Starting phenix.real_space_refine on Sat Feb 17 05:54:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2c_31640/02_2024/7v2c_31640_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2c_31640/02_2024/7v2c_31640.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2c_31640/02_2024/7v2c_31640_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2c_31640/02_2024/7v2c_31640_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2c_31640/02_2024/7v2c_31640_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2c_31640/02_2024/7v2c_31640.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2c_31640/02_2024/7v2c_31640.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2c_31640/02_2024/7v2c_31640_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2c_31640/02_2024/7v2c_31640_neut_updated.pdb" } resolution = 2.9 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= 0.005 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: 8 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 48 5.49 5 Mg 1 5.21 5 S 482 5.16 5 C 44273 2.51 5 N 11236 2.21 5 O 12246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 140": "OE1" <-> "OE2" Residue "A GLU 377": "OE1" <-> "OE2" Residue "A GLU 445": "OE1" <-> "OE2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "E GLU 34": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "H GLU 54": "OE1" <-> "OE2" Residue "I GLU 30": "OE1" <-> "OE2" Residue "I GLU 105": "OE1" <-> "OE2" Residue "J GLU 107": "OE1" <-> "OE2" Residue "J PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "M GLU 44": "OE1" <-> "OE2" Residue "M GLU 396": "OE1" <-> "OE2" Residue "M GLU 468": "OE1" <-> "OE2" Residue "P GLU 85": "OE1" <-> "OE2" Residue "P TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 104": "OE1" <-> "OE2" Residue "Q TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 35": "OE1" <-> "OE2" Residue "T GLU 73": "OE1" <-> "OE2" Residue "W GLU 92": "OE1" <-> "OE2" Residue "X GLU 123": "OE1" <-> "OE2" Residue "Y GLU 41": "OE1" <-> "OE2" Residue "Y GLU 59": "OE1" <-> "OE2" Residue "Z GLU 49": "OE1" <-> "OE2" Residue "Z GLU 85": "OE1" <-> "OE2" Residue "a GLU 155": "OE1" <-> "OE2" Residue "b GLU 8": "OE1" <-> "OE2" Residue "c GLU 85": "OE1" <-> "OE2" Residue "c GLU 169": "OE1" <-> "OE2" Residue "d ASP 3": "OD1" <-> "OD2" Residue "e GLU 64": "OE1" <-> "OE2" Residue "f GLU 68": "OE1" <-> "OE2" Residue "g GLU 19": "OE1" <-> "OE2" Residue "g GLU 101": "OE1" <-> "OE2" Residue "g GLU 117": "OE1" <-> "OE2" Residue "h GLU 39": "OE1" <-> "OE2" Residue "h GLU 53": "OE1" <-> "OE2" Residue "h GLU 102": "OE1" <-> "OE2" Residue "i GLU 34": "OE1" <-> "OE2" Residue "i GLU 269": "OE1" <-> "OE2" Residue "j GLU 32": "OE1" <-> "OE2" Residue "j GLU 115": "OE1" <-> "OE2" Residue "l TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 503": "OE1" <-> "OE2" Residue "l GLU 559": "OE1" <-> "OE2" Residue "n GLU 33": "OE1" <-> "OE2" Residue "o GLU 35": "OE1" <-> "OE2" Residue "o ARG 56": "NH1" <-> "NH2" Residue "p GLU 69": "OE1" <-> "OE2" Residue "p GLU 95": "OE1" <-> "OE2" Residue "r GLU 87": "OE1" <-> "OE2" Residue "r GLU 114": "OE1" <-> "OE2" Residue "r GLU 123": "OE1" <-> "OE2" Residue "r GLU 335": "OE1" <-> "OE2" Residue "s GLU 202": "OE1" <-> "OE2" Residue "s GLU 204": "OE1" <-> "OE2" Residue "s GLU 206": "OE1" <-> "OE2" Residue "u ASP 113": "OD1" <-> "OD2" Residue "u GLU 155": "OE1" <-> "OE2" Residue "v GLU 36": "OE1" <-> "OE2" Residue "w GLU 303": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 68315 Number of models: 1 Model: "" Number of chains: 70 Chain: "A" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3330 Classifications: {'peptide': 433} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 410} Chain: "B" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1412 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "C" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1248 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 971 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "F" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 687 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 690 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASP:plan': 3} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 910 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "I" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 11, 'TRANS': 85} Chain breaks: 1 Chain: "J" Number of atoms: 2751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2751 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 22, 'TRANS': 319} Chain: "K" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 366 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 3, 'TRANS': 39} Chain: "L" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "M" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5296 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 32, 'TRANS': 657} Chain: "N" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1204 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "O" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1671 Classifications: {'peptide': 217} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 195} Chain: "P" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1738 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "Q" Number of atoms: 3459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3459 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 401} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 566 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "U" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 643 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 11, 'TRANS': 71} Chain: "V" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1021 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "W" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1161 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 133} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "X" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 694 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Y" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 584 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 6, 'TRANS': 60} Chain: "Z" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "a" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1151 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 10, 'TRANS': 127} Chain: "b" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 819 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "c" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1315 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 20, 'TRANS': 135} Chain: "d" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1461 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 10, 'TRANS': 164} Chain: "e" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 867 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 8, 'TRANS': 95} Chain: "f" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 378 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "g" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1000 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 11, 'TRANS': 109} Chain: "h" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 867 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "i" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2710 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 328} Chain: "j" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 914 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "k" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "l" Number of atoms: 4816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4816 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 28, 'TRANS': 577} Chain: "m" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1291 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 171} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "n" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 479 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "o" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1062 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 11, 'TRANS': 116} Chain: "p" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1534 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 17, 'TRANS': 160} Chain: "r" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3631 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Chain: "s" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2508 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 296} Chain: "u" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1398 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "v" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1028 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "w" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2590 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 16, 'TRANS': 303} Chain: "A" 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: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'PEE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'PEE': 1, 'PLX': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 222 Unusual residues: {' UQ': 1, 'CDL': 1, 'NDP': 1, 'PLX': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {' UQ:plan-2': 1, ' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 30 Chain: "M" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' MG': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 194 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "W" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "X" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "g" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 68 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Chain: "j" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 144 Unusual residues: {'PEE': 2, 'PLX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "l" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 290 Unusual residues: {'CDL': 2, 'PEE': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "m" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 255 Unusual residues: {'CDL': 1, 'PEE': 1, 'PLX': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "s" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 63 Unusual residues: {' UQ': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 55 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Chain: "w" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2718 SG CYS A 382 48.130 49.070 174.160 1.00 41.46 S ATOM 3060 SG CYS A 425 47.412 45.909 180.045 1.00 46.19 S ATOM 2738 SG CYS A 385 44.784 44.762 174.253 1.00 43.02 S ATOM 2699 SG CYS A 379 42.856 49.665 178.245 1.00 44.75 S ATOM 3961 SG CYS B 113 35.729 64.058 139.313 1.00 37.37 S ATOM 3980 SG CYS B 116 40.975 61.832 142.936 1.00 34.05 S ATOM 4003 SG CYS B 119 41.800 64.452 137.392 1.00 33.15 S ATOM 4332 SG CYS B 162 39.332 58.540 138.360 1.00 33.12 S ATOM 4030 SG CYS B 123 47.815 67.159 132.578 1.00 29.88 S ATOM 4256 SG CYS B 152 45.837 65.348 126.820 1.00 30.05 S ATOM 4303 SG CYS B 158 44.042 61.583 131.729 1.00 32.29 S ATOM 4282 SG CYS B 155 50.044 61.836 130.159 1.00 32.12 S ATOM 5724 SG CYS C 166 52.344 65.144 122.301 1.00 34.38 S ATOM 4996 SG CYS C 72 52.750 66.598 115.933 1.00 37.52 S ATOM 4990 SG CYS C 71 58.007 64.904 118.939 1.00 36.77 S ATOM 5494 SG CYS C 136 54.784 70.260 121.065 1.00 31.01 S ATOM 14946 SG CYS M 131 40.623 62.319 154.973 1.00 36.25 S ATOM 14925 SG CYS M 128 44.044 57.632 151.935 1.00 33.36 S ATOM 14986 SG CYS M 137 46.287 61.118 157.112 1.00 35.34 S ATOM 15318 SG CYS M 179 44.778 61.494 168.247 1.00 40.20 S ATOM 15672 SG CYS M 226 41.656 64.222 163.866 1.00 37.16 S ATOM 15342 SG CYS M 182 39.699 63.879 169.636 1.00 39.06 S ATOM 15295 SG CYS M 176 39.400 59.249 166.559 1.00 37.69 S ATOM 14543 SG CYS M 78 56.601 57.231 171.609 1.00 40.86 S ATOM 14644 SG CYS M 92 54.784 59.296 174.140 1.00 40.36 S ATOM 14432 SG CYS M 64 50.271 59.175 171.882 1.00 38.19 S ATOM 14518 SG CYS M 75 51.367 57.308 169.127 1.00 40.49 S ATOM 21481 SG CYS O 135 32.243 31.812 183.060 1.00 67.31 S ATOM 21515 SG CYS O 140 32.454 28.349 184.217 1.00 68.20 S ATOM 21795 SG CYS O 176 36.685 33.273 185.570 1.00 66.25 S ATOM 21818 SG CYS O 180 37.593 29.885 186.706 1.00 71.67 S ATOM 28557 SG CYS T 86 28.721 50.744 147.432 1.00 45.25 S ATOM 28735 SG CYS T 111 29.832 54.205 148.550 1.00 46.38 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.50 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.50 Time building chain proxies: 25.75, per 1000 atoms: 0.38 Number of scatterers: 68315 At special positions: 0 Unit cell: (210.543, 218.063, 230.953, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 482 16.00 P 48 15.00 Mg 1 11.99 O 12246 8.00 N 11236 7.00 C 44273 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 58 " distance=2.03 Simple disulfide: pdb=" SG CYS V 18 " - pdb=" SG CYS V 75 " distance=2.03 Simple disulfide: pdb=" SG CYS V 95 " - pdb=" SG CYS V 115 " distance=2.03 Simple disulfide: pdb=" SG CYS d 113 " - pdb=" SG CYS d 125 " distance=2.02 Simple disulfide: pdb=" SG CYS h 33 " - pdb=" SG CYS h 66 " distance=2.03 Simple disulfide: pdb=" SG CYS h 43 " - pdb=" SG CYS h 56 " distance=1.58 Simple disulfide: pdb=" SG CYS u 46 " - pdb=" SG CYS u 56 " distance=2.03 Simple disulfide: pdb=" SG CYS u 78 " - pdb=" SG CYS u 110 " distance=2.03 Simple disulfide: pdb=" SG CYS u 88 " - pdb=" SG CYS u 100 " 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=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.66 Conformation dependent library (CDL) restraints added in 8.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " pdb=" FES O 301 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 135 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " pdb=" SF4 A 501 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb=" SF4 C 301 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb=" SF4 M 801 " pdb="FE3 SF4 M 801 " - pdb=" NE2 HIS M 124 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " pdb="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " pdb="FE1 SF4 M 801 " - pdb=" SG CYS M 131 " pdb=" SF4 M 802 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 86 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 111 " pdb="ZN ZN T 201 " - pdb=" NE2 HIS T 95 " 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15530 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 341 helices and 29 sheets defined 51.8% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.77 Creating SS restraints... Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 53 through 58 removed outlier: 3.772A pdb=" N SER A 58 " --> pdb=" O LYS A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 73 through 83 Processing helix chain 'A' and resid 95 through 102 removed outlier: 4.606A pdb=" N MET A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 133 Processing helix chain 'A' and resid 135 through 149 Processing helix chain 'A' and resid 163 through 178 Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 245 through 257 removed outlier: 3.596A pdb=" N SER A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 296 through 303 Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 363 through 376 Processing helix chain 'A' and resid 383 through 400 removed outlier: 4.375A pdb=" N ASP A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 419 Processing helix chain 'A' and resid 427 through 456 Proline residue: A 434 - end of helix removed outlier: 3.653A pdb=" N ARG A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) Proline residue: A 444 - end of helix Processing helix chain 'B' and resid 50 through 62 Processing helix chain 'B' and resid 64 through 78 removed outlier: 3.543A pdb=" N PHE B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 187 through 206 removed outlier: 5.460A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'C' and resid 43 through 60 Processing helix chain 'C' and resid 71 through 80 Processing helix chain 'C' and resid 86 through 89 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 111 through 122 Proline residue: C 115 - end of helix Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 189 through 194 Processing helix chain 'E' and resid 25 through 50 Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 56 through 70 removed outlier: 4.321A pdb=" N ASN E 70 " --> pdb=" O MET E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 94 Processing helix chain 'E' and resid 100 through 106 removed outlier: 4.312A pdb=" N PHE E 106 " --> pdb=" O HIS E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 124 Processing helix chain 'F' and resid 28 through 47 removed outlier: 4.800A pdb=" N GLY F 32 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ARG F 40 " --> pdb=" O ILE F 37 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N TYR F 41 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N VAL F 42 " --> pdb=" O LYS F 39 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLU F 43 " --> pdb=" O ARG F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'F' and resid 84 through 95 Processing helix chain 'G' and resid 76 through 89 Processing helix chain 'G' and resid 112 through 126 Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'H' and resid 20 through 37 removed outlier: 3.959A pdb=" N GLN H 37 " --> pdb=" O ASP H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 60 Processing helix chain 'H' and resid 65 through 72 Processing helix chain 'H' and resid 78 through 97 Processing helix chain 'I' and resid 6 through 16 Processing helix chain 'I' and resid 54 through 56 No H-bonds generated for 'chain 'I' and resid 54 through 56' Processing helix chain 'I' and resid 60 through 62 No H-bonds generated for 'chain 'I' and resid 60 through 62' Processing helix chain 'J' and resid 38 through 40 No H-bonds generated for 'chain 'J' and resid 38 through 40' Processing helix chain 'J' and resid 65 through 75 Processing helix chain 'J' and resid 88 through 97 removed outlier: 5.138A pdb=" N HIS J 93 " --> pdb=" O ASP J 90 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 113 through 119 Processing helix chain 'J' and resid 141 through 145 Processing helix chain 'J' and resid 147 through 158 Processing helix chain 'J' and resid 179 through 194 Processing helix chain 'J' and resid 212 through 223 removed outlier: 3.788A pdb=" N PHE J 217 " --> pdb=" O PHE J 213 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG J 221 " --> pdb=" O PHE J 217 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N TRP J 222 " --> pdb=" O ALA J 218 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N PHE J 223 " --> pdb=" O SER J 219 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 232 Processing helix chain 'J' and resid 242 through 253 Processing helix chain 'J' and resid 273 through 283 Processing helix chain 'J' and resid 295 through 307 removed outlier: 3.837A pdb=" N VAL J 307 " --> pdb=" O ARG J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 316 through 322 Processing helix chain 'J' and resid 335 through 338 Processing helix chain 'J' and resid 350 through 356 removed outlier: 5.583A pdb=" N ARG J 355 " --> pdb=" O GLU J 351 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N HIS J 356 " --> pdb=" O VAL J 352 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 80 removed outlier: 3.800A pdb=" N GLU K 80 " --> pdb=" O GLN K 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 77 through 80' Processing helix chain 'K' and resid 85 through 95 removed outlier: 4.389A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 71 No H-bonds generated for 'chain 'L' and resid 69 through 71' Processing helix chain 'L' and resid 131 through 141 Processing helix chain 'L' and resid 161 through 164 Processing helix chain 'M' and resid 49 through 56 removed outlier: 4.010A pdb=" N VAL M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 122 Processing helix chain 'M' and resid 138 through 146 Processing helix chain 'M' and resid 173 through 175 No H-bonds generated for 'chain 'M' and resid 173 through 175' Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'M' and resid 219 through 225 removed outlier: 3.644A pdb=" N ILE M 222 " --> pdb=" O SER M 219 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE M 225 " --> pdb=" O ILE M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 292 Processing helix chain 'M' and resid 294 through 296 No H-bonds generated for 'chain 'M' and resid 294 through 296' Processing helix chain 'M' and resid 319 through 332 removed outlier: 3.520A pdb=" N SER M 332 " --> pdb=" O GLY M 328 " (cutoff:3.500A) Processing helix chain 'M' and resid 348 through 361 removed outlier: 3.830A pdb=" N VAL M 361 " --> pdb=" O LEU M 357 " (cutoff:3.500A) Processing helix chain 'M' and resid 378 through 380 No H-bonds generated for 'chain 'M' and resid 378 through 380' Processing helix chain 'M' and resid 383 through 385 No H-bonds generated for 'chain 'M' and resid 383 through 385' Processing helix chain 'M' and resid 392 through 396 removed outlier: 3.619A pdb=" N GLU M 395 " --> pdb=" O ALA M 392 " (cutoff:3.500A) Processing helix chain 'M' and resid 407 through 410 No H-bonds generated for 'chain 'M' and resid 407 through 410' Processing helix chain 'M' and resid 412 through 424 Processing helix chain 'M' and resid 449 through 457 Processing helix chain 'M' and resid 461 through 468 Processing helix chain 'M' and resid 478 through 481 Processing helix chain 'M' and resid 486 through 503 Processing helix chain 'M' and resid 522 through 528 Processing helix chain 'M' and resid 535 through 539 Processing helix chain 'M' and resid 589 through 591 No H-bonds generated for 'chain 'M' and resid 589 through 591' Processing helix chain 'M' and resid 619 through 629 Processing helix chain 'M' and resid 639 through 649 Processing helix chain 'M' and resid 651 through 653 No H-bonds generated for 'chain 'M' and resid 651 through 653' Processing helix chain 'M' and resid 665 through 672 Processing helix chain 'M' and resid 691 through 695 removed outlier: 3.616A pdb=" N TYR M 695 " --> pdb=" O LYS M 692 " (cutoff:3.500A) Processing helix chain 'M' and resid 699 through 702 No H-bonds generated for 'chain 'M' and resid 699 through 702' Processing helix chain 'M' and resid 705 through 715 Processing helix chain 'N' and resid 4 through 17 removed outlier: 3.751A pdb=" N HIS N 17 " --> pdb=" O GLN N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 30 Processing helix chain 'N' and resid 79 through 81 No H-bonds generated for 'chain 'N' and resid 79 through 81' Processing helix chain 'N' and resid 84 through 90 Processing helix chain 'O' and resid 57 through 69 removed outlier: 3.797A pdb=" N ASN O 69 " --> pdb=" O ALA O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 90 removed outlier: 4.594A pdb=" N LEU O 80 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Proline residue: O 81 - end of helix Processing helix chain 'O' and resid 95 through 104 Processing helix chain 'O' and resid 109 through 118 Processing helix chain 'O' and resid 138 through 141 No H-bonds generated for 'chain 'O' and resid 138 through 141' Processing helix chain 'O' and resid 145 through 156 Processing helix chain 'O' and resid 198 through 210 Processing helix chain 'P' and resid 52 through 68 Processing helix chain 'P' and resid 90 through 102 removed outlier: 3.634A pdb=" N VAL P 93 " --> pdb=" O PRO P 90 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ILE P 94 " --> pdb=" O ASP P 91 " (cutoff:3.500A) Proline residue: P 95 - end of helix Processing helix chain 'P' and resid 161 through 174 removed outlier: 3.658A pdb=" N TRP P 165 " --> pdb=" O ALA P 162 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU P 167 " --> pdb=" O ASN P 164 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE P 174 " --> pdb=" O TRP P 171 " (cutoff:3.500A) Processing helix chain 'P' and resid 243 through 245 No H-bonds generated for 'chain 'P' and resid 243 through 245' Processing helix chain 'Q' and resid 41 through 47 removed outlier: 4.243A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N PHE Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 120 through 126 Processing helix chain 'Q' and resid 133 through 139 removed outlier: 3.828A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG Q 138 " --> pdb=" O PRO Q 134 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 159 Processing helix chain 'Q' and resid 165 through 194 Processing helix chain 'Q' and resid 198 through 218 removed outlier: 3.970A pdb=" N GLU Q 205 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 240 through 262 removed outlier: 3.691A pdb=" N ASN Q 250 " --> pdb=" O GLU Q 246 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER Q 252 " --> pdb=" O SER Q 248 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N PHE Q 253 " --> pdb=" O LYS Q 249 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG Q 254 " --> pdb=" O ASN Q 250 " (cutoff:3.500A) Processing helix chain 'Q' and resid 266 through 272 Processing helix chain 'Q' and resid 280 through 285 Processing helix chain 'Q' and resid 290 through 296 removed outlier: 4.402A pdb=" N GLY Q 295 " --> pdb=" O MET Q 292 " (cutoff:3.500A) Processing helix chain 'Q' and resid 302 through 305 No H-bonds generated for 'chain 'Q' and resid 302 through 305' Processing helix chain 'Q' and resid 311 through 313 No H-bonds generated for 'chain 'Q' and resid 311 through 313' Processing helix chain 'Q' and resid 326 through 349 Processing helix chain 'Q' and resid 368 through 371 No H-bonds generated for 'chain 'Q' and resid 368 through 371' Processing helix chain 'Q' and resid 375 through 386 Processing helix chain 'Q' and resid 427 through 439 removed outlier: 4.691A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 453 Processing helix chain 'Q' and resid 458 through 462 Processing helix chain 'S' and resid 2 through 4 No H-bonds generated for 'chain 'S' and resid 2 through 4' Processing helix chain 'S' and resid 6 through 31 removed outlier: 3.614A pdb=" N ILE S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) Proline residue: S 19 - end of helix Processing helix chain 'S' and resid 42 through 55 Processing helix chain 'S' and resid 66 through 68 No H-bonds generated for 'chain 'S' and resid 66 through 68' Processing helix chain 'T' and resid 50 through 55 Processing helix chain 'T' and resid 67 through 72 Processing helix chain 'T' and resid 91 through 93 No H-bonds generated for 'chain 'T' and resid 91 through 93' Processing helix chain 'U' and resid 4 through 15 Processing helix chain 'U' and resid 17 through 35 Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 39 through 47 Processing helix chain 'U' and resid 79 through 82 No H-bonds generated for 'chain 'U' and resid 79 through 82' Processing helix chain 'V' and resid 3 through 10 Processing helix chain 'V' and resid 18 through 43 Processing helix chain 'V' and resid 49 through 80 Processing helix chain 'V' and resid 87 through 105 Processing helix chain 'V' and resid 108 through 131 Processing helix chain 'W' and resid 32 through 99 Proline residue: W 73 - end of helix removed outlier: 3.602A pdb=" N LYS W 99 " --> pdb=" O ALA W 95 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 137 Processing helix chain 'X' and resid 76 through 88 Processing helix chain 'X' and resid 95 through 97 No H-bonds generated for 'chain 'X' and resid 95 through 97' Processing helix chain 'X' and resid 112 through 126 Processing helix chain 'X' and resid 141 through 152 Processing helix chain 'Y' and resid 52 through 75 Processing helix chain 'Y' and resid 77 through 81 Processing helix chain 'Y' and resid 89 through 91 No H-bonds generated for 'chain 'Y' and resid 89 through 91' Processing helix chain 'Z' and resid 19 through 21 No H-bonds generated for 'chain 'Z' and resid 19 through 21' Processing helix chain 'Z' and resid 28 through 39 removed outlier: 4.097A pdb=" N ARG Z 39 " --> pdb=" O LYS Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 46 through 54 removed outlier: 4.599A pdb=" N TRP Z 51 " --> pdb=" O ARG Z 47 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ARG Z 52 " --> pdb=" O ASN Z 48 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TYR Z 53 " --> pdb=" O GLU Z 49 " (cutoff:3.500A) Processing helix chain 'Z' and resid 63 through 67 Processing helix chain 'Z' and resid 71 through 86 Processing helix chain 'a' and resid 62 through 92 Proline residue: a 81 - end of helix Processing helix chain 'a' and resid 109 through 112 removed outlier: 4.025A pdb=" N TYR a 112 " --> pdb=" O HIS a 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 109 through 112' Processing helix chain 'a' and resid 116 through 125 Processing helix chain 'a' and resid 129 through 163 Processing helix chain 'a' and resid 176 through 178 No H-bonds generated for 'chain 'a' and resid 176 through 178' Processing helix chain 'b' and resid 6 through 26 Processing helix chain 'b' and resid 69 through 74 Processing helix chain 'b' and resid 76 through 88 Processing helix chain 'c' and resid 34 through 36 No H-bonds generated for 'chain 'c' and resid 34 through 36' Processing helix chain 'c' and resid 45 through 54 Processing helix chain 'c' and resid 109 through 111 No H-bonds generated for 'chain 'c' and resid 109 through 111' Processing helix chain 'c' and resid 129 through 148 Processing helix chain 'd' and resid 29 through 57 removed outlier: 4.874A pdb=" N ARG d 43 " --> pdb=" O LEU d 39 " (cutoff:3.500A) Proline residue: d 44 - end of helix Processing helix chain 'd' and resid 74 through 76 No H-bonds generated for 'chain 'd' and resid 74 through 76' Processing helix chain 'd' and resid 82 through 116 Processing helix chain 'd' and resid 121 through 124 No H-bonds generated for 'chain 'd' and resid 121 through 124' Processing helix chain 'd' and resid 126 through 143 Processing helix chain 'd' and resid 152 through 175 removed outlier: 3.522A pdb=" N ALA d 175 " --> pdb=" O LYS d 171 " (cutoff:3.500A) Processing helix chain 'e' and resid 80 through 94 Processing helix chain 'e' and resid 98 through 106 Processing helix chain 'e' and resid 116 through 132 Processing helix chain 'e' and resid 144 through 146 No H-bonds generated for 'chain 'e' and resid 144 through 146' Processing helix chain 'f' and resid 41 through 73 Processing helix chain 'g' and resid 18 through 22 removed outlier: 3.635A pdb=" N SER g 22 " --> pdb=" O GLU g 19 " (cutoff:3.500A) Processing helix chain 'g' and resid 31 through 50 Processing helix chain 'g' and resid 60 through 98 removed outlier: 3.802A pdb=" N TYR g 76 " --> pdb=" O PHE g 72 " (cutoff:3.500A) Processing helix chain 'g' and resid 100 through 102 No H-bonds generated for 'chain 'g' and resid 100 through 102' Processing helix chain 'h' and resid 6 through 10 Processing helix chain 'h' and resid 16 through 18 No H-bonds generated for 'chain 'h' and resid 16 through 18' Processing helix chain 'h' and resid 26 through 28 No H-bonds generated for 'chain 'h' and resid 26 through 28' Processing helix chain 'h' and resid 34 through 44 Processing helix chain 'h' and resid 49 through 52 No H-bonds generated for 'chain 'h' and resid 49 through 52' Processing helix chain 'h' and resid 57 through 68 Processing helix chain 'h' and resid 70 through 89 Processing helix chain 'h' and resid 96 through 98 No H-bonds generated for 'chain 'h' and resid 96 through 98' Processing helix chain 'i' and resid 3 through 22 Processing helix chain 'i' and resid 26 through 44 Proline residue: i 42 - end of helix Processing helix chain 'i' and resid 50 through 80 Processing helix chain 'i' and resid 92 through 106 Processing helix chain 'i' and resid 112 through 121 Proline residue: i 116 - end of helix removed outlier: 3.580A pdb=" N THR i 119 " --> pdb=" O PRO i 116 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 144 removed outlier: 3.779A pdb=" N GLN i 134 " --> pdb=" O LEU i 130 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LYS i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ALA i 137 " --> pdb=" O TRP i 133 " (cutoff:3.500A) Proline residue: i 138 - end of helix Processing helix chain 'i' and resid 151 through 169 Processing helix chain 'i' and resid 175 through 192 Processing helix chain 'i' and resid 198 through 221 Processing helix chain 'i' and resid 227 through 235 removed outlier: 3.648A pdb=" N HIS i 232 " --> pdb=" O LEU i 228 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR i 233 " --> pdb=" O SER i 229 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N TRP i 234 " --> pdb=" O LEU i 230 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ASN i 235 " --> pdb=" O SER i 231 " (cutoff:3.500A) Processing helix chain 'i' and resid 238 through 252 Processing helix chain 'i' and resid 258 through 271 Proline residue: i 262 - end of helix Processing helix chain 'i' and resid 277 through 300 removed outlier: 4.479A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 309 through 316 Processing helix chain 'i' and resid 326 through 334 Processing helix chain 'i' and resid 337 through 346 Proline residue: i 341 - end of helix Processing helix chain 'j' and resid 2 through 23 Processing helix chain 'j' and resid 56 through 80 removed outlier: 3.527A pdb=" N LEU j 64 " --> pdb=" O ILE j 60 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU j 67 " --> pdb=" O LEU j 63 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU j 68 " --> pdb=" O LEU j 64 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE j 69 " --> pdb=" O PHE j 65 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA j 70 " --> pdb=" O ASP j 66 " (cutoff:3.500A) Proline residue: j 74 - end of helix removed outlier: 5.579A pdb=" N TRP j 77 " --> pdb=" O LEU j 73 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLN j 80 " --> pdb=" O PRO j 76 " (cutoff:3.500A) Processing helix chain 'j' and resid 84 through 107 removed outlier: 3.508A pdb=" N THR j 89 " --> pdb=" O LYS j 85 " (cutoff:3.500A) Processing helix chain 'k' and resid 3 through 21 Processing helix chain 'k' and resid 27 through 50 Processing helix chain 'k' and resid 55 through 85 removed outlier: 3.646A pdb=" N MET k 58 " --> pdb=" O LEU k 55 " (cutoff:3.500A) Proline residue: k 60 - end of helix Processing helix chain 'k' and resid 90 through 92 No H-bonds generated for 'chain 'k' and resid 90 through 92' Processing helix chain 'l' and resid 3 through 13 removed outlier: 3.806A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) Processing helix chain 'l' and resid 17 through 22 Processing helix chain 'l' and resid 32 through 57 removed outlier: 4.652A pdb=" N VAL l 49 " --> pdb=" O THR l 45 " (cutoff:3.500A) Proline residue: l 50 - end of helix Processing helix chain 'l' and resid 84 through 107 Proline residue: l 91 - end of helix removed outlier: 3.863A pdb=" N TRP l 106 " --> pdb=" O GLU l 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 114 through 132 Processing helix chain 'l' and resid 137 through 155 Processing helix chain 'l' and resid 162 through 193 removed outlier: 3.891A pdb=" N GLY l 181 " --> pdb=" O ILE l 177 " (cutoff:3.500A) Processing helix chain 'l' and resid 198 through 204 Processing helix chain 'l' and resid 210 through 224 Processing helix chain 'l' and resid 227 through 229 No H-bonds generated for 'chain 'l' and resid 227 through 229' Processing helix chain 'l' and resid 231 through 238 removed outlier: 3.545A pdb=" N SER l 235 " --> pdb=" O PRO l 231 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N GLU l 238 " --> pdb=" O PRO l 234 " (cutoff:3.500A) Processing helix chain 'l' and resid 241 through 246 Processing helix chain 'l' and resid 252 through 262 removed outlier: 4.524A pdb=" N GLY l 256 " --> pdb=" O VAL l 253 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL l 257 " --> pdb=" O VAL l 254 " (cutoff:3.500A) Processing helix chain 'l' and resid 264 through 269 removed outlier: 4.115A pdb=" N THR l 269 " --> pdb=" O PRO l 265 " (cutoff:3.500A) Processing helix chain 'l' and resid 272 through 294 removed outlier: 4.549A pdb=" N THR l 294 " --> pdb=" O LEU l 290 " (cutoff:3.500A) Processing helix chain 'l' and resid 298 through 318 Processing helix chain 'l' and resid 322 through 349 removed outlier: 4.041A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE l 335 " --> pdb=" O MET l 331 " (cutoff:3.500A) Processing helix chain 'l' and resid 356 through 358 No H-bonds generated for 'chain 'l' and resid 356 through 358' Processing helix chain 'l' and resid 367 through 381 Processing helix chain 'l' and resid 389 through 400 removed outlier: 4.883A pdb=" N LEU l 394 " --> pdb=" O TYR l 390 " (cutoff:3.500A) Processing helix chain 'l' and resid 406 through 431 removed outlier: 3.622A pdb=" N ALA l 420 " --> pdb=" O THR l 416 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG l 425 " --> pdb=" O ALA l 421 " (cutoff:3.500A) Processing helix chain 'l' and resid 448 through 469 removed outlier: 5.778A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N PHE l 466 " --> pdb=" O ILE l 462 " (cutoff:3.500A) Processing helix chain 'l' and resid 484 through 487 No H-bonds generated for 'chain 'l' and resid 484 through 487' Processing helix chain 'l' and resid 489 through 508 removed outlier: 3.952A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) Processing helix chain 'l' and resid 518 through 524 Processing helix chain 'l' and resid 526 through 533 Proline residue: l 530 - end of helix removed outlier: 4.116A pdb=" N MET l 533 " --> pdb=" O PRO l 530 " (cutoff:3.500A) Processing helix chain 'l' and resid 536 through 547 Processing helix chain 'l' and resid 557 through 561 Processing helix chain 'l' and resid 563 through 577 Processing helix chain 'l' and resid 584 through 600 Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 25 through 47 removed outlier: 3.958A pdb=" N GLY m 29 " --> pdb=" O SER m 25 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE m 47 " --> pdb=" O ILE m 43 " (cutoff:3.500A) Processing helix chain 'm' and resid 50 through 74 Processing helix chain 'm' and resid 87 through 109 Processing helix chain 'm' and resid 125 through 127 No H-bonds generated for 'chain 'm' and resid 125 through 127' Processing helix chain 'm' and resid 138 through 146 removed outlier: 4.304A pdb=" N LEU m 146 " --> pdb=" O GLY m 142 " (cutoff:3.500A) Processing helix chain 'm' and resid 151 through 173 Processing helix chain 'n' and resid 4 through 34 removed outlier: 6.515A pdb=" N VAL n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N HIS n 14 " --> pdb=" O ASP n 10 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ILE n 15 " --> pdb=" O HIS n 11 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU n 16 " --> pdb=" O TRP n 12 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N VAL n 17 " --> pdb=" O VAL n 13 " (cutoff:3.500A) Proline residue: n 18 - end of helix removed outlier: 3.509A pdb=" N LYS n 34 " --> pdb=" O ARG n 30 " (cutoff:3.500A) Processing helix chain 'o' and resid 20 through 23 No H-bonds generated for 'chain 'o' and resid 20 through 23' Processing helix chain 'o' and resid 27 through 51 removed outlier: 3.708A pdb=" N GLN o 50 " --> pdb=" O GLU o 46 " (cutoff:3.500A) Processing helix chain 'o' and resid 63 through 73 Processing helix chain 'o' and resid 77 through 79 No H-bonds generated for 'chain 'o' and resid 77 through 79' Processing helix chain 'o' and resid 84 through 118 Proline residue: o 97 - end of helix Processing helix chain 'p' and resid 12 through 30 Processing helix chain 'p' and resid 34 through 51 removed outlier: 4.428A pdb=" N HIS p 51 " --> pdb=" O ARG p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 57 through 74 Processing helix chain 'p' and resid 93 through 96 removed outlier: 4.383A pdb=" N CYS p 96 " --> pdb=" O ARG p 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 93 through 96' Processing helix chain 'p' and resid 101 through 106 Processing helix chain 'p' and resid 109 through 113 Processing helix chain 'p' and resid 116 through 142 removed outlier: 4.733A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ARG p 135 " --> pdb=" O GLU p 131 " (cutoff:3.500A) Processing helix chain 'p' and resid 168 through 171 No H-bonds generated for 'chain 'p' and resid 168 through 171' Processing helix chain 'r' and resid 2 through 16 Proline residue: r 7 - end of helix Proline residue: r 13 - end of helix Processing helix chain 'r' and resid 23 through 42 removed outlier: 4.259A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N LEU r 42 " --> pdb=" O SER r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 60 through 80 Proline residue: r 64 - end of helix Proline residue: r 74 - end of helix Processing helix chain 'r' and resid 89 through 111 removed outlier: 3.765A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 115 through 136 removed outlier: 4.765A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL r 127 " --> pdb=" O GLU r 123 " (cutoff:3.500A) Proline residue: r 128 - end of helix Processing helix chain 'r' and resid 140 through 171 removed outlier: 4.031A pdb=" N LEU r 143 " --> pdb=" O THR r 140 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TYR r 152 " --> pdb=" O PHE r 149 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA r 155 " --> pdb=" O TYR r 152 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LEU r 158 " --> pdb=" O ALA r 155 " (cutoff:3.500A) Proline residue: r 159 - end of helix removed outlier: 4.039A pdb=" N THR r 171 " --> pdb=" O GLN r 168 " (cutoff:3.500A) Processing helix chain 'r' and resid 176 through 181 Processing helix chain 'r' and resid 190 through 206 removed outlier: 4.542A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 222 removed outlier: 4.194A pdb=" N LYS r 218 " --> pdb=" O LEU r 214 " (cutoff:3.500A) Processing helix chain 'r' and resid 225 through 233 Processing helix chain 'r' and resid 237 through 250 removed outlier: 5.127A pdb=" N THR r 248 " --> pdb=" O MET r 244 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ILE r 249 " --> pdb=" O ARG r 245 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU r 250 " --> pdb=" O ILE r 246 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 257 Processing helix chain 'r' and resid 259 through 277 removed outlier: 3.826A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) Processing helix chain 'r' and resid 283 through 303 Processing helix chain 'r' and resid 306 through 337 removed outlier: 3.598A pdb=" N ASN r 333 " --> pdb=" O LEU r 329 " (cutoff:3.500A) Processing helix chain 'r' and resid 353 through 366 Processing helix chain 'r' and resid 373 through 388 Processing helix chain 'r' and resid 390 through 415 removed outlier: 3.875A pdb=" N ILE r 393 " --> pdb=" O ASN r 390 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR r 414 " --> pdb=" O LEU r 411 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN r 415 " --> pdb=" O ILE r 412 " (cutoff:3.500A) Processing helix chain 'r' and resid 431 through 449 Proline residue: r 443 - end of helix Processing helix chain 'r' and resid 451 through 454 Processing helix chain 's' and resid 2 through 32 Proline residue: s 12 - end of helix removed outlier: 3.712A pdb=" N LEU s 22 " --> pdb=" O ALA s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 42 through 44 No H-bonds generated for 'chain 's' and resid 42 through 44' Processing helix chain 's' and resid 47 through 57 Processing helix chain 's' and resid 68 through 86 Proline residue: s 75 - end of helix removed outlier: 4.574A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 123 removed outlier: 3.831A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 5.131A pdb=" N VAL s 144 " --> pdb=" O ILE s 140 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 168 removed outlier: 3.940A pdb=" N THR s 168 " --> pdb=" O LEU s 165 " (cutoff:3.500A) Processing helix chain 's' and resid 174 through 176 No H-bonds generated for 'chain 's' and resid 174 through 176' Processing helix chain 's' and resid 179 through 192 Processing helix chain 's' and resid 210 through 212 No H-bonds generated for 'chain 's' and resid 210 through 212' Processing helix chain 's' and resid 218 through 242 Processing helix chain 's' and resid 252 through 276 Processing helix chain 's' and resid 282 through 291 removed outlier: 3.697A pdb=" N MET s 286 " --> pdb=" O TYR s 282 " (cutoff:3.500A) Processing helix chain 's' and resid 293 through 311 Proline residue: s 308 - end of helix Processing helix chain 'u' and resid 10 through 13 Processing helix chain 'u' and resid 22 through 27 Processing helix chain 'u' and resid 29 through 35 Processing helix chain 'u' and resid 37 through 50 Processing helix chain 'u' and resid 53 through 55 No H-bonds generated for 'chain 'u' and resid 53 through 55' Processing helix chain 'u' and resid 57 through 77 Processing helix chain 'u' and resid 79 through 91 Processing helix chain 'u' and resid 102 through 114 Processing helix chain 'v' and resid 4 through 10 Processing helix chain 'v' and resid 43 through 49 Processing helix chain 'v' and resid 60 through 72 Processing helix chain 'v' and resid 82 through 124 Processing helix chain 'w' and resid 40 through 44 Processing helix chain 'w' and resid 50 through 52 No H-bonds generated for 'chain 'w' and resid 50 through 52' Processing helix chain 'w' and resid 70 through 81 Processing helix chain 'w' and resid 94 through 96 No H-bonds generated for 'chain 'w' and resid 94 through 96' Processing helix chain 'w' and resid 114 through 119 Processing helix chain 'w' and resid 127 through 153 Processing helix chain 'w' and resid 163 through 165 No H-bonds generated for 'chain 'w' and resid 163 through 165' Processing helix chain 'w' and resid 167 through 175 Processing helix chain 'w' and resid 181 through 197 removed outlier: 4.266A pdb=" N CYS w 196 " --> pdb=" O LYS w 192 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N GLU w 197 " --> pdb=" O VAL w 193 " (cutoff:3.500A) Processing helix chain 'w' and resid 211 through 221 Processing helix chain 'w' and resid 226 through 228 No H-bonds generated for 'chain 'w' and resid 226 through 228' Processing helix chain 'w' and resid 231 through 251 removed outlier: 4.381A pdb=" N LEU w 246 " --> pdb=" O LYS w 242 " (cutoff:3.500A) Proline residue: w 247 - end of helix removed outlier: 4.019A pdb=" N GLU w 251 " --> pdb=" O PRO w 247 " (cutoff:3.500A) Processing helix chain 'w' and resid 266 through 275 Processing helix chain 'w' and resid 282 through 285 Processing helix chain 'w' and resid 288 through 298 Processing helix chain 'w' and resid 301 through 309 removed outlier: 5.136A pdb=" N TYR w 307 " --> pdb=" O GLU w 303 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N THR w 308 " --> pdb=" O VAL w 304 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR w 309 " --> pdb=" O LEU w 305 " (cutoff:3.500A) Processing helix chain 'w' and resid 321 through 332 Processing helix chain 'w' and resid 345 through 347 No H-bonds generated for 'chain 'w' and resid 345 through 347' Processing helix chain 'w' and resid 352 through 354 No H-bonds generated for 'chain 'w' and resid 352 through 354' Processing sheet with id= A, first strand: chain 'A' and resid 240 through 244 removed outlier: 7.195A pdb=" N TYR A 112 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N ALA A 243 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL A 114 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL A 198 " --> pdb=" O ILE A 158 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 286 through 291 Processing sheet with id= C, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= D, first strand: chain 'B' and resid 128 through 134 removed outlier: 6.049A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N THR B 142 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 102 through 106 removed outlier: 6.521A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE C 161 " --> pdb=" O SER C 132 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'F' and resid 52 through 57 removed outlier: 6.819A pdb=" N ARG F 68 " --> pdb=" O ARG F 17 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ILE F 19 " --> pdb=" O TRP F 66 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP F 66 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ILE F 21 " --> pdb=" O LYS F 64 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LYS F 64 " --> pdb=" O ILE F 21 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 262 through 265 removed outlier: 6.665A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE J 167 " --> pdb=" O ASN J 128 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLN J 79 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE J 81 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 226 through 228 Processing sheet with id= I, first strand: chain 'L' and resid 144 through 147 removed outlier: 3.566A pdb=" N ILE L 79 " --> pdb=" O ASP L 146 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'L' and resid 106 through 108 Processing sheet with id= K, first strand: chain 'M' and resid 32 through 36 Processing sheet with id= L, first strand: chain 'M' and resid 169 through 171 Processing sheet with id= M, first strand: chain 'M' and resid 196 through 200 removed outlier: 3.572A pdb=" N ARG M 200 " --> pdb=" O ASP M 203 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'M' and resid 246 through 251 Processing sheet with id= O, first strand: chain 'M' and resid 306 through 308 Processing sheet with id= P, first strand: chain 'M' and resid 365 through 368 removed outlier: 4.585A pdb=" N SER M 365 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU M 584 " --> pdb=" O GLY M 570 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'M' and resid 513 through 516 removed outlier: 8.316A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LYS M 428 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N LEU M 402 " --> pdb=" O LYS M 428 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALA M 430 " --> pdb=" O LEU M 402 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASP M 443 " --> pdb=" O LEU M 431 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'M' and resid 595 through 597 Processing sheet with id= S, first strand: chain 'N' and resid 60 through 63 removed outlier: 6.752A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N LEU N 38 " --> pdb=" O GLU N 50 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'O' and resid 169 through 174 removed outlier: 6.685A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'P' and resid 110 through 118 removed outlier: 3.620A pdb=" N SER P 110 " --> pdb=" O LEU P 133 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LEU P 84 " --> pdb=" O ARG P 140 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N TYR P 146 " --> pdb=" O ILE P 88 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU P 83 " --> pdb=" O SER P 79 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'P' and resid 208 through 213 removed outlier: 3.519A pdb=" N ARG P 218 " --> pdb=" O ASP P 213 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'Q' and resid 80 through 84 removed outlier: 3.727A pdb=" N LYS Q 108 " --> pdb=" O GLU Q 100 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id= Y, first strand: chain 'T' and resid 83 through 86 Processing sheet with id= Z, first strand: chain 'l' and resid 69 through 71 Processing sheet with id= AA, first strand: chain 'l' and resid 62 through 67 removed outlier: 6.465A pdb=" N LEU l 78 " --> pdb=" O ASN l 65 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'w' and resid 60 through 64 removed outlier: 6.918A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N GLU w 254 " --> pdb=" O VAL w 204 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N TYR w 206 " --> pdb=" O GLU w 254 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU w 256 " --> pdb=" O TYR w 206 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'w' and resid 84 through 86 2907 hydrogen bonds defined for protein. 8121 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: 22.66 Time building geometry restraints manager: 23.89 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: 27756 1.40 - 1.62: 41301 1.62 - 1.84: 855 1.84 - 2.06: 4 2.06 - 2.28: 80 Bond restraints: 69996 Sorted by residual: bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.297 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" CB7 CDL i 401 " pdb=" OB8 CDL i 401 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.20e+02 bond pdb=" C18 UQ s 501 " pdb=" C19 UQ s 501 " ideal model delta sigma weight residual 1.336 1.554 -0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" CA7 CDL i 401 " pdb=" OA8 CDL i 401 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.19e+02 bond pdb=" C18 UQ J 402 " pdb=" C19 UQ J 402 " ideal model delta sigma weight residual 1.336 1.554 -0.218 2.00e-02 2.50e+03 1.19e+02 ... (remaining 69991 not shown) Histogram of bond angle deviations from ideal: 73.57 - 85.74: 76 85.74 - 97.91: 4 97.91 - 110.09: 12124 110.09 - 122.26: 72809 122.26 - 134.44: 9564 Bond angle restraints: 94577 Sorted by residual: angle pdb=" N ALA s 216 " pdb=" CA ALA s 216 " pdb=" C ALA s 216 " ideal model delta sigma weight residual 111.36 123.12 -11.76 1.09e+00 8.42e-01 1.16e+02 angle pdb=" N LEU r 250 " pdb=" CA LEU r 250 " pdb=" C LEU r 250 " ideal model delta sigma weight residual 111.28 120.76 -9.48 1.09e+00 8.42e-01 7.57e+01 angle pdb=" N GLU s 206 " pdb=" CA GLU s 206 " pdb=" C GLU s 206 " ideal model delta sigma weight residual 111.14 120.34 -9.20 1.08e+00 8.57e-01 7.26e+01 angle pdb=" N HIS l 192 " pdb=" CA HIS l 192 " pdb=" C HIS l 192 " ideal model delta sigma weight residual 111.36 120.20 -8.84 1.09e+00 8.42e-01 6.58e+01 angle pdb=" N ASN M 74 " pdb=" CA ASN M 74 " pdb=" C ASN M 74 " ideal model delta sigma weight residual 111.36 120.17 -8.81 1.09e+00 8.42e-01 6.54e+01 ... (remaining 94572 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.94: 41158 33.94 - 67.87: 1376 67.87 - 101.81: 105 101.81 - 135.74: 22 135.74 - 169.68: 23 Dihedral angle restraints: 42684 sinusoidal: 18593 harmonic: 24091 Sorted by residual: dihedral pdb=" CA PRO i 255 " pdb=" C PRO i 255 " pdb=" N PRO i 256 " pdb=" CA PRO i 256 " ideal model delta harmonic sigma weight residual 0.00 39.56 -39.56 0 5.00e+00 4.00e-02 6.26e+01 dihedral pdb=" C5' ADP w 401 " pdb=" O5' ADP w 401 " pdb=" PA ADP w 401 " pdb=" O2A ADP w 401 " ideal model delta sinusoidal sigma weight residual -60.00 105.08 -165.08 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C10 FMN A 502 " pdb=" C1' FMN A 502 " pdb=" N10 FMN A 502 " pdb=" C2' FMN A 502 " ideal model delta sinusoidal sigma weight residual -102.41 59.17 -161.58 1 2.00e+01 2.50e-03 4.68e+01 ... (remaining 42681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 9950 0.120 - 0.240: 208 0.240 - 0.361: 21 0.361 - 0.481: 5 0.481 - 0.601: 2 Chirality restraints: 10186 Sorted by residual: chirality pdb=" CA SER s 209 " pdb=" N SER s 209 " pdb=" C SER s 209 " pdb=" CB SER s 209 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.03e+00 chirality pdb=" CA MET Q 222 " pdb=" N MET Q 222 " pdb=" C MET Q 222 " pdb=" CB MET Q 222 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.49 2.00e-01 2.50e+01 5.89e+00 chirality pdb=" CA MET M 173 " pdb=" N MET M 173 " pdb=" C MET M 173 " pdb=" CB MET M 173 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.33e+00 ... (remaining 10183 not shown) Planarity restraints: 11775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 UQ J 402 " -0.504 2.00e-02 2.50e+03 4.34e-01 2.36e+03 pdb=" C18 UQ J 402 " 0.573 2.00e-02 2.50e+03 pdb=" C19 UQ J 402 " 0.416 2.00e-02 2.50e+03 pdb=" C20 UQ J 402 " -0.057 2.00e-02 2.50e+03 pdb=" C21 UQ J 402 " -0.428 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ s 501 " 0.308 2.00e-02 2.50e+03 3.14e-01 1.23e+03 pdb=" C18 UQ s 501 " -0.583 2.00e-02 2.50e+03 pdb=" C19 UQ s 501 " 0.238 2.00e-02 2.50e+03 pdb=" C20 UQ s 501 " 0.022 2.00e-02 2.50e+03 pdb=" C21 UQ s 501 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ J 402 " 0.044 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C11 UQ J 402 " -0.063 2.00e-02 2.50e+03 pdb=" C7 UQ J 402 " -0.292 2.00e-02 2.50e+03 pdb=" C8 UQ J 402 " 0.546 2.00e-02 2.50e+03 pdb=" C9 UQ J 402 " -0.235 2.00e-02 2.50e+03 ... (remaining 11772 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.29: 95 2.29 - 2.94: 29181 2.94 - 3.59: 98894 3.59 - 4.25: 163629 4.25 - 4.90: 280097 Nonbonded interactions: 571896 Sorted by model distance: nonbonded pdb=" OE1 GLU a 97 " pdb=" NH2 ARG d 60 " model vdw 1.632 2.520 nonbonded pdb=" OD1 ASN d 104 " pdb=" O THR l 73 " model vdw 1.806 3.040 nonbonded pdb=" ND2 ASN O 182 " pdb=" OE1 GLU O 194 " model vdw 1.875 2.520 nonbonded pdb=" ND2 ASN S 31 " pdb=" OH TYR S 60 " model vdw 1.875 2.520 nonbonded pdb=" OH TYR Q 226 " pdb=" O GLN Q 234 " model vdw 1.920 2.440 ... (remaining 571891 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 'G' and (resid 69 through 93 or (resid 94 through 97 and (name N or name \ CA or name C or name O or name CB )) or resid 98 through 156)) selection = (chain 'X' and (resid 69 through 106 or (resid 107 and (name N or name CA or nam \ e C or name O or name CB )) or resid 108 through 149 or (resid 150 through 153 a \ nd (name N or name CA or name C or name O or name CB )) or resid 154 through 156 \ )) } 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=0.50 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: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 9.710 Check model and map are aligned: 0.740 Set scattering table: 0.470 Process input model: 156.730 Find NCS groups from input model: 2.140 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 184.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 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 : 0.007 0.227 69996 Z= 0.455 Angle : 0.874 16.850 94577 Z= 0.479 Chirality : 0.050 0.601 10186 Planarity : 0.010 0.434 11775 Dihedral : 16.598 169.677 27127 Min Nonbonded Distance : 1.632 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.98 % Favored : 95.90 % Rotamer: Outliers : 0.39 % Allowed : 0.78 % Favored : 98.83 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.79 % Cis-general : 0.00 % Twisted Proline : 0.40 % 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: 0.64 (0.09), residues: 8172 helix: 1.57 (0.08), residues: 4300 sheet: -0.44 (0.25), residues: 440 loop : -0.94 (0.11), residues: 3432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP M 100 HIS 0.011 0.001 HIS p 51 PHE 0.038 0.001 PHE Q 204 TYR 0.039 0.001 TYR C 142 ARG 0.005 0.000 ARG a 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1317 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 1289 time to evaluate : 5.849 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 55 ASP cc_start: 0.8268 (m-30) cc_final: 0.7743 (m-30) REVERT: F 64 LYS cc_start: 0.8670 (mtpp) cc_final: 0.8262 (mtpp) REVERT: G 81 ASP cc_start: 0.7380 (m-30) cc_final: 0.7146 (m-30) REVERT: G 114 ASP cc_start: 0.8178 (m-30) cc_final: 0.7930 (m-30) REVERT: G 144 ILE cc_start: 0.8431 (mt) cc_final: 0.8141 (mt) REVERT: J 303 ARG cc_start: 0.8088 (tmt-80) cc_final: 0.7774 (tpt-90) REVERT: J 323 HIS cc_start: 0.7922 (m90) cc_final: 0.7553 (t-90) REVERT: K 80 GLU cc_start: 0.8279 (mp0) cc_final: 0.8069 (pm20) REVERT: L 78 ARG cc_start: 0.8612 (ttt-90) cc_final: 0.8214 (ttt180) REVERT: L 105 GLU cc_start: 0.8873 (tt0) cc_final: 0.8669 (tt0) REVERT: L 146 ASP cc_start: 0.7762 (p0) cc_final: 0.7508 (p0) REVERT: L 149 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7956 (mm-30) REVERT: M 395 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8166 (mt-10) REVERT: M 470 LYS cc_start: 0.8032 (ptpp) cc_final: 0.7673 (ptpp) REVERT: M 530 TYR cc_start: 0.8911 (OUTLIER) cc_final: 0.8340 (t80) REVERT: N 8 ARG cc_start: 0.7457 (mmt90) cc_final: 0.6409 (tpt170) REVERT: P 236 ASN cc_start: 0.9201 (m-40) cc_final: 0.8854 (m110) REVERT: Q 282 ASP cc_start: 0.8550 (m-30) cc_final: 0.8213 (m-30) REVERT: T 106 THR cc_start: 0.9192 (p) cc_final: 0.8974 (t) REVERT: U 79 GLU cc_start: 0.8450 (tp30) cc_final: 0.8197 (mm-30) REVERT: V 106 ARG cc_start: 0.7156 (tpm170) cc_final: 0.6748 (tpp-160) REVERT: W 24 ASN cc_start: 0.8216 (t0) cc_final: 0.7903 (t0) REVERT: Z 23 LYS cc_start: 0.8464 (mttp) cc_final: 0.8185 (mttt) REVERT: b 120 MET cc_start: 0.7914 (ptm) cc_final: 0.7692 (ptm) REVERT: b 121 LYS cc_start: 0.8265 (tmtt) cc_final: 0.7818 (tmtm) REVERT: d 64 TYR cc_start: 0.9134 (OUTLIER) cc_final: 0.8339 (m-80) REVERT: d 81 ASP cc_start: 0.8423 (t0) cc_final: 0.8157 (t0) REVERT: f 61 GLN cc_start: 0.8340 (tp40) cc_final: 0.7920 (tp40) REVERT: f 65 ASP cc_start: 0.8344 (m-30) cc_final: 0.8105 (m-30) REVERT: h 13 ASP cc_start: 0.8970 (t70) cc_final: 0.8708 (t0) REVERT: i 18 MET cc_start: 0.7877 (mmm) cc_final: 0.7624 (mmt) REVERT: i 89 MET cc_start: 0.8267 (ttt) cc_final: 0.7826 (ttt) REVERT: i 154 MET cc_start: 0.9118 (tpt) cc_final: 0.8820 (tpt) REVERT: j 52 SER cc_start: 0.9115 (t) cc_final: 0.8885 (t) REVERT: l 108 MET cc_start: 0.9253 (mmm) cc_final: 0.8936 (mmt) REVERT: o 113 GLU cc_start: 0.8040 (tp30) cc_final: 0.7832 (mm-30) REVERT: p 51 HIS cc_start: 0.8594 (m-70) cc_final: 0.8372 (m170) REVERT: r 201 MET cc_start: 0.8956 (mmm) cc_final: 0.8625 (mmm) REVERT: s 62 ARG cc_start: 0.7829 (ttp80) cc_final: 0.7379 (ttp80) REVERT: s 233 MET cc_start: 0.8471 (tmm) cc_final: 0.8150 (tmt) REVERT: v 33 GLU cc_start: 0.7458 (tm-30) cc_final: 0.7208 (tm-30) REVERT: v 59 CYS cc_start: 0.8148 (m) cc_final: 0.7802 (m) outliers start: 28 outliers final: 11 residues processed: 1311 average time/residue: 1.5977 time to fit residues: 2702.7683 Evaluate side-chains 1098 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1085 time to evaluate : 5.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain P residue 201 ASP Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain d residue 64 TYR Chi-restraints excluded: chain h residue 43 CYS Chi-restraints excluded: chain h residue 45 HIS Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 601 LEU Chi-restraints excluded: chain r residue 248 THR Chi-restraints excluded: chain s residue 202 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 679 optimal weight: 4.9990 chunk 610 optimal weight: 1.9990 chunk 338 optimal weight: 3.9990 chunk 208 optimal weight: 7.9990 chunk 411 optimal weight: 6.9990 chunk 325 optimal weight: 3.9990 chunk 630 optimal weight: 0.0370 chunk 244 optimal weight: 10.0000 chunk 383 optimal weight: 0.9980 chunk 469 optimal weight: 10.0000 chunk 731 optimal weight: 0.7980 overall best weight: 1.5662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 GLN E 48 HIS F 25 GLN F 81 ASN F 93 ASN G 101 ASN H 37 GLN H 41 ASN H 73 GLN H 86 ASN J 109 ASN J 269 ASN J 356 HIS K 75 ASN K 79 HIS L 109 ASN M 331 GLN ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 116 ASN ** N 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 123 ASN P 51 ASN P 105 ASN ** P 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 60 HIS S 31 ASN T 122 HIS U 11 ASN V 89 ASN b 13 GLN b 26 GLN d 107 GLN d 149 HIS e 148 GLN ** g 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 27 HIS h 98 HIS i 47 ASN i 319 HIS j 10 ASN j 28 ASN ** l 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 471 ASN l 524 ASN ** l 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 580 GLN m 86 ASN n 3 ASN p 66 GLN p 124 GLN ** u 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 219 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.0813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 69996 Z= 0.224 Angle : 0.560 10.705 94577 Z= 0.283 Chirality : 0.042 0.202 10186 Planarity : 0.005 0.054 11775 Dihedral : 16.098 176.920 10948 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.82 % Favored : 96.12 % Rotamer: Outliers : 1.75 % Allowed : 8.66 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 0.68 (0.09), residues: 8172 helix: 1.58 (0.08), residues: 4289 sheet: -0.40 (0.25), residues: 439 loop : -0.87 (0.11), residues: 3444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP u 86 HIS 0.007 0.001 HIS r 30 PHE 0.031 0.001 PHE i 292 TYR 0.025 0.001 TYR C 142 ARG 0.007 0.000 ARG J 179 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1263 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 1138 time to evaluate : 5.892 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: B 55 ASP cc_start: 0.8252 (m-30) cc_final: 0.7708 (m-30) REVERT: F 64 LYS cc_start: 0.8703 (mtpp) cc_final: 0.8256 (mtpp) REVERT: G 81 ASP cc_start: 0.7376 (m-30) cc_final: 0.7153 (m-30) REVERT: G 92 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8129 (mtmt) REVERT: G 111 ASP cc_start: 0.7891 (p0) cc_final: 0.7389 (p0) REVERT: G 114 ASP cc_start: 0.8354 (m-30) cc_final: 0.7953 (m-30) REVERT: G 144 ILE cc_start: 0.8399 (mt) cc_final: 0.8084 (mt) REVERT: I 108 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8850 (mtpt) REVERT: J 323 HIS cc_start: 0.7931 (m90) cc_final: 0.7573 (t70) REVERT: L 78 ARG cc_start: 0.8636 (ttt-90) cc_final: 0.8217 (ttt180) REVERT: L 105 GLU cc_start: 0.8849 (tt0) cc_final: 0.8636 (tt0) REVERT: L 149 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7964 (mm-30) REVERT: M 42 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8010 (mmm) REVERT: M 395 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8275 (mt-10) REVERT: M 530 TYR cc_start: 0.8957 (OUTLIER) cc_final: 0.8196 (t80) REVERT: N 8 ARG cc_start: 0.7394 (mmt90) cc_final: 0.6428 (tpt170) REVERT: N 53 LYS cc_start: 0.8699 (mmtp) cc_final: 0.8307 (tppp) REVERT: P 50 ARG cc_start: 0.7597 (ttm170) cc_final: 0.7231 (mpt-90) REVERT: P 236 ASN cc_start: 0.9178 (m-40) cc_final: 0.8861 (m110) REVERT: Q 282 ASP cc_start: 0.8573 (m-30) cc_final: 0.8194 (m-30) REVERT: T 64 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7258 (mp0) REVERT: T 105 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6602 (tp30) REVERT: T 106 THR cc_start: 0.9179 (p) cc_final: 0.8972 (t) REVERT: U 15 LYS cc_start: 0.8580 (mtmm) cc_final: 0.8060 (mtpp) REVERT: U 79 GLU cc_start: 0.8452 (tp30) cc_final: 0.8203 (mm-30) REVERT: V 106 ARG cc_start: 0.7337 (tpm170) cc_final: 0.6946 (mmm160) REVERT: V 140 LYS cc_start: 0.8547 (ptmt) cc_final: 0.8302 (pttt) REVERT: W 24 ASN cc_start: 0.8228 (t0) cc_final: 0.7851 (t0) REVERT: W 80 ASP cc_start: 0.7758 (m-30) cc_final: 0.7471 (m-30) REVERT: W 98 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7127 (mpt) REVERT: Y 95 GLU cc_start: 0.7944 (pp20) cc_final: 0.7669 (pp20) REVERT: Z 14 MET cc_start: 0.5756 (OUTLIER) cc_final: 0.5131 (ptm) REVERT: a 52 LYS cc_start: 0.7782 (tppp) cc_final: 0.7266 (tppp) REVERT: a 114 LYS cc_start: 0.8541 (ptmt) cc_final: 0.7884 (ttpt) REVERT: e 121 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8242 (tp30) REVERT: f 61 GLN cc_start: 0.8369 (tp40) cc_final: 0.7954 (tp40) REVERT: f 65 ASP cc_start: 0.8377 (m-30) cc_final: 0.8130 (m-30) REVERT: f 68 GLU cc_start: 0.8661 (tp30) cc_final: 0.8419 (mm-30) REVERT: h 13 ASP cc_start: 0.8911 (t70) cc_final: 0.8660 (t0) REVERT: i 18 MET cc_start: 0.7877 (mmm) cc_final: 0.7618 (mmt) REVERT: i 269 GLU cc_start: 0.8574 (tp30) cc_final: 0.8367 (tp30) REVERT: j 52 SER cc_start: 0.9124 (t) cc_final: 0.8892 (t) REVERT: l 108 MET cc_start: 0.9188 (mmm) cc_final: 0.8817 (mmt) REVERT: l 271 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8001 (mttp) REVERT: l 405 ASN cc_start: 0.7516 (t0) cc_final: 0.7288 (t0) REVERT: o 113 GLU cc_start: 0.8080 (tp30) cc_final: 0.7827 (mm-30) REVERT: p 51 HIS cc_start: 0.8533 (m-70) cc_final: 0.8298 (m170) REVERT: r 22 MET cc_start: 0.8577 (mmm) cc_final: 0.8289 (mmm) REVERT: r 201 MET cc_start: 0.9024 (mmm) cc_final: 0.8752 (mmm) REVERT: s 151 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8790 (tp) REVERT: s 233 MET cc_start: 0.8523 (tmm) cc_final: 0.8212 (tmt) REVERT: v 70 LYS cc_start: 0.8800 (tppp) cc_final: 0.8456 (tttp) REVERT: w 227 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.7935 (mtt) outliers start: 125 outliers final: 58 residues processed: 1190 average time/residue: 1.5927 time to fit residues: 2442.5603 Evaluate side-chains 1156 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1087 time to evaluate : 5.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 108 LYS Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 690 THR Chi-restraints excluded: chain Q residue 417 SER Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain T residue 105 GLU Chi-restraints excluded: chain T residue 122 HIS Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 98 MET Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain X residue 132 ASP Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 74 ASP Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 141 LEU Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain e residue 68 GLU Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 271 LYS Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 544 MET Chi-restraints excluded: chain l residue 599 MET Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain o residue 73 SER Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain p residue 117 ASP Chi-restraints excluded: chain p residue 141 GLN Chi-restraints excluded: chain r residue 31 SER Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 246 ILE Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 156 MET Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 267 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 406 optimal weight: 4.9990 chunk 226 optimal weight: 6.9990 chunk 608 optimal weight: 6.9990 chunk 497 optimal weight: 9.9990 chunk 201 optimal weight: 10.0000 chunk 732 optimal weight: 2.9990 chunk 791 optimal weight: 9.9990 chunk 652 optimal weight: 5.9990 chunk 726 optimal weight: 1.9990 chunk 249 optimal weight: 5.9990 chunk 587 optimal weight: 0.6980 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 303 HIS E 48 HIS E 72 HIS F 81 ASN F 93 ASN G 101 ASN H 37 GLN H 41 ASN H 73 GLN I 25 GLN J 109 ASN K 75 ASN L 109 ASN M 598 ASN ** M 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 113 HIS N 116 ASN P 51 ASN ** P 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 GLN Q 60 HIS Q 285 ASN U 11 ASN b 13 GLN d 149 HIS e 132 ASN g 18 ASN h 21 GLN i 47 ASN i 83 GLN i 319 HIS ** l 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 86 ASN n 3 ASN p 66 GLN r 255 ASN u 151 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 69996 Z= 0.394 Angle : 0.614 12.093 94577 Z= 0.309 Chirality : 0.046 0.241 10186 Planarity : 0.005 0.056 11775 Dihedral : 15.477 176.989 10937 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.33 % Favored : 95.63 % Rotamer: Outliers : 2.42 % Allowed : 10.39 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 0.47 (0.09), residues: 8172 helix: 1.36 (0.08), residues: 4291 sheet: -0.31 (0.25), residues: 430 loop : -0.93 (0.10), residues: 3451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.009 0.001 HIS i 232 PHE 0.032 0.002 PHE i 292 TYR 0.027 0.002 TYR C 142 ARG 0.010 0.000 ARG n 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1276 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 1103 time to evaluate : 5.857 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 ASP cc_start: 0.8261 (m-30) cc_final: 0.7712 (m-30) REVERT: F 64 LYS cc_start: 0.8721 (mtpp) cc_final: 0.8254 (mtpp) REVERT: G 81 ASP cc_start: 0.7433 (m-30) cc_final: 0.7154 (m-30) REVERT: G 92 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8136 (mtmt) REVERT: G 111 ASP cc_start: 0.7906 (p0) cc_final: 0.7379 (p0) REVERT: G 114 ASP cc_start: 0.8390 (m-30) cc_final: 0.7993 (m-30) REVERT: G 122 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8228 (mmp) REVERT: G 144 ILE cc_start: 0.8451 (mt) cc_final: 0.8183 (mt) REVERT: J 323 HIS cc_start: 0.8177 (m90) cc_final: 0.7697 (t70) REVERT: L 105 GLU cc_start: 0.8876 (tt0) cc_final: 0.8581 (tt0) REVERT: L 149 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7906 (mm-30) REVERT: M 39 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7090 (tp40) REVERT: M 42 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8049 (mmm) REVERT: M 150 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.7728 (mtp85) REVERT: M 530 TYR cc_start: 0.8983 (OUTLIER) cc_final: 0.8160 (t80) REVERT: N 8 ARG cc_start: 0.7463 (mmt90) cc_final: 0.6529 (tpt170) REVERT: N 53 LYS cc_start: 0.8624 (mmtp) cc_final: 0.8331 (tppp) REVERT: N 76 ASP cc_start: 0.7554 (p0) cc_final: 0.7318 (p0) REVERT: N 107 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8429 (ptpp) REVERT: Q 52 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.7193 (mtp) REVERT: Q 282 ASP cc_start: 0.8612 (m-30) cc_final: 0.8228 (m-30) REVERT: T 64 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7183 (mp0) REVERT: T 76 VAL cc_start: 0.8880 (m) cc_final: 0.8563 (t) REVERT: T 78 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.6667 (mp0) REVERT: T 105 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6770 (tp30) REVERT: T 106 THR cc_start: 0.9159 (p) cc_final: 0.8946 (t) REVERT: U 79 GLU cc_start: 0.8463 (tp30) cc_final: 0.8204 (mm-30) REVERT: V 106 ARG cc_start: 0.7399 (tpm170) cc_final: 0.6923 (mmm160) REVERT: W 80 ASP cc_start: 0.7874 (m-30) cc_final: 0.7599 (m-30) REVERT: W 98 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7181 (mpt) REVERT: Z 14 MET cc_start: 0.5973 (OUTLIER) cc_final: 0.5324 (ptm) REVERT: Z 20 LYS cc_start: 0.8783 (mtmp) cc_final: 0.8523 (mtmp) REVERT: a 114 LYS cc_start: 0.8509 (ptmt) cc_final: 0.7852 (ttpt) REVERT: b 24 LYS cc_start: 0.9067 (tptm) cc_final: 0.8830 (tptt) REVERT: e 121 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8228 (tp30) REVERT: f 61 GLN cc_start: 0.8472 (tp40) cc_final: 0.8072 (tp40) REVERT: f 65 ASP cc_start: 0.8427 (m-30) cc_final: 0.8164 (m-30) REVERT: f 68 GLU cc_start: 0.8780 (tp30) cc_final: 0.8492 (mm-30) REVERT: h 13 ASP cc_start: 0.9017 (t70) cc_final: 0.8756 (t0) REVERT: i 18 MET cc_start: 0.7844 (mmm) cc_final: 0.7582 (mmt) REVERT: i 269 GLU cc_start: 0.8606 (tp30) cc_final: 0.8311 (tp30) REVERT: j 52 SER cc_start: 0.9190 (t) cc_final: 0.8968 (t) REVERT: k 57 ASN cc_start: 0.9262 (m110) cc_final: 0.9032 (m110) REVERT: l 108 MET cc_start: 0.9189 (mmm) cc_final: 0.8707 (mmt) REVERT: l 197 ASP cc_start: 0.8391 (p0) cc_final: 0.7994 (p0) REVERT: l 271 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8142 (mttp) REVERT: m 109 LYS cc_start: 0.7189 (OUTLIER) cc_final: 0.6908 (mttm) REVERT: o 113 GLU cc_start: 0.8087 (tp30) cc_final: 0.7795 (mm-30) REVERT: p 49 ASP cc_start: 0.8381 (m-30) cc_final: 0.7909 (p0) REVERT: r 201 MET cc_start: 0.9062 (mmm) cc_final: 0.8828 (mmm) REVERT: s 151 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8875 (tp) REVERT: s 233 MET cc_start: 0.8470 (tmm) cc_final: 0.8205 (tmt) REVERT: w 227 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.7831 (mtt) outliers start: 173 outliers final: 85 residues processed: 1172 average time/residue: 1.5771 time to fit residues: 2384.0071 Evaluate side-chains 1167 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1065 time to evaluate : 5.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 39 GLN Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 562 LYS Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain M residue 690 THR Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain O residue 224 SER Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 417 SER Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 105 GLU Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain W residue 98 MET Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain X residue 132 ASP Chi-restraints excluded: chain X residue 151 LYS Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Y residue 100 LEU Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain a residue 185 THR Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain b residue 113 THR Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 141 LEU Chi-restraints excluded: chain d residue 52 ILE Chi-restraints excluded: chain d residue 135 VAL Chi-restraints excluded: chain e residue 62 GLU Chi-restraints excluded: chain e residue 68 GLU Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain i residue 281 LEU Chi-restraints excluded: chain k residue 80 MET Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 204 LEU Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 271 LYS Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 544 MET Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain m residue 109 LYS Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain o residue 73 SER Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain p residue 117 ASP Chi-restraints excluded: chain p residue 141 GLN Chi-restraints excluded: chain r residue 31 SER Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 246 ILE Chi-restraints excluded: chain r residue 250 LEU Chi-restraints excluded: chain r residue 454 ILE Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 156 MET Chi-restraints excluded: chain s residue 168 THR Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 267 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 723 optimal weight: 3.9990 chunk 550 optimal weight: 2.9990 chunk 380 optimal weight: 0.5980 chunk 81 optimal weight: 5.9990 chunk 349 optimal weight: 2.9990 chunk 491 optimal weight: 4.9990 chunk 734 optimal weight: 0.9990 chunk 778 optimal weight: 6.9990 chunk 383 optimal weight: 5.9990 chunk 696 optimal weight: 3.9990 chunk 209 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN E 48 HIS F 93 ASN G 101 ASN G 115 GLN H 41 ASN H 73 GLN I 25 GLN J 341 GLN K 75 ASN ** M 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 69 ASN O 133 GLN P 51 ASN Q 60 HIS U 11 ASN W 24 ASN b 13 GLN d 23 GLN ** g 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 GLN i 47 ASN i 319 HIS ** l 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 86 ASN n 3 ASN p 66 GLN p 124 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 69996 Z= 0.284 Angle : 0.567 10.713 94577 Z= 0.285 Chirality : 0.043 0.219 10186 Planarity : 0.004 0.059 11775 Dihedral : 14.853 177.539 10935 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.06 % Favored : 95.89 % Rotamer: Outliers : 2.44 % Allowed : 11.87 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 0.50 (0.09), residues: 8172 helix: 1.41 (0.08), residues: 4286 sheet: -0.29 (0.26), residues: 408 loop : -0.94 (0.10), residues: 3478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.011 0.001 HIS p 51 PHE 0.032 0.001 PHE i 292 TYR 0.023 0.001 TYR l 587 ARG 0.016 0.000 ARG s 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1305 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1130 time to evaluate : 9.463 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 ASP cc_start: 0.8246 (m-30) cc_final: 0.7710 (m-30) REVERT: G 81 ASP cc_start: 0.7502 (m-30) cc_final: 0.7212 (m-30) REVERT: G 92 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8176 (mtmt) REVERT: G 111 ASP cc_start: 0.7913 (p0) cc_final: 0.7313 (p0) REVERT: G 114 ASP cc_start: 0.8360 (m-30) cc_final: 0.8077 (m-30) REVERT: G 122 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8200 (mmp) REVERT: G 144 ILE cc_start: 0.8481 (mt) cc_final: 0.8198 (mt) REVERT: H 105 GLU cc_start: 0.8002 (tp30) cc_final: 0.7798 (tt0) REVERT: J 323 HIS cc_start: 0.8179 (m90) cc_final: 0.7653 (t70) REVERT: L 78 ARG cc_start: 0.8563 (ttt-90) cc_final: 0.8327 (ttt180) REVERT: L 105 GLU cc_start: 0.8877 (tt0) cc_final: 0.8576 (tt0) REVERT: L 149 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7835 (mm-30) REVERT: M 39 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7089 (tp40) REVERT: M 42 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8029 (mmm) REVERT: M 75 CYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8374 (p) REVERT: M 150 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.7619 (mtp85) REVERT: M 530 TYR cc_start: 0.8952 (OUTLIER) cc_final: 0.7995 (t80) REVERT: N 8 ARG cc_start: 0.7383 (mmt90) cc_final: 0.6300 (tpt170) REVERT: N 53 LYS cc_start: 0.8618 (mmtp) cc_final: 0.8330 (tppp) REVERT: Q 282 ASP cc_start: 0.8597 (m-30) cc_final: 0.8208 (m-30) REVERT: Q 308 TYR cc_start: 0.8757 (OUTLIER) cc_final: 0.8040 (p90) REVERT: T 64 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7154 (mp0) REVERT: T 76 VAL cc_start: 0.8863 (m) cc_final: 0.8579 (t) REVERT: T 78 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.6690 (mp0) REVERT: T 105 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6770 (tp30) REVERT: T 106 THR cc_start: 0.9152 (p) cc_final: 0.8947 (t) REVERT: U 79 GLU cc_start: 0.8450 (tp30) cc_final: 0.8185 (mm-30) REVERT: V 106 ARG cc_start: 0.7448 (tpm170) cc_final: 0.6921 (mmm160) REVERT: V 140 LYS cc_start: 0.8662 (ptmt) cc_final: 0.8430 (pttt) REVERT: W 80 ASP cc_start: 0.7862 (m-30) cc_final: 0.7578 (m-30) REVERT: Z 14 MET cc_start: 0.6018 (OUTLIER) cc_final: 0.5431 (ptm) REVERT: Z 20 LYS cc_start: 0.8823 (mtmp) cc_final: 0.8533 (mtmp) REVERT: a 114 LYS cc_start: 0.8509 (ptmt) cc_final: 0.7849 (ttpt) REVERT: c 84 GLN cc_start: 0.9278 (tp40) cc_final: 0.9062 (tp40) REVERT: c 185 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8106 (mm-30) REVERT: d 163 MET cc_start: 0.8592 (mtp) cc_final: 0.8348 (mtm) REVERT: e 121 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8184 (tp30) REVERT: f 61 GLN cc_start: 0.8461 (tp40) cc_final: 0.8046 (tp40) REVERT: f 65 ASP cc_start: 0.8452 (m-30) cc_final: 0.8205 (m-30) REVERT: f 68 GLU cc_start: 0.8775 (tp30) cc_final: 0.8495 (mm-30) REVERT: h 13 ASP cc_start: 0.8947 (t70) cc_final: 0.8702 (t0) REVERT: i 18 MET cc_start: 0.7829 (mmm) cc_final: 0.7577 (mmt) REVERT: i 217 MET cc_start: 0.8995 (mtp) cc_final: 0.8778 (mtp) REVERT: i 269 GLU cc_start: 0.8564 (tp30) cc_final: 0.8304 (tp30) REVERT: j 52 SER cc_start: 0.9178 (t) cc_final: 0.8955 (t) REVERT: k 57 ASN cc_start: 0.9279 (m110) cc_final: 0.9003 (m110) REVERT: l 72 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.7782 (mp10) REVERT: l 108 MET cc_start: 0.9114 (mmm) cc_final: 0.8815 (mmm) REVERT: l 271 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8098 (mttp) REVERT: l 482 MET cc_start: 0.8693 (mtp) cc_final: 0.8419 (ttm) REVERT: m 109 LYS cc_start: 0.7068 (OUTLIER) cc_final: 0.6804 (mttm) REVERT: n 41 LYS cc_start: 0.9294 (mtpm) cc_final: 0.8989 (mtpt) REVERT: o 113 GLU cc_start: 0.8085 (tp30) cc_final: 0.7874 (mm-30) REVERT: p 49 ASP cc_start: 0.8351 (m-30) cc_final: 0.7939 (p0) REVERT: p 50 GLU cc_start: 0.8097 (tt0) cc_final: 0.7891 (tt0) REVERT: p 51 HIS cc_start: 0.8605 (m-70) cc_final: 0.7896 (m170) REVERT: p 65 ARG cc_start: 0.7844 (tpp80) cc_final: 0.7530 (mtp180) REVERT: r 22 MET cc_start: 0.8555 (mmm) cc_final: 0.8321 (mmm) REVERT: r 201 MET cc_start: 0.9042 (mmm) cc_final: 0.8743 (mmm) REVERT: s 151 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8881 (tp) REVERT: s 233 MET cc_start: 0.8429 (tmm) cc_final: 0.8189 (tmt) REVERT: w 227 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.7893 (mtt) REVERT: w 252 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8281 (mtpt) outliers start: 175 outliers final: 95 residues processed: 1215 average time/residue: 1.6102 time to fit residues: 2539.1524 Evaluate side-chains 1192 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 1078 time to evaluate : 5.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 40 LYS Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 39 GLN Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 75 CYS Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 562 LYS Chi-restraints excluded: chain M residue 674 LEU Chi-restraints excluded: chain M residue 690 THR Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain O residue 224 SER Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 417 SER Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 105 GLU Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain X residue 132 ASP Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Y residue 100 LEU Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain a residue 185 THR Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 141 LEU Chi-restraints excluded: chain c residue 146 VAL Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain d residue 52 ILE Chi-restraints excluded: chain d residue 99 ASP Chi-restraints excluded: chain e residue 62 GLU Chi-restraints excluded: chain e residue 68 GLU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain i residue 281 LEU Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 72 GLN Chi-restraints excluded: chain l residue 271 LYS Chi-restraints excluded: chain l residue 286 LEU Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 480 THR Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 544 MET Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain m residue 109 LYS Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain o residue 73 SER Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain p residue 117 ASP Chi-restraints excluded: chain p residue 124 GLN Chi-restraints excluded: chain r residue 31 SER Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 158 LEU Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 246 ILE Chi-restraints excluded: chain r residue 250 LEU Chi-restraints excluded: chain r residue 454 ILE Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 156 MET Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain w residue 219 GLN Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 252 LYS Chi-restraints excluded: chain w residue 267 GLU Chi-restraints excluded: chain w residue 297 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 648 optimal weight: 0.7980 chunk 441 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 579 optimal weight: 3.9990 chunk 321 optimal weight: 1.9990 chunk 664 optimal weight: 6.9990 chunk 537 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 397 optimal weight: 0.6980 chunk 698 optimal weight: 0.9980 chunk 196 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN E 48 HIS ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 ASN H 37 GLN H 41 ASN H 73 GLN I 25 GLN J 109 ASN J 341 GLN K 75 ASN M 425 ASN ** M 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 116 ASN P 51 ASN Q 60 HIS U 11 ASN W 24 ASN b 13 GLN b 14 GLN g 18 ASN h 21 GLN i 47 ASN i 319 HIS ** l 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 86 ASN n 3 ASN p 124 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 69996 Z= 0.194 Angle : 0.531 10.531 94577 Z= 0.268 Chirality : 0.041 0.250 10186 Planarity : 0.004 0.055 11775 Dihedral : 14.343 179.001 10935 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.99 % Favored : 95.96 % Rotamer: Outliers : 2.51 % Allowed : 12.81 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 0.64 (0.09), residues: 8172 helix: 1.54 (0.08), residues: 4282 sheet: -0.27 (0.25), residues: 415 loop : -0.89 (0.10), residues: 3475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.008 0.001 HIS r 30 PHE 0.030 0.001 PHE i 292 TYR 0.021 0.001 TYR l 587 ARG 0.009 0.000 ARG w 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1296 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1116 time to evaluate : 5.965 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 ASP cc_start: 0.8230 (m-30) cc_final: 0.7693 (m-30) REVERT: E 42 GLU cc_start: 0.7970 (tp30) cc_final: 0.7689 (tm-30) REVERT: F 76 ASN cc_start: 0.8861 (p0) cc_final: 0.8629 (p0) REVERT: G 81 ASP cc_start: 0.7524 (m-30) cc_final: 0.7213 (m-30) REVERT: G 92 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8282 (mtmt) REVERT: G 111 ASP cc_start: 0.7896 (p0) cc_final: 0.7275 (p0) REVERT: G 114 ASP cc_start: 0.8310 (m-30) cc_final: 0.8036 (m-30) REVERT: G 122 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8228 (mmp) REVERT: G 144 ILE cc_start: 0.8471 (mt) cc_final: 0.8179 (mt) REVERT: J 323 HIS cc_start: 0.8127 (m90) cc_final: 0.7591 (t70) REVERT: L 78 ARG cc_start: 0.8544 (ttt-90) cc_final: 0.8292 (ttt180) REVERT: L 105 GLU cc_start: 0.8854 (tt0) cc_final: 0.8580 (tt0) REVERT: L 149 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7887 (mm-30) REVERT: M 39 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7134 (tp40) REVERT: M 42 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8005 (mmm) REVERT: M 75 CYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8409 (p) REVERT: M 150 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8514 (mtp85) REVERT: M 395 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8224 (mt-10) REVERT: M 530 TYR cc_start: 0.8902 (OUTLIER) cc_final: 0.7876 (t80) REVERT: N 8 ARG cc_start: 0.7367 (mmt90) cc_final: 0.6277 (tpt170) REVERT: N 53 LYS cc_start: 0.8603 (mmtp) cc_final: 0.8327 (tppp) REVERT: N 107 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8449 (ptpp) REVERT: P 236 ASN cc_start: 0.9216 (m-40) cc_final: 0.8905 (m110) REVERT: Q 52 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.7200 (mtp) REVERT: Q 282 ASP cc_start: 0.8586 (m-30) cc_final: 0.8177 (m-30) REVERT: Q 308 TYR cc_start: 0.8726 (OUTLIER) cc_final: 0.8025 (p90) REVERT: S 4 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8173 (mt-10) REVERT: T 64 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7147 (mp0) REVERT: T 76 VAL cc_start: 0.8866 (m) cc_final: 0.8619 (t) REVERT: T 78 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.6732 (mp0) REVERT: U 79 GLU cc_start: 0.8419 (tp30) cc_final: 0.8151 (mm-30) REVERT: V 106 ARG cc_start: 0.7453 (tpm170) cc_final: 0.6921 (mmm160) REVERT: W 80 ASP cc_start: 0.7831 (m-30) cc_final: 0.7547 (m-30) REVERT: W 98 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7738 (mpt) REVERT: a 114 LYS cc_start: 0.8486 (ptmt) cc_final: 0.7794 (ttpt) REVERT: c 84 GLN cc_start: 0.9267 (tp40) cc_final: 0.8953 (tp40) REVERT: c 185 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8138 (mm-30) REVERT: d 163 MET cc_start: 0.8572 (mtp) cc_final: 0.8334 (mtm) REVERT: e 116 GLU cc_start: 0.7461 (pm20) cc_final: 0.7052 (pm20) REVERT: e 121 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8239 (tp30) REVERT: f 61 GLN cc_start: 0.8422 (tp40) cc_final: 0.8004 (tp40) REVERT: f 65 ASP cc_start: 0.8488 (m-30) cc_final: 0.8232 (m-30) REVERT: f 68 GLU cc_start: 0.8723 (tp30) cc_final: 0.8464 (mm-30) REVERT: h 13 ASP cc_start: 0.8910 (t70) cc_final: 0.8662 (t0) REVERT: i 18 MET cc_start: 0.7854 (mmm) cc_final: 0.7605 (mmt) REVERT: i 269 GLU cc_start: 0.8571 (tp30) cc_final: 0.8293 (tp30) REVERT: j 52 SER cc_start: 0.9124 (t) cc_final: 0.8895 (t) REVERT: l 72 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.7770 (mp10) REVERT: l 108 MET cc_start: 0.9060 (mmm) cc_final: 0.8686 (mmm) REVERT: l 271 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8018 (mttp) REVERT: l 482 MET cc_start: 0.8650 (mtp) cc_final: 0.8441 (mtp) REVERT: m 109 LYS cc_start: 0.7104 (OUTLIER) cc_final: 0.6864 (mttm) REVERT: o 113 GLU cc_start: 0.8098 (tp30) cc_final: 0.7823 (mm-30) REVERT: p 49 ASP cc_start: 0.8300 (m-30) cc_final: 0.7922 (p0) REVERT: p 65 ARG cc_start: 0.7816 (tpp80) cc_final: 0.7521 (mtp180) REVERT: r 22 MET cc_start: 0.8539 (mmm) cc_final: 0.8299 (mmm) REVERT: r 201 MET cc_start: 0.9069 (mmm) cc_final: 0.8784 (mmm) REVERT: s 151 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8859 (tp) REVERT: v 70 LYS cc_start: 0.8714 (tppp) cc_final: 0.8413 (tttm) REVERT: w 252 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8286 (mtpt) outliers start: 180 outliers final: 98 residues processed: 1207 average time/residue: 1.5842 time to fit residues: 2471.9759 Evaluate side-chains 1195 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1077 time to evaluate : 5.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 40 LYS Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 146 ASP Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 39 GLN Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 54 GLU Chi-restraints excluded: chain M residue 75 CYS Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 674 LEU Chi-restraints excluded: chain M residue 690 THR Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 260 GLU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 417 SER Chi-restraints excluded: chain S residue 4 GLU Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 98 MET Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain X residue 132 ASP Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain a residue 185 THR Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 146 VAL Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain d residue 52 ILE Chi-restraints excluded: chain e residue 62 GLU Chi-restraints excluded: chain e residue 68 GLU Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 93 THR Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 72 GLN Chi-restraints excluded: chain l residue 271 LYS Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 480 THR Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 544 MET Chi-restraints excluded: chain l residue 599 MET Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain m residue 109 LYS Chi-restraints excluded: chain n residue 3 ASN Chi-restraints excluded: chain n residue 30 ARG Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain o residue 73 SER Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain p residue 117 ASP Chi-restraints excluded: chain r residue 31 SER Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 158 LEU Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 246 ILE Chi-restraints excluded: chain r residue 250 LEU Chi-restraints excluded: chain r residue 454 ILE Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 156 MET Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 18 VAL Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 219 GLN Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 252 LYS Chi-restraints excluded: chain w residue 267 GLU Chi-restraints excluded: chain w residue 297 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 261 optimal weight: 1.9990 chunk 700 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 chunk 456 optimal weight: 3.9990 chunk 192 optimal weight: 4.9990 chunk 778 optimal weight: 8.9990 chunk 646 optimal weight: 7.9990 chunk 360 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 257 optimal weight: 2.9990 chunk 408 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 45 ASN E 48 HIS ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 ASN H 41 ASN H 73 GLN I 25 GLN K 75 ASN ** M 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 116 ASN P 51 ASN Q 60 HIS U 11 ASN Z 91 GLN b 13 GLN b 14 GLN g 18 ASN i 47 ASN i 319 HIS ** l 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 86 ASN n 3 ASN p 66 GLN p 124 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 69996 Z= 0.399 Angle : 0.616 11.028 94577 Z= 0.309 Chirality : 0.046 0.249 10186 Planarity : 0.005 0.056 11775 Dihedral : 14.270 177.739 10932 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.49 % Favored : 95.46 % Rotamer: Outliers : 2.91 % Allowed : 13.54 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 0.44 (0.09), residues: 8172 helix: 1.34 (0.08), residues: 4282 sheet: -0.26 (0.25), residues: 410 loop : -0.96 (0.10), residues: 3480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.009 0.001 HIS i 232 PHE 0.032 0.002 PHE i 292 TYR 0.028 0.002 TYR l 587 ARG 0.008 0.000 ARG w 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1297 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1089 time to evaluate : 6.225 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 ASP cc_start: 0.8258 (m-30) cc_final: 0.7718 (m-30) REVERT: E 23 ARG cc_start: 0.8176 (mmm160) cc_final: 0.7918 (mtp85) REVERT: F 57 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7242 (mt-10) REVERT: F 76 ASN cc_start: 0.8859 (p0) cc_final: 0.8593 (p0) REVERT: G 92 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8202 (mtmt) REVERT: G 114 ASP cc_start: 0.8316 (m-30) cc_final: 0.8041 (m-30) REVERT: G 122 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8160 (mmp) REVERT: G 139 MET cc_start: 0.7908 (tpp) cc_final: 0.7595 (tpt) REVERT: G 144 ILE cc_start: 0.8528 (mt) cc_final: 0.8264 (mt) REVERT: J 323 HIS cc_start: 0.8164 (m90) cc_final: 0.7655 (t70) REVERT: L 78 ARG cc_start: 0.8577 (ttt-90) cc_final: 0.8341 (ttt180) REVERT: L 105 GLU cc_start: 0.8888 (tt0) cc_final: 0.8538 (tt0) REVERT: L 149 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7793 (mm-30) REVERT: M 39 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7119 (tp40) REVERT: M 42 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8066 (mmm) REVERT: M 75 CYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8395 (p) REVERT: M 150 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.7599 (mtp85) REVERT: M 530 TYR cc_start: 0.8954 (OUTLIER) cc_final: 0.7891 (t80) REVERT: N 8 ARG cc_start: 0.7405 (mmt90) cc_final: 0.6497 (tpt170) REVERT: N 41 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.7699 (tp30) REVERT: N 53 LYS cc_start: 0.8626 (mmtp) cc_final: 0.8335 (tppp) REVERT: N 107 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8445 (ptpp) REVERT: Q 52 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7173 (mtp) REVERT: Q 282 ASP cc_start: 0.8587 (m-30) cc_final: 0.8196 (m-30) REVERT: Q 308 TYR cc_start: 0.8893 (OUTLIER) cc_final: 0.8098 (p90) REVERT: T 64 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7157 (mp0) REVERT: T 76 VAL cc_start: 0.8870 (m) cc_final: 0.8600 (t) REVERT: T 78 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.6769 (mp0) REVERT: U 79 GLU cc_start: 0.8461 (tp30) cc_final: 0.8169 (mm-30) REVERT: V 106 ARG cc_start: 0.7273 (tpm170) cc_final: 0.6786 (mmm160) REVERT: W 80 ASP cc_start: 0.7911 (m-30) cc_final: 0.7626 (m-30) REVERT: X 155 TYR cc_start: 0.6341 (OUTLIER) cc_final: 0.6043 (m-10) REVERT: Z 14 MET cc_start: 0.6026 (OUTLIER) cc_final: 0.5381 (ptm) REVERT: a 114 LYS cc_start: 0.8504 (ptmt) cc_final: 0.7840 (ttpt) REVERT: c 84 GLN cc_start: 0.9288 (tp40) cc_final: 0.8964 (tp40) REVERT: c 185 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8115 (mm-30) REVERT: d 163 MET cc_start: 0.8590 (mtp) cc_final: 0.8334 (mtm) REVERT: e 116 GLU cc_start: 0.7557 (pm20) cc_final: 0.6973 (pm20) REVERT: e 121 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8224 (tp30) REVERT: f 60 LYS cc_start: 0.8695 (ttpt) cc_final: 0.8464 (tttp) REVERT: f 61 GLN cc_start: 0.8532 (tp40) cc_final: 0.8151 (tp40) REVERT: f 65 ASP cc_start: 0.8477 (m-30) cc_final: 0.8225 (m-30) REVERT: f 68 GLU cc_start: 0.8799 (tp30) cc_final: 0.8525 (mm-30) REVERT: h 13 ASP cc_start: 0.8979 (t70) cc_final: 0.8723 (t0) REVERT: i 18 MET cc_start: 0.7875 (mmm) cc_final: 0.7583 (mmt) REVERT: i 269 GLU cc_start: 0.8620 (tp30) cc_final: 0.8402 (tp30) REVERT: j 52 SER cc_start: 0.9186 (t) cc_final: 0.8971 (t) REVERT: l 72 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.7906 (mp10) REVERT: l 108 MET cc_start: 0.9122 (mmm) cc_final: 0.8717 (mmm) REVERT: l 271 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8150 (mttp) REVERT: l 411 MET cc_start: 0.8357 (mmp) cc_final: 0.8048 (mmm) REVERT: m 109 LYS cc_start: 0.7114 (OUTLIER) cc_final: 0.6851 (mttm) REVERT: n 41 LYS cc_start: 0.9268 (mtpm) cc_final: 0.8950 (mtpt) REVERT: p 49 ASP cc_start: 0.8306 (m-30) cc_final: 0.8025 (p0) REVERT: p 65 ARG cc_start: 0.7870 (tpp80) cc_final: 0.7564 (mtp180) REVERT: s 151 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8882 (tp) REVERT: v 52 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7710 (mmt) REVERT: w 227 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.7917 (mtt) REVERT: w 252 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8302 (mtpt) outliers start: 208 outliers final: 126 residues processed: 1197 average time/residue: 1.5622 time to fit residues: 2418.9465 Evaluate side-chains 1211 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 1061 time to evaluate : 5.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 40 LYS Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 146 ASP Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 39 GLN Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 54 GLU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 75 CYS Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 674 LEU Chi-restraints excluded: chain M residue 690 THR Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain O residue 224 SER Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 260 GLU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 417 SER Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 76 ILE Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain X residue 132 ASP Chi-restraints excluded: chain X residue 155 TYR Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain a residue 185 THR Chi-restraints excluded: chain b residue 113 THR Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 146 VAL Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain d residue 52 ILE Chi-restraints excluded: chain d residue 135 VAL Chi-restraints excluded: chain e residue 62 GLU Chi-restraints excluded: chain e residue 68 GLU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 93 THR Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain k residue 63 LEU Chi-restraints excluded: chain k residue 80 MET Chi-restraints excluded: chain k residue 82 SER Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 72 GLN Chi-restraints excluded: chain l residue 119 LYS Chi-restraints excluded: chain l residue 204 LEU Chi-restraints excluded: chain l residue 271 LYS Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 480 THR Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 544 MET Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain m residue 109 LYS Chi-restraints excluded: chain m residue 167 VAL Chi-restraints excluded: chain n residue 30 ARG Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 73 SER Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain p residue 117 ASP Chi-restraints excluded: chain p residue 124 GLN Chi-restraints excluded: chain p residue 141 GLN Chi-restraints excluded: chain r residue 31 SER Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 158 LEU Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 246 ILE Chi-restraints excluded: chain r residue 250 LEU Chi-restraints excluded: chain r residue 400 MET Chi-restraints excluded: chain r residue 454 ILE Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 156 MET Chi-restraints excluded: chain s residue 168 THR Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 18 VAL Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 52 MET Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 59 CYS Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 219 GLN Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 252 LYS Chi-restraints excluded: chain w residue 267 GLU Chi-restraints excluded: chain w residue 297 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 750 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 443 optimal weight: 6.9990 chunk 568 optimal weight: 0.9990 chunk 440 optimal weight: 3.9990 chunk 655 optimal weight: 3.9990 chunk 434 optimal weight: 3.9990 chunk 775 optimal weight: 7.9990 chunk 485 optimal weight: 3.9990 chunk 473 optimal weight: 7.9990 chunk 358 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN E 48 HIS ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 ASN H 37 GLN H 41 ASN H 73 GLN I 25 GLN J 109 ASN J 341 GLN K 75 ASN M 425 ASN ** M 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 116 ASN P 51 ASN Q 60 HIS U 11 ASN b 13 GLN g 18 ASN h 21 GLN i 47 ASN i 319 HIS j 10 ASN ** l 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 86 ASN n 3 ASN v 110 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 69996 Z= 0.397 Angle : 0.620 11.392 94577 Z= 0.311 Chirality : 0.046 0.263 10186 Planarity : 0.005 0.059 11775 Dihedral : 14.105 179.948 10932 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.43 % Favored : 95.51 % Rotamer: Outliers : 2.89 % Allowed : 14.29 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 0.36 (0.09), residues: 8172 helix: 1.26 (0.08), residues: 4281 sheet: -0.28 (0.25), residues: 410 loop : -0.98 (0.10), residues: 3481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.009 0.001 HIS p 51 PHE 0.032 0.002 PHE i 292 TYR 0.028 0.002 TYR l 587 ARG 0.009 0.000 ARG w 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1283 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1076 time to evaluate : 5.926 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: B 55 ASP cc_start: 0.8262 (m-30) cc_final: 0.7725 (m-30) REVERT: E 23 ARG cc_start: 0.8163 (mmm160) cc_final: 0.7905 (mtp85) REVERT: E 42 GLU cc_start: 0.7988 (tp30) cc_final: 0.7640 (tm-30) REVERT: F 57 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7245 (mt-10) REVERT: F 76 ASN cc_start: 0.8847 (p0) cc_final: 0.8582 (p0) REVERT: G 92 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8159 (mtmt) REVERT: G 111 ASP cc_start: 0.7973 (p0) cc_final: 0.7466 (p0) REVERT: G 114 ASP cc_start: 0.8445 (m-30) cc_final: 0.8175 (m-30) REVERT: G 139 MET cc_start: 0.7875 (tpp) cc_final: 0.7530 (tpt) REVERT: G 144 ILE cc_start: 0.8575 (mt) cc_final: 0.8317 (mt) REVERT: J 323 HIS cc_start: 0.8160 (m90) cc_final: 0.7658 (t70) REVERT: L 105 GLU cc_start: 0.8891 (tt0) cc_final: 0.8527 (tt0) REVERT: L 149 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7769 (mm-30) REVERT: M 39 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7170 (tp40) REVERT: M 42 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8063 (mmm) REVERT: M 75 CYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8402 (p) REVERT: M 150 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.7607 (mtp85) REVERT: M 530 TYR cc_start: 0.8907 (OUTLIER) cc_final: 0.7831 (t80) REVERT: N 8 ARG cc_start: 0.7364 (mmt90) cc_final: 0.6497 (tpt170) REVERT: N 41 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.7747 (tp30) REVERT: N 53 LYS cc_start: 0.8699 (mmtp) cc_final: 0.8336 (tppp) REVERT: N 107 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8466 (ptpp) REVERT: Q 52 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.7187 (mtp) REVERT: Q 282 ASP cc_start: 0.8592 (m-30) cc_final: 0.8176 (m-30) REVERT: Q 308 TYR cc_start: 0.8912 (OUTLIER) cc_final: 0.8132 (p90) REVERT: T 64 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7152 (mp0) REVERT: T 76 VAL cc_start: 0.8897 (m) cc_final: 0.8640 (t) REVERT: T 78 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.6686 (mp0) REVERT: U 79 GLU cc_start: 0.8427 (tp30) cc_final: 0.8124 (mm-30) REVERT: V 106 ARG cc_start: 0.7157 (tpm170) cc_final: 0.6595 (mmm160) REVERT: W 80 ASP cc_start: 0.7947 (m-30) cc_final: 0.7660 (m-30) REVERT: X 155 TYR cc_start: 0.6335 (OUTLIER) cc_final: 0.5952 (m-10) REVERT: Z 14 MET cc_start: 0.6223 (OUTLIER) cc_final: 0.5607 (ptm) REVERT: a 114 LYS cc_start: 0.8509 (ptmt) cc_final: 0.7850 (ttpt) REVERT: c 84 GLN cc_start: 0.9304 (tp40) cc_final: 0.8988 (tp40) REVERT: c 185 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8148 (mm-30) REVERT: d 163 MET cc_start: 0.8582 (mtp) cc_final: 0.8334 (mtm) REVERT: e 121 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8254 (tp30) REVERT: f 60 LYS cc_start: 0.8703 (ttpt) cc_final: 0.8475 (tttp) REVERT: f 61 GLN cc_start: 0.8594 (tp40) cc_final: 0.8218 (tp40) REVERT: f 65 ASP cc_start: 0.8484 (m-30) cc_final: 0.8233 (m-30) REVERT: f 68 GLU cc_start: 0.8782 (tp30) cc_final: 0.8509 (mm-30) REVERT: h 13 ASP cc_start: 0.8967 (t70) cc_final: 0.8710 (t0) REVERT: i 18 MET cc_start: 0.7891 (mmm) cc_final: 0.7557 (mmt) REVERT: j 52 SER cc_start: 0.9182 (t) cc_final: 0.8961 (t) REVERT: l 72 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.7930 (mp10) REVERT: l 108 MET cc_start: 0.9112 (mmm) cc_final: 0.8690 (mmm) REVERT: l 271 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8166 (mttp) REVERT: l 411 MET cc_start: 0.8350 (mmp) cc_final: 0.8081 (mmm) REVERT: l 475 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.6368 (mpt) REVERT: m 109 LYS cc_start: 0.7183 (OUTLIER) cc_final: 0.6924 (mttm) REVERT: n 41 LYS cc_start: 0.9270 (mtpm) cc_final: 0.8970 (mtpt) REVERT: o 113 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7845 (mm-30) REVERT: p 49 ASP cc_start: 0.8291 (m-30) cc_final: 0.8024 (p0) REVERT: p 57 MET cc_start: 0.7975 (mmp) cc_final: 0.7769 (tpp) REVERT: p 65 ARG cc_start: 0.7812 (tpp80) cc_final: 0.7496 (mtp180) REVERT: r 336 ARG cc_start: 0.8659 (tpp-160) cc_final: 0.8439 (ttm170) REVERT: r 396 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.7644 (mmt) REVERT: s 151 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8881 (tp) REVERT: v 52 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7635 (mmt) REVERT: w 252 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8328 (mtpt) outliers start: 207 outliers final: 130 residues processed: 1190 average time/residue: 1.5942 time to fit residues: 2447.0306 Evaluate side-chains 1203 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1049 time to evaluate : 5.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 40 LYS Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 146 ASP Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 39 GLN Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 54 GLU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 75 CYS Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 674 LEU Chi-restraints excluded: chain M residue 690 THR Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain O residue 224 SER Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 260 GLU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 417 SER Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 76 ILE Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain X residue 132 ASP Chi-restraints excluded: chain X residue 155 TYR Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain a residue 185 THR Chi-restraints excluded: chain b residue 113 THR Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 146 VAL Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain d residue 52 ILE Chi-restraints excluded: chain d residue 135 VAL Chi-restraints excluded: chain e residue 62 GLU Chi-restraints excluded: chain e residue 68 GLU Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain f residue 46 LEU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 93 THR Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain i residue 273 ASN Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain k residue 80 MET Chi-restraints excluded: chain k residue 82 SER Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 72 GLN Chi-restraints excluded: chain l residue 204 LEU Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 271 LYS Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 475 MET Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 480 THR Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 544 MET Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain m residue 109 LYS Chi-restraints excluded: chain m residue 167 VAL Chi-restraints excluded: chain n residue 30 ARG Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain o residue 73 SER Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain p residue 117 ASP Chi-restraints excluded: chain p residue 141 GLN Chi-restraints excluded: chain r residue 31 SER Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 158 LEU Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 246 ILE Chi-restraints excluded: chain r residue 250 LEU Chi-restraints excluded: chain r residue 396 MET Chi-restraints excluded: chain r residue 400 MET Chi-restraints excluded: chain r residue 454 ILE Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 156 MET Chi-restraints excluded: chain s residue 168 THR Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 18 VAL Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 52 MET Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 59 CYS Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 219 GLN Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 252 LYS Chi-restraints excluded: chain w residue 267 GLU Chi-restraints excluded: chain w residue 297 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 480 optimal weight: 0.9990 chunk 309 optimal weight: 0.9990 chunk 463 optimal weight: 0.7980 chunk 233 optimal weight: 0.6980 chunk 152 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 493 optimal weight: 0.9990 chunk 528 optimal weight: 0.9990 chunk 383 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 609 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 GLN E 45 ASN E 48 HIS ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 ASN H 41 ASN H 73 GLN I 13 ASN I 25 GLN J 341 GLN K 75 ASN ** M 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 ASN Q 60 HIS U 11 ASN b 13 GLN h 21 GLN i 47 ASN i 319 HIS j 10 ASN l 2 ASN ** l 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 86 ASN n 3 ASN v 110 GLN w 300 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 69996 Z= 0.161 Angle : 0.533 11.288 94577 Z= 0.268 Chirality : 0.040 0.286 10186 Planarity : 0.004 0.057 11775 Dihedral : 13.345 179.729 10932 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.90 % Favored : 96.04 % Rotamer: Outliers : 2.17 % Allowed : 15.35 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 0.70 (0.09), residues: 8172 helix: 1.58 (0.08), residues: 4257 sheet: -0.25 (0.25), residues: 433 loop : -0.84 (0.10), residues: 3482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP u 86 HIS 0.009 0.001 HIS r 30 PHE 0.027 0.001 PHE i 292 TYR 0.020 0.001 TYR l 422 ARG 0.010 0.000 ARG J 179 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1254 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1099 time to evaluate : 7.474 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: B 55 ASP cc_start: 0.8215 (m-30) cc_final: 0.7694 (m-30) REVERT: B 160 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8174 (mt-10) REVERT: E 23 ARG cc_start: 0.8100 (mmm160) cc_final: 0.7862 (mtp85) REVERT: E 42 GLU cc_start: 0.7952 (tp30) cc_final: 0.7618 (tm-30) REVERT: F 76 ASN cc_start: 0.8771 (p0) cc_final: 0.8525 (p0) REVERT: G 111 ASP cc_start: 0.7896 (p0) cc_final: 0.7300 (p0) REVERT: G 139 MET cc_start: 0.7901 (tpp) cc_final: 0.7588 (tpt) REVERT: G 144 ILE cc_start: 0.8524 (mt) cc_final: 0.8249 (mt) REVERT: J 323 HIS cc_start: 0.7924 (m90) cc_final: 0.7553 (t70) REVERT: L 78 ARG cc_start: 0.8408 (ttt180) cc_final: 0.8150 (ttt180) REVERT: L 105 GLU cc_start: 0.8861 (tt0) cc_final: 0.8565 (tt0) REVERT: L 149 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7739 (mm-30) REVERT: M 75 CYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8377 (p) REVERT: M 530 TYR cc_start: 0.8824 (OUTLIER) cc_final: 0.7660 (t80) REVERT: M 559 ASP cc_start: 0.8281 (m-30) cc_final: 0.8080 (m-30) REVERT: N 8 ARG cc_start: 0.7397 (mmt90) cc_final: 0.6327 (tpt170) REVERT: N 53 LYS cc_start: 0.8631 (mmtp) cc_final: 0.8330 (tppp) REVERT: N 107 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8404 (ptpp) REVERT: P 236 ASN cc_start: 0.9205 (m-40) cc_final: 0.8892 (m110) REVERT: Q 52 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.7147 (mtp) REVERT: Q 282 ASP cc_start: 0.8538 (m-30) cc_final: 0.8109 (m-30) REVERT: Q 308 TYR cc_start: 0.8774 (OUTLIER) cc_final: 0.7914 (p90) REVERT: T 64 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7127 (mp0) REVERT: U 79 GLU cc_start: 0.8397 (tp30) cc_final: 0.8121 (mm-30) REVERT: V 106 ARG cc_start: 0.7049 (tpm170) cc_final: 0.6526 (mmm160) REVERT: W 80 ASP cc_start: 0.7834 (m-30) cc_final: 0.7548 (m-30) REVERT: b 24 LYS cc_start: 0.9003 (tptm) cc_final: 0.8653 (tptp) REVERT: c 84 GLN cc_start: 0.9237 (tp40) cc_final: 0.8911 (tp40) REVERT: d 163 MET cc_start: 0.8566 (mtp) cc_final: 0.8331 (mtm) REVERT: f 61 GLN cc_start: 0.8560 (tp40) cc_final: 0.8157 (tp40) REVERT: f 65 ASP cc_start: 0.8503 (m-30) cc_final: 0.8234 (m-30) REVERT: f 68 GLU cc_start: 0.8783 (tp30) cc_final: 0.8554 (mm-30) REVERT: h 13 ASP cc_start: 0.8856 (t70) cc_final: 0.8615 (t0) REVERT: i 18 MET cc_start: 0.7854 (mmm) cc_final: 0.7579 (mmt) REVERT: l 108 MET cc_start: 0.8986 (mmm) cc_final: 0.8563 (mmm) REVERT: l 145 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8023 (mp0) REVERT: l 482 MET cc_start: 0.8585 (mtp) cc_final: 0.8237 (ttp) REVERT: m 109 LYS cc_start: 0.7133 (OUTLIER) cc_final: 0.6880 (mttm) REVERT: o 75 ASN cc_start: 0.9007 (t0) cc_final: 0.8784 (t0) REVERT: o 113 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7953 (mm-30) REVERT: p 49 ASP cc_start: 0.8266 (m-30) cc_final: 0.8033 (p0) REVERT: v 70 LYS cc_start: 0.8696 (tppp) cc_final: 0.8453 (tttp) REVERT: w 252 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8316 (mtpt) outliers start: 155 outliers final: 84 residues processed: 1184 average time/residue: 1.5887 time to fit residues: 2438.8269 Evaluate side-chains 1133 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 1041 time to evaluate : 5.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 54 GLU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 75 CYS Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 674 LEU Chi-restraints excluded: chain M residue 690 THR Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain O residue 224 SER Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 260 GLU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 417 SER Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 76 ILE Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain a residue 185 THR Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 146 VAL Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain d residue 52 ILE Chi-restraints excluded: chain f residue 46 LEU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 93 THR Chi-restraints excluded: chain i residue 273 ASN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 480 THR Chi-restraints excluded: chain l residue 544 MET Chi-restraints excluded: chain m residue 109 LYS Chi-restraints excluded: chain m residue 167 VAL Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain o residue 73 SER Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain p residue 117 ASP Chi-restraints excluded: chain r residue 158 LEU Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 246 ILE Chi-restraints excluded: chain r residue 454 ILE Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 156 MET Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 252 LYS Chi-restraints excluded: chain w residue 267 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 705 optimal weight: 0.9980 chunk 743 optimal weight: 1.9990 chunk 678 optimal weight: 0.7980 chunk 723 optimal weight: 1.9990 chunk 435 optimal weight: 0.7980 chunk 314 optimal weight: 0.9980 chunk 567 optimal weight: 0.9980 chunk 221 optimal weight: 5.9990 chunk 653 optimal weight: 6.9990 chunk 683 optimal weight: 1.9990 chunk 720 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 GLN E 45 ASN E 48 HIS ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 ASN H 41 ASN H 73 GLN I 47 HIS J 109 ASN K 75 ASN M 425 ASN ** M 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 116 ASN P 51 ASN Q 60 HIS U 11 ASN b 13 GLN b 14 GLN c 100 ASN e 148 GLN i 47 ASN i 319 HIS l 2 ASN ** l 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 479 ASN l 541 ASN m 86 ASN n 3 ASN p 124 GLN r 44 GLN s 235 ASN v 110 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 69996 Z= 0.167 Angle : 0.538 12.617 94577 Z= 0.269 Chirality : 0.041 0.277 10186 Planarity : 0.004 0.053 11775 Dihedral : 13.011 179.152 10932 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.93 % Favored : 96.02 % Rotamer: Outliers : 1.69 % Allowed : 16.19 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 0.82 (0.09), residues: 8172 helix: 1.65 (0.08), residues: 4268 sheet: -0.18 (0.25), residues: 444 loop : -0.75 (0.11), residues: 3460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.009 0.001 HIS r 30 PHE 0.031 0.001 PHE i 292 TYR 0.020 0.001 TYR G 147 ARG 0.009 0.000 ARG w 175 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1193 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1072 time to evaluate : 5.936 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: B 55 ASP cc_start: 0.8213 (m-30) cc_final: 0.7695 (m-30) REVERT: B 160 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8172 (mt-10) REVERT: E 23 ARG cc_start: 0.8086 (mmm160) cc_final: 0.7854 (mtp85) REVERT: E 42 GLU cc_start: 0.7961 (tp30) cc_final: 0.7647 (tm-30) REVERT: F 76 ASN cc_start: 0.8732 (p0) cc_final: 0.8488 (p0) REVERT: G 139 MET cc_start: 0.7872 (tpp) cc_final: 0.7605 (tpt) REVERT: G 144 ILE cc_start: 0.8522 (mt) cc_final: 0.8247 (mt) REVERT: J 97 MET cc_start: 0.9192 (mtt) cc_final: 0.8783 (mtt) REVERT: J 323 HIS cc_start: 0.7929 (m90) cc_final: 0.7563 (t70) REVERT: L 105 GLU cc_start: 0.8850 (tt0) cc_final: 0.8572 (tt0) REVERT: L 149 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7802 (mm-30) REVERT: M 75 CYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8379 (p) REVERT: M 150 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7348 (mtp85) REVERT: M 530 TYR cc_start: 0.8832 (OUTLIER) cc_final: 0.7647 (t80) REVERT: M 559 ASP cc_start: 0.8252 (m-30) cc_final: 0.8045 (m-30) REVERT: N 8 ARG cc_start: 0.7296 (mmt90) cc_final: 0.6293 (tpt170) REVERT: N 53 LYS cc_start: 0.8628 (mmtp) cc_final: 0.8339 (tppp) REVERT: N 107 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8430 (ptpp) REVERT: P 236 ASN cc_start: 0.9171 (m-40) cc_final: 0.8848 (m110) REVERT: Q 52 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.7141 (mtp) REVERT: Q 282 ASP cc_start: 0.8554 (m-30) cc_final: 0.8128 (m-30) REVERT: Q 308 TYR cc_start: 0.8751 (OUTLIER) cc_final: 0.7876 (p90) REVERT: T 64 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7116 (mp0) REVERT: U 79 GLU cc_start: 0.8369 (tp30) cc_final: 0.8108 (mm-30) REVERT: V 106 ARG cc_start: 0.7051 (tpm170) cc_final: 0.6539 (mmm160) REVERT: W 80 ASP cc_start: 0.7797 (m-30) cc_final: 0.7498 (m-30) REVERT: W 98 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7052 (mpt) REVERT: X 129 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8326 (tt0) REVERT: Z 14 MET cc_start: 0.6277 (OUTLIER) cc_final: 0.5508 (ptm) REVERT: c 84 GLN cc_start: 0.9223 (tp40) cc_final: 0.8895 (tp40) REVERT: d 163 MET cc_start: 0.8532 (mtp) cc_final: 0.8300 (mtm) REVERT: f 61 GLN cc_start: 0.8568 (tp40) cc_final: 0.8147 (tp40) REVERT: f 65 ASP cc_start: 0.8498 (m-30) cc_final: 0.8227 (m-30) REVERT: f 68 GLU cc_start: 0.8801 (tp30) cc_final: 0.8578 (mm-30) REVERT: h 13 ASP cc_start: 0.8846 (t70) cc_final: 0.8625 (t0) REVERT: i 18 MET cc_start: 0.7882 (mmm) cc_final: 0.7612 (mmt) REVERT: i 274 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7831 (mt-10) REVERT: l 145 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8035 (mp0) REVERT: m 55 MET cc_start: 0.7769 (tpp) cc_final: 0.7507 (mmp) REVERT: m 109 LYS cc_start: 0.7120 (OUTLIER) cc_final: 0.6878 (mttm) REVERT: o 113 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7959 (mm-30) REVERT: p 49 ASP cc_start: 0.8251 (m-30) cc_final: 0.8040 (p0) REVERT: v 70 LYS cc_start: 0.8693 (tppp) cc_final: 0.8443 (tttp) REVERT: w 227 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.8024 (mtt) REVERT: w 241 TYR cc_start: 0.8624 (OUTLIER) cc_final: 0.6059 (t80) REVERT: w 252 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8311 (mtpt) outliers start: 121 outliers final: 82 residues processed: 1143 average time/residue: 1.6210 time to fit residues: 2393.2431 Evaluate side-chains 1147 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 1051 time to evaluate : 5.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain J residue 220 MET Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 54 GLU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 75 CYS Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 674 LEU Chi-restraints excluded: chain M residue 690 THR Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain O residue 224 SER Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 260 GLU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 417 SER Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 76 ILE Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 98 MET Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain a residue 185 THR Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 141 LEU Chi-restraints excluded: chain c residue 146 VAL Chi-restraints excluded: chain f residue 46 LEU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain h residue 93 THR Chi-restraints excluded: chain i residue 273 ASN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 480 THR Chi-restraints excluded: chain m residue 109 LYS Chi-restraints excluded: chain m residue 167 VAL Chi-restraints excluded: chain n residue 3 ASN Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain o residue 73 SER Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain p residue 117 ASP Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 246 ILE Chi-restraints excluded: chain r residue 454 ILE Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 156 MET Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 252 LYS Chi-restraints excluded: chain w residue 267 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 474 optimal weight: 6.9990 chunk 764 optimal weight: 3.9990 chunk 466 optimal weight: 8.9990 chunk 362 optimal weight: 0.5980 chunk 531 optimal weight: 0.7980 chunk 801 optimal weight: 1.9990 chunk 738 optimal weight: 2.9990 chunk 638 optimal weight: 0.0770 chunk 66 optimal weight: 1.9990 chunk 493 optimal weight: 0.3980 chunk 391 optimal weight: 0.0470 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 GLN A 451 GLN E 45 ASN E 48 HIS F 76 ASN G 101 ASN H 41 ASN H 73 GLN K 75 ASN M 425 ASN ** M 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 ASN ** P 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 60 HIS U 11 ASN b 13 GLN b 14 GLN c 100 ASN ** e 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 148 GLN i 47 ASN i 319 HIS l 135 ASN l 139 GLN l 199 GLN l 205 ASN l 479 ASN m 86 ASN ** n 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 124 GLN s 235 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.120 69996 Z= 0.140 Angle : 0.533 17.818 94577 Z= 0.265 Chirality : 0.040 0.314 10186 Planarity : 0.004 0.054 11775 Dihedral : 12.540 177.149 10932 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.73 % Favored : 96.21 % Rotamer: Outliers : 1.31 % Allowed : 16.75 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 0.97 (0.10), residues: 8172 helix: 1.77 (0.08), residues: 4254 sheet: -0.09 (0.25), residues: 443 loop : -0.67 (0.11), residues: 3475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP l 144 HIS 0.009 0.001 HIS r 30 PHE 0.030 0.001 PHE i 292 TYR 0.021 0.001 TYR l 422 ARG 0.010 0.000 ARG w 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1214 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1120 time to evaluate : 6.070 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8090 (mm-30) REVERT: B 50 MET cc_start: 0.8158 (tpt) cc_final: 0.7856 (tpp) REVERT: B 55 ASP cc_start: 0.8233 (m-30) cc_final: 0.7720 (m-30) REVERT: E 23 ARG cc_start: 0.8066 (mmm160) cc_final: 0.7845 (mtp85) REVERT: E 42 GLU cc_start: 0.7961 (tp30) cc_final: 0.7750 (tm-30) REVERT: F 76 ASN cc_start: 0.8740 (p0) cc_final: 0.8524 (p0) REVERT: G 97 LYS cc_start: 0.7376 (tptm) cc_final: 0.7163 (tptp) REVERT: G 139 MET cc_start: 0.7869 (tpp) cc_final: 0.7616 (tpt) REVERT: G 144 ILE cc_start: 0.8512 (mt) cc_final: 0.8242 (mt) REVERT: J 323 HIS cc_start: 0.7932 (m90) cc_final: 0.7541 (t70) REVERT: L 78 ARG cc_start: 0.8393 (ttt180) cc_final: 0.8091 (ttt180) REVERT: L 105 GLU cc_start: 0.8822 (tt0) cc_final: 0.8559 (tt0) REVERT: L 133 ASP cc_start: 0.8317 (m-30) cc_final: 0.7913 (m-30) REVERT: L 149 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7788 (mm-30) REVERT: M 75 CYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8374 (p) REVERT: M 395 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8125 (mt-10) REVERT: M 530 TYR cc_start: 0.8792 (OUTLIER) cc_final: 0.7706 (t80) REVERT: M 559 ASP cc_start: 0.8212 (m-30) cc_final: 0.8004 (m-30) REVERT: N 8 ARG cc_start: 0.7377 (mmt90) cc_final: 0.6261 (tpt170) REVERT: N 53 LYS cc_start: 0.8623 (mmtp) cc_final: 0.8330 (tppp) REVERT: P 236 ASN cc_start: 0.9116 (m-40) cc_final: 0.8815 (m110) REVERT: Q 282 ASP cc_start: 0.8537 (m-30) cc_final: 0.8106 (m-30) REVERT: Q 308 TYR cc_start: 0.8653 (OUTLIER) cc_final: 0.7834 (p90) REVERT: U 79 GLU cc_start: 0.8305 (tp30) cc_final: 0.8044 (mm-30) REVERT: V 106 ARG cc_start: 0.7004 (tpm170) cc_final: 0.6514 (mmm160) REVERT: W 80 ASP cc_start: 0.7751 (m-30) cc_final: 0.7458 (m-30) REVERT: W 98 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7044 (mpt) REVERT: X 129 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8299 (tt0) REVERT: Z 20 LYS cc_start: 0.8909 (mtmp) cc_final: 0.8563 (mtmp) REVERT: c 84 GLN cc_start: 0.9142 (tp40) cc_final: 0.8802 (tp40) REVERT: d 163 MET cc_start: 0.8515 (mtp) cc_final: 0.8291 (mtm) REVERT: e 137 MET cc_start: 0.8586 (tpp) cc_final: 0.7882 (tpt) REVERT: f 60 LYS cc_start: 0.8668 (ttpt) cc_final: 0.8392 (mtpm) REVERT: f 61 GLN cc_start: 0.8554 (tp40) cc_final: 0.8211 (tp40) REVERT: f 65 ASP cc_start: 0.8486 (m-30) cc_final: 0.8219 (m-30) REVERT: h 13 ASP cc_start: 0.8797 (t70) cc_final: 0.8546 (t0) REVERT: i 18 MET cc_start: 0.7878 (mmm) cc_final: 0.7614 (mmt) REVERT: l 1 MET cc_start: 0.6964 (OUTLIER) cc_final: 0.6691 (pp-130) REVERT: l 145 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8049 (mp0) REVERT: r 82 SER cc_start: 0.8743 (t) cc_final: 0.8437 (p) REVERT: v 46 MET cc_start: 0.8668 (mtm) cc_final: 0.8387 (ttm) REVERT: v 70 LYS cc_start: 0.8701 (tppp) cc_final: 0.8398 (tttm) REVERT: w 227 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.8072 (mtt) REVERT: w 241 TYR cc_start: 0.8555 (OUTLIER) cc_final: 0.6091 (t80) outliers start: 94 outliers final: 62 residues processed: 1172 average time/residue: 1.5726 time to fit residues: 2392.0199 Evaluate side-chains 1133 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1063 time to evaluate : 5.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 75 CYS Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 530 TYR Chi-restraints excluded: chain M residue 690 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain O residue 224 SER Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 417 SER Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 76 ILE Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 98 MET Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain a residue 185 THR Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 146 VAL Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain f residue 46 LEU Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain h residue 93 THR Chi-restraints excluded: chain i residue 215 MET Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 480 THR Chi-restraints excluded: chain m residue 78 MET Chi-restraints excluded: chain m residue 167 VAL Chi-restraints excluded: chain o residue 73 SER Chi-restraints excluded: chain p residue 124 GLN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 246 ILE Chi-restraints excluded: chain r residue 454 ILE Chi-restraints excluded: chain s residue 156 MET Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 267 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 507 optimal weight: 0.0970 chunk 680 optimal weight: 1.9990 chunk 195 optimal weight: 5.9990 chunk 588 optimal weight: 2.9990 chunk 94 optimal weight: 0.0030 chunk 177 optimal weight: 4.9990 chunk 639 optimal weight: 0.7980 chunk 267 optimal weight: 4.9990 chunk 656 optimal weight: 0.1980 chunk 80 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN E 45 ASN F 25 GLN G 101 ASN H 37 GLN H 41 ASN H 73 GLN J 109 ASN K 75 ASN M 425 ASN ** M 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 116 ASN O 153 GLN P 51 ASN ** P 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 60 HIS Q 83 ASN U 11 ASN b 13 GLN b 14 GLN ** e 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 47 ASN i 319 HIS l 135 ASN l 139 GLN l 199 GLN l 471 ASN l 479 ASN m 86 ASN n 3 ASN p 124 GLN r 44 GLN u 99 HIS v 110 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.103211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.079535 restraints weight = 103351.245| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 1.91 r_work: 0.2782 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.206 69996 Z= 0.195 Angle : 0.631 59.176 94577 Z= 0.330 Chirality : 0.040 0.284 10186 Planarity : 0.005 0.236 11775 Dihedral : 12.533 177.155 10932 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.79 % Favored : 96.16 % Rotamer: Outliers : 1.20 % Allowed : 17.28 % Favored : 81.52 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.19 % 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: 0.97 (0.10), residues: 8172 helix: 1.77 (0.08), residues: 4254 sheet: -0.10 (0.25), residues: 449 loop : -0.67 (0.11), residues: 3469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP W 48 HIS 0.020 0.001 HIS Q 233 PHE 0.030 0.001 PHE i 292 TYR 0.020 0.001 TYR l 422 ARG 0.016 0.000 ARG s 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31569.96 seconds wall clock time: 546 minutes 15.18 seconds (32775.18 seconds total)