through 511 removed outlier: 4.008A pdb=" N PHE L 505 " --> pdb=" O ARG L 502 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ASP L 506 " --> pdb=" O GLY L 503 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL L 507 " --> pdb=" O GLY L 504 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE L 508 " --> pdb=" O PHE L 505 " (cutoff:3.500A) Processing helix chain 'L' and resid 513 through 525 Processing helix chain 'M' and resid 2 through 17 Proline residue: M 12 - end of helix removed outlier: 3.749A pdb=" N LEU M 15 " --> pdb=" O GLN M 11 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER M 16 " --> pdb=" O PRO M 12 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE M 17 " --> pdb=" O LEU M 13 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 43 Processing helix chain 'M' and resid 69 through 87 Proline residue: M 83 - end of helix Processing helix chain 'M' and resid 92 through 110 removed outlier: 3.836A pdb=" N VAL M 110 " --> pdb=" O SER M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 114 through 123 Processing helix chain 'M' and resid 126 through 132 Processing helix chain 'M' and resid 140 through 167 Processing helix chain 'M' and resid 182 through 195 removed outlier: 4.254A pdb=" N LEU M 191 " --> pdb=" O GLY M 187 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU M 192 " --> pdb=" O ILE M 188 " (cutoff:3.500A) Processing helix chain 'M' and resid 203 through 211 removed outlier: 4.074A pdb=" N GLU M 207 " --> pdb=" O LEU M 203 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 222 Processing helix chain 'M' and resid 226 through 235 removed outlier: 3.609A pdb=" N HIS M 233 " --> pdb=" O VAL M 230 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL M 234 " --> pdb=" O GLY M 231 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE M 235 " --> pdb=" O LEU M 232 " (cutoff:3.500A) Processing helix chain 'M' and resid 241 through 246 Processing helix chain 'M' and resid 248 through 268 removed outlier: 3.512A pdb=" N LEU M 267 " --> pdb=" O SER M 263 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS M 268 " --> pdb=" O PHE M 264 " (cutoff:3.500A) Processing helix chain 'M' and resid 272 through 292 removed outlier: 3.745A pdb=" N ALA M 285 " --> pdb=" O ILE M 281 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE M 286 " --> pdb=" O SER M 282 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL M 287 " --> pdb=" O HIS M 283 " (cutoff:3.500A) Processing helix chain 'M' and resid 296 through 327 Proline residue: M 314 - end of helix Processing helix chain 'M' and resid 338 through 341 No H-bonds generated for 'chain 'M' and resid 338 through 341' Processing helix chain 'M' and resid 343 through 356 Processing helix chain 'M' and resid 363 through 378 Processing helix chain 'M' and resid 380 through 405 removed outlier: 4.476A pdb=" N PHE M 391 " --> pdb=" O ILE M 387 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N VAL M 392 " --> pdb=" O PHE M 388 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY M 393 " --> pdb=" O PHE M 389 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR M 394 " --> pdb=" O SER M 390 " (cutoff:3.500A) Processing helix chain 'M' and resid 417 through 434 Proline residue: M 425 - end of helix Processing helix chain 'N' and resid 2 through 23 removed outlier: 3.734A pdb=" N TRP N 6 " --> pdb=" O TRP N 2 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TYR N 7 " --> pdb=" O GLU N 3 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE N 10 " --> pdb=" O TRP N 6 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU N 11 " --> pdb=" O TYR N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 33 through 46 removed outlier: 3.519A pdb=" N VAL N 44 " --> pdb=" O ILE N 40 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY N 45 " --> pdb=" O ILE N 41 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLY N 46 " --> pdb=" O SER N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 65 removed outlier: 4.084A pdb=" N ASN N 65 " --> pdb=" O LEU N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 69 through 87 Processing helix chain 'N' and resid 91 through 112 Processing helix chain 'N' and resid 115 through 150 removed outlier: 4.729A pdb=" N TRP N 119 " --> pdb=" O ASN N 116 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE N 120 " --> pdb=" O GLN N 117 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA N 121 " --> pdb=" O ARG N 118 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N TYR N 122 " --> pdb=" O TRP N 119 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER N 150 " --> pdb=" O TYR N 147 " (cutoff:3.500A) Processing helix chain 'N' and resid 158 through 168 Processing helix chain 'N' and resid 171 through 173 No H-bonds generated for 'chain 'N' and resid 171 through 173' Processing helix chain 'N' and resid 175 through 183 removed outlier: 4.009A pdb=" N VAL N 183 " --> pdb=" O GLU N 179 " (cutoff:3.500A) Processing helix chain 'N' and resid 186 through 207 removed outlier: 3.509A pdb=" N THR N 194 " --> pdb=" O PHE N 190 " (cutoff:3.500A) Proline residue: N 196 - end of helix removed outlier: 4.213A pdb=" N SER N 199 " --> pdb=" O LEU N 195 " (cutoff:3.500A) Processing helix chain 'N' and resid 215 through 230 Processing helix chain 'N' and resid 234 through 255 removed outlier: 3.552A pdb=" N SER N 242 " --> pdb=" O LEU N 238 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL N 243 " --> pdb=" O LEU N 239 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU N 255 " --> pdb=" O LEU N 251 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 276 removed outlier: 3.805A pdb=" N SER N 266 " --> pdb=" O PHE N 262 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLY N 274 " --> pdb=" O LEU N 270 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL N 275 " --> pdb=" O SER N 271 " (cutoff:3.500A) Processing helix chain 'N' and resid 281 through 292 Processing helix chain 'N' and resid 298 through 313 removed outlier: 3.522A pdb=" N ILE N 306 " --> pdb=" O GLY N 302 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER N 312 " --> pdb=" O LYS N 308 " (cutoff:3.500A) Processing helix chain 'N' and resid 316 through 341 removed outlier: 3.598A pdb=" N GLY N 332 " --> pdb=" O ILE N 328 " (cutoff:3.500A) Processing helix chain 'N' and resid 357 through 374 removed outlier: 4.499A pdb=" N THR N 368 " --> pdb=" O LEU N 364 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N LEU N 369 " --> pdb=" O THR N 365 " (cutoff:3.500A) Proline residue: N 370 - end of helix removed outlier: 5.131A pdb=" N TYR N 373 " --> pdb=" O LEU N 369 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N SER N 374 " --> pdb=" O PRO N 370 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 84 Processing helix chain 'O' and resid 88 through 90 No H-bonds generated for 'chain 'O' and resid 88 through 90' Processing helix chain 'O' and resid 111 through 116 removed outlier: 4.519A pdb=" N LYS O 115 " --> pdb=" O GLU O 112 " (cutoff:3.500A) Processing helix chain 'O' and resid 126 through 136 Processing helix chain 'O' and resid 139 through 141 No H-bonds generated for 'chain 'O' and resid 139 through 141' Processing helix chain 'O' and resid 149 through 151 No H-bonds generated for 'chain 'O' and resid 149 through 151' Processing helix chain 'O' and resid 156 through 158 No H-bonds generated for 'chain 'O' and resid 156 through 158' Processing helix chain 'P' and resid 12 through 15 No H-bonds generated for 'chain 'P' and resid 12 through 15' Processing helix chain 'P' and resid 38 through 50 removed outlier: 3.941A pdb=" N TYR P 42 " --> pdb=" O PHE P 38 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG P 50 " --> pdb=" O GLU P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 66 through 71 removed outlier: 4.079A pdb=" N GLN P 70 " --> pdb=" O GLN P 66 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET P 71 " --> pdb=" O PRO P 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 66 through 71' Processing helix chain 'P' and resid 88 through 94 Processing helix chain 'P' and resid 116 through 134 removed outlier: 4.193A pdb=" N PHE P 123 " --> pdb=" O VAL P 119 " (cutoff:3.500A) Proline residue: P 124 - end of helix removed outlier: 3.561A pdb=" N SER P 134 " --> pdb=" O ILE P 130 " (cutoff:3.500A) Processing helix chain 'P' and resid 155 through 170 removed outlier: 3.534A pdb=" N ALA P 161 " --> pdb=" O LEU P 157 " (cutoff:3.500A) Processing helix chain 'P' and resid 190 through 199 Processing helix chain 'P' and resid 218 through 229 Processing helix chain 'P' and resid 249 through 260 Processing helix chain 'P' and resid 275 through 278 No H-bonds generated for 'chain 'P' and resid 275 through 278' Processing helix chain 'P' and resid 280 through 288 removed outlier: 3.806A pdb=" N THR P 284 " --> pdb=" O LYS P 280 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS P 288 " --> pdb=" O THR P 284 " (cutoff:3.500A) Processing helix chain 'P' and resid 301 through 306 Processing helix chain 'P' and resid 333 through 342 removed outlier: 4.411A pdb=" N GLY P 338 " --> pdb=" O ALA P 335 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 40 Processing helix chain 'Q' and resid 50 through 55 removed outlier: 3.507A pdb=" N SER Q 54 " --> pdb=" O ASP Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 59 through 61 No H-bonds generated for 'chain 'Q' and resid 59 through 61' Processing helix chain 'Q' and resid 120 through 124 Processing helix chain 'Q' and resid 130 through 140 Processing helix chain 'Q' and resid 163 through 167 removed outlier: 4.237A pdb=" N TYR Q 167 " --> pdb=" O TYR Q 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 163 through 167' Processing helix chain 'Q' and resid 169 through 171 No H-bonds generated for 'chain 'Q' and resid 169 through 171' Processing helix chain 'Q' and resid 181 through 184 No H-bonds generated for 'chain 'Q' and resid 181 through 184' Processing helix chain 'R' and resid 54 through 58 removed outlier: 3.954A pdb=" N TRP R 58 " --> pdb=" O HIS R 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 54 through 58' Processing helix chain 'R' and resid 66 through 72 Processing helix chain 'R' and resid 124 through 126 No H-bonds generated for 'chain 'R' and resid 124 through 126' Processing helix chain 'S' and resid 4 through 10 removed outlier: 3.790A pdb=" N LEU S 7 " --> pdb=" O LYS S 4 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR S 8 " --> pdb=" O THR S 5 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR S 9 " --> pdb=" O ALA S 6 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 42 removed outlier: 3.530A pdb=" N TYR S 36 " --> pdb=" O VAL S 32 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA S 37 " --> pdb=" O LEU S 33 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N GLU S 38 " --> pdb=" O GLY S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 67 No H-bonds generated for 'chain 'S' and resid 65 through 67' Processing helix chain 'S' and resid 79 through 95 Processing helix chain 'T' and resid 45 through 58 removed outlier: 4.249A pdb=" N HIS T 58 " --> pdb=" O HIS T 54 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 76 No H-bonds generated for 'chain 'T' and resid 73 through 76' Processing helix chain 'T' and resid 80 through 94 Processing helix chain 'T' and resid 100 through 105 removed outlier: 3.512A pdb=" N LYS T 105 " --> pdb=" O ASN T 101 " (cutoff:3.500A) Processing helix chain 'T' and resid 109 through 118 Processing helix chain 'U' and resid 44 through 57 Processing helix chain 'U' and resid 80 through 93 Processing helix chain 'U' and resid 100 through 105 Processing helix chain 'U' and resid 109 through 118 Processing helix chain 'V' and resid 41 through 46 Processing helix chain 'V' and resid 48 through 51 No H-bonds generated for 'chain 'V' and resid 48 through 51' Processing helix chain 'V' and resid 58 through 73 removed outlier: 3.762A pdb=" N LYS V 73 " --> pdb=" O LEU V 69 " (cutoff:3.500A) Processing helix chain 'V' and resid 80 through 98 Processing helix chain 'V' and resid 102 through 109 Processing helix chain 'V' and resid 113 through 133 removed outlier: 3.731A pdb=" N SER V 120 " --> pdb=" O LEU V 116 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS V 121 " --> pdb=" O ILE V 117 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE V 126 " --> pdb=" O GLU V 122 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU V 127 " --> pdb=" O GLU V 123 " (cutoff:3.500A) Proline residue: V 128 - end of helix removed outlier: 3.678A pdb=" N SER V 133 " --> pdb=" O VAL V 129 " (cutoff:3.500A) Processing helix chain 'V' and resid 152 through 157 Processing helix chain 'W' and resid 22 through 40 Proline residue: W 35 - end of helix Processing helix chain 'W' and resid 49 through 63 removed outlier: 3.518A pdb=" N ILE W 55 " --> pdb=" O GLU W 51 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS W 57 " --> pdb=" O ARG W 53 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP W 58 " --> pdb=" O LEU W 54 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ASN W 63 " --> pdb=" O LYS W 59 " (cutoff:3.500A) Processing helix chain 'W' and resid 69 through 87 removed outlier: 3.756A pdb=" N TYR W 86 " --> pdb=" O GLU W 82 " (cutoff:3.500A) Processing helix chain 'W' and resid 93 through 99 Processing helix chain 'W' and resid 101 through 109 Processing helix chain 'W' and resid 119 through 126 Processing helix chain 'X' and resid 8 through 13 Processing helix chain 'X' and resid 15 through 21 removed outlier: 3.798A pdb=" N VAL X 19 " --> pdb=" O ALA X 15 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE X 20 " --> pdb=" O LYS X 16 " (cutoff:3.500A) Processing helix chain 'X' and resid 23 through 35 Processing helix chain 'X' and resid 43 through 63 Processing helix chain 'X' and resid 65 through 77 Processing helix chain 'X' and resid 83 through 95 removed outlier: 3.794A pdb=" N ARG X 86 " --> pdb=" O SER X 83 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N GLU X 87 " --> pdb=" O LYS X 84 " (cutoff:3.500A) Processing helix chain 'Y' and resid 37 through 43 Processing helix chain 'Y' and resid 48 through 77 Proline residue: Y 57 - end of helix removed outlier: 3.656A pdb=" N ARG Y 77 " --> pdb=" O LEU Y 73 " (cutoff:3.500A) Processing helix chain 'Y' and resid 88 through 121 Proline residue: Y 94 - end of helix Processing helix chain 'Y' and resid 126 through 140 Processing helix chain 'Y' and resid 146 through 167 removed outlier: 4.254A pdb=" N LEU Y 150 " --> pdb=" O LEU Y 146 " (cutoff:3.500A) Proline residue: Y 153 - end of helix Proline residue: Y 160 - end of helix Processing helix chain 'Y' and resid 169 through 173 Processing helix chain 'Z' and resid 46 through 113 removed outlier: 3.647A pdb=" N ARG Z 72 " --> pdb=" O LYS Z 68 " (cutoff:3.500A) Proline residue: Z 87 - end of helix Processing helix chain 'a' and resid 5 through 31 Processing helix chain 'a' and resid 34 through 36 No H-bonds generated for 'chain 'a' and resid 34 through 36' Processing helix chain 'a' and resid 42 through 62 Processing helix chain 'b' and resid 3 through 53 removed outlier: 3.885A pdb=" N UNK b 10 " --> pdb=" O UNK b 6 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N UNK b 53 " --> pdb=" O UNK b 49 " (cutoff:3.500A) Processing helix chain 'c' and resid 15 through 18 Processing helix chain 'c' and resid 51 through 76 Processing helix chain 'c' and resid 88 through 91 Processing helix chain 'd' and resid 6 through 24 Processing helix chain 'd' and resid 33 through 68 removed outlier: 3.676A pdb=" N VAL d 37 " --> pdb=" O PRO d 33 " (cutoff:3.500A) Processing helix chain 'd' and resid 74 through 79 Processing helix chain 'e' and resid 14 through 26 Processing helix chain 'e' and resid 32 through 38 Processing helix chain 'e' and resid 40 through 51 Processing helix chain 'e' and resid 53 through 71 Processing helix chain 'f' and resid 35 through 41 Processing helix chain 'f' and resid 44 through 68 removed outlier: 3.763A pdb=" N LYS f 67 " --> pdb=" O TYR f 63 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY f 68 " --> pdb=" O LEU f 64 " (cutoff:3.500A) Processing helix chain 'f' and resid 71 through 99 Processing helix chain 'f' and resid 105 through 110 Processing helix chain 'g' and resid 46 through 48 No H-bonds generated for 'chain 'g' and resid 46 through 48' Processing helix chain 'g' and resid 64 through 84 Processing helix chain 'g' and resid 92 through 116 removed outlier: 3.736A pdb=" N ALA g 96 " --> pdb=" O PRO g 92 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR g 97 " --> pdb=" O SER g 93 " (cutoff:3.500A) Proline residue: g 98 - end of helix Processing helix chain 'g' and resid 118 through 130 Processing helix chain 'g' and resid 135 through 143 removed outlier: 4.127A pdb=" N TYR g 139 " --> pdb=" O GLU g 136 " (cutoff:3.500A) Processing helix chain 'g' and resid 148 through 156 removed outlier: 3.576A pdb=" N HIS g 155 " --> pdb=" O LEU g 151 " (cutoff:3.500A) Processing helix chain 'g' and resid 161 through 170 Processing helix chain 'h' and resid 16 through 19 No H-bonds generated for 'chain 'h' and resid 16 through 19' Processing helix chain 'h' and resid 35 through 49 Proline residue: h 47 - end of helix Processing helix chain 'h' and resid 51 through 80 removed outlier: 3.528A pdb=" N SER h 80 " --> pdb=" O ALA h 76 " (cutoff:3.500A) Processing helix chain 'i' and resid 20 through 41 Processing helix chain 'i' and resid 84 through 92 Processing helix chain 'i' and resid 103 through 119 Processing helix chain 'j' and resid 38 through 61 Processing helix chain 'j' and resid 63 through 67 Processing helix chain 'j' and resid 70 through 79 removed outlier: 3.798A pdb=" N UNK j 79 " --> pdb=" O UNK j 75 " (cutoff:3.500A) Processing helix chain 'k' and resid 9 through 12 No H-bonds generated for 'chain 'k' and resid 9 through 12' Processing helix chain 'k' and resid 14 through 17 removed outlier: 3.780A pdb=" N TYR k 17 " --> pdb=" O ALA k 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 14 through 17' Processing helix chain 'k' and resid 19 through 21 No H-bonds generated for 'chain 'k' and resid 19 through 21' Processing helix chain 'k' and resid 25 through 28 No H-bonds generated for 'chain 'k' and resid 25 through 28' Processing helix chain 'k' and resid 32 through 46 Processing helix chain 'l' and resid 45 through 47 No H-bonds generated for 'chain 'l' and resid 45 through 47' Processing helix chain 'l' and resid 68 through 70 No H-bonds generated for 'chain 'l' and resid 68 through 70' Processing helix chain 'l' and resid 73 through 95 Proline residue: l 85 - end of helix Proline residue: l 90 - end of helix removed outlier: 3.596A pdb=" N TYR l 93 " --> pdb=" O ALA l 89 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU l 94 " --> pdb=" O PRO l 90 " (cutoff:3.500A) Processing helix chain 'l' and resid 100 through 103 No H-bonds generated for 'chain 'l' and resid 100 through 103' Processing helix chain 'l' and resid 113 through 121 removed outlier: 3.503A pdb=" N PHE l 118 " --> pdb=" O GLU l 114 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU l 121 " --> pdb=" O GLU l 117 " (cutoff:3.500A) Processing helix chain 'l' and resid 136 through 143 Processing helix chain 'm' and resid 52 through 55 removed outlier: 3.561A pdb=" N SER m 55 " --> pdb=" O ARG m 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 52 through 55' Processing helix chain 'm' and resid 61 through 71 Processing helix chain 'm' and resid 81 through 113 removed outlier: 3.717A pdb=" N GLY m 93 " --> pdb=" O THR m 89 " (cutoff:3.500A) Processing helix chain 'n' and resid 4 through 7 No H-bonds generated for 'chain 'n' and resid 4 through 7' Processing helix chain 'n' and resid 11 through 29 Processing helix chain 'n' and resid 33 through 50 removed outlier: 3.848A pdb=" N TYR n 37 " --> pdb=" O ARG n 33 " (cutoff:3.500A) Proline residue: n 38 - end of helix removed outlier: 4.105A pdb=" N ASN n 50 " --> pdb=" O GLU n 46 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 72 Processing helix chain 'n' and resid 106 through 108 No H-bonds generated for 'chain 'n' and resid 106 through 108' Processing helix chain 'o' and resid 14 through 19 Processing helix chain 'o' and resid 24 through 26 No H-bonds generated for 'chain 'o' and resid 24 through 26' Processing helix chain 'o' and resid 31 through 43 Processing helix chain 'o' and resid 48 through 51 No H-bonds generated for 'chain 'o' and resid 48 through 51' Processing helix chain 'o' and resid 54 through 80 Processing helix chain 'p' and resid 6 through 25 Processing helix chain 'p' and resid 45 through 47 No H-bonds generated for 'chain 'p' and resid 45 through 47' Processing helix chain 'p' and resid 49 through 84 Processing helix chain 'p' and resid 88 through 91 No H-bonds generated for 'chain 'p' and resid 88 through 91' Processing helix chain 'p' and resid 93 through 109 Processing helix chain 'p' and resid 123 through 139 Processing helix chain 'r' and resid 70 through 72 No H-bonds generated for 'chain 'r' and resid 70 through 72' Processing helix chain 'r' and resid 93 through 98 Processing helix chain 'r' and resid 104 through 106 No H-bonds generated for 'chain 'r' and resid 104 through 106' Processing helix chain 's' and resid 5 through 8 No H-bonds generated for 'chain 's' and resid 5 through 8' Processing helix chain 's' and resid 48 through 53 Processing helix chain 's' and resid 67 through 70 Processing helix chain 's' and resid 72 through 105 removed outlier: 3.576A pdb=" N ILE s 90 " --> pdb=" O LEU s 86 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N HIS s 93 " --> pdb=" O ALA s 89 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N TYR s 94 " --> pdb=" O ILE s 90 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL s 104 " --> pdb=" O ILE s 100 " (cutoff:3.500A) Processing helix chain 't' and resid 63 through 73 removed outlier: 4.380A pdb=" N TYR t 73 " --> pdb=" O PHE t 69 " (cutoff:3.500A) Processing helix chain 't' and resid 81 through 100 removed outlier: 3.581A pdb=" N TYR t 86 " --> pdb=" O HIS t 82 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA t 99 " --> pdb=" O VAL t 95 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP t 100 " --> pdb=" O TYR t 96 " (cutoff:3.500A) Processing helix chain 't' and resid 106 through 119 Processing helix chain 't' and resid 123 through 129 Processing helix chain 'u' and resid 2 through 49 removed outlier: 3.885A pdb=" N UNK u 6 " --> pdb=" O UNK u 2 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N UNK u 49 " --> pdb=" O UNK u 45 " (cutoff:3.500A) Processing helix chain 'w' and resid 5 through 26 Processing helix chain 'w' and resid 31 through 40 Processing helix chain 'x' and resid 47 through 49 No H-bonds generated for 'chain 'x' and resid 47 through 49' Processing helix chain 'x' and resid 207 through 230 removed outlier: 4.920A pdb=" N ILE x 214 " --> pdb=" O THR x 210 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ARG x 215 " --> pdb=" O SER x 211 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA x 218 " --> pdb=" O ILE x 214 " (cutoff:3.500A) Processing helix chain 'x' and resid 239 through 251 Processing helix chain 'x' and resid 260 through 277 Processing helix chain 'y' and resid 9 through 12 No H-bonds generated for 'chain 'y' and resid 9 through 12' Processing helix chain 'y' and resid 23 through 50 removed outlier: 3.635A pdb=" N MET y 49 " --> pdb=" O LEU y 45 " (cutoff:3.500A) Processing helix chain 'y' and resid 86 through 92 Processing helix chain 'y' and resid 241 through 265 removed outlier: 3.936A pdb=" N GLY y 245 " --> pdb=" O PRO y 241 " (cutoff:3.500A) Processing helix chain 'y' and resid 269 through 286 Processing helix chain 'y' and resid 291 through 295 Processing helix chain 'z' and resid 3 through 31 Processing helix chain 'z' and resid 35 through 37 No H-bonds generated for 'chain 'z' and resid 35 through 37' Processing helix chain 'z' and resid 191 through 226 removed outlier: 3.758A pdb=" N PHE z 197 " --> pdb=" O GLU z 193 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ASN z 198 " --> pdb=" O LEU z 194 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR z 199 " --> pdb=" O ALA z 195 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE z 225 " --> pdb=" O LYS z 221 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 32 through 36 removed outlier: 6.639A pdb=" N VAL B 70 " --> pdb=" O MET B 33 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N PHE B 35 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE B 72 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TRP B 97 " --> pdb=" O MET B 71 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N VAL B 73 " --> pdb=" O TRP B 97 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL B 99 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL B 129 " --> pdb=" O SER B 100 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 83 through 91 removed outlier: 6.823A pdb=" N HIS C 104 " --> pdb=" O ILE C 85 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE C 87 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL C 102 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA C 89 " --> pdb=" O GLU C 100 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLU C 100 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ARG C 113 " --> pdb=" O GLN C 55 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL C 119 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY C 46 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET C 42 " --> pdb=" O TYR C 60 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 125 through 127 removed outlier: 6.605A pdb=" N PHE C 150 " --> pdb=" O VAL C 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'C' and resid 181 through 186 removed outlier: 3.923A pdb=" N ARG C 191 " --> pdb=" O ASP C 186 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 326 through 334 removed outlier: 3.523A pdb=" N GLY D 340 " --> pdb=" O ARG D 357 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 11 through 16 removed outlier: 3.830A pdb=" N ASN D 11 " --> pdb=" O MET D 33 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR D 13 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LEU D 31 " --> pdb=" O THR D 13 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASN D 15 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU D 29 " --> pdb=" O ASN D 15 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG D 28 " --> pdb=" O HIS D 44 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ASP D 34 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ILE D 38 " --> pdb=" O ASP D 34 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 177 through 182 removed outlier: 6.744A pdb=" N TYR E 138 " --> pdb=" O THR E 178 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N GLY E 180 " --> pdb=" O TYR E 138 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL E 140 " --> pdb=" O GLY E 180 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N MET E 182 " --> pdb=" O VAL E 140 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ILE E 142 " --> pdb=" O MET E 182 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 247 through 249 Processing sheet with id= I, first strand: chain 'F' and resid 248 through 252 removed outlier: 6.989A pdb=" N TYR F 120 " --> pdb=" O THR F 249 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N THR F 251 " --> pdb=" O TYR F 120 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL F 122 " --> pdb=" O THR F 251 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA F 161 " --> pdb=" O LEU F 121 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N VAL F 123 " --> pdb=" O ALA F 161 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TYR F 163 " --> pdb=" O VAL F 123 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLY F 125 " --> pdb=" O TYR F 163 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N TYR F 165 " --> pdb=" O GLY F 125 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASP F 202 " --> pdb=" O GLY F 162 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ILE F 164 " --> pdb=" O ASP F 202 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N PHE F 204 " --> pdb=" O ILE F 164 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE F 166 " --> pdb=" O PHE F 204 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N HIS F 206 " --> pdb=" O ILE F 166 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'F' and resid 294 through 299 removed outlier: 3.829A pdb=" N ALA F 324 " --> pdb=" O MET F 365 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 43 through 48 Processing sheet with id= L, first strand: chain 'G' and resid 181 through 183 Processing sheet with id= M, first strand: chain 'G' and resid 208 through 210 removed outlier: 3.699A pdb=" N GLY G 208 " --> pdb=" O GLY G 219 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 258 through 263 removed outlier: 6.274A pdb=" N ARG G 278 " --> pdb=" O VAL G 282 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N VAL G 282 " --> pdb=" O ARG G 278 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 318 through 321 Processing sheet with id= P, first strand: chain 'G' and resid 376 through 379 removed outlier: 4.504A pdb=" N ASN G 376 " --> pdb=" O LEU G 349 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL G 550 " --> pdb=" O LYS G 350 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE G 352 " --> pdb=" O VAL G 550 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N TYR G 552 " --> pdb=" O ILE G 352 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N PHE G 569 " --> pdb=" O VAL G 551 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU G 553 " --> pdb=" O PHE G 569 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE G 571 " --> pdb=" O LEU G 553 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL G 586 " --> pdb=" O TYR G 572 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N GLY G 574 " --> pdb=" O VAL G 586 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU G 588 " --> pdb=" O GLY G 574 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 436 through 439 Processing sheet with id= R, first strand: chain 'G' and resid 599 through 601 Processing sheet with id= S, first strand: chain 'I' and resid 118 through 120 Processing sheet with id= T, first strand: chain 'I' and resid 145 through 151 removed outlier: 6.065A pdb=" N GLU I 150 " --> pdb=" O THR I 159 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N THR I 159 " --> pdb=" O GLU I 150 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'L' and resid 66 through 68 Processing sheet with id= V, first strand: chain 'L' and resid 57 through 62 removed outlier: 3.560A pdb=" N THR L 57 " --> pdb=" O TYR L 79 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ALA L 75 " --> pdb=" O LEU L 61 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'M' and resid 54 through 57 removed outlier: 3.819A pdb=" N GLN M 54 " --> pdb=" O VAL M 67 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'O' and resid 66 through 72 Processing sheet with id= Y, first strand: chain 'O' and resid 106 through 108 Processing sheet with id= Z, first strand: chain 'P' and resid 238 through 241 removed outlier: 6.594A pdb=" N ILE P 176 " --> pdb=" O TYR P 239 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU P 241 " --> pdb=" O ILE P 176 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ARG P 178 " --> pdb=" O LEU P 241 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLN P 53 " --> pdb=" O ALA P 30 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL P 32 " --> pdb=" O GLN P 53 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL P 55 " --> pdb=" O VAL P 32 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'P' and resid 203 through 206 Processing sheet with id= AB, first strand: chain 'Q' and resid 93 through 97 removed outlier: 4.335A pdb=" N CYS Q 70 " --> pdb=" O ASP Q 147 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'Q' and resid 102 through 104 Processing sheet with id= AD, first strand: chain 'R' and resid 76 through 78 Processing sheet with id= AE, first strand: chain 'R' and resid 82 through 85 Processing sheet with id= AF, first strand: chain 'S' and resid 47 through 53 removed outlier: 3.553A pdb=" N GLU S 13 " --> pdb=" O ARG S 63 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'i' and resid 60 through 64 Processing sheet with id= AH, first strand: chain 'j' and resid 24 through 26 Processing sheet with id= AI, first strand: chain 'x' and resid 79 through 82 Processing sheet with id= AJ, first strand: chain 'x' and resid 84 through 86 removed outlier: 6.776A pdb=" N ILE x 105 " --> pdb=" O ASP x 85 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR x 133 " --> pdb=" O ARG x 106 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain 'x' and resid 192 through 195 removed outlier: 3.621A pdb=" N ARG x 203 " --> pdb=" O LEU x 193 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA x 195 " --> pdb=" O PHE x 201 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE x 201 " --> pdb=" O ALA x 195 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'y' and resid 80 through 83 Processing sheet with id= AM, first strand: chain 'y' and resid 113 through 116 Processing sheet with id= AN, first strand: chain 'y' and resid 118 through 120 removed outlier: 6.573A pdb=" N ILE y 139 " --> pdb=" O LYS y 119 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N THR y 167 " --> pdb=" O GLU y 140 " (cutoff:3.500A) No H-bonds generated for sheet with id= AN Processing sheet with id= AO, first strand: chain 'y' and resid 226 through 229 removed outlier: 3.855A pdb=" N ARG y 237 " --> pdb=" O VAL y 227 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL y 229 " --> pdb=" O PHE y 235 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N PHE y 235 " --> pdb=" O VAL y 229 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'y' and resid 296 through 298 Processing sheet with id= AQ, first strand: chain 'z' and resid 67 through 70 Processing sheet with id= AR, first strand: chain 'z' and resid 72 through 74 removed outlier: 6.706A pdb=" N VAL z 93 " --> pdb=" O ILE z 73 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR z 117 " --> pdb=" O THR z 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= AR Processing sheet with id= AS, first strand: chain 'z' and resid 140 through 142 removed outlier: 6.574A pdb=" N THR z 158 " --> pdb=" O LEU z 141 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLU z 176 " --> pdb=" O ILE z 159 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG z 187 " --> pdb=" O LEU z 177 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N SER z 179 " --> pdb=" O LYS z 185 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LYS z 185 " --> pdb=" O SER z 179 " (cutoff:3.500A) 3035 hydrogen bonds defined for protein. 8547 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 24.53 Time building geometry restraints manager: 24.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 29208 1.40 - 1.62: 41558 1.62 - 1.84: 577 1.84 - 2.06: 0 2.06 - 2.28: 80 Bond restraints: 71423 Sorted by residual: bond pdb=" CA7 CDL N 401 " pdb=" OA8 CDL N 401 " ideal model delta sigma weight residual 1.334 1.405 -0.071 1.10e-02 8.26e+03 4.17e+01 bond pdb=" CB7 CDL N 401 " pdb=" OB8 CDL N 401 " ideal model delta sigma weight residual 1.334 1.403 -0.069 1.10e-02 8.26e+03 3.94e+01 bond pdb=" CA7 CDL L 601 " pdb=" OA8 CDL L 601 " ideal model delta sigma weight residual 1.334 1.403 -0.069 1.10e-02 8.26e+03 3.91e+01 bond pdb=" CA7 CDL t 201 " pdb=" OA8 CDL t 201 " ideal model delta sigma weight residual 1.334 1.402 -0.068 1.10e-02 8.26e+03 3.87e+01 bond pdb=" CB7 CDL L 601 " pdb=" OB8 CDL L 601 " ideal model delta sigma weight residual 1.334 1.402 -0.068 1.10e-02 8.26e+03 3.86e+01 ... (remaining 71418 not shown) Histogram of bond angle deviations from ideal: 73.22 - 85.44: 76 85.44 - 97.67: 3 97.67 - 109.90: 10157 109.90 - 122.13: 75142 122.13 - 134.36: 11330 Bond angle restraints: 96708 Sorted by residual: angle pdb=" C11 CDL N 401 " pdb=" CA5 CDL N 401 " pdb=" OA6 CDL N 401 " ideal model delta sigma weight residual 111.33 120.98 -9.65 1.32e+00 5.72e-01 5.33e+01 angle pdb=" C11 CDL L 601 " pdb=" CA5 CDL L 601 " pdb=" OA6 CDL L 601 " ideal model delta sigma weight residual 111.33 120.50 -9.17 1.32e+00 5.72e-01 4.81e+01 angle pdb=" C11 CDL t 201 " pdb=" CA5 CDL t 201 " pdb=" OA6 CDL t 201 " ideal model delta sigma weight residual 111.33 120.28 -8.95 1.32e+00 5.72e-01 4.58e+01 angle pdb=" C51 CDL N 401 " pdb=" CB5 CDL N 401 " pdb=" OB6 CDL N 401 " ideal model delta sigma weight residual 111.33 120.12 -8.79 1.32e+00 5.72e-01 4.42e+01 angle pdb=" C51 CDL t 201 " pdb=" CB5 CDL t 201 " pdb=" OB6 CDL t 201 " ideal model delta sigma weight residual 111.33 119.87 -8.54 1.32e+00 5.72e-01 4.18e+01 ... (remaining 96703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.84: 41660 34.84 - 69.68: 916 69.68 - 104.52: 78 104.52 - 139.35: 1 139.35 - 174.19: 4 Dihedral angle restraints: 42659 sinusoidal: 17239 harmonic: 25420 Sorted by residual: dihedral pdb=" CA UNK b 8 " pdb=" C UNK b 8 " pdb=" N UNK b 9 " pdb=" CA UNK b 9 " ideal model delta harmonic sigma weight residual 180.00 134.60 45.40 0 5.00e+00 4.00e-02 8.25e+01 dihedral pdb=" CA UNK u 4 " pdb=" C UNK u 4 " pdb=" N UNK u 5 " pdb=" CA UNK u 5 " ideal model delta harmonic sigma weight residual 180.00 134.61 45.39 0 5.00e+00 4.00e-02 8.24e+01 dihedral pdb=" CB CYS e 13 " pdb=" SG CYS e 13 " pdb=" SG CYS e 49 " pdb=" CB CYS e 49 " ideal model delta sinusoidal sigma weight residual 93.00 159.04 -66.04 1 1.00e+01 1.00e-02 5.70e+01 ... (remaining 42656 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 9122 0.067 - 0.135: 1366 0.135 - 0.202: 98 0.202 - 0.269: 14 0.269 - 0.337: 1 Chirality restraints: 10601 Sorted by residual: chirality pdb=" CA4 CDL M 502 " pdb=" CA3 CDL M 502 " pdb=" CA6 CDL M 502 " pdb=" OA6 CDL M 502 " both_signs ideal model delta sigma weight residual False -2.57 -2.24 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CB ILE B 60 " pdb=" CA ILE B 60 " pdb=" CG1 ILE B 60 " pdb=" CG2 ILE B 60 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA GLU N 99 " pdb=" N GLU N 99 " pdb=" C GLU N 99 " pdb=" CB GLU N 99 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 10598 not shown) Planarity restraints: 12183 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA UNK u 3 " 0.029 2.00e-02 2.50e+03 5.73e-02 3.29e+01 pdb=" C UNK u 3 " -0.099 2.00e-02 2.50e+03 pdb=" O UNK u 3 " 0.038 2.00e-02 2.50e+03 pdb=" N UNK u 4 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK b 7 " 0.028 2.00e-02 2.50e+03 5.69e-02 3.24e+01 pdb=" C UNK b 7 " -0.098 2.00e-02 2.50e+03 pdb=" O UNK b 7 " 0.038 2.00e-02 2.50e+03 pdb=" N UNK b 8 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK u 38 " 0.027 2.00e-02 2.50e+03 5.28e-02 2.79e+01 pdb=" C UNK u 38 " -0.091 2.00e-02 2.50e+03 pdb=" O UNK u 38 " 0.033 2.00e-02 2.50e+03 pdb=" N UNK u 39 " 0.031 2.00e-02 2.50e+03 ... (remaining 12180 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 293 2.46 - 3.07: 49278 3.07 - 3.68: 110430 3.68 - 4.29: 176298 4.29 - 4.90: 284481 Nonbonded interactions: 620780 Sorted by model distance: nonbonded pdb=" O LEU H 286 " pdb=" OG SER H 290 " model vdw 1.852 2.440 nonbonded pdb=" O UNK b 41 " pdb=" N UNK b 43 " model vdw 2.026 2.520 nonbonded pdb=" O UNK u 37 " pdb=" N UNK u 39 " model vdw 2.027 2.520 nonbonded pdb=" OG1 THR G 398 " pdb=" O ASN G 516 " model vdw 2.041 2.440 nonbonded pdb=" O ALA L 245 " pdb=" OG1 THR L 249 " model vdw 2.046 2.440 ... (remaining 620775 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 'b' and resid 5 through 54) selection = chain 'u' } 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: 9.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 41.760 Check model and map are aligned: 0.760 Set scattering table: 0.510 Process input model: 168.530 Find NCS groups from input model: 2.200 Set up NCS constraints: 0.230 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: 0.010 Load rotamer database and sin/cos tables:2.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 226.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 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 : 0.005 0.105 71423 Z= 0.329 Angle : 0.896 18.717 96708 Z= 0.444 Chirality : 0.047 0.337 10601 Planarity : 0.006 0.153 12183 Dihedral : 14.390 174.193 26344 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.09 % Favored : 97.89 % Rotamer: Outliers : 0.04 % Allowed : 0.25 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.94 (0.09), residues: 8417 helix: 1.58 (0.08), residues: 4273 sheet: -0.12 (0.22), residues: 544 loop : -0.36 (0.10), residues: 3600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP M 423 HIS 0.010 0.001 HIS B 112 PHE 0.054 0.002 PHE D 132 TYR 0.061 0.002 TYR B 110 ARG 0.035 0.001 ARG n 17 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16834 Ramachandran restraints generated. 8417 Oldfield, 0 Emsley, 8417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16834 Ramachandran restraints generated. 8417 Oldfield, 0 Emsley, 8417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1726 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1723 time to evaluate : 5.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 THR cc_start: 0.8140 (m) cc_final: 0.7862 (p) REVERT: D 77 MET cc_start: 0.8036 (mmt) cc_final: 0.7732 (mmt) REVERT: D 283 MET cc_start: 0.8924 (tpp) cc_final: 0.8615 (tpp) REVERT: D 375 MET cc_start: 0.7746 (mpp) cc_final: 0.7321 (mmm) REVERT: E 243 GLU cc_start: 0.7084 (mp0) cc_final: 0.6844 (mp0) REVERT: F 137 GLU cc_start: 0.7172 (mp0) cc_final: 0.6966 (mp0) REVERT: F 459 LYS cc_start: 0.7466 (mttt) cc_final: 0.7263 (pttt) REVERT: G 264 ASP cc_start: 0.7506 (t0) cc_final: 0.7295 (t0) REVERT: G 269 LEU cc_start: 0.8840 (tp) cc_final: 0.8575 (tp) REVERT: G 506 ASP cc_start: 0.7574 (m-30) cc_final: 0.7268 (t70) REVERT: G 619 ASP cc_start: 0.7823 (t0) cc_final: 0.7507 (t70) REVERT: H 27 MET cc_start: 0.6495 (mmm) cc_final: 0.6039 (ttp) REVERT: H 197 PRO cc_start: 0.5476 (Cg_exo) cc_final: 0.5171 (Cg_endo) REVERT: P 145 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7497 (mm-30) REVERT: P 295 LEU cc_start: 0.6271 (pp) cc_final: 0.5905 (pp) REVERT: X 33 LYS cc_start: 0.8491 (mmmt) cc_final: 0.8244 (mmtm) REVERT: d 81 SER cc_start: 0.7618 (m) cc_final: 0.7104 (p) REVERT: e 65 GLU cc_start: 0.7649 (tp30) cc_final: 0.7331 (tp30) REVERT: g 113 LYS cc_start: 0.8428 (mtpp) cc_final: 0.7880 (tttm) REVERT: h 44 THR cc_start: 0.9391 (m) cc_final: 0.9130 (m) REVERT: m 119 ASN cc_start: 0.8849 (t0) cc_final: 0.8568 (t0) REVERT: y 49 MET cc_start: 0.8521 (mtm) cc_final: 0.8256 (mtp) REVERT: y 281 ASP cc_start: 0.8196 (p0) cc_final: 0.7978 (m-30) REVERT: y 296 TYR cc_start: 0.8562 (m-80) cc_final: 0.8337 (m-80) REVERT: y 307 ARG cc_start: 0.7833 (ptt180) cc_final: 0.7398 (ptm-80) outliers start: 3 outliers final: 1 residues processed: 1725 average time/residue: 0.7935 time to fit residues: 2227.2367 Evaluate side-chains 1188 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1187 time to evaluate : 5.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 49 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 721 optimal weight: 3.9990 chunk 647 optimal weight: 3.9990 chunk 359 optimal weight: 0.6980 chunk 221 optimal weight: 3.9990 chunk 436 optimal weight: 1.9990 chunk 345 optimal weight: 0.8980 chunk 669 optimal weight: 0.9980 chunk 259 optimal weight: 1.9990 chunk 407 optimal weight: 3.9990 chunk 498 optimal weight: 4.9990 chunk 775 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN C 111 ASN C 112 ASN ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 GLN F 52 ASN F 87 GLN F 228 GLN G 78 HIS G 519 ASN ** G 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 ASN J 120 GLN L 243 HIS L 459 GLN L 520 ASN M 300 GLN N 279 ASN N 305 GLN O 160 ASN ** Q 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 22 ASN ** Y 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 86 HIS a 39 ASN a 44 GLN a 58 GLN f 8 ASN g 132 ASN h 42 ASN i 81 ASN l 129 ASN p 84 HIS ** s 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 39 GLN x 44 GLN x 247 GLN x 270 GLN y 113 ASN y 137 ASN y 146 ASN y 154 HIS ** y 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 303 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 71423 Z= 0.301 Angle : 0.603 9.877 96708 Z= 0.313 Chirality : 0.044 0.222 10601 Planarity : 0.005 0.068 12183 Dihedral : 11.730 171.752 10650 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.53 % Favored : 97.46 % Rotamer: Outliers : 1.88 % Allowed : 6.51 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.96 (0.09), residues: 8417 helix: 1.55 (0.08), residues: 4303 sheet: 0.02 (0.21), residues: 562 loop : -0.33 (0.10), residues: 3552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP M 423 HIS 0.010 0.001 HIS Q 154 PHE 0.046 0.002 PHE D 132 TYR 0.062 0.002 TYR B 110 ARG 0.009 0.001 ARG q 142 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16834 Ramachandran restraints generated. 8417 Oldfield, 0 Emsley, 8417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16834 Ramachandran restraints generated. 8417 Oldfield, 0 Emsley, 8417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1388 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1252 time to evaluate : 6.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8780 (m-80) cc_final: 0.8547 (m-80) REVERT: C 146 MET cc_start: 0.8828 (mmt) cc_final: 0.8566 (mmt) REVERT: D 283 MET cc_start: 0.8877 (tpp) cc_final: 0.8581 (tpp) REVERT: E 185 MET cc_start: 0.8686 (mmt) cc_final: 0.8391 (mmt) REVERT: F 127 GLU cc_start: 0.7193 (tm-30) cc_final: 0.6993 (tm-30) REVERT: F 344 ILE cc_start: 0.8638 (tp) cc_final: 0.8309 (tp) REVERT: G 506 ASP cc_start: 0.7764 (m-30) cc_final: 0.7417 (m-30) REVERT: H 27 MET cc_start: 0.6407 (mmm) cc_final: 0.6143 (ttp) REVERT: H 116 TYR cc_start: 0.6830 (t80) cc_final: 0.6328 (t80) REVERT: H 197 PRO cc_start: 0.5661 (Cg_exo) cc_final: 0.5210 (Cg_endo) REVERT: I 49 ARG cc_start: 0.6088 (mmt90) cc_final: 0.5660 (mtt180) REVERT: J 67 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8465 (tt) REVERT: L 205 ASP cc_start: 0.6855 (m-30) cc_final: 0.6602 (m-30) REVERT: L 222 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8495 (mp) REVERT: M 13 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8410 (mp) REVERT: P 145 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7465 (mm-30) REVERT: P 295 LEU cc_start: 0.6699 (pp) cc_final: 0.6416 (pp) REVERT: P 299 MET cc_start: 0.7868 (mtp) cc_final: 0.7568 (mtm) REVERT: T 57 LYS cc_start: 0.8562 (mtpt) cc_final: 0.8142 (mttt) REVERT: T 72 THR cc_start: 0.9072 (p) cc_final: 0.8804 (p) REVERT: T 101 ASN cc_start: 0.7962 (p0) cc_final: 0.7656 (p0) REVERT: U 46 GLU cc_start: 0.5729 (mm-30) cc_final: 0.5117 (mm-30) REVERT: X 40 GLU cc_start: 0.7427 (mp0) cc_final: 0.7223 (mp0) REVERT: d 81 SER cc_start: 0.7613 (m) cc_final: 0.7191 (p) REVERT: f 44 LYS cc_start: 0.7385 (tppt) cc_final: 0.6815 (tptp) REVERT: l 88 SER cc_start: 0.8927 (p) cc_final: 0.8707 (p) REVERT: m 51 ASP cc_start: 0.8548 (p0) cc_final: 0.8343 (p0) REVERT: n 51 LYS cc_start: 0.8338 (ptmt) cc_final: 0.8111 (ptmt) REVERT: y 49 MET cc_start: 0.8339 (mtm) cc_final: 0.8114 (mtp) REVERT: y 56 GLN cc_start: 0.8724 (mm-40) cc_final: 0.8515 (mm-40) REVERT: y 281 ASP cc_start: 0.8224 (p0) cc_final: 0.7987 (m-30) REVERT: y 307 ARG cc_start: 0.7773 (ptt180) cc_final: 0.7331 (ptm-80) outliers start: 136 outliers final: 89 residues processed: 1318 average time/residue: 0.6970 time to fit residues: 1540.2566 Evaluate side-chains 1249 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 1157 time to evaluate : 5.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain F residue 320 ASP Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 215 ASP Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 299 SER Chi-restraints excluded: chain G residue 387 SER Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 617 LEU Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 154 ASP Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain K residue 55 ASN Chi-restraints excluded: chain L residue 222 LEU Chi-restraints excluded: chain L residue 310 ASP Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain M residue 13 LEU Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 305 GLN Chi-restraints excluded: chain N residue 312 SER Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain O residue 115 LYS Chi-restraints excluded: chain O residue 144 GLU Chi-restraints excluded: chain P residue 13 ASN Chi-restraints excluded: chain P residue 118 ASP Chi-restraints excluded: chain P residue 339 VAL Chi-restraints excluded: chain Q residue 129 THR Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 16 ILE Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain U residue 122 SER Chi-restraints excluded: chain V residue 125 ARG Chi-restraints excluded: chain V residue 127 LEU Chi-restraints excluded: chain W residue 38 HIS Chi-restraints excluded: chain W residue 64 SER Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 73 LEU Chi-restraints excluded: chain Z residue 115 VAL Chi-restraints excluded: chain Z residue 137 ASP Chi-restraints excluded: chain a residue 35 SER Chi-restraints excluded: chain a residue 58 GLN Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain e residue 2 SER Chi-restraints excluded: chain f residue 25 SER Chi-restraints excluded: chain f residue 105 SER Chi-restraints excluded: chain g residue 147 ASP Chi-restraints excluded: chain g residue 152 LEU Chi-restraints excluded: chain h residue 14 SER Chi-restraints excluded: chain i residue 47 ASP Chi-restraints excluded: chain i residue 57 GLU Chi-restraints excluded: chain i residue 66 SER Chi-restraints excluded: chain i residue 73 VAL Chi-restraints excluded: chain i residue 97 THR Chi-restraints excluded: chain i residue 99 THR Chi-restraints excluded: chain l residue 49 MET Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 113 SER Chi-restraints excluded: chain m residue 29 SER Chi-restraints excluded: chain o residue 39 GLU Chi-restraints excluded: chain p residue 5 THR Chi-restraints excluded: chain x residue 49 ASP Chi-restraints excluded: chain x residue 67 SER Chi-restraints excluded: chain x residue 71 ASP Chi-restraints excluded: chain y residue 81 VAL Chi-restraints excluded: chain y residue 137 ASN Chi-restraints excluded: chain y residue 149 ASP Chi-restraints excluded: chain y residue 280 LYS Chi-restraints excluded: chain y residue 284 LEU Chi-restraints excluded: chain z residue 103 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 431 optimal weight: 1.9990 chunk 240 optimal weight: 3.9990 chunk 645 optimal weight: 2.9990 chunk 528 optimal weight: 0.6980 chunk 213 optimal weight: 0.7980 chunk 776 optimal weight: 9.9990 chunk 839 optimal weight: 0.7980 chunk 691 optimal weight: 1.9990 chunk 770 optimal weight: 9.9990 chunk 264 optimal weight: 0.4980 chunk 623 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 HIS ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 HIS E 240 GLN F 460 ASN I 210 ASN J 10 ASN J 37 ASN L 392 GLN ** M 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 279 ASN N 305 GLN P 307 GLN ** Q 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 101 ASN Y 87 ASN Z 90 GLN g 132 ASN i 36 GLN l 129 ASN ** s 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 39 GLN x 247 GLN x 270 GLN y 137 ASN y 154 HIS y 172 ASN y 301 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 71423 Z= 0.228 Angle : 0.525 9.830 96708 Z= 0.272 Chirality : 0.041 0.185 10601 Planarity : 0.005 0.060 12183 Dihedral : 10.982 170.512 10648 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.46 % Favored : 97.52 % Rotamer: Outliers : 2.11 % Allowed : 8.69 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.01 (0.09), residues: 8417 helix: 1.59 (0.08), residues: 4310 sheet: -0.04 (0.22), residues: 564 loop : -0.28 (0.10), residues: 3543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP M 423 HIS 0.007 0.001 HIS Q 154 PHE 0.031 0.001 PHE D 132 TYR 0.038 0.001 TYR R 121 ARG 0.013 0.000 ARG Z 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16834 Ramachandran restraints generated. 8417 Oldfield, 0 Emsley, 8417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16834 Ramachandran restraints generated. 8417 Oldfield, 0 Emsley, 8417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1359 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1207 time to evaluate : 6.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 TYR cc_start: 0.6453 (OUTLIER) cc_final: 0.5029 (t80) REVERT: D 33 MET cc_start: 0.7522 (mtp) cc_final: 0.7308 (mtp) REVERT: D 129 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.6412 (mt) REVERT: D 260 ASP cc_start: 0.7621 (m-30) cc_final: 0.7305 (m-30) REVERT: D 375 MET cc_start: 0.7776 (mpp) cc_final: 0.7401 (mmm) REVERT: E 185 MET cc_start: 0.8673 (mmt) cc_final: 0.8342 (mmt) REVERT: F 344 ILE cc_start: 0.8573 (tp) cc_final: 0.8287 (tp) REVERT: G 506 ASP cc_start: 0.7830 (m-30) cc_final: 0.7410 (t70) REVERT: H 116 TYR cc_start: 0.6828 (t80) cc_final: 0.6364 (t80) REVERT: H 165 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7528 (mm-30) REVERT: H 197 PRO cc_start: 0.5821 (Cg_exo) cc_final: 0.5350 (Cg_endo) REVERT: I 49 ARG cc_start: 0.6311 (mmt90) cc_final: 0.5926 (mtt180) REVERT: J 26 MET cc_start: 0.7920 (mmm) cc_final: 0.7645 (mmm) REVERT: L 205 ASP cc_start: 0.6885 (m-30) cc_final: 0.6670 (m-30) REVERT: L 222 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8543 (mp) REVERT: L 258 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8058 (pp) REVERT: M 13 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8423 (mp) REVERT: N 116 ASN cc_start: 0.7695 (OUTLIER) cc_final: 0.7435 (p0) REVERT: P 76 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8604 (mm110) REVERT: P 145 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7439 (mm-30) REVERT: P 295 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6608 (pp) REVERT: P 299 MET cc_start: 0.7855 (mtp) cc_final: 0.7567 (mtm) REVERT: R 23 LYS cc_start: 0.7988 (tttt) cc_final: 0.7269 (mttm) REVERT: T 57 LYS cc_start: 0.8539 (mtpt) cc_final: 0.8112 (mttt) REVERT: U 105 LYS cc_start: 0.7052 (mmtp) cc_final: 0.6603 (mmtp) REVERT: X 40 GLU cc_start: 0.7412 (mp0) cc_final: 0.7207 (mp0) REVERT: Y 164 ASP cc_start: 0.7422 (m-30) cc_final: 0.7210 (m-30) REVERT: Z 47 LEU cc_start: 0.6397 (tp) cc_final: 0.6094 (tp) REVERT: c 81 ARG cc_start: 0.8572 (ttt90) cc_final: 0.8345 (ttt90) REVERT: d 81 SER cc_start: 0.7493 (m) cc_final: 0.7111 (p) REVERT: e 55 LEU cc_start: 0.8328 (tt) cc_final: 0.7920 (mt) REVERT: f 44 LYS cc_start: 0.7371 (tppt) cc_final: 0.6867 (tptp) REVERT: m 111 LYS cc_start: 0.8579 (ttmt) cc_final: 0.8343 (tppt) REVERT: n 77 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7271 (tt0) REVERT: s 99 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6512 (mt-10) REVERT: y 49 MET cc_start: 0.8208 (mtm) cc_final: 0.7990 (mtp) REVERT: y 246 PHE cc_start: 0.7711 (t80) cc_final: 0.7273 (t80) REVERT: y 281 ASP cc_start: 0.8266 (p0) cc_final: 0.8041 (m-30) REVERT: y 307 ARG cc_start: 0.7771 (ptt180) cc_final: 0.7314 (ptm-80) outliers start: 152 outliers final: 102 residues processed: 1278 average time/residue: 0.7808 time to fit residues: 1663.1769 Evaluate side-chains 1246 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 1135 time to evaluate : 5.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 73 TYR Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 320 ASP Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 459 LYS Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 215 ASP Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 299 SER Chi-restraints excluded: chain G residue 387 SER Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 617 LEU Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 272 ILE Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 88 MET Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 154 ASP Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 55 ASN Chi-restraints excluded: chain L residue 222 LEU Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 310 ASP Chi-restraints excluded: chain L residue 314 ASP Chi-restraints excluded: chain M residue 13 LEU Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 224 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 116 ASN Chi-restraints excluded: chain N residue 194 THR Chi-restraints excluded: chain N residue 372 VAL Chi-restraints excluded: chain O residue 115 LYS Chi-restraints excluded: chain O residue 144 GLU Chi-restraints excluded: chain P residue 13 ASN Chi-restraints excluded: chain P residue 118 ASP Chi-restraints excluded: chain P residue 151 SER Chi-restraints excluded: chain P residue 295 LEU Chi-restraints excluded: chain P residue 339 VAL Chi-restraints excluded: chain Q residue 129 THR Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 9 THR Chi-restraints excluded: chain S residue 16 ILE Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain U residue 98 VAL Chi-restraints excluded: chain U residue 122 SER Chi-restraints excluded: chain V residue 125 ARG Chi-restraints excluded: chain V residue 127 LEU Chi-restraints excluded: chain W residue 38 HIS Chi-restraints excluded: chain W residue 64 SER Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 70 ASP Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Y residue 23 LYS Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 73 LEU Chi-restraints excluded: chain Z residue 115 VAL Chi-restraints excluded: chain Z residue 137 ASP Chi-restraints excluded: chain a residue 30 LYS Chi-restraints excluded: chain a residue 35 SER Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain e residue 2 SER Chi-restraints excluded: chain f residue 25 SER Chi-restraints excluded: chain f residue 105 SER Chi-restraints excluded: chain i residue 57 GLU Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 81 ASN Chi-restraints excluded: chain i residue 97 THR Chi-restraints excluded: chain l residue 49 MET Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 87 LEU Chi-restraints excluded: chain l residue 113 SER Chi-restraints excluded: chain n residue 77 GLU Chi-restraints excluded: chain o residue 39 GLU Chi-restraints excluded: chain p residue 154 ILE Chi-restraints excluded: chain s residue 99 GLU Chi-restraints excluded: chain x residue 49 ASP Chi-restraints excluded: chain x residue 67 SER Chi-restraints excluded: chain x residue 71 ASP Chi-restraints excluded: chain y residue 81 VAL Chi-restraints excluded: chain y residue 135 ASP Chi-restraints excluded: chain y residue 146 ASN Chi-restraints excluded: chain y residue 149 ASP Chi-restraints excluded: chain y residue 280 LYS Chi-restraints excluded: chain y residue 284 LEU Chi-restraints excluded: chain z residue 89 GLU Chi-restraints excluded: chain z residue 103 ASP Chi-restraints excluded: chain z residue 156 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 767 optimal weight: 0.6980 chunk 584 optimal weight: 6.9990 chunk 403 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 370 optimal weight: 0.9980 chunk 521 optimal weight: 4.9990 chunk 779 optimal weight: 0.6980 chunk 825 optimal weight: 0.4980 chunk 407 optimal weight: 2.9990 chunk 738 optimal weight: 0.9990 chunk 222 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 GLN ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 HIS E 240 GLN G 327 ASN G 608 GLN ** H 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 288 GLN J 37 ASN J 132 ASN ** M 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 305 GLN Q 154 HIS Q 166 ASN Y 202 ASN ** a 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 132 ASN i 36 GLN l 129 ASN p 84 HIS s 13 ASN s 39 GLN x 270 GLN y 137 ASN y 154 HIS y 238 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 71423 Z= 0.180 Angle : 0.486 8.737 96708 Z= 0.251 Chirality : 0.040 0.196 10601 Planarity : 0.004 0.058 12183 Dihedral : 10.266 169.610 10648 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.46 % Favored : 97.52 % Rotamer: Outliers : 2.22 % Allowed : 9.78 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.14 (0.09), residues: 8417 helix: 1.72 (0.08), residues: 4307 sheet: 0.06 (0.22), residues: 565 loop : -0.28 (0.10), residues: 3545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP M 423 HIS 0.005 0.001 HIS Q 154 PHE 0.027 0.001 PHE D 132 TYR 0.024 0.001 TYR L 408 ARG 0.010 0.000 ARG Z 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16834 Ramachandran restraints generated. 8417 Oldfield, 0 Emsley, 8417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16834 Ramachandran restraints generated. 8417 Oldfield, 0 Emsley, 8417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1345 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1185 time to evaluate : 6.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 TYR cc_start: 0.6465 (OUTLIER) cc_final: 0.4912 (t80) REVERT: B 151 LYS cc_start: 0.8760 (tttt) cc_final: 0.8461 (tttt) REVERT: B 160 LEU cc_start: 0.7941 (mt) cc_final: 0.7662 (mp) REVERT: D 42 ASP cc_start: 0.7519 (t70) cc_final: 0.7286 (t70) REVERT: D 129 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.6237 (mt) REVERT: D 260 ASP cc_start: 0.7590 (m-30) cc_final: 0.7299 (m-30) REVERT: D 375 MET cc_start: 0.7805 (mpp) cc_final: 0.7417 (mmm) REVERT: E 185 MET cc_start: 0.8687 (mmt) cc_final: 0.8376 (mmt) REVERT: F 127 GLU cc_start: 0.6968 (tm-30) cc_final: 0.6505 (tm-30) REVERT: F 459 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7380 (mtpt) REVERT: G 280 THR cc_start: 0.9029 (p) cc_final: 0.8682 (m) REVERT: G 506 ASP cc_start: 0.7828 (m-30) cc_final: 0.7382 (t70) REVERT: H 116 TYR cc_start: 0.6814 (t80) cc_final: 0.6464 (t80) REVERT: H 197 PRO cc_start: 0.6030 (Cg_exo) cc_final: 0.5489 (Cg_endo) REVERT: I 49 ARG cc_start: 0.6408 (mmt90) cc_final: 0.6176 (mtt180) REVERT: J 67 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8533 (tt) REVERT: L 205 ASP cc_start: 0.6884 (m-30) cc_final: 0.6670 (m-30) REVERT: M 13 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8372 (mp) REVERT: N 116 ASN cc_start: 0.7730 (OUTLIER) cc_final: 0.7469 (p0) REVERT: P 145 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7443 (mm-30) REVERT: P 299 MET cc_start: 0.7824 (mtp) cc_final: 0.7527 (mtm) REVERT: R 23 LYS cc_start: 0.7926 (tttt) cc_final: 0.7248 (mttm) REVERT: R 52 TYR cc_start: 0.8658 (m-80) cc_final: 0.8274 (m-80) REVERT: T 57 LYS cc_start: 0.8545 (mtpt) cc_final: 0.8116 (mttt) REVERT: T 92 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7229 (mt-10) REVERT: T 96 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8344 (pp) REVERT: U 105 LYS cc_start: 0.7042 (mmtp) cc_final: 0.6572 (mmtp) REVERT: X 40 GLU cc_start: 0.7404 (mp0) cc_final: 0.7197 (mp0) REVERT: Y 118 GLU cc_start: 0.8098 (tt0) cc_final: 0.7835 (tt0) REVERT: Y 124 LYS cc_start: 0.7969 (mptt) cc_final: 0.7583 (mptt) REVERT: Z 47 LEU cc_start: 0.6390 (tp) cc_final: 0.6021 (tp) REVERT: d 81 SER cc_start: 0.7476 (m) cc_final: 0.7083 (p) REVERT: e 55 LEU cc_start: 0.8341 (tt) cc_final: 0.7902 (mt) REVERT: e 59 LYS cc_start: 0.8328 (mmmt) cc_final: 0.8025 (mmtt) REVERT: e 65 GLU cc_start: 0.7755 (tp30) cc_final: 0.7444 (tp30) REVERT: f 44 LYS cc_start: 0.7329 (tppt) cc_final: 0.6922 (tptp) REVERT: i 102 ASP cc_start: 0.6847 (t0) cc_final: 0.6613 (t0) REVERT: n 56 ARG cc_start: 0.7540 (mmp-170) cc_final: 0.7291 (mmp-170) REVERT: r 116 MET cc_start: 0.7489 (mmp) cc_final: 0.7131 (mmp) REVERT: s 99 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6487 (mt-10) REVERT: x 58 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6766 (mt-10) REVERT: y 56 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8510 (mm-40) outliers start: 160 outliers final: 107 residues processed: 1265 average time/residue: 0.7521 time to fit residues: 1619.4833 Evaluate side-chains 1249 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 1132 time to evaluate : 5.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 16 PHE Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 320 ASP Chi-restraints excluded: chain F residue 456 ASP Chi-restraints excluded: chain F residue 459 LYS Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 215 ASP Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 299 SER Chi-restraints excluded: chain G residue 387 SER Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 272 ILE Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 55 ASN Chi-restraints excluded: chain L residue 310 ASP Chi-restraints excluded: chain L residue 314 ASP Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain M residue 13 LEU Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 179 GLU Chi-restraints excluded: chain M residue 224 LEU Chi-restraints excluded: chain M residue 227 ILE Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 116 ASN Chi-restraints excluded: chain N residue 194 THR Chi-restraints excluded: chain N residue 372 VAL Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain O residue 115 LYS Chi-restraints excluded: chain O residue 144 GLU Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 13 ASN Chi-restraints excluded: chain P residue 118 ASP Chi-restraints excluded: chain P residue 273 GLU Chi-restraints excluded: chain P residue 282 LEU Chi-restraints excluded: chain Q residue 129 THR Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain S residue 9 THR Chi-restraints excluded: chain S residue 16 ILE Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 92 GLU Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain U residue 122 SER Chi-restraints excluded: chain V residue 125 ARG Chi-restraints excluded: chain V residue 127 LEU Chi-restraints excluded: chain W residue 38 HIS Chi-restraints excluded: chain W residue 64 SER Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 70 ASP Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Y residue 23 LYS Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 73 LEU Chi-restraints excluded: chain Z residue 115 VAL Chi-restraints excluded: chain Z residue 137 ASP Chi-restraints excluded: chain a residue 30 LYS Chi-restraints excluded: chain a residue 35 SER Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain e residue 2 SER Chi-restraints excluded: chain f residue 25 SER Chi-restraints excluded: chain f residue 105 SER Chi-restraints excluded: chain g residue 152 LEU Chi-restraints excluded: chain h residue 16 ASP Chi-restraints excluded: chain i residue 57 GLU Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain l residue 46 ASP Chi-restraints excluded: chain l residue 49 MET Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 113 SER Chi-restraints excluded: chain m residue 29 SER Chi-restraints excluded: chain o residue 39 GLU Chi-restraints excluded: chain p residue 5 THR Chi-restraints excluded: chain p residue 109 LEU Chi-restraints excluded: chain p residue 154 ILE Chi-restraints excluded: chain s residue 16 SER Chi-restraints excluded: chain s residue 38 THR Chi-restraints excluded: chain s residue 99 GLU Chi-restraints excluded: chain x residue 49 ASP Chi-restraints excluded: chain x residue 58 GLU Chi-restraints excluded: chain x residue 67 SER Chi-restraints excluded: chain x residue 71 ASP Chi-restraints excluded: chain y residue 81 VAL Chi-restraints excluded: chain y residue 135 ASP Chi-restraints excluded: chain y residue 146 ASN Chi-restraints excluded: chain y residue 149 ASP Chi-restraints excluded: chain y residue 284 LEU Chi-restraints excluded: chain z residue 89 GLU Chi-restraints excluded: chain z residue 103 ASP Chi-restraints excluded: chain z residue 217 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 687 optimal weight: 1.9990 chunk 468 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 614 optimal weight: 0.9990 chunk 340 optimal weight: 0.9980 chunk 704 optimal weight: 0.7980 chunk 570 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 421 optimal weight: 0.9990 chunk 740 optimal weight: 0.0370 chunk 208 optimal weight: 1.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 ASN ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 HIS E 240 GLN ** H 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 271 GLN H 288 GLN J 37 ASN L 319 HIS L 387 ASN ** M 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 305 GLN a 58 GLN i 36 GLN l 129 ASN p 84 HIS p 93 GLN s 39 GLN ** s 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 270 GLN y 137 ASN y 146 ASN y 154 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 71423 Z= 0.189 Angle : 0.484 8.525 96708 Z= 0.250 Chirality : 0.040 0.207 10601 Planarity : 0.004 0.057 12183 Dihedral : 9.915 169.830 10648 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.55 % Favored : 97.42 % Rotamer: Outliers : 2.26 % Allowed : 10.80 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.17 (0.09), residues: 8417 helix: 1.76 (0.08), residues: 4314 sheet: -0.07 (0.21), residues: 571 loop : -0.25 (0.10), residues: 3532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 141 HIS 0.005 0.001 HIS B 112 PHE 0.023 0.001 PHE B 13 TYR 0.025 0.001 TYR R 121 ARG 0.006 0.000 ARG Z 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16834 Ramachandran restraints generated. 8417 Oldfield, 0 Emsley, 8417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16834 Ramachandran restraints generated. 8417 Oldfield, 0 Emsley, 8417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1347 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1184 time to evaluate : 6.146 Fit side-chains revert: symmetry clash REVERT: A 98 TYR cc_start: 0.6507 (OUTLIER) cc_final: 0.5007 (t80) REVERT: B 45 MET cc_start: 0.6485 (mtp) cc_final: 0.5824 (mmm) REVERT: B 151 LYS cc_start: 0.8767 (tttt) cc_final: 0.8487 (tttt) REVERT: D 42 ASP cc_start: 0.7505 (t70) cc_final: 0.7256 (t70) REVERT: D 129 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6133 (mt) REVERT: D 260 ASP cc_start: 0.7630 (m-30) cc_final: 0.7333 (m-30) REVERT: D 375 MET cc_start: 0.7870 (mpp) cc_final: 0.7478 (mmm) REVERT: E 185 MET cc_start: 0.8695 (mmt) cc_final: 0.8419 (mmt) REVERT: F 127 GLU cc_start: 0.6975 (tm-30) cc_final: 0.6544 (tm-30) REVERT: F 241 MET cc_start: 0.7844 (mtm) cc_final: 0.7572 (mtt) REVERT: F 344 ILE cc_start: 0.8594 (tp) cc_final: 0.8256 (tp) REVERT: F 459 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7390 (mtpt) REVERT: G 280 THR cc_start: 0.9041 (p) cc_final: 0.8699 (m) REVERT: G 506 ASP cc_start: 0.7836 (m-30) cc_final: 0.7377 (t70) REVERT: H 116 TYR cc_start: 0.6790 (t80) cc_final: 0.6493 (t80) REVERT: H 138 GLU cc_start: 0.7845 (tp30) cc_final: 0.7569 (tp30) REVERT: H 188 GLU cc_start: 0.8278 (mm-30) cc_final: 0.8067 (mm-30) REVERT: H 197 PRO cc_start: 0.6176 (Cg_exo) cc_final: 0.5638 (Cg_endo) REVERT: I 49 ARG cc_start: 0.6446 (mmt90) cc_final: 0.6193 (mtt180) REVERT: I 98 LYS cc_start: 0.4258 (pttp) cc_final: 0.3179 (mmtt) REVERT: J 67 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8555 (tt) REVERT: L 205 ASP cc_start: 0.6902 (m-30) cc_final: 0.6678 (m-30) REVERT: M 13 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8377 (mp) REVERT: P 273 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6594 (mp0) REVERT: P 299 MET cc_start: 0.7841 (mtp) cc_final: 0.7562 (mtm) REVERT: R 23 LYS cc_start: 0.7932 (tttt) cc_final: 0.7221 (mttm) REVERT: R 52 TYR cc_start: 0.8677 (m-80) cc_final: 0.8302 (m-80) REVERT: T 57 LYS cc_start: 0.8550 (mtpt) cc_final: 0.8113 (mttt) REVERT: T 92 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7289 (mt-10) REVERT: T 96 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8194 (pp) REVERT: U 105 LYS cc_start: 0.7024 (mmtp) cc_final: 0.6571 (mmtp) REVERT: U 110 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7152 (pp20) REVERT: W 1 MET cc_start: -0.0442 (ttm) cc_final: -0.0738 (ttt) REVERT: X 40 GLU cc_start: 0.7413 (mp0) cc_final: 0.7211 (mp0) REVERT: Y 118 GLU cc_start: 0.8103 (tt0) cc_final: 0.7858 (tt0) REVERT: Y 124 LYS cc_start: 0.8029 (mptt) cc_final: 0.7542 (mptt) REVERT: Z 66 ASP cc_start: 0.7633 (t0) cc_final: 0.7334 (t0) REVERT: d 15 MET cc_start: 0.8521 (tpt) cc_final: 0.8262 (tpt) REVERT: d 81 SER cc_start: 0.7466 (m) cc_final: 0.7089 (p) REVERT: e 55 LEU cc_start: 0.8360 (tt) cc_final: 0.7919 (mt) REVERT: e 59 LYS cc_start: 0.8339 (mmmt) cc_final: 0.8039 (mmtt) REVERT: e 65 GLU cc_start: 0.7819 (tp30) cc_final: 0.7472 (tp30) REVERT: f 44 LYS cc_start: 0.7356 (tppt) cc_final: 0.6989 (tptp) REVERT: s 99 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6506 (mt-10) REVERT: x 58 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6795 (mp0) outliers start: 163 outliers final: 122 residues processed: 1268 average time/residue: 0.6887 time to fit residues: 1469.9447 Evaluate side-chains 1276 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1144 time to evaluate : 6.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 320 ASP Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 456 ASP Chi-restraints excluded: chain F residue 459 LYS Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 215 ASP Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 299 SER Chi-restraints excluded: chain G residue 326 GLU Chi-restraints excluded: chain G residue 387 SER Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 617 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 272 ILE Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 94 PHE Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain K residue 55 ASN Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain L residue 176 ASP Chi-restraints excluded: chain L residue 222 LEU Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 286 ASP Chi-restraints excluded: chain L residue 310 ASP Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain M residue 13 LEU Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 224 LEU Chi-restraints excluded: chain M residue 227 ILE Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 194 THR Chi-restraints excluded: chain N residue 372 VAL Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain O residue 115 LYS Chi-restraints excluded: chain O residue 144 GLU Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 13 ASN Chi-restraints excluded: chain P residue 118 ASP Chi-restraints excluded: chain P residue 151 SER Chi-restraints excluded: chain P residue 273 GLU Chi-restraints excluded: chain P residue 344 VAL Chi-restraints excluded: chain Q residue 129 THR Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 9 THR Chi-restraints excluded: chain S residue 16 ILE Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 92 GLU Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain U residue 122 SER Chi-restraints excluded: chain V residue 72 VAL Chi-restraints excluded: chain V residue 125 ARG Chi-restraints excluded: chain V residue 127 LEU Chi-restraints excluded: chain W residue 38 HIS Chi-restraints excluded: chain W residue 64 SER Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 70 ASP Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 73 LEU Chi-restraints excluded: chain Z residue 92 GLU Chi-restraints excluded: chain Z residue 115 VAL Chi-restraints excluded: chain Z residue 137 ASP Chi-restraints excluded: chain a residue 30 LYS Chi-restraints excluded: chain a residue 35 SER Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain e residue 2 SER Chi-restraints excluded: chain e residue 38 GLU Chi-restraints excluded: chain f residue 25 SER Chi-restraints excluded: chain f residue 105 SER Chi-restraints excluded: chain g residue 152 LEU Chi-restraints excluded: chain h residue 16 ASP Chi-restraints excluded: chain i residue 57 GLU Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain l residue 49 MET Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 113 SER Chi-restraints excluded: chain m residue 29 SER Chi-restraints excluded: chain o residue 39 GLU Chi-restraints excluded: chain p residue 5 THR Chi-restraints excluded: chain p residue 109 LEU Chi-restraints excluded: chain p residue 154 ILE Chi-restraints excluded: chain s residue 38 THR Chi-restraints excluded: chain s residue 99 GLU Chi-restraints excluded: chain x residue 49 ASP Chi-restraints excluded: chain x residue 58 GLU Chi-restraints excluded: chain x residue 67 SER Chi-restraints excluded: chain x residue 71 ASP Chi-restraints excluded: chain y residue 81 VAL Chi-restraints excluded: chain y residue 135 ASP Chi-restraints excluded: chain y residue 146 ASN Chi-restraints excluded: chain y residue 149 ASP Chi-restraints excluded: chain y residue 216 VAL Chi-restraints excluded: chain y residue 284 LEU Chi-restraints excluded: chain z residue 89 GLU Chi-restraints excluded: chain z residue 103 ASP Chi-restraints excluded: chain z residue 156 ASP Chi-restraints excluded: chain z residue 217 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 277 optimal weight: 7.9990 chunk 743 optimal weight: 10.0000 chunk 163 optimal weight: 0.9980 chunk 484 optimal weight: 0.9990 chunk 203 optimal weight: 0.4980 chunk 826 optimal weight: 0.5980 chunk 685 optimal weight: 0.8980 chunk 382 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 273 optimal weight: 0.9980 chunk 433 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 HIS E 240 GLN ** H 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 271 GLN H 288 GLN J 37 ASN ** M 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 305 GLN P 63 ASN P 120 HIS a 58 GLN i 36 GLN l 129 ASN p 84 HIS s 39 GLN ** x 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 270 GLN y 137 ASN y 146 ASN y 154 HIS z 145 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 71423 Z= 0.177 Angle : 0.476 12.224 96708 Z= 0.244 Chirality : 0.039 0.207 10601 Planarity : 0.004 0.055 12183 Dihedral : 9.683 170.082 10648 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.55 % Favored : 97.42 % Rotamer: Outliers : 2.40 % Allowed : 11.36 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.21 (0.09), residues: 8417 helix: 1.81 (0.08), residues: 4310 sheet: -0.08 (0.21), residues: 575 loop : -0.24 (0.10), residues: 3532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 141 HIS 0.004 0.001 HIS B 112 PHE 0.021 0.001 PHE H 269 TYR 0.022 0.001 TYR M 396 ARG 0.008 0.000 ARG c 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16834 Ramachandran restraints generated. 8417 Oldfield, 0 Emsley, 8417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16834 Ramachandran restraints generated. 8417 Oldfield, 0 Emsley, 8417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1344 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 1171 time to evaluate : 6.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 TYR cc_start: 0.6507 (OUTLIER) cc_final: 0.5023 (t80) REVERT: B 45 MET cc_start: 0.6474 (mtp) cc_final: 0.5896 (mmm) REVERT: B 151 LYS cc_start: 0.8775 (tttt) cc_final: 0.8524 (tttt) REVERT: D 1 MET cc_start: -0.0802 (mtp) cc_final: -0.1197 (mtp) REVERT: D 42 ASP cc_start: 0.7496 (t70) cc_final: 0.7270 (t70) REVERT: D 129 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6104 (mt) REVERT: D 368 ASP cc_start: 0.8081 (t0) cc_final: 0.7733 (t0) REVERT: D 375 MET cc_start: 0.7931 (mpp) cc_final: 0.7519 (mmm) REVERT: E 185 MET cc_start: 0.8687 (mmt) cc_final: 0.8381 (mmt) REVERT: F 127 GLU cc_start: 0.6952 (tm-30) cc_final: 0.6554 (tm-30) REVERT: F 216 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7241 (tt0) REVERT: G 280 THR cc_start: 0.9028 (p) cc_final: 0.8684 (m) REVERT: G 506 ASP cc_start: 0.7817 (m-30) cc_final: 0.7377 (t70) REVERT: H 116 TYR cc_start: 0.6802 (t80) cc_final: 0.6597 (t80) REVERT: H 151 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7246 (mm-30) REVERT: H 197 PRO cc_start: 0.6234 (Cg_exo) cc_final: 0.5700 (Cg_endo) REVERT: I 49 ARG cc_start: 0.6471 (mmt90) cc_final: 0.6034 (mtp180) REVERT: I 98 LYS cc_start: 0.4194 (pttp) cc_final: 0.3116 (mmtt) REVERT: J 67 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8548 (tt) REVERT: L 205 ASP cc_start: 0.6911 (m-30) cc_final: 0.6697 (m-30) REVERT: L 341 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7778 (mm-30) REVERT: M 13 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8371 (mp) REVERT: P 273 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6704 (mp0) REVERT: P 299 MET cc_start: 0.7839 (mtp) cc_final: 0.7554 (mtm) REVERT: T 57 LYS cc_start: 0.8527 (mtpt) cc_final: 0.8109 (mttt) REVERT: T 92 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7290 (mt-10) REVERT: T 96 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8350 (pp) REVERT: U 46 GLU cc_start: 0.5684 (mm-30) cc_final: 0.5014 (mm-30) REVERT: U 105 LYS cc_start: 0.7025 (mmtp) cc_final: 0.6590 (mmtp) REVERT: U 110 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7157 (pp20) REVERT: W 1 MET cc_start: -0.1058 (ttm) cc_final: -0.1768 (ttt) REVERT: X 40 GLU cc_start: 0.7417 (mp0) cc_final: 0.7215 (mp0) REVERT: Y 124 LYS cc_start: 0.8061 (mptt) cc_final: 0.7550 (mptt) REVERT: Z 66 ASP cc_start: 0.7645 (t0) cc_final: 0.7328 (t0) REVERT: d 81 SER cc_start: 0.7429 (m) cc_final: 0.7043 (p) REVERT: e 55 LEU cc_start: 0.8376 (tt) cc_final: 0.7935 (mt) REVERT: e 59 LYS cc_start: 0.8319 (mmmt) cc_final: 0.8063 (mmtt) REVERT: e 65 GLU cc_start: 0.7834 (tp30) cc_final: 0.7481 (tp30) REVERT: f 44 LYS cc_start: 0.7355 (tppt) cc_final: 0.6996 (tptp) REVERT: h 61 ASN cc_start: 0.8146 (m-40) cc_final: 0.7945 (t0) REVERT: i 116 LEU cc_start: 0.8199 (mm) cc_final: 0.7993 (mp) REVERT: s 99 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6486 (mt-10) REVERT: x 58 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6821 (mp0) outliers start: 173 outliers final: 134 residues processed: 1264 average time/residue: 0.6875 time to fit residues: 1464.8418 Evaluate side-chains 1287 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1143 time to evaluate : 6.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 73 TYR Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 306 GLU Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 456 ASP Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 215 ASP Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 299 SER Chi-restraints excluded: chain G residue 326 GLU Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 617 LEU Chi-restraints excluded: chain G residue 669 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 272 ILE Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 88 MET Chi-restraints excluded: chain I residue 94 PHE Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 55 ASN Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain L residue 176 ASP Chi-restraints excluded: chain L residue 222 LEU Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 310 ASP Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain M residue 13 LEU Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 224 LEU Chi-restraints excluded: chain M residue 227 ILE Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 194 THR Chi-restraints excluded: chain N residue 372 VAL Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain O residue 115 LYS Chi-restraints excluded: chain O residue 144 GLU Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 13 ASN Chi-restraints excluded: chain P residue 118 ASP Chi-restraints excluded: chain P residue 151 SER Chi-restraints excluded: chain P residue 273 GLU Chi-restraints excluded: chain P residue 344 VAL Chi-restraints excluded: chain Q residue 120 VAL Chi-restraints excluded: chain Q residue 129 THR Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 9 THR Chi-restraints excluded: chain S residue 16 ILE Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 92 GLU Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain U residue 122 SER Chi-restraints excluded: chain V residue 72 VAL Chi-restraints excluded: chain V residue 125 ARG Chi-restraints excluded: chain V residue 127 LEU Chi-restraints excluded: chain W residue 38 HIS Chi-restraints excluded: chain W residue 64 SER Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 62 GLN Chi-restraints excluded: chain X residue 70 ASP Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Y residue 23 LYS Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 73 LEU Chi-restraints excluded: chain Z residue 92 GLU Chi-restraints excluded: chain Z residue 115 VAL Chi-restraints excluded: chain Z residue 137 ASP Chi-restraints excluded: chain a residue 30 LYS Chi-restraints excluded: chain a residue 35 SER Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain e residue 2 SER Chi-restraints excluded: chain e residue 38 GLU Chi-restraints excluded: chain f residue 25 SER Chi-restraints excluded: chain f residue 105 SER Chi-restraints excluded: chain g residue 152 LEU Chi-restraints excluded: chain h residue 16 ASP Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 57 GLU Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 81 ASN Chi-restraints excluded: chain l residue 49 MET Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 113 SER Chi-restraints excluded: chain m residue 29 SER Chi-restraints excluded: chain o residue 39 GLU Chi-restraints excluded: chain p residue 5 THR Chi-restraints excluded: chain p residue 109 LEU Chi-restraints excluded: chain p residue 154 ILE Chi-restraints excluded: chain s residue 38 THR Chi-restraints excluded: chain s residue 99 GLU Chi-restraints excluded: chain t residue 98 VAL Chi-restraints excluded: chain x residue 49 ASP Chi-restraints excluded: chain x residue 58 GLU Chi-restraints excluded: chain x residue 67 SER Chi-restraints excluded: chain x residue 71 ASP Chi-restraints excluded: chain x residue 115 ASP Chi-restraints excluded: chain y residue 48 LEU Chi-restraints excluded: chain y residue 81 VAL Chi-restraints excluded: chain y residue 135 ASP Chi-restraints excluded: chain y residue 149 ASP Chi-restraints excluded: chain y residue 284 LEU Chi-restraints excluded: chain z residue 89 GLU Chi-restraints excluded: chain z residue 103 ASP Chi-restraints excluded: chain z residue 156 ASP Chi-restraints excluded: chain z residue 217 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 796 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 470 optimal weight: 5.9990 chunk 603 optimal weight: 9.9990 chunk 467 optimal weight: 0.2980 chunk 695 optimal weight: 3.9990 chunk 461 optimal weight: 0.7980 chunk 823 optimal weight: 0.2980 chunk 515 optimal weight: 4.9990 chunk 501 optimal weight: 1.9990 chunk 380 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 293 GLN ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 HIS E 240 GLN G 78 HIS ** H 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 288 GLN J 37 ASN N 305 GLN Q 150 ASN a 58 GLN ** h 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 129 ASN s 39 GLN ** x 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 270 GLN y 137 ASN y 146 ASN y 154 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 71423 Z= 0.211 Angle : 0.488 10.328 96708 Z= 0.251 Chirality : 0.040 0.218 10601 Planarity : 0.004 0.055 12183 Dihedral : 9.557 170.846 10648 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.67 % Favored : 97.30 % Rotamer: Outliers : 2.35 % Allowed : 11.84 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.19 (0.09), residues: 8417 helix: 1.79 (0.08), residues: 4308 sheet: -0.11 (0.21), residues: 575 loop : -0.26 (0.10), residues: 3534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 141 HIS 0.004 0.001 HIS B 112 PHE 0.022 0.001 PHE H 269 TYR 0.029 0.001 TYR R 121 ARG 0.009 0.000 ARG c 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16834 Ramachandran restraints generated. 8417 Oldfield, 0 Emsley, 8417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16834 Ramachandran restraints generated. 8417 Oldfield, 0 Emsley, 8417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1340 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1170 time to evaluate : 6.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 TYR cc_start: 0.6574 (OUTLIER) cc_final: 0.5133 (t80) REVERT: B 45 MET cc_start: 0.6449 (mtp) cc_final: 0.5934 (mmm) REVERT: B 151 LYS cc_start: 0.8796 (tttt) cc_final: 0.8527 (tttt) REVERT: D 1 MET cc_start: -0.1045 (mtp) cc_final: -0.1350 (mtp) REVERT: D 42 ASP cc_start: 0.7531 (t70) cc_final: 0.7277 (t70) REVERT: D 129 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6160 (mt) REVERT: D 368 ASP cc_start: 0.8085 (t0) cc_final: 0.7670 (t0) REVERT: D 375 MET cc_start: 0.7979 (mpp) cc_final: 0.7606 (mmm) REVERT: E 185 MET cc_start: 0.8653 (mmt) cc_final: 0.8329 (mmt) REVERT: F 127 GLU cc_start: 0.6939 (tm-30) cc_final: 0.6601 (tm-30) REVERT: F 369 THR cc_start: 0.8215 (m) cc_final: 0.8004 (m) REVERT: G 280 THR cc_start: 0.9040 (p) cc_final: 0.8694 (m) REVERT: G 506 ASP cc_start: 0.7814 (m-30) cc_final: 0.7376 (t70) REVERT: G 523 ASP cc_start: 0.7704 (p0) cc_final: 0.7117 (p0) REVERT: H 151 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7276 (mm-30) REVERT: H 197 PRO cc_start: 0.6178 (Cg_exo) cc_final: 0.5659 (Cg_endo) REVERT: I 49 ARG cc_start: 0.6481 (mmt90) cc_final: 0.5949 (mtp180) REVERT: I 98 LYS cc_start: 0.4180 (pttp) cc_final: 0.3135 (mmtt) REVERT: J 67 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8547 (tt) REVERT: L 205 ASP cc_start: 0.6897 (m-30) cc_final: 0.6693 (m-30) REVERT: M 13 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8382 (mp) REVERT: P 273 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6790 (mp0) REVERT: P 299 MET cc_start: 0.7915 (mtp) cc_final: 0.7627 (mtm) REVERT: T 57 LYS cc_start: 0.8553 (mtpt) cc_final: 0.8130 (mttt) REVERT: T 92 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7340 (mt-10) REVERT: T 96 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8196 (pp) REVERT: U 46 GLU cc_start: 0.5612 (mm-30) cc_final: 0.4978 (mm-30) REVERT: U 105 LYS cc_start: 0.7002 (mmtp) cc_final: 0.6590 (mmtp) REVERT: U 110 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7145 (pp20) REVERT: W 1 MET cc_start: -0.1014 (ttm) cc_final: -0.1251 (ttt) REVERT: Z 66 ASP cc_start: 0.7673 (t0) cc_final: 0.7367 (t0) REVERT: d 81 SER cc_start: 0.7480 (m) cc_final: 0.7075 (p) REVERT: e 55 LEU cc_start: 0.8414 (tt) cc_final: 0.7966 (mt) REVERT: e 59 LYS cc_start: 0.8329 (mmmt) cc_final: 0.8060 (mmtt) REVERT: e 65 GLU cc_start: 0.7909 (tp30) cc_final: 0.7559 (tp30) REVERT: f 44 LYS cc_start: 0.7391 (tppt) cc_final: 0.7056 (tptp) REVERT: g 136 GLU cc_start: 0.8031 (mp0) cc_final: 0.7410 (mt-10) REVERT: i 116 LEU cc_start: 0.8200 (mm) cc_final: 0.7993 (mp) REVERT: t 89 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9020 (mp) REVERT: x 58 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6786 (mp0) outliers start: 170 outliers final: 133 residues processed: 1262 average time/residue: 0.7099 time to fit residues: 1505.5255 Evaluate side-chains 1282 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1140 time to evaluate : 5.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 39 CYS Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 215 ASP Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 299 SER Chi-restraints excluded: chain G residue 326 GLU Chi-restraints excluded: chain G residue 387 SER Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 617 LEU Chi-restraints excluded: chain G residue 669 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 272 ILE Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 94 PHE Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 55 ASN Chi-restraints excluded: chain K residue 68 ILE Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain L residue 222 LEU Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 310 ASP Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain M residue 13 LEU Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 224 LEU Chi-restraints excluded: chain M residue 227 ILE Chi-restraints excluded: chain M residue 423 TRP Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 194 THR Chi-restraints excluded: chain N residue 372 VAL Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain O residue 115 LYS Chi-restraints excluded: chain O residue 144 GLU Chi-restraints excluded: chain P residue 13 ASN Chi-restraints excluded: chain P residue 118 ASP Chi-restraints excluded: chain P residue 151 SER Chi-restraints excluded: chain P residue 273 GLU Chi-restraints excluded: chain P residue 282 LEU Chi-restraints excluded: chain P residue 344 VAL Chi-restraints excluded: chain Q residue 120 VAL Chi-restraints excluded: chain Q residue 129 THR Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 9 THR Chi-restraints excluded: chain S residue 16 ILE Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 92 GLU Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain U residue 122 SER Chi-restraints excluded: chain V residue 72 VAL Chi-restraints excluded: chain V residue 125 ARG Chi-restraints excluded: chain V residue 127 LEU Chi-restraints excluded: chain W residue 38 HIS Chi-restraints excluded: chain W residue 64 SER Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 62 GLN Chi-restraints excluded: chain X residue 70 ASP Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 69 SER Chi-restraints excluded: chain Z residue 73 LEU Chi-restraints excluded: chain Z residue 85 LEU Chi-restraints excluded: chain Z residue 92 GLU Chi-restraints excluded: chain Z residue 115 VAL Chi-restraints excluded: chain Z residue 137 ASP Chi-restraints excluded: chain a residue 30 LYS Chi-restraints excluded: chain a residue 35 SER Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain e residue 2 SER Chi-restraints excluded: chain e residue 38 GLU Chi-restraints excluded: chain f residue 25 SER Chi-restraints excluded: chain f residue 105 SER Chi-restraints excluded: chain h residue 16 ASP Chi-restraints excluded: chain i residue 47 ASP Chi-restraints excluded: chain i residue 57 GLU Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 81 ASN Chi-restraints excluded: chain l residue 49 MET Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 113 SER Chi-restraints excluded: chain m residue 29 SER Chi-restraints excluded: chain o residue 39 GLU Chi-restraints excluded: chain p residue 5 THR Chi-restraints excluded: chain p residue 109 LEU Chi-restraints excluded: chain p residue 154 ILE Chi-restraints excluded: chain s residue 16 SER Chi-restraints excluded: chain s residue 38 THR Chi-restraints excluded: chain t residue 89 LEU Chi-restraints excluded: chain t residue 98 VAL Chi-restraints excluded: chain x residue 49 ASP Chi-restraints excluded: chain x residue 58 GLU Chi-restraints excluded: chain x residue 67 SER Chi-restraints excluded: chain x residue 71 ASP Chi-restraints excluded: chain x residue 115 ASP Chi-restraints excluded: chain y residue 48 LEU Chi-restraints excluded: chain y residue 81 VAL Chi-restraints excluded: chain y residue 135 ASP Chi-restraints excluded: chain y residue 149 ASP Chi-restraints excluded: chain y residue 216 VAL Chi-restraints excluded: chain y residue 284 LEU Chi-restraints excluded: chain z residue 103 ASP Chi-restraints excluded: chain z residue 156 ASP Chi-restraints excluded: chain z residue 217 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 509 optimal weight: 0.6980 chunk 328 optimal weight: 3.9990 chunk 491 optimal weight: 3.9990 chunk 247 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 chunk 523 optimal weight: 0.7980 chunk 560 optimal weight: 1.9990 chunk 406 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 646 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 GLN ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 HIS E 240 GLN H 271 GLN H 288 GLN J 37 ASN N 305 GLN a 58 GLN ** h 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 129 ASN n 34 HIS s 39 GLN ** x 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 270 GLN y 137 ASN y 154 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 71423 Z= 0.195 Angle : 0.484 10.467 96708 Z= 0.249 Chirality : 0.040 0.233 10601 Planarity : 0.004 0.054 12183 Dihedral : 9.399 171.151 10648 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.63 % Favored : 97.35 % Rotamer: Outliers : 2.37 % Allowed : 12.18 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.20 (0.09), residues: 8417 helix: 1.81 (0.08), residues: 4307 sheet: -0.08 (0.22), residues: 563 loop : -0.26 (0.10), residues: 3547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 141 HIS 0.005 0.001 HIS B 112 PHE 0.023 0.001 PHE H 269 TYR 0.022 0.001 TYR M 396 ARG 0.008 0.000 ARG c 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16834 Ramachandran restraints generated. 8417 Oldfield, 0 Emsley, 8417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16834 Ramachandran restraints generated. 8417 Oldfield, 0 Emsley, 8417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1336 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1165 time to evaluate : 6.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 TYR cc_start: 0.6534 (OUTLIER) cc_final: 0.5174 (t80) REVERT: B 151 LYS cc_start: 0.8800 (tttt) cc_final: 0.8539 (tttt) REVERT: D 42 ASP cc_start: 0.7511 (t70) cc_final: 0.7260 (t70) REVERT: D 368 ASP cc_start: 0.8084 (t0) cc_final: 0.7732 (t0) REVERT: D 375 MET cc_start: 0.7997 (mpp) cc_final: 0.7587 (mmm) REVERT: F 216 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7267 (tt0) REVERT: F 344 ILE cc_start: 0.8621 (tp) cc_final: 0.8349 (tp) REVERT: F 369 THR cc_start: 0.8176 (m) cc_final: 0.7964 (m) REVERT: F 459 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7393 (mtpt) REVERT: G 280 THR cc_start: 0.9041 (p) cc_final: 0.8681 (m) REVERT: G 506 ASP cc_start: 0.7805 (m-30) cc_final: 0.7382 (t70) REVERT: H 116 TYR cc_start: 0.6829 (t80) cc_final: 0.6503 (t80) REVERT: H 151 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7288 (mm-30) REVERT: H 197 PRO cc_start: 0.6247 (Cg_exo) cc_final: 0.5838 (Cg_endo) REVERT: I 49 ARG cc_start: 0.6498 (mmt90) cc_final: 0.5948 (mtp180) REVERT: I 55 GLU cc_start: 0.7244 (pt0) cc_final: 0.6665 (pp20) REVERT: I 98 LYS cc_start: 0.4184 (pttp) cc_final: 0.3082 (mmtt) REVERT: J 67 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8610 (tt) REVERT: M 13 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8384 (mp) REVERT: M 313 SER cc_start: 0.8934 (OUTLIER) cc_final: 0.8724 (p) REVERT: P 273 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6851 (mp0) REVERT: P 299 MET cc_start: 0.7902 (mtp) cc_final: 0.7619 (mtm) REVERT: P 341 PHE cc_start: 0.7548 (OUTLIER) cc_final: 0.6663 (t80) REVERT: R 74 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7418 (mp0) REVERT: T 57 LYS cc_start: 0.8537 (mtpt) cc_final: 0.8121 (mttt) REVERT: T 92 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7310 (mt-10) REVERT: T 96 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8243 (pp) REVERT: U 46 GLU cc_start: 0.5637 (mm-30) cc_final: 0.5007 (mm-30) REVERT: U 105 LYS cc_start: 0.6998 (mmtp) cc_final: 0.6602 (mmtp) REVERT: U 110 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7150 (pp20) REVERT: Z 56 PHE cc_start: 0.8136 (t80) cc_final: 0.7886 (t80) REVERT: Z 66 ASP cc_start: 0.7681 (t0) cc_final: 0.7370 (t0) REVERT: a 60 THR cc_start: 0.7899 (m) cc_final: 0.7675 (m) REVERT: d 81 SER cc_start: 0.7460 (m) cc_final: 0.7056 (p) REVERT: e 55 LEU cc_start: 0.8394 (tt) cc_final: 0.7952 (mt) REVERT: e 59 LYS cc_start: 0.8309 (mmmt) cc_final: 0.8027 (mmtt) REVERT: e 65 GLU cc_start: 0.7903 (tp30) cc_final: 0.7570 (tp30) REVERT: f 44 LYS cc_start: 0.7392 (tppt) cc_final: 0.7051 (tptp) REVERT: g 136 GLU cc_start: 0.8029 (mp0) cc_final: 0.7427 (mt-10) REVERT: t 56 LYS cc_start: 0.8359 (mtmt) cc_final: 0.8060 (mptt) REVERT: t 89 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.9021 (mp) REVERT: x 58 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6797 (mp0) outliers start: 171 outliers final: 139 residues processed: 1256 average time/residue: 0.6939 time to fit residues: 1463.3051 Evaluate side-chains 1288 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 1137 time to evaluate : 5.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 39 CYS Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 459 LYS Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 215 ASP Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 299 SER Chi-restraints excluded: chain G residue 326 GLU Chi-restraints excluded: chain G residue 387 SER Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 617 LEU Chi-restraints excluded: chain G residue 669 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 272 ILE Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 94 PHE Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 55 ASN Chi-restraints excluded: chain K residue 68 ILE Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 176 ASP Chi-restraints excluded: chain L residue 222 LEU Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 286 ASP Chi-restraints excluded: chain L residue 310 ASP Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain M residue 13 LEU Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 224 LEU Chi-restraints excluded: chain M residue 227 ILE Chi-restraints excluded: chain M residue 313 SER Chi-restraints excluded: chain M residue 423 TRP Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 194 THR Chi-restraints excluded: chain N residue 372 VAL Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain O residue 115 LYS Chi-restraints excluded: chain O residue 144 GLU Chi-restraints excluded: chain P residue 13 ASN Chi-restraints excluded: chain P residue 118 ASP Chi-restraints excluded: chain P residue 151 SER Chi-restraints excluded: chain P residue 273 GLU Chi-restraints excluded: chain P residue 282 LEU Chi-restraints excluded: chain P residue 341 PHE Chi-restraints excluded: chain P residue 344 VAL Chi-restraints excluded: chain Q residue 120 VAL Chi-restraints excluded: chain Q residue 129 THR Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 9 THR Chi-restraints excluded: chain S residue 16 ILE Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 92 GLU Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain U residue 91 GLU Chi-restraints excluded: chain U residue 122 SER Chi-restraints excluded: chain V residue 72 VAL Chi-restraints excluded: chain V residue 125 ARG Chi-restraints excluded: chain V residue 127 LEU Chi-restraints excluded: chain W residue 38 HIS Chi-restraints excluded: chain W residue 64 SER Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 62 GLN Chi-restraints excluded: chain X residue 70 ASP Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 73 LEU Chi-restraints excluded: chain Z residue 85 LEU Chi-restraints excluded: chain Z residue 92 GLU Chi-restraints excluded: chain Z residue 115 VAL Chi-restraints excluded: chain Z residue 137 ASP Chi-restraints excluded: chain a residue 30 LYS Chi-restraints excluded: chain a residue 35 SER Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain e residue 2 SER Chi-restraints excluded: chain e residue 38 GLU Chi-restraints excluded: chain f residue 25 SER Chi-restraints excluded: chain f residue 105 SER Chi-restraints excluded: chain g residue 152 LEU Chi-restraints excluded: chain h residue 16 ASP Chi-restraints excluded: chain h residue 34 SER Chi-restraints excluded: chain i residue 57 GLU Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain l residue 49 MET Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 113 SER Chi-restraints excluded: chain m residue 29 SER Chi-restraints excluded: chain o residue 39 GLU Chi-restraints excluded: chain p residue 5 THR Chi-restraints excluded: chain p residue 109 LEU Chi-restraints excluded: chain p residue 154 ILE Chi-restraints excluded: chain s residue 36 LEU Chi-restraints excluded: chain s residue 38 THR Chi-restraints excluded: chain t residue 89 LEU Chi-restraints excluded: chain t residue 98 VAL Chi-restraints excluded: chain x residue 49 ASP Chi-restraints excluded: chain x residue 58 GLU Chi-restraints excluded: chain x residue 67 SER Chi-restraints excluded: chain x residue 71 ASP Chi-restraints excluded: chain x residue 88 GLN Chi-restraints excluded: chain x residue 115 ASP Chi-restraints excluded: chain y residue 48 LEU Chi-restraints excluded: chain y residue 81 VAL Chi-restraints excluded: chain y residue 135 ASP Chi-restraints excluded: chain y residue 149 ASP Chi-restraints excluded: chain y residue 216 VAL Chi-restraints excluded: chain y residue 284 LEU Chi-restraints excluded: chain z residue 103 ASP Chi-restraints excluded: chain z residue 156 ASP Chi-restraints excluded: chain z residue 217 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 748 optimal weight: 0.6980 chunk 788 optimal weight: 3.9990 chunk 719 optimal weight: 4.9990 chunk 767 optimal weight: 2.9990 chunk 461 optimal weight: 0.8980 chunk 334 optimal weight: 0.7980 chunk 602 optimal weight: 10.0000 chunk 235 optimal weight: 0.9980 chunk 693 optimal weight: 2.9990 chunk 725 optimal weight: 0.9980 chunk 764 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 HIS F 278 ASN H 271 GLN H 288 GLN J 37 ASN J 120 GLN N 305 GLN P 152 HIS X 36 HIS a 58 GLN ** h 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 129 ASN n 34 HIS s 39 GLN ** x 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 270 GLN y 137 ASN y 154 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 71423 Z= 0.210 Angle : 0.490 10.550 96708 Z= 0.252 Chirality : 0.040 0.234 10601 Planarity : 0.004 0.054 12183 Dihedral : 9.324 171.490 10648 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.76 % Favored : 97.22 % Rotamer: Outliers : 2.29 % Allowed : 12.36 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.19 (0.09), residues: 8417 helix: 1.79 (0.08), residues: 4309 sheet: -0.04 (0.22), residues: 551 loop : -0.27 (0.10), residues: 3557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 141 HIS 0.005 0.001 HIS B 112 PHE 0.023 0.001 PHE H 269 TYR 0.027 0.001 TYR R 121 ARG 0.009 0.000 ARG c 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16834 Ramachandran restraints generated. 8417 Oldfield, 0 Emsley, 8417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16834 Ramachandran restraints generated. 8417 Oldfield, 0 Emsley, 8417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1328 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1163 time to evaluate : 6.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 TYR cc_start: 0.6524 (OUTLIER) cc_final: 0.5207 (t80) REVERT: B 151 LYS cc_start: 0.8798 (tttt) cc_final: 0.8530 (tttt) REVERT: D 42 ASP cc_start: 0.7595 (t70) cc_final: 0.7345 (t70) REVERT: D 368 ASP cc_start: 0.8092 (t0) cc_final: 0.7742 (t0) REVERT: D 375 MET cc_start: 0.8039 (mpp) cc_final: 0.7618 (mmm) REVERT: F 369 THR cc_start: 0.8196 (m) cc_final: 0.7991 (m) REVERT: F 459 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7373 (mtpt) REVERT: G 280 THR cc_start: 0.9047 (p) cc_final: 0.8691 (m) REVERT: G 506 ASP cc_start: 0.7804 (m-30) cc_final: 0.7380 (t70) REVERT: H 151 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7296 (mm-30) REVERT: H 197 PRO cc_start: 0.6291 (Cg_exo) cc_final: 0.5821 (Cg_endo) REVERT: I 49 ARG cc_start: 0.6469 (mmt90) cc_final: 0.5922 (mtp180) REVERT: I 94 PHE cc_start: 0.4326 (OUTLIER) cc_final: 0.3954 (m-80) REVERT: I 98 LYS cc_start: 0.4202 (pttp) cc_final: 0.3066 (mmtt) REVERT: J 67 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8611 (tt) REVERT: M 13 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8431 (mp) REVERT: P 273 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6780 (mp0) REVERT: P 299 MET cc_start: 0.7897 (mtp) cc_final: 0.7612 (mtm) REVERT: P 341 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.6719 (t80) REVERT: R 74 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7405 (mp0) REVERT: T 57 LYS cc_start: 0.8532 (mtpt) cc_final: 0.8116 (mttt) REVERT: T 92 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7334 (mt-10) REVERT: T 96 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8267 (pp) REVERT: U 46 GLU cc_start: 0.5640 (mm-30) cc_final: 0.5006 (mm-30) REVERT: U 105 LYS cc_start: 0.7014 (mmtp) cc_final: 0.6631 (mmtp) REVERT: U 110 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7175 (pp20) REVERT: V 80 GLU cc_start: 0.7407 (tp30) cc_final: 0.7143 (tp30) REVERT: Y 84 ARG cc_start: 0.7501 (mtm180) cc_final: 0.7266 (mtm180) REVERT: Y 124 LYS cc_start: 0.7900 (mptt) cc_final: 0.7691 (mttt) REVERT: Z 56 PHE cc_start: 0.8160 (t80) cc_final: 0.7904 (t80) REVERT: Z 65 ARG cc_start: 0.8417 (tpp80) cc_final: 0.7855 (mtt90) REVERT: Z 66 ASP cc_start: 0.7693 (t0) cc_final: 0.7387 (t0) REVERT: a 60 THR cc_start: 0.7895 (m) cc_final: 0.7680 (m) REVERT: d 81 SER cc_start: 0.7465 (m) cc_final: 0.7049 (p) REVERT: e 55 LEU cc_start: 0.8412 (tt) cc_final: 0.7960 (mt) REVERT: e 59 LYS cc_start: 0.8318 (mmmt) cc_final: 0.8044 (mmtt) REVERT: e 65 GLU cc_start: 0.7938 (tp30) cc_final: 0.7590 (tp30) REVERT: f 44 LYS cc_start: 0.7409 (tppt) cc_final: 0.7066 (tptp) REVERT: g 136 GLU cc_start: 0.8041 (mp0) cc_final: 0.7418 (mt-10) REVERT: t 56 LYS cc_start: 0.8379 (mtmt) cc_final: 0.8042 (mptt) REVERT: t 89 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9027 (mp) REVERT: x 58 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6760 (mp0) outliers start: 165 outliers final: 139 residues processed: 1249 average time/residue: 0.7146 time to fit residues: 1506.2423 Evaluate side-chains 1282 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 1132 time to evaluate : 6.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 39 CYS Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain F residue 306 GLU Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 459 LYS Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 215 ASP Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 299 SER Chi-restraints excluded: chain G residue 326 GLU Chi-restraints excluded: chain G residue 387 SER Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 617 LEU Chi-restraints excluded: chain G residue 669 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 272 ILE Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 94 PHE Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 55 ASN Chi-restraints excluded: chain K residue 68 ILE Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain L residue 176 ASP Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 286 ASP Chi-restraints excluded: chain L residue 310 ASP Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain M residue 13 LEU Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 224 LEU Chi-restraints excluded: chain M residue 227 ILE Chi-restraints excluded: chain M residue 423 TRP Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 194 THR Chi-restraints excluded: chain N residue 372 VAL Chi-restraints excluded: chain O residue 115 LYS Chi-restraints excluded: chain O residue 144 GLU Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 118 ASP Chi-restraints excluded: chain P residue 151 SER Chi-restraints excluded: chain P residue 273 GLU Chi-restraints excluded: chain P residue 282 LEU Chi-restraints excluded: chain P residue 341 PHE Chi-restraints excluded: chain Q residue 120 VAL Chi-restraints excluded: chain Q residue 124 THR Chi-restraints excluded: chain Q residue 129 THR Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain R residue 68 ASP Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 9 THR Chi-restraints excluded: chain S residue 16 ILE Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 92 GLU Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain U residue 122 SER Chi-restraints excluded: chain V residue 72 VAL Chi-restraints excluded: chain V residue 125 ARG Chi-restraints excluded: chain V residue 127 LEU Chi-restraints excluded: chain W residue 38 HIS Chi-restraints excluded: chain W residue 64 SER Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 70 ASP Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 69 SER Chi-restraints excluded: chain Z residue 73 LEU Chi-restraints excluded: chain Z residue 85 LEU Chi-restraints excluded: chain Z residue 92 GLU Chi-restraints excluded: chain Z residue 115 VAL Chi-restraints excluded: chain Z residue 137 ASP Chi-restraints excluded: chain a residue 30 LYS Chi-restraints excluded: chain a residue 35 SER Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain e residue 2 SER Chi-restraints excluded: chain e residue 38 GLU Chi-restraints excluded: chain f residue 25 SER Chi-restraints excluded: chain f residue 105 SER Chi-restraints excluded: chain h residue 16 ASP Chi-restraints excluded: chain h residue 34 SER Chi-restraints excluded: chain i residue 57 GLU Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 81 ASN Chi-restraints excluded: chain l residue 49 MET Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 113 SER Chi-restraints excluded: chain m residue 29 SER Chi-restraints excluded: chain o residue 39 GLU Chi-restraints excluded: chain p residue 5 THR Chi-restraints excluded: chain p residue 109 LEU Chi-restraints excluded: chain p residue 154 ILE Chi-restraints excluded: chain s residue 16 SER Chi-restraints excluded: chain s residue 36 LEU Chi-restraints excluded: chain s residue 38 THR Chi-restraints excluded: chain t residue 62 ASN Chi-restraints excluded: chain t residue 89 LEU Chi-restraints excluded: chain t residue 98 VAL Chi-restraints excluded: chain x residue 49 ASP Chi-restraints excluded: chain x residue 58 GLU Chi-restraints excluded: chain x residue 67 SER Chi-restraints excluded: chain x residue 71 ASP Chi-restraints excluded: chain x residue 88 GLN Chi-restraints excluded: chain x residue 115 ASP Chi-restraints excluded: chain y residue 48 LEU Chi-restraints excluded: chain y residue 81 VAL Chi-restraints excluded: chain y residue 135 ASP Chi-restraints excluded: chain y residue 149 ASP Chi-restraints excluded: chain y residue 216 VAL Chi-restraints excluded: chain y residue 284 LEU Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain z residue 103 ASP Chi-restraints excluded: chain z residue 156 ASP Chi-restraints excluded: chain z residue 217 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 503 optimal weight: 0.7980 chunk 811 optimal weight: 1.9990 chunk 495 optimal weight: 0.6980 chunk 384 optimal weight: 0.8980 chunk 563 optimal weight: 3.9990 chunk 850 optimal weight: 1.9990 chunk 783 optimal weight: 0.9980 chunk 677 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 523 optimal weight: 0.9990 chunk 415 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 HIS F 278 ASN H 271 GLN H 288 GLN J 37 ASN N 305 GLN a 58 GLN c 25 HIS ** h 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 8 GLN l 129 ASN s 39 GLN ** x 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 270 GLN y 154 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 71423 Z= 0.200 Angle : 0.486 11.229 96708 Z= 0.250 Chirality : 0.040 0.241 10601 Planarity : 0.004 0.054 12183 Dihedral : 9.231 171.594 10648 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.63 % Favored : 97.35 % Rotamer: Outliers : 2.26 % Allowed : 12.55 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.20 (0.09), residues: 8417 helix: 1.80 (0.08), residues: 4307 sheet: -0.02 (0.22), residues: 551 loop : -0.27 (0.10), residues: 3559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 141 HIS 0.004 0.001 HIS B 112 PHE 0.023 0.001 PHE H 269 TYR 0.022 0.001 TYR M 396 ARG 0.010 0.000 ARG c 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16834 Ramachandran restraints generated. 8417 Oldfield, 0 Emsley, 8417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16834 Ramachandran restraints generated. 8417 Oldfield, 0 Emsley, 8417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1314 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1151 time to evaluate : 6.113 Fit side-chains revert: symmetry clash REVERT: A 98 TYR cc_start: 0.6459 (OUTLIER) cc_final: 0.5303 (t80) REVERT: B 151 LYS cc_start: 0.8779 (tttt) cc_final: 0.8525 (tttt) REVERT: D 42 ASP cc_start: 0.7598 (t70) cc_final: 0.7341 (t70) REVERT: D 193 LEU cc_start: 0.8556 (tp) cc_final: 0.8323 (tt) REVERT: D 368 ASP cc_start: 0.8088 (t0) cc_final: 0.7741 (t0) REVERT: D 375 MET cc_start: 0.8030 (mpp) cc_final: 0.7611 (mmm) REVERT: F 216 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7251 (tt0) REVERT: F 369 THR cc_start: 0.8211 (m) cc_final: 0.8002 (m) REVERT: F 459 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7362 (mtpt) REVERT: G 280 THR cc_start: 0.9042 (p) cc_final: 0.8685 (m) REVERT: G 506 ASP cc_start: 0.7799 (m-30) cc_final: 0.7384 (t70) REVERT: H 116 TYR cc_start: 0.6868 (t80) cc_final: 0.6643 (t80) REVERT: H 151 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7318 (mm-30) REVERT: H 197 PRO cc_start: 0.6391 (Cg_exo) cc_final: 0.5934 (Cg_endo) REVERT: I 49 ARG cc_start: 0.6445 (mmt90) cc_final: 0.5949 (mtp180) REVERT: I 94 PHE cc_start: 0.4289 (OUTLIER) cc_final: 0.3940 (m-80) REVERT: I 98 LYS cc_start: 0.4120 (pttp) cc_final: 0.3057 (mmtt) REVERT: J 67 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8612 (tt) REVERT: M 13 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8413 (mp) REVERT: P 273 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6821 (mp0) REVERT: P 299 MET cc_start: 0.7897 (mtp) cc_final: 0.7613 (mtm) REVERT: P 341 PHE cc_start: 0.7535 (OUTLIER) cc_final: 0.6692 (t80) REVERT: R 74 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7408 (mp0) REVERT: T 57 LYS cc_start: 0.8540 (mtpt) cc_final: 0.8076 (mttt) REVERT: T 96 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8286 (pp) REVERT: U 46 GLU cc_start: 0.5638 (mm-30) cc_final: 0.5035 (mm-30) REVERT: U 105 LYS cc_start: 0.6987 (mmtp) cc_final: 0.6610 (mmtp) REVERT: U 110 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7181 (pp20) REVERT: V 80 GLU cc_start: 0.7418 (tp30) cc_final: 0.7106 (tp30) REVERT: W 1 MET cc_start: -0.0902 (ttt) cc_final: -0.1236 (ttt) REVERT: X 58 GLN cc_start: 0.8227 (mt0) cc_final: 0.7989 (mt0) REVERT: Y 84 ARG cc_start: 0.7524 (mtm180) cc_final: 0.7272 (mtm180) REVERT: Z 56 PHE cc_start: 0.8161 (t80) cc_final: 0.7925 (t80) REVERT: Z 65 ARG cc_start: 0.8425 (tpp80) cc_final: 0.7874 (mtt90) REVERT: Z 66 ASP cc_start: 0.7723 (t0) cc_final: 0.7411 (t0) REVERT: a 60 THR cc_start: 0.7896 (m) cc_final: 0.7689 (m) REVERT: d 81 SER cc_start: 0.7439 (m) cc_final: 0.7030 (p) REVERT: e 55 LEU cc_start: 0.8409 (tt) cc_final: 0.7962 (mt) REVERT: e 59 LYS cc_start: 0.8323 (mmmt) cc_final: 0.8044 (mmtt) REVERT: e 65 GLU cc_start: 0.7944 (tp30) cc_final: 0.7597 (tp30) REVERT: f 44 LYS cc_start: 0.7417 (tppt) cc_final: 0.7064 (tptp) REVERT: i 116 LEU cc_start: 0.8180 (mm) cc_final: 0.7973 (mp) REVERT: s 98 LYS cc_start: 0.8634 (mmtm) cc_final: 0.8228 (mmmt) REVERT: t 56 LYS cc_start: 0.8371 (mtmt) cc_final: 0.8042 (mptt) REVERT: t 89 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9024 (mp) REVERT: x 58 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6733 (mp0) REVERT: y 273 LEU cc_start: 0.8678 (tp) cc_final: 0.8340 (tt) outliers start: 163 outliers final: 141 residues processed: 1237 average time/residue: 0.7052 time to fit residues: 1463.2074 Evaluate side-chains 1286 residues out of total 7219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1134 time to evaluate : 6.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 MET Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 39 CYS Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 456 ASP Chi-restraints excluded: chain F residue 459 LYS Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 215 ASP Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 299 SER Chi-restraints excluded: chain G residue 326 GLU Chi-restraints excluded: chain G residue 387 SER Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 617 LEU Chi-restraints excluded: chain G residue 669 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 272 ILE Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 94 PHE Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 55 ASN Chi-restraints excluded: chain K residue 68 ILE Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 176 ASP Chi-restraints excluded: chain L residue 222 LEU Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 286 ASP Chi-restraints excluded: chain L residue 310 ASP Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain M residue 13 LEU Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 224 LEU Chi-restraints excluded: chain M residue 227 ILE Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 194 THR Chi-restraints excluded: chain N residue 366 VAL Chi-restraints excluded: chain N residue 372 VAL Chi-restraints excluded: chain O residue 115 LYS Chi-restraints excluded: chain O residue 144 GLU Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 118 ASP Chi-restraints excluded: chain P residue 151 SER Chi-restraints excluded: chain P residue 273 GLU Chi-restraints excluded: chain P residue 282 LEU Chi-restraints excluded: chain P residue 341 PHE Chi-restraints excluded: chain P residue 344 VAL Chi-restraints excluded: chain Q residue 120 VAL Chi-restraints excluded: chain Q residue 124 THR Chi-restraints excluded: chain Q residue 129 THR Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 9 THR Chi-restraints excluded: chain S residue 16 ILE Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain U residue 122 SER Chi-restraints excluded: chain V residue 72 VAL Chi-restraints excluded: chain V residue 125 ARG Chi-restraints excluded: chain V residue 127 LEU Chi-restraints excluded: chain W residue 38 HIS Chi-restraints excluded: chain W residue 64 SER Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 70 ASP Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 73 LEU Chi-restraints excluded: chain Z residue 85 LEU Chi-restraints excluded: chain Z residue 92 GLU Chi-restraints excluded: chain Z residue 115 VAL Chi-restraints excluded: chain Z residue 137 ASP Chi-restraints excluded: chain a residue 30 LYS Chi-restraints excluded: chain a residue 35 SER Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain e residue 2 SER Chi-restraints excluded: chain e residue 38 GLU Chi-restraints excluded: chain f residue 25 SER Chi-restraints excluded: chain f residue 105 SER Chi-restraints excluded: chain h residue 34 SER Chi-restraints excluded: chain i residue 57 GLU Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 81 ASN Chi-restraints excluded: chain l residue 49 MET Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 113 SER Chi-restraints excluded: chain m residue 29 SER Chi-restraints excluded: chain o residue 39 GLU Chi-restraints excluded: chain p residue 5 THR Chi-restraints excluded: chain p residue 109 LEU Chi-restraints excluded: chain p residue 154 ILE Chi-restraints excluded: chain s residue 16 SER Chi-restraints excluded: chain s residue 38 THR Chi-restraints excluded: chain t residue 62 ASN Chi-restraints excluded: chain t residue 89 LEU Chi-restraints excluded: chain t residue 98 VAL Chi-restraints excluded: chain x residue 49 ASP Chi-restraints excluded: chain x residue 58 GLU Chi-restraints excluded: chain x residue 67 SER Chi-restraints excluded: chain x residue 71 ASP Chi-restraints excluded: chain x residue 88 GLN Chi-restraints excluded: chain x residue 115 ASP Chi-restraints excluded: chain y residue 48 LEU Chi-restraints excluded: chain y residue 81 VAL Chi-restraints excluded: chain y residue 135 ASP Chi-restraints excluded: chain y residue 149 ASP Chi-restraints excluded: chain y residue 216 VAL Chi-restraints excluded: chain y residue 284 LEU Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain z residue 103 ASP Chi-restraints excluded: chain z residue 217 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 538 optimal weight: 0.0170 chunk 721 optimal weight: 0.6980 chunk 207 optimal weight: 0.6980 chunk 624 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 188 optimal weight: 0.9990 chunk 678 optimal weight: 8.9990 chunk 283 optimal weight: 4.9990 chunk 696 optimal weight: 0.0980 chunk 85 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 278 ASN H 288 GLN J 37 ASN J 120 GLN N 305 GLN a 58 GLN h 17 HIS ** h 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 8 GLN l 129 ASN s 39 GLN ** x 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 270 GLN y 154 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.119720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.095961 restraints weight = 95892.442| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.46 r_work: 0.2852 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 71423 Z= 0.156 Angle : 0.467 10.793 96708 Z= 0.240 Chirality : 0.039 0.252 10601 Planarity : 0.004 0.054 12183 Dihedral : 9.017 171.358 10648 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.47 % Favored : 97.51 % Rotamer: Outliers : 1.99 % Allowed : 12.83 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.28 (0.09), residues: 8417 helix: 1.88 (0.08), residues: 4312 sheet: -0.06 (0.22), residues: 571 loop : -0.24 (0.10), residues: 3534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 141 HIS 0.004 0.001 HIS B 112 PHE 0.022 0.001 PHE H 269 TYR 0.028 0.001 TYR R 121 ARG 0.010 0.000 ARG c 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24244.03 seconds wall clock time: 422 minutes 35.03 seconds (25355.03 seconds total)