Starting phenix.real_space_refine on Fri Sep 27 22:45:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6shb_10197/09_2024/6shb_10197.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6shb_10197/09_2024/6shb_10197.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6shb_10197/09_2024/6shb_10197.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6shb_10197/09_2024/6shb_10197.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6shb_10197/09_2024/6shb_10197.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6shb_10197/09_2024/6shb_10197.cif" } resolution = 3.07 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= 0.591 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 3 7.51 5 Zn 1 6.06 5 P 97 5.49 5 S 111 5.16 5 C 43130 2.51 5 N 11156 2.21 5 O 13202 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 468 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 67700 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 1253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1253 Classifications: {'peptide': 153} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 150} Chain: "B" Number of atoms: 1261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1261 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain: "C" Number of atoms: 1261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1261 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain: "D" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2274 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain: "E" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2274 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain: "F" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2274 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain: "G" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2273 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 274} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "I" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2282 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 12, 'TRANS': 271} Chain: "J" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3889 Classifications: {'peptide': 475} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 469} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "U" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 911 Classifications: {'RNA': 43} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 17, 'rna3p_pyr': 19} Link IDs: {'rna2p': 7, 'rna3p': 35} Chain: "V" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1045 Classifications: {'RNA': 49} Modifications used: {'5*END': 1, 'rna2p_pur': 12, 'rna2p_pyr': 7, 'rna3p_pur': 17, 'rna3p_pyr': 13} Link IDs: {'rna2p': 19, 'rna3p': 29} Chain: "L" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "M" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "N" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "O" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "P" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "Q" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "R" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "S" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "T" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "W" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "X" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "l" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "m" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "n" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "o" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "p" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "q" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "r" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "s" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "t" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "w" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "x" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "K" Number of atoms: 8282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1009, 8282 Classifications: {'peptide': 1009} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 973} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "Z" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "z" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "H" Number of atoms: 2527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2527 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain: "Y" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "y" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "K" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {' MN': 3, ' ZN': 1, 'ANP': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 54947 SG CYS K 464 77.887 109.284 39.230 1.00 31.95 S ATOM 55314 SG CYS K 512 75.361 108.655 36.301 1.00 32.71 S Time building chain proxies: 29.84, per 1000 atoms: 0.44 Number of scatterers: 67700 At special positions: 0 Unit cell: (163.072, 180.544, 244.608, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Mn 3 24.99 S 111 16.00 P 97 15.00 O 13202 8.00 N 11156 7.00 C 43130 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS R 63 " distance=2.03 Simple disulfide: pdb=" SG CYS B 115 " - pdb=" SG CYS Q 63 " distance=2.03 Simple disulfide: pdb=" SG CYS C 115 " - pdb=" SG CYS S 63 " distance=2.03 Simple disulfide: pdb=" SG CYS D 256 " - pdb=" SG CYS O 63 " distance=2.03 Simple disulfide: pdb=" SG CYS E 256 " - pdb=" SG CYS l 63 " distance=2.03 Simple disulfide: pdb=" SG CYS F 256 " - pdb=" SG CYS m 63 " distance=2.04 Simple disulfide: pdb=" SG CYS G 256 " - pdb=" SG CYS N 63 " distance=2.03 Simple disulfide: pdb=" SG CYS I 252 " - pdb=" SG CYS p 63 " distance=2.03 Simple disulfide: pdb=" SG CYS J 262 " - pdb=" SG CYS J 268 " distance=2.03 Simple disulfide: pdb=" SG CYS J 356 " - pdb=" SG CYS J 474 " distance=2.04 Simple disulfide: pdb=" SG CYS J 396 " - pdb=" SG CYS J 399 " distance=2.04 Simple disulfide: pdb=" SG CYS J 466 " - pdb=" SG CYS w 63 " distance=2.04 Simple disulfide: pdb=" SG CYS X 63 " - pdb=" SG CYS H 304 " distance=2.04 Simple disulfide: pdb=" SG CYS K 578 " - pdb=" SG CYS K 587 " distance=2.04 Simple disulfide: pdb=" SG CYS K 711 " - pdb=" SG CYS K 721 " distance=2.04 Simple disulfide: pdb=" SG CYS K 836 " - pdb=" SG CYS Y 63 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.86 Conformation dependent library (CDL) restraints added in 6.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K1101 " pdb="ZN ZN K1101 " - pdb=" SG CYS K 464 " pdb="ZN ZN K1101 " - pdb=" SG CYS K 512 " 16206 Ramachandran restraints generated. 8103 Oldfield, 0 Emsley, 8103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15584 Finding SS restraints... Secondary structure from input PDB file: 195 helices and 0 sheets defined 24.5% alpha, 0.0% beta 29 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 17.63 Creating SS restraints... Processing helix chain 'A' and resid 6 through 20 Processing helix chain 'A' and resid 24 through 43 removed outlier: 3.934A pdb=" N VAL A 38 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLU A 39 " --> pdb=" O ARG A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 55 Processing helix chain 'A' and resid 63 through 70 Processing helix chain 'A' and resid 82 through 102 removed outlier: 4.083A pdb=" N ARG A 101 " --> pdb=" O TYR A 97 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 114 Processing helix chain 'A' and resid 116 through 151 removed outlier: 5.082A pdb=" N LEU A 120 " --> pdb=" O LYS A 117 " (cutoff:3.500A) Proline residue: A 131 - end of helix removed outlier: 4.082A pdb=" N SER A 134 " --> pdb=" O PRO A 131 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE A 137 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG A 138 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR A 139 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 151 " --> pdb=" O SER A 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 20 removed outlier: 3.591A pdb=" N LEU B 9 " --> pdb=" O ASP B 6 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B 13 " --> pdb=" O ALA B 10 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA B 20 " --> pdb=" O VAL B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 44 removed outlier: 4.212A pdb=" N VAL B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU B 39 " --> pdb=" O ARG B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 57 Processing helix chain 'B' and resid 61 through 72 Processing helix chain 'B' and resid 82 through 100 Processing helix chain 'B' and resid 106 through 114 Processing helix chain 'B' and resid 116 through 136 removed outlier: 4.090A pdb=" N LEU B 120 " --> pdb=" O GLU B 116 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) Proline residue: B 131 - end of helix Processing helix chain 'B' and resid 138 through 151 Processing helix chain 'C' and resid 6 through 20 removed outlier: 3.648A pdb=" N LYS C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 44 removed outlier: 3.638A pdb=" N SER C 32 " --> pdb=" O GLN C 28 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL C 38 " --> pdb=" O ALA C 34 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLU C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 57 Processing helix chain 'C' and resid 63 through 71 removed outlier: 3.778A pdb=" N PHE C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 100 removed outlier: 3.580A pdb=" N TYR C 87 " --> pdb=" O GLU C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 114 Processing helix chain 'C' and resid 117 through 128 removed outlier: 4.031A pdb=" N ASP C 121 " --> pdb=" O LYS C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 134 Processing helix chain 'C' and resid 138 through 151 Processing helix chain 'D' and resid 46 through 60 Processing helix chain 'D' and resid 62 through 72 removed outlier: 4.015A pdb=" N ARG D 65 " --> pdb=" O PRO D 62 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ASP D 66 " --> pdb=" O ASP D 63 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU D 72 " --> pdb=" O TYR D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 130 Processing helix chain 'D' and resid 137 through 149 removed outlier: 4.637A pdb=" N LYS D 149 " --> pdb=" O THR D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 204 removed outlier: 4.370A pdb=" N GLU D 200 " --> pdb=" O SER D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 260 removed outlier: 4.471A pdb=" N LEU D 258 " --> pdb=" O ALA D 254 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ARG D 259 " --> pdb=" O SER D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 272 No H-bonds generated for 'chain 'D' and resid 270 through 272' Processing helix chain 'D' and resid 282 through 284 No H-bonds generated for 'chain 'D' and resid 282 through 284' Processing helix chain 'E' and resid 46 through 60 Processing helix chain 'E' and resid 65 through 71 Processing helix chain 'E' and resid 115 through 130 removed outlier: 3.530A pdb=" N GLN E 130 " --> pdb=" O ASP E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 149 removed outlier: 4.481A pdb=" N LYS E 149 " --> pdb=" O THR E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 205 removed outlier: 4.418A pdb=" N GLU E 200 " --> pdb=" O SER E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 256 Processing helix chain 'E' and resid 282 through 285 No H-bonds generated for 'chain 'E' and resid 282 through 285' Processing helix chain 'F' and resid 46 through 60 removed outlier: 3.868A pdb=" N LYS F 59 " --> pdb=" O SER F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 72 removed outlier: 3.857A pdb=" N ARG F 65 " --> pdb=" O PRO F 62 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ASP F 66 " --> pdb=" O ASP F 63 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE F 68 " --> pdb=" O ARG F 65 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS F 70 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU F 72 " --> pdb=" O TYR F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 128 Processing helix chain 'F' and resid 137 through 149 removed outlier: 4.347A pdb=" N LYS F 149 " --> pdb=" O THR F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 167 No H-bonds generated for 'chain 'F' and resid 165 through 167' Processing helix chain 'F' and resid 195 through 205 removed outlier: 3.888A pdb=" N GLU F 200 " --> pdb=" O SER F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 256 Processing helix chain 'F' and resid 258 through 260 No H-bonds generated for 'chain 'F' and resid 258 through 260' Processing helix chain 'F' and resid 270 through 272 No H-bonds generated for 'chain 'F' and resid 270 through 272' Processing helix chain 'F' and resid 282 through 285 No H-bonds generated for 'chain 'F' and resid 282 through 285' Processing helix chain 'G' and resid 46 through 60 Processing helix chain 'G' and resid 64 through 71 removed outlier: 3.640A pdb=" N ILE G 68 " --> pdb=" O ARG G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 129 Processing helix chain 'G' and resid 137 through 149 removed outlier: 3.865A pdb=" N LYS G 149 " --> pdb=" O THR G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 205 removed outlier: 3.625A pdb=" N GLU G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 256 Processing helix chain 'G' and resid 258 through 260 No H-bonds generated for 'chain 'G' and resid 258 through 260' Processing helix chain 'I' and resid 3 through 15 removed outlier: 4.719A pdb=" N LEU I 10 " --> pdb=" O LEU I 6 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N GLU I 11 " --> pdb=" O VAL I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 34 removed outlier: 3.811A pdb=" N ILE I 31 " --> pdb=" O SER I 27 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 39 No H-bonds generated for 'chain 'I' and resid 36 through 39' Processing helix chain 'I' and resid 53 through 57 removed outlier: 3.602A pdb=" N ILE I 57 " --> pdb=" O LYS I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 87 Processing helix chain 'I' and resid 93 through 108 Processing helix chain 'I' and resid 154 through 178 removed outlier: 7.515A pdb=" N GLU I 171 " --> pdb=" O GLY I 167 " (cutoff:3.500A) removed outlier: 9.568A pdb=" N GLN I 172 " --> pdb=" O LYS I 168 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLU I 173 " --> pdb=" O LEU I 169 " (cutoff:3.500A) Processing helix chain 'I' and resid 248 through 258 Proline residue: I 256 - end of helix Processing helix chain 'I' and resid 267 through 269 No H-bonds generated for 'chain 'I' and resid 267 through 269' Processing helix chain 'J' and resid 35 through 58 Processing helix chain 'J' and resid 64 through 70 Processing helix chain 'J' and resid 152 through 158 Processing helix chain 'J' and resid 162 through 165 No H-bonds generated for 'chain 'J' and resid 162 through 165' Processing helix chain 'J' and resid 167 through 169 No H-bonds generated for 'chain 'J' and resid 167 through 169' Processing helix chain 'J' and resid 182 through 200 removed outlier: 3.545A pdb=" N TYR J 199 " --> pdb=" O ASN J 195 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N PHE J 200 " --> pdb=" O TYR J 196 " (cutoff:3.500A) Processing helix chain 'J' and resid 224 through 241 Processing helix chain 'J' and resid 248 through 250 No H-bonds generated for 'chain 'J' and resid 248 through 250' Processing helix chain 'J' and resid 265 through 278 removed outlier: 6.569A pdb=" N LYS J 270 " --> pdb=" O SER J 266 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ILE J 271 " --> pdb=" O ILE J 267 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP J 273 " --> pdb=" O LYS J 269 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU J 274 " --> pdb=" O LYS J 270 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N PHE J 278 " --> pdb=" O LEU J 274 " (cutoff:3.500A) Processing helix chain 'J' and resid 284 through 299 removed outlier: 3.821A pdb=" N ILE J 298 " --> pdb=" O ILE J 294 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS J 299 " --> pdb=" O LEU J 295 " (cutoff:3.500A) Processing helix chain 'J' and resid 307 through 309 No H-bonds generated for 'chain 'J' and resid 307 through 309' Processing helix chain 'J' and resid 339 through 350 removed outlier: 4.615A pdb=" N TYR J 347 " --> pdb=" O LEU J 343 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LYS J 348 " --> pdb=" O ALA J 344 " (cutoff:3.500A) Processing helix chain 'J' and resid 365 through 374 Processing helix chain 'J' and resid 390 through 395 Processing helix chain 'J' and resid 418 through 422 Processing helix chain 'J' and resid 461 through 474 removed outlier: 4.278A pdb=" N CYS J 466 " --> pdb=" O LYS J 462 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU J 469 " --> pdb=" O ARG J 465 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 140 Processing helix chain 'L' and resid 156 through 166 Processing helix chain 'M' and resid 132 through 141 removed outlier: 4.201A pdb=" N LYS M 139 " --> pdb=" O ASN M 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 156 through 164 removed outlier: 4.050A pdb=" N ILE M 163 " --> pdb=" O VAL M 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 131 through 140 Processing helix chain 'N' and resid 156 through 166 removed outlier: 3.601A pdb=" N LYS N 160 " --> pdb=" O ILE N 156 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N GLU N 161 " --> pdb=" O GLU N 157 " (cutoff:3.500A) Processing helix chain 'O' and resid 131 through 145 removed outlier: 3.562A pdb=" N ASN O 136 " --> pdb=" O THR O 132 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASP O 143 " --> pdb=" O LYS O 139 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LYS O 144 " --> pdb=" O GLU O 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 157 through 164 Processing helix chain 'P' and resid 132 through 140 Processing helix chain 'P' and resid 155 through 162 removed outlier: 3.830A pdb=" N ASP P 162 " --> pdb=" O VAL P 159 " (cutoff:3.500A) Processing helix chain 'Q' and resid 131 through 144 removed outlier: 3.878A pdb=" N LYS Q 139 " --> pdb=" O ASN Q 135 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE Q 142 " --> pdb=" O ILE Q 138 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP Q 143 " --> pdb=" O LYS Q 139 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS Q 144 " --> pdb=" O GLU Q 140 " (cutoff:3.500A) Processing helix chain 'Q' and resid 156 through 166 removed outlier: 3.571A pdb=" N GLU Q 161 " --> pdb=" O GLU Q 157 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP Q 162 " --> pdb=" O LYS Q 158 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE Q 163 " --> pdb=" O VAL Q 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 132 through 140 Processing helix chain 'R' and resid 156 through 166 removed outlier: 3.743A pdb=" N ILE R 163 " --> pdb=" O VAL R 159 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS R 164 " --> pdb=" O LYS R 160 " (cutoff:3.500A) Processing helix chain 'S' and resid 131 through 145 removed outlier: 4.918A pdb=" N ASN S 136 " --> pdb=" O THR S 132 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE S 137 " --> pdb=" O ILE S 133 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LYS S 139 " --> pdb=" O ASN S 135 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASP S 143 " --> pdb=" O LYS S 139 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LYS S 144 " --> pdb=" O GLU S 140 " (cutoff:3.500A) Processing helix chain 'S' and resid 157 through 165 Processing helix chain 'T' and resid 131 through 145 removed outlier: 4.875A pdb=" N ASP T 143 " --> pdb=" O LYS T 139 " (cutoff:3.500A) Processing helix chain 'T' and resid 157 through 166 Processing helix chain 'W' and resid 131 through 140 removed outlier: 3.665A pdb=" N ASN W 135 " --> pdb=" O THR W 132 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ASN W 136 " --> pdb=" O ILE W 133 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS W 139 " --> pdb=" O ASN W 136 " (cutoff:3.500A) Processing helix chain 'W' and resid 142 through 145 No H-bonds generated for 'chain 'W' and resid 142 through 145' Processing helix chain 'W' and resid 157 through 165 Processing helix chain 'X' and resid 131 through 137 Processing helix chain 'X' and resid 156 through 166 Processing helix chain 'l' and resid 131 through 144 removed outlier: 3.581A pdb=" N ASN l 136 " --> pdb=" O THR l 132 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP l 143 " --> pdb=" O LYS l 139 " (cutoff:3.500A) Processing helix chain 'l' and resid 156 through 166 removed outlier: 3.673A pdb=" N ASP l 162 " --> pdb=" O LYS l 158 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE l 163 " --> pdb=" O VAL l 159 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LYS l 164 " --> pdb=" O LYS l 160 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU l 165 " --> pdb=" O GLU l 161 " (cutoff:3.500A) Processing helix chain 'm' and resid 131 through 140 Processing helix chain 'm' and resid 156 through 166 Processing helix chain 'n' and resid 131 through 139 removed outlier: 3.703A pdb=" N ASN n 136 " --> pdb=" O THR n 132 " (cutoff:3.500A) Processing helix chain 'n' and resid 156 through 166 removed outlier: 4.041A pdb=" N ILE n 163 " --> pdb=" O VAL n 159 " (cutoff:3.500A) Processing helix chain 'o' and resid 131 through 140 removed outlier: 3.556A pdb=" N ASN o 135 " --> pdb=" O ASP o 131 " (cutoff:3.500A) Processing helix chain 'o' and resid 156 through 165 Processing helix chain 'p' and resid 131 through 140 Processing helix chain 'p' and resid 156 through 163 removed outlier: 3.851A pdb=" N ASP p 162 " --> pdb=" O LYS p 158 " (cutoff:3.500A) Processing helix chain 'q' and resid 132 through 140 removed outlier: 3.681A pdb=" N LYS q 139 " --> pdb=" O ASN q 135 " (cutoff:3.500A) Processing helix chain 'q' and resid 156 through 166 Processing helix chain 'r' and resid 131 through 145 removed outlier: 4.028A pdb=" N PHE r 142 " --> pdb=" O ILE r 138 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP r 143 " --> pdb=" O LYS r 139 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS r 144 " --> pdb=" O GLU r 140 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE r 145 " --> pdb=" O VAL r 141 " (cutoff:3.500A) Processing helix chain 'r' and resid 156 through 165 Processing helix chain 's' and resid 131 through 140 Processing helix chain 's' and resid 142 through 145 No H-bonds generated for 'chain 's' and resid 142 through 145' Processing helix chain 's' and resid 160 through 165 Processing helix chain 't' and resid 131 through 140 removed outlier: 4.412A pdb=" N ASN t 136 " --> pdb=" O THR t 132 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LYS t 139 " --> pdb=" O ASN t 135 " (cutoff:3.500A) Processing helix chain 't' and resid 157 through 159 No H-bonds generated for 'chain 't' and resid 157 through 159' Processing helix chain 't' and resid 161 through 166 Processing helix chain 'w' and resid 131 through 140 removed outlier: 3.918A pdb=" N LYS w 139 " --> pdb=" O ASN w 135 " (cutoff:3.500A) Processing helix chain 'w' and resid 156 through 163 Processing helix chain 'x' and resid 131 through 140 removed outlier: 4.618A pdb=" N LYS x 139 " --> pdb=" O ASN x 135 " (cutoff:3.500A) Processing helix chain 'x' and resid 142 through 145 No H-bonds generated for 'chain 'x' and resid 142 through 145' Processing helix chain 'x' and resid 156 through 161 removed outlier: 3.816A pdb=" N LYS x 160 " --> pdb=" O ILE x 156 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU x 161 " --> pdb=" O GLU x 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 156 through 161' Processing helix chain 'x' and resid 163 through 166 No H-bonds generated for 'chain 'x' and resid 163 through 166' Processing helix chain 'K' and resid 14 through 18 Processing helix chain 'K' and resid 68 through 74 removed outlier: 3.857A pdb=" N ALA K 72 " --> pdb=" O LYS K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 82 No H-bonds generated for 'chain 'K' and resid 79 through 82' Processing helix chain 'K' and resid 87 through 90 No H-bonds generated for 'chain 'K' and resid 87 through 90' Processing helix chain 'K' and resid 121 through 133 removed outlier: 5.209A pdb=" N ASP K 125 " --> pdb=" O SER K 122 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU K 127 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS K 133 " --> pdb=" O GLU K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 143 through 146 No H-bonds generated for 'chain 'K' and resid 143 through 146' Processing helix chain 'K' and resid 148 through 160 removed outlier: 3.764A pdb=" N LEU K 152 " --> pdb=" O GLN K 148 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE K 153 " --> pdb=" O LEU K 149 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU K 155 " --> pdb=" O TYR K 151 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU K 156 " --> pdb=" O LEU K 152 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP K 158 " --> pdb=" O TYR K 154 " (cutoff:3.500A) Processing helix chain 'K' and resid 170 through 172 No H-bonds generated for 'chain 'K' and resid 170 through 172' Processing helix chain 'K' and resid 177 through 196 removed outlier: 3.821A pdb=" N ALA K 185 " --> pdb=" O LEU K 181 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET K 187 " --> pdb=" O ALA K 183 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASN K 189 " --> pdb=" O ALA K 185 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N TRP K 190 " --> pdb=" O ALA K 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 213 No H-bonds generated for 'chain 'K' and resid 210 through 213' Processing helix chain 'K' and resid 221 through 244 removed outlier: 3.843A pdb=" N VAL K 237 " --> pdb=" O LEU K 233 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE K 238 " --> pdb=" O LEU K 234 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TRP K 240 " --> pdb=" O TYR K 236 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE K 241 " --> pdb=" O VAL K 237 " (cutoff:3.500A) Processing helix chain 'K' and resid 259 through 272 removed outlier: 3.785A pdb=" N PHE K 263 " --> pdb=" O GLN K 259 " (cutoff:3.500A) Processing helix chain 'K' and resid 276 through 287 removed outlier: 4.209A pdb=" N GLU K 281 " --> pdb=" O ASP K 277 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ILE K 282 " --> pdb=" O VAL K 278 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU K 284 " --> pdb=" O ASP K 280 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU K 285 " --> pdb=" O GLU K 281 " (cutoff:3.500A) Processing helix chain 'K' and resid 333 through 361 removed outlier: 3.785A pdb=" N SER K 337 " --> pdb=" O ASN K 333 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS K 338 " --> pdb=" O CYS K 334 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS K 340 " --> pdb=" O ILE K 336 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG K 342 " --> pdb=" O LYS K 338 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TRP K 347 " --> pdb=" O TYR K 343 " (cutoff:3.500A) Processing helix chain 'K' and resid 367 through 376 Processing helix chain 'K' and resid 380 through 382 No H-bonds generated for 'chain 'K' and resid 380 through 382' Processing helix chain 'K' and resid 414 through 430 removed outlier: 4.358A pdb=" N LEU K 430 " --> pdb=" O LYS K 426 " (cutoff:3.500A) Processing helix chain 'K' and resid 435 through 438 Processing helix chain 'K' and resid 442 through 446 Processing helix chain 'K' and resid 482 through 489 removed outlier: 3.832A pdb=" N LEU K 486 " --> pdb=" O LEU K 482 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE K 487 " --> pdb=" O GLU K 483 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU K 489 " --> pdb=" O LYS K 485 " (cutoff:3.500A) Processing helix chain 'K' and resid 498 through 504 removed outlier: 3.869A pdb=" N MET K 504 " --> pdb=" O SER K 500 " (cutoff:3.500A) Processing helix chain 'K' and resid 513 through 523 Processing helix chain 'K' and resid 526 through 532 Processing helix chain 'K' and resid 539 through 548 removed outlier: 3.715A pdb=" N SER K 548 " --> pdb=" O ASN K 544 " (cutoff:3.500A) Processing helix chain 'K' and resid 558 through 568 removed outlier: 3.753A pdb=" N SER K 563 " --> pdb=" O SER K 559 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE K 564 " --> pdb=" O ASP K 560 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LYS K 565 " --> pdb=" O ILE K 561 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N THR K 566 " --> pdb=" O ALA K 562 " (cutoff:3.500A) Processing helix chain 'K' and resid 580 through 583 removed outlier: 3.766A pdb=" N GLU K 583 " --> pdb=" O ASP K 580 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 580 through 583' Processing helix chain 'K' and resid 599 through 602 No H-bonds generated for 'chain 'K' and resid 599 through 602' Processing helix chain 'K' and resid 615 through 617 No H-bonds generated for 'chain 'K' and resid 615 through 617' Processing helix chain 'K' and resid 625 through 634 removed outlier: 3.884A pdb=" N ARG K 633 " --> pdb=" O PHE K 629 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG K 634 " --> pdb=" O SER K 630 " (cutoff:3.500A) Processing helix chain 'K' and resid 654 through 659 Processing helix chain 'K' and resid 672 through 675 Processing helix chain 'K' and resid 678 through 681 Processing helix chain 'K' and resid 690 through 696 removed outlier: 3.820A pdb=" N ASN K 695 " --> pdb=" O GLU K 691 " (cutoff:3.500A) Processing helix chain 'K' and resid 701 through 708 removed outlier: 3.819A pdb=" N VAL K 708 " --> pdb=" O TYR K 704 " (cutoff:3.500A) Processing helix chain 'K' and resid 721 through 732 removed outlier: 4.126A pdb=" N ILE K 725 " --> pdb=" O CYS K 721 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N SER K 727 " --> pdb=" O GLU K 723 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ASN K 728 " --> pdb=" O LYS K 724 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLU K 729 " --> pdb=" O ILE K 725 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL K 730 " --> pdb=" O TYR K 726 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LYS K 732 " --> pdb=" O ASN K 728 " (cutoff:3.500A) Processing helix chain 'K' and resid 747 through 759 removed outlier: 3.512A pdb=" N SER K 751 " --> pdb=" O GLU K 747 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE K 755 " --> pdb=" O SER K 751 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE K 758 " --> pdb=" O TYR K 754 " (cutoff:3.500A) Processing helix chain 'K' and resid 768 through 791 removed outlier: 3.860A pdb=" N ASN K 790 " --> pdb=" O LEU K 786 " (cutoff:3.500A) Processing helix chain 'K' and resid 814 through 825 removed outlier: 3.724A pdb=" N ARG K 822 " --> pdb=" O LYS K 818 " (cutoff:3.500A) Processing helix chain 'K' and resid 870 through 885 removed outlier: 3.658A pdb=" N LEU K 880 " --> pdb=" O ASP K 876 " (cutoff:3.500A) Processing helix chain 'K' and resid 931 through 933 No H-bonds generated for 'chain 'K' and resid 931 through 933' Processing helix chain 'K' and resid 937 through 950 removed outlier: 3.805A pdb=" N ARG K 948 " --> pdb=" O GLU K 944 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP K 950 " --> pdb=" O LYS K 946 " (cutoff:3.500A) Processing helix chain 'K' and resid 956 through 959 Processing helix chain 'K' and resid 962 through 971 removed outlier: 5.762A pdb=" N HIS K 967 " --> pdb=" O GLU K 963 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LEU K 968 " --> pdb=" O LYS K 964 " (cutoff:3.500A) Processing helix chain 'K' and resid 975 through 988 Processing helix chain 'K' and resid 1001 through 1003 No H-bonds generated for 'chain 'K' and resid 1001 through 1003' Processing helix chain 'K' and resid 1021 through 1034 Processing helix chain 'Z' and resid 131 through 133 No H-bonds generated for 'chain 'Z' and resid 131 through 133' Processing helix chain 'Z' and resid 138 through 141 No H-bonds generated for 'chain 'Z' and resid 138 through 141' Processing helix chain 'Z' and resid 156 through 158 No H-bonds generated for 'chain 'Z' and resid 156 through 158' Processing helix chain 'z' and resid 131 through 141 removed outlier: 4.061A pdb=" N ASN z 135 " --> pdb=" O THR z 132 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN z 136 " --> pdb=" O ILE z 133 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE z 137 " --> pdb=" O VAL z 134 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL z 141 " --> pdb=" O ILE z 138 " (cutoff:3.500A) Processing helix chain 'z' and resid 156 through 164 removed outlier: 3.834A pdb=" N GLU z 161 " --> pdb=" O GLU z 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 50 Processing helix chain 'H' and resid 60 through 67 Processing helix chain 'H' and resid 97 through 99 No H-bonds generated for 'chain 'H' and resid 97 through 99' Processing helix chain 'H' and resid 103 through 107 Processing helix chain 'H' and resid 111 through 123 Processing helix chain 'H' and resid 178 through 181 Processing helix chain 'H' and resid 226 through 232 removed outlier: 3.527A pdb=" N ASN H 232 " --> pdb=" O ASN H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 271 through 277 Processing helix chain 'H' and resid 283 through 295 Processing helix chain 'Y' and resid 132 through 140 removed outlier: 3.860A pdb=" N LYS Y 139 " --> pdb=" O ASN Y 135 " (cutoff:3.500A) Processing helix chain 'Y' and resid 142 through 145 No H-bonds generated for 'chain 'Y' and resid 142 through 145' Processing helix chain 'Y' and resid 156 through 166 removed outlier: 4.125A pdb=" N ASP Y 162 " --> pdb=" O LYS Y 158 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE Y 163 " --> pdb=" O VAL Y 159 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS Y 164 " --> pdb=" O LYS Y 160 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU Y 165 " --> pdb=" O GLU Y 161 " (cutoff:3.500A) Processing helix chain 'y' and resid 132 through 140 removed outlier: 3.924A pdb=" N ASN y 136 " --> pdb=" O THR y 132 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS y 139 " --> pdb=" O ASN y 135 " (cutoff:3.500A) Processing helix chain 'y' and resid 156 through 165 removed outlier: 3.550A pdb=" N ILE y 163 " --> pdb=" O VAL y 159 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LYS y 164 " --> pdb=" O LYS y 160 " (cutoff:3.500A) 1067 hydrogen bonds defined for protein. 2949 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 68 hydrogen bonds 128 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 17.58 Time building geometry restraints manager: 15.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 14975 1.33 - 1.45: 15603 1.45 - 1.58: 38155 1.58 - 1.70: 177 1.70 - 1.83: 162 Bond restraints: 69072 Sorted by residual: bond pdb=" N3B ANP K1102 " pdb=" PG ANP K1102 " ideal model delta sigma weight residual 1.795 1.603 0.192 2.00e-02 2.50e+03 9.20e+01 bond pdb=" N3B ANP K1103 " pdb=" PG ANP K1103 " ideal model delta sigma weight residual 1.795 1.615 0.180 2.00e-02 2.50e+03 8.06e+01 bond pdb=" O3A ANP K1102 " pdb=" PB ANP K1102 " ideal model delta sigma weight residual 1.700 1.572 0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" O3A ANP K1103 " pdb=" PB ANP K1103 " ideal model delta sigma weight residual 1.700 1.582 0.118 2.00e-02 2.50e+03 3.49e+01 bond pdb=" N3B ANP K1102 " pdb=" PB ANP K1102 " ideal model delta sigma weight residual 1.669 1.602 0.067 2.00e-02 2.50e+03 1.12e+01 ... (remaining 69067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.98: 93445 3.98 - 7.95: 433 7.95 - 11.93: 15 11.93 - 15.91: 0 15.91 - 19.88: 2 Bond angle restraints: 93895 Sorted by residual: angle pdb=" N ILE J 360 " pdb=" CA ILE J 360 " pdb=" C ILE J 360 " ideal model delta sigma weight residual 113.71 107.43 6.28 9.50e-01 1.11e+00 4.38e+01 angle pdb=" N GLY r 73 " pdb=" CA GLY r 73 " pdb=" C GLY r 73 " ideal model delta sigma weight residual 110.38 118.04 -7.66 1.28e+00 6.10e-01 3.58e+01 angle pdb=" N ILE X 16 " pdb=" CA ILE X 16 " pdb=" C ILE X 16 " ideal model delta sigma weight residual 113.71 108.02 5.69 9.50e-01 1.11e+00 3.58e+01 angle pdb=" C GLY s 73 " pdb=" N THR s 74 " pdb=" CA THR s 74 " ideal model delta sigma weight residual 122.15 142.03 -19.88 3.47e+00 8.31e-02 3.28e+01 angle pdb=" N GLU K 659 " pdb=" CA GLU K 659 " pdb=" C GLU K 659 " ideal model delta sigma weight residual 111.28 105.28 6.00 1.09e+00 8.42e-01 3.03e+01 ... (remaining 93890 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 41424 35.28 - 70.56: 1019 70.56 - 105.84: 113 105.84 - 141.12: 2 141.12 - 176.40: 4 Dihedral angle restraints: 42562 sinusoidal: 18408 harmonic: 24154 Sorted by residual: dihedral pdb=" CB CYS J 396 " pdb=" SG CYS J 396 " pdb=" SG CYS J 399 " pdb=" CB CYS J 399 " ideal model delta sinusoidal sigma weight residual -86.00 -170.32 84.32 1 1.00e+01 1.00e-02 8.65e+01 dihedral pdb=" O4' U V 3 " pdb=" C1' U V 3 " pdb=" N1 U V 3 " pdb=" C2 U V 3 " ideal model delta sinusoidal sigma weight residual 200.00 37.18 162.82 1 1.50e+01 4.44e-03 8.34e+01 dihedral pdb=" CB CYS K 836 " pdb=" SG CYS K 836 " pdb=" SG CYS Y 63 " pdb=" CB CYS Y 63 " ideal model delta sinusoidal sigma weight residual 93.00 168.46 -75.46 1 1.00e+01 1.00e-02 7.19e+01 ... (remaining 42559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 10134 0.096 - 0.193: 832 0.193 - 0.289: 20 0.289 - 0.386: 4 0.386 - 0.482: 2 Chirality restraints: 10992 Sorted by residual: chirality pdb=" C3' ANP K1102 " pdb=" C2' ANP K1102 " pdb=" C4' ANP K1102 " pdb=" O3' ANP K1102 " both_signs ideal model delta sigma weight residual False -2.36 -2.84 0.48 2.00e-01 2.50e+01 5.81e+00 chirality pdb=" C3' ANP K1103 " pdb=" C2' ANP K1103 " pdb=" C4' ANP K1103 " pdb=" O3' ANP K1103 " both_signs ideal model delta sigma weight residual False -2.36 -2.74 0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" CB VAL D 232 " pdb=" CA VAL D 232 " pdb=" CG1 VAL D 232 " pdb=" CG2 VAL D 232 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.75e+00 ... (remaining 10989 not shown) Planarity restraints: 11507 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A V 19 " 0.056 2.00e-02 2.50e+03 2.67e-02 1.95e+01 pdb=" N9 A V 19 " -0.065 2.00e-02 2.50e+03 pdb=" C8 A V 19 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A V 19 " 0.007 2.00e-02 2.50e+03 pdb=" C5 A V 19 " 0.005 2.00e-02 2.50e+03 pdb=" C6 A V 19 " 0.008 2.00e-02 2.50e+03 pdb=" N6 A V 19 " 0.009 2.00e-02 2.50e+03 pdb=" N1 A V 19 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A V 19 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A V 19 " -0.009 2.00e-02 2.50e+03 pdb=" C4 A V 19 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A V 13 " -0.049 2.00e-02 2.50e+03 2.11e-02 1.23e+01 pdb=" N9 A V 13 " 0.044 2.00e-02 2.50e+03 pdb=" C8 A V 13 " 0.006 2.00e-02 2.50e+03 pdb=" N7 A V 13 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A V 13 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A V 13 " -0.006 2.00e-02 2.50e+03 pdb=" N6 A V 13 " -0.013 2.00e-02 2.50e+03 pdb=" N1 A V 13 " -0.005 2.00e-02 2.50e+03 pdb=" C2 A V 13 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A V 13 " 0.011 2.00e-02 2.50e+03 pdb=" C4 A V 13 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C V 25 " 0.044 2.00e-02 2.50e+03 2.32e-02 1.21e+01 pdb=" N1 C V 25 " -0.050 2.00e-02 2.50e+03 pdb=" C2 C V 25 " -0.004 2.00e-02 2.50e+03 pdb=" O2 C V 25 " -0.007 2.00e-02 2.50e+03 pdb=" N3 C V 25 " 0.008 2.00e-02 2.50e+03 pdb=" C4 C V 25 " 0.010 2.00e-02 2.50e+03 pdb=" N4 C V 25 " 0.007 2.00e-02 2.50e+03 pdb=" C5 C V 25 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C V 25 " -0.010 2.00e-02 2.50e+03 ... (remaining 11504 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 942 2.55 - 3.14: 59036 3.14 - 3.73: 107557 3.73 - 4.31: 161659 4.31 - 4.90: 255519 Nonbonded interactions: 584713 Sorted by model distance: nonbonded pdb=" O2B ANP K1103 " pdb="MN MN K1104 " model vdw 1.963 2.320 nonbonded pdb=" O3G ANP K1102 " pdb="MN MN K1106 " model vdw 1.967 2.320 nonbonded pdb=" O3A ANP K1102 " pdb="MN MN K1106 " model vdw 1.968 2.320 nonbonded pdb=" O1A ANP K1103 " pdb="MN MN K1104 " model vdw 1.977 2.320 nonbonded pdb=" OE2 GLU K 882 " pdb="MN MN K1105 " model vdw 2.006 2.320 ... (remaining 584708 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 3 through 155) selection = (chain 'C' and resid 3 through 155) } ncs_group { reference = (chain 'D' and (resid 2 through 157 or (resid 158 and (name N or name CA or name \ C or name O or name CB )) or resid 159 through 286)) selection = (chain 'E' and (resid 2 through 157 or (resid 158 and (name N or name CA or name \ C or name O or name CB )) or resid 159 through 286)) selection = (chain 'F' and (resid 2 through 157 or (resid 158 and (name N or name CA or name \ C or name O or name CB )) or resid 159 through 286)) selection = chain 'G' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 2.150 Check model and map are aligned: 0.420 Set scattering table: 0.480 Process input model: 135.450 Find NCS groups from input model: 2.290 Set up NCS constraints: 0.700 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 155.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 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 : 0.009 0.192 69072 Z= 0.571 Angle : 0.867 19.882 93895 Z= 0.477 Chirality : 0.054 0.482 10992 Planarity : 0.005 0.057 11507 Dihedral : 16.244 176.396 26930 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 21.45 Ramachandran Plot: Outliers : 0.42 % Allowed : 17.22 % Favored : 82.36 % Rotamer: Outliers : 0.48 % Allowed : 13.45 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.14 % 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: -5.08 (0.07), residues: 8103 helix: -3.12 (0.08), residues: 2223 sheet: -2.39 (0.13), residues: 1376 loop : -3.99 (0.07), residues: 4504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP E 281 HIS 0.007 0.001 HIS K 865 PHE 0.042 0.003 PHE J 123 TYR 0.034 0.002 TYR B 42 ARG 0.010 0.001 ARG H 15 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16206 Ramachandran restraints generated. 8103 Oldfield, 0 Emsley, 8103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16206 Ramachandran restraints generated. 8103 Oldfield, 0 Emsley, 8103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1814 residues out of total 7446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1778 time to evaluate : 5.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 TYR cc_start: 0.6288 (t80) cc_final: 0.5825 (t80) REVERT: J 125 ASP cc_start: 0.6907 (m-30) cc_final: 0.6516 (m-30) REVERT: J 437 ILE cc_start: 0.8180 (mp) cc_final: 0.7910 (mp) REVERT: L 102 ILE cc_start: 0.7498 (mm) cc_final: 0.7233 (mm) REVERT: Q 166 LEU cc_start: 0.8547 (tp) cc_final: 0.8331 (tt) REVERT: S 7 TYR cc_start: 0.5994 (t80) cc_final: 0.5746 (t80) REVERT: S 121 MET cc_start: 0.7170 (mpp) cc_final: 0.6951 (mtm) REVERT: l 86 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7648 (pp) REVERT: r 29 HIS cc_start: 0.5866 (m-70) cc_final: 0.5590 (m-70) REVERT: K 158 TRP cc_start: 0.3724 (m100) cc_final: 0.3282 (m100) REVERT: K 282 ILE cc_start: 0.8118 (mm) cc_final: 0.7842 (mm) REVERT: z 144 LYS cc_start: 0.5936 (pttt) cc_final: 0.5184 (tptt) outliers start: 36 outliers final: 20 residues processed: 1807 average time/residue: 0.6933 time to fit residues: 2082.7196 Evaluate side-chains 1287 residues out of total 7446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 1266 time to evaluate : 5.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain Q residue 102 ILE Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain l residue 86 LEU Chi-restraints excluded: chain p residue 63 CYS Chi-restraints excluded: chain q residue 154 VAL Chi-restraints excluded: chain s residue 8 VAL Chi-restraints excluded: chain x residue 12 ILE Chi-restraints excluded: chain x residue 123 THR Chi-restraints excluded: chain K residue 277 ASP Chi-restraints excluded: chain K residue 651 SER Chi-restraints excluded: chain K residue 657 LEU Chi-restraints excluded: chain K residue 737 VAL Chi-restraints excluded: chain K residue 803 ASP Chi-restraints excluded: chain K residue 883 GLU Chi-restraints excluded: chain H residue 242 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 813 random chunks: chunk 686 optimal weight: 6.9990 chunk 616 optimal weight: 8.9990 chunk 341 optimal weight: 1.9990 chunk 210 optimal weight: 0.7980 chunk 415 optimal weight: 2.9990 chunk 329 optimal weight: 3.9990 chunk 637 optimal weight: 4.9990 chunk 246 optimal weight: 0.9990 chunk 387 optimal weight: 0.7980 chunk 474 optimal weight: 5.9990 chunk 738 optimal weight: 0.0020 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 128 ASN C 84 ASN C 128 ASN ** D 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 ASN D 153 ASN E 13 HIS ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 ASN G 19 HIS I 74 ASN I 87 ASN I 97 ASN J 126 ASN J 285 ASN J 337 ASN J 345 ASN J 393 ASN J 424 GLN J 452 HIS L 40 ASN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 14 ASN O 174 GLN ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 101 ASN Q 40 ASN Q 135 ASN ** R 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 ASN R 79 GLN S 77 GLN T 32 ASN T 40 ASN T 101 ASN ** W 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 135 ASN W 147 ASN X 14 ASN X 29 HIS ** X 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 91 ASN l 4 GLN m 91 ASN ** m 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 174 GLN ** n 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 4 GLN ** o 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 135 ASN p 174 GLN q 29 HIS q 76 GLN ** r 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 81 ASN t 4 GLN ** t 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 174 GLN x 4 GLN K 108 ASN K 126 ASN K 175 HIS K 292 ASN K 344 ASN K 602 ASN K 875 ASN K1024 ASN Z 14 ASN Z 40 ASN Z 135 ASN ** z 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 53 ASN z 79 GLN z 135 ASN H 66 ASN H 130 GLN H 253 ASN H 279 ASN ** H 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 14 ASN Y 29 HIS Y 32 ASN Y 39 HIS Y 77 GLN y 4 GLN y 81 ASN y 136 ASN Total number of N/Q/H flips: 74 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 69072 Z= 0.219 Angle : 0.717 10.885 93895 Z= 0.374 Chirality : 0.049 0.313 10992 Planarity : 0.005 0.081 11507 Dihedral : 11.710 175.000 10394 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.53 % Favored : 87.42 % Rotamer: Outliers : 2.78 % Allowed : 17.15 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.06 % 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: -4.14 (0.08), residues: 8103 helix: -2.11 (0.10), residues: 2251 sheet: -1.93 (0.14), residues: 1293 loop : -3.49 (0.08), residues: 4559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP K 240 HIS 0.009 0.001 HIS O 29 PHE 0.020 0.002 PHE z 142 TYR 0.032 0.002 TYR S 112 ARG 0.009 0.001 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16206 Ramachandran restraints generated. 8103 Oldfield, 0 Emsley, 8103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16206 Ramachandran restraints generated. 8103 Oldfield, 0 Emsley, 8103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1779 residues out of total 7446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1572 time to evaluate : 6.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 GLU cc_start: 0.6491 (pt0) cc_final: 0.6162 (pt0) REVERT: B 74 ASP cc_start: 0.6552 (p0) cc_final: 0.6289 (p0) REVERT: D 30 ILE cc_start: 0.7343 (OUTLIER) cc_final: 0.7008 (tt) REVERT: J 125 ASP cc_start: 0.6252 (m-30) cc_final: 0.5322 (m-30) REVERT: J 311 ASN cc_start: 0.6882 (p0) cc_final: 0.6646 (p0) REVERT: J 405 PHE cc_start: 0.6840 (OUTLIER) cc_final: 0.5896 (p90) REVERT: T 93 LEU cc_start: 0.7203 (mp) cc_final: 0.6960 (mp) REVERT: o 44 ILE cc_start: 0.8083 (mp) cc_final: 0.7712 (mp) REVERT: q 35 GLU cc_start: 0.5416 (tm-30) cc_final: 0.5174 (tm-30) REVERT: K 158 TRP cc_start: 0.3406 (m100) cc_final: 0.3193 (m100) REVERT: K 282 ILE cc_start: 0.8113 (mm) cc_final: 0.7910 (mm) REVERT: z 121 MET cc_start: 0.2583 (mtt) cc_final: 0.2266 (ptp) REVERT: z 144 LYS cc_start: 0.5960 (pttt) cc_final: 0.5311 (tptt) REVERT: z 162 ASP cc_start: 0.5686 (OUTLIER) cc_final: 0.5402 (t0) REVERT: y 30 ILE cc_start: 0.4417 (mt) cc_final: 0.4151 (mt) outliers start: 207 outliers final: 105 residues processed: 1695 average time/residue: 0.6694 time to fit residues: 1934.6242 Evaluate side-chains 1394 residues out of total 7446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1286 time to evaluate : 5.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 182 GLU Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 174 ILE Chi-restraints excluded: chain J residue 226 ASP Chi-restraints excluded: chain J residue 405 PHE Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 121 MET Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 102 ILE Chi-restraints excluded: chain Q residue 132 THR Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain T residue 45 THR Chi-restraints excluded: chain T residue 132 THR Chi-restraints excluded: chain W residue 103 SER Chi-restraints excluded: chain W residue 129 SER Chi-restraints excluded: chain W residue 133 ILE Chi-restraints excluded: chain X residue 14 ASN Chi-restraints excluded: chain X residue 109 TYR Chi-restraints excluded: chain l residue 86 LEU Chi-restraints excluded: chain m residue 8 VAL Chi-restraints excluded: chain n residue 16 ILE Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain n residue 134 VAL Chi-restraints excluded: chain o residue 8 VAL Chi-restraints excluded: chain o residue 16 ILE Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain q residue 49 VAL Chi-restraints excluded: chain q residue 154 VAL Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 49 VAL Chi-restraints excluded: chain r residue 57 VAL Chi-restraints excluded: chain r residue 108 ILE Chi-restraints excluded: chain s residue 8 VAL Chi-restraints excluded: chain s residue 53 ASN Chi-restraints excluded: chain s residue 60 LEU Chi-restraints excluded: chain s residue 86 LEU Chi-restraints excluded: chain s residue 105 ASP Chi-restraints excluded: chain s residue 132 THR Chi-restraints excluded: chain t residue 42 LEU Chi-restraints excluded: chain t residue 108 ILE Chi-restraints excluded: chain t residue 166 LEU Chi-restraints excluded: chain w residue 60 LEU Chi-restraints excluded: chain w residue 108 ILE Chi-restraints excluded: chain w residue 149 THR Chi-restraints excluded: chain x residue 12 ILE Chi-restraints excluded: chain x residue 141 VAL Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 364 ASP Chi-restraints excluded: chain K residue 517 VAL Chi-restraints excluded: chain K residue 657 LEU Chi-restraints excluded: chain K residue 663 THR Chi-restraints excluded: chain K residue 694 VAL Chi-restraints excluded: chain K residue 737 VAL Chi-restraints excluded: chain K residue 748 VAL Chi-restraints excluded: chain K residue 765 ILE Chi-restraints excluded: chain K residue 766 VAL Chi-restraints excluded: chain K residue 785 GLU Chi-restraints excluded: chain K residue 788 LEU Chi-restraints excluded: chain K residue 860 SER Chi-restraints excluded: chain K residue 926 VAL Chi-restraints excluded: chain Z residue 17 THR Chi-restraints excluded: chain Z residue 74 THR Chi-restraints excluded: chain Z residue 154 VAL Chi-restraints excluded: chain z residue 43 VAL Chi-restraints excluded: chain z residue 88 LEU Chi-restraints excluded: chain z residue 162 ASP Chi-restraints excluded: chain H residue 242 VAL Chi-restraints excluded: chain H residue 251 ILE Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 20 VAL Chi-restraints excluded: chain y residue 108 ILE Chi-restraints excluded: chain y residue 154 VAL Chi-restraints excluded: chain y residue 159 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 813 random chunks: chunk 410 optimal weight: 8.9990 chunk 229 optimal weight: 6.9990 chunk 614 optimal weight: 30.0000 chunk 502 optimal weight: 4.9990 chunk 203 optimal weight: 5.9990 chunk 739 optimal weight: 9.9990 chunk 799 optimal weight: 5.9990 chunk 658 optimal weight: 5.9990 chunk 733 optimal weight: 0.9990 chunk 252 optimal weight: 8.9990 chunk 593 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN C 23 HIS D 17 HIS ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 HIS I 43 ASN I 87 ASN J 157 HIS J 337 ASN M 79 GLN M 150 GLN N 174 GLN ** O 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 GLN P 135 ASN Q 174 GLN R 14 ASN ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 135 ASN ** n 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 53 ASN o 4 GLN ** o 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 4 GLN p 40 ASN ** r 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 32 ASN s 4 GLN ** s 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 175 HIS K 846 ASN ** z 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 HIS H 187 ASN ** H 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 29 HIS ** y 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 69072 Z= 0.450 Angle : 0.762 13.385 93895 Z= 0.394 Chirality : 0.050 0.333 10992 Planarity : 0.005 0.076 11507 Dihedral : 11.243 173.425 10378 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 13.64 % Favored : 86.29 % Rotamer: Outliers : 3.83 % Allowed : 19.79 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.87 (0.08), residues: 8103 helix: -1.90 (0.10), residues: 2263 sheet: -1.68 (0.14), residues: 1252 loop : -3.33 (0.08), residues: 4588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP K 240 HIS 0.007 0.001 HIS K 175 PHE 0.021 0.002 PHE C 51 TYR 0.034 0.002 TYR t 112 ARG 0.012 0.001 ARG O 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16206 Ramachandran restraints generated. 8103 Oldfield, 0 Emsley, 8103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16206 Ramachandran restraints generated. 8103 Oldfield, 0 Emsley, 8103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1603 residues out of total 7446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 1318 time to evaluate : 5.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 ASP cc_start: 0.6803 (p0) cc_final: 0.6566 (p0) REVERT: D 30 ILE cc_start: 0.7519 (OUTLIER) cc_final: 0.7259 (tt) REVERT: E 38 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.6976 (pm20) REVERT: G 246 GLU cc_start: 0.6648 (OUTLIER) cc_final: 0.6277 (mt-10) REVERT: J 125 ASP cc_start: 0.6579 (m-30) cc_final: 0.6360 (m-30) REVERT: J 311 ASN cc_start: 0.7048 (p0) cc_final: 0.6723 (p0) REVERT: J 405 PHE cc_start: 0.7019 (OUTLIER) cc_final: 0.6005 (p90) REVERT: T 93 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.7002 (mp) REVERT: w 170 TYR cc_start: 0.5155 (m-80) cc_final: 0.4896 (m-80) REVERT: K 158 TRP cc_start: 0.3577 (m100) cc_final: 0.3360 (m100) REVERT: K 187 MET cc_start: 0.5193 (ppp) cc_final: 0.4383 (ppp) REVERT: K 282 ILE cc_start: 0.8155 (mm) cc_final: 0.7935 (mm) REVERT: K 291 PHE cc_start: 0.7133 (m-80) cc_final: 0.6807 (m-80) REVERT: z 144 LYS cc_start: 0.5992 (pttt) cc_final: 0.5419 (tptt) REVERT: z 162 ASP cc_start: 0.5758 (OUTLIER) cc_final: 0.5552 (t0) outliers start: 285 outliers final: 187 residues processed: 1505 average time/residue: 0.6522 time to fit residues: 1682.1290 Evaluate side-chains 1396 residues out of total 7446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1203 time to evaluate : 5.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain G residue 66 ASP Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 256 CYS Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 182 GLU Chi-restraints excluded: chain I residue 200 PHE Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 283 SER Chi-restraints excluded: chain J residue 405 PHE Chi-restraints excluded: chain J residue 437 ILE Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 34 ASP Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 131 ASP Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 81 ASN Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain N residue 132 THR Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 149 THR Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain P residue 56 LEU Chi-restraints excluded: chain P residue 77 GLN Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 30 ILE Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain Q residue 102 ILE Chi-restraints excluded: chain Q residue 132 THR Chi-restraints excluded: chain Q residue 174 GLN Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain R residue 145 ILE Chi-restraints excluded: chain S residue 9 PHE Chi-restraints excluded: chain S residue 18 ILE Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 49 VAL Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain T residue 45 THR Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 132 THR Chi-restraints excluded: chain W residue 30 ILE Chi-restraints excluded: chain W residue 32 ASN Chi-restraints excluded: chain W residue 43 VAL Chi-restraints excluded: chain W residue 103 SER Chi-restraints excluded: chain W residue 129 SER Chi-restraints excluded: chain W residue 133 ILE Chi-restraints excluded: chain X residue 17 THR Chi-restraints excluded: chain X residue 109 TYR Chi-restraints excluded: chain l residue 86 LEU Chi-restraints excluded: chain l residue 126 VAL Chi-restraints excluded: chain m residue 8 VAL Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain m residue 165 GLU Chi-restraints excluded: chain n residue 16 ILE Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain o residue 16 ILE Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain o residue 96 ILE Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 74 THR Chi-restraints excluded: chain q residue 45 THR Chi-restraints excluded: chain q residue 49 VAL Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 74 THR Chi-restraints excluded: chain q residue 88 LEU Chi-restraints excluded: chain q residue 134 VAL Chi-restraints excluded: chain q residue 154 VAL Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 16 ILE Chi-restraints excluded: chain r residue 42 LEU Chi-restraints excluded: chain r residue 49 VAL Chi-restraints excluded: chain r residue 57 VAL Chi-restraints excluded: chain r residue 74 THR Chi-restraints excluded: chain r residue 108 ILE Chi-restraints excluded: chain s residue 8 VAL Chi-restraints excluded: chain s residue 60 LEU Chi-restraints excluded: chain s residue 86 LEU Chi-restraints excluded: chain s residue 95 LEU Chi-restraints excluded: chain s residue 105 ASP Chi-restraints excluded: chain s residue 106 LEU Chi-restraints excluded: chain t residue 8 VAL Chi-restraints excluded: chain t residue 42 LEU Chi-restraints excluded: chain t residue 120 SER Chi-restraints excluded: chain t residue 149 THR Chi-restraints excluded: chain w residue 8 VAL Chi-restraints excluded: chain w residue 16 ILE Chi-restraints excluded: chain w residue 108 ILE Chi-restraints excluded: chain w residue 149 THR Chi-restraints excluded: chain x residue 3 THR Chi-restraints excluded: chain x residue 12 ILE Chi-restraints excluded: chain x residue 24 ILE Chi-restraints excluded: chain x residue 66 VAL Chi-restraints excluded: chain x residue 134 VAL Chi-restraints excluded: chain x residue 141 VAL Chi-restraints excluded: chain x residue 166 LEU Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 166 THR Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain K residue 307 ILE Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 517 VAL Chi-restraints excluded: chain K residue 545 GLU Chi-restraints excluded: chain K residue 638 THR Chi-restraints excluded: chain K residue 657 LEU Chi-restraints excluded: chain K residue 694 VAL Chi-restraints excluded: chain K residue 705 VAL Chi-restraints excluded: chain K residue 709 LEU Chi-restraints excluded: chain K residue 737 VAL Chi-restraints excluded: chain K residue 748 VAL Chi-restraints excluded: chain K residue 765 ILE Chi-restraints excluded: chain K residue 766 VAL Chi-restraints excluded: chain K residue 785 GLU Chi-restraints excluded: chain K residue 860 SER Chi-restraints excluded: chain K residue 886 GLU Chi-restraints excluded: chain K residue 919 LEU Chi-restraints excluded: chain K residue 926 VAL Chi-restraints excluded: chain K residue 954 ILE Chi-restraints excluded: chain Z residue 17 THR Chi-restraints excluded: chain Z residue 74 THR Chi-restraints excluded: chain Z residue 154 VAL Chi-restraints excluded: chain z residue 43 VAL Chi-restraints excluded: chain z residue 88 LEU Chi-restraints excluded: chain z residue 162 ASP Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain H residue 247 LEU Chi-restraints excluded: chain H residue 251 ILE Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 20 VAL Chi-restraints excluded: chain y residue 108 ILE Chi-restraints excluded: chain y residue 154 VAL Chi-restraints excluded: chain y residue 159 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 813 random chunks: chunk 730 optimal weight: 6.9990 chunk 556 optimal weight: 9.9990 chunk 383 optimal weight: 10.0000 chunk 81 optimal weight: 0.5980 chunk 352 optimal weight: 8.9990 chunk 496 optimal weight: 20.0000 chunk 742 optimal weight: 20.0000 chunk 785 optimal weight: 20.0000 chunk 387 optimal weight: 7.9990 chunk 703 optimal weight: 6.9990 chunk 211 optimal weight: 1.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN B 111 GLN ** D 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN M 174 GLN ** O 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 GLN ** P 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 4 GLN T 135 ASN ** W 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 147 ASN ** l 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 14 ASN p 4 GLN q 29 HIS ** r 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 4 GLN ** s 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 39 HIS ** t 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 76 GLN t 77 GLN ** w 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 175 HIS ** K 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 259 GLN ** z 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 29 HIS ** y 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.090 69072 Z= 0.555 Angle : 0.791 12.546 93895 Z= 0.410 Chirality : 0.051 0.367 10992 Planarity : 0.005 0.073 11507 Dihedral : 11.238 172.987 10377 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 14.33 % Favored : 85.57 % Rotamer: Outliers : 5.03 % Allowed : 21.51 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.76 (0.08), residues: 8103 helix: -1.85 (0.10), residues: 2274 sheet: -1.63 (0.15), residues: 1230 loop : -3.23 (0.08), residues: 4599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 240 HIS 0.006 0.001 HIS K 175 PHE 0.024 0.002 PHE J 123 TYR 0.028 0.002 TYR B 42 ARG 0.011 0.001 ARG O 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16206 Ramachandran restraints generated. 8103 Oldfield, 0 Emsley, 8103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16206 Ramachandran restraints generated. 8103 Oldfield, 0 Emsley, 8103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1668 residues out of total 7446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 374 poor density : 1294 time to evaluate : 6.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 TYR cc_start: 0.6209 (t80) cc_final: 0.5728 (t80) REVERT: B 114 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8072 (mmt90) REVERT: E 38 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7004 (pm20) REVERT: G 29 GLU cc_start: 0.6955 (pp20) cc_final: 0.6380 (pp20) REVERT: G 246 GLU cc_start: 0.6700 (OUTLIER) cc_final: 0.6375 (mt-10) REVERT: J 125 ASP cc_start: 0.6599 (m-30) cc_final: 0.6303 (m-30) REVERT: J 311 ASN cc_start: 0.7005 (p0) cc_final: 0.6643 (p0) REVERT: J 405 PHE cc_start: 0.7128 (OUTLIER) cc_final: 0.6088 (p90) REVERT: T 93 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.7035 (mp) REVERT: w 102 ILE cc_start: 0.6588 (OUTLIER) cc_final: 0.6116 (mm) REVERT: K 187 MET cc_start: 0.5150 (ppp) cc_final: 0.4870 (ppp) REVERT: K 208 ILE cc_start: 0.8466 (mm) cc_final: 0.8256 (mm) REVERT: z 60 LEU cc_start: 0.4521 (OUTLIER) cc_final: 0.3779 (mm) REVERT: z 144 LYS cc_start: 0.6175 (pttt) cc_final: 0.5625 (tptt) outliers start: 374 outliers final: 256 residues processed: 1557 average time/residue: 0.7102 time to fit residues: 1917.7517 Evaluate side-chains 1430 residues out of total 7446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 1167 time to evaluate : 5.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 114 ARG Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain G residue 66 ASP Chi-restraints excluded: chain G residue 141 ASN Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 168 ASP Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 256 CYS Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 182 GLU Chi-restraints excluded: chain I residue 191 ASP Chi-restraints excluded: chain I residue 200 PHE Chi-restraints excluded: chain I residue 252 CYS Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 111 CYS Chi-restraints excluded: chain J residue 114 ASN Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 283 SER Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 356 CYS Chi-restraints excluded: chain J residue 405 PHE Chi-restraints excluded: chain J residue 437 ILE Chi-restraints excluded: chain L residue 35 GLU Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 165 GLU Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 34 ASP Chi-restraints excluded: chain M residue 55 ARG Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 131 ASP Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 121 MET Chi-restraints excluded: chain N residue 132 THR Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 140 GLU Chi-restraints excluded: chain N residue 141 VAL Chi-restraints excluded: chain N residue 149 THR Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain P residue 113 SER Chi-restraints excluded: chain P residue 121 MET Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain P residue 163 ILE Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 30 ILE Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 84 LEU Chi-restraints excluded: chain Q residue 102 ILE Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 132 THR Chi-restraints excluded: chain Q residue 159 VAL Chi-restraints excluded: chain Q residue 174 GLN Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 145 ILE Chi-restraints excluded: chain S residue 4 GLN Chi-restraints excluded: chain S residue 9 PHE Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 18 ILE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 49 VAL Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain T residue 45 THR Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 132 THR Chi-restraints excluded: chain W residue 30 ILE Chi-restraints excluded: chain W residue 32 ASN Chi-restraints excluded: chain W residue 43 VAL Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 110 ILE Chi-restraints excluded: chain W residue 129 SER Chi-restraints excluded: chain W residue 133 ILE Chi-restraints excluded: chain X residue 16 ILE Chi-restraints excluded: chain X residue 17 THR Chi-restraints excluded: chain X residue 33 ILE Chi-restraints excluded: chain X residue 109 TYR Chi-restraints excluded: chain l residue 86 LEU Chi-restraints excluded: chain l residue 126 VAL Chi-restraints excluded: chain m residue 8 VAL Chi-restraints excluded: chain m residue 23 THR Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain m residue 121 MET Chi-restraints excluded: chain m residue 165 GLU Chi-restraints excluded: chain n residue 14 ASN Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain n residue 95 LEU Chi-restraints excluded: chain n residue 127 SER Chi-restraints excluded: chain o residue 16 ILE Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain o residue 93 LEU Chi-restraints excluded: chain o residue 96 ILE Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 74 THR Chi-restraints excluded: chain p residue 132 THR Chi-restraints excluded: chain p residue 137 ILE Chi-restraints excluded: chain q residue 29 HIS Chi-restraints excluded: chain q residue 45 THR Chi-restraints excluded: chain q residue 49 VAL Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 74 THR Chi-restraints excluded: chain q residue 88 LEU Chi-restraints excluded: chain q residue 154 VAL Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 16 ILE Chi-restraints excluded: chain r residue 42 LEU Chi-restraints excluded: chain r residue 49 VAL Chi-restraints excluded: chain r residue 57 VAL Chi-restraints excluded: chain r residue 74 THR Chi-restraints excluded: chain s residue 8 VAL Chi-restraints excluded: chain s residue 9 PHE Chi-restraints excluded: chain s residue 43 VAL Chi-restraints excluded: chain s residue 60 LEU Chi-restraints excluded: chain s residue 86 LEU Chi-restraints excluded: chain s residue 95 LEU Chi-restraints excluded: chain s residue 105 ASP Chi-restraints excluded: chain s residue 132 THR Chi-restraints excluded: chain t residue 8 VAL Chi-restraints excluded: chain t residue 42 LEU Chi-restraints excluded: chain t residue 74 THR Chi-restraints excluded: chain t residue 120 SER Chi-restraints excluded: chain t residue 121 MET Chi-restraints excluded: chain t residue 129 SER Chi-restraints excluded: chain t residue 149 THR Chi-restraints excluded: chain w residue 16 ILE Chi-restraints excluded: chain w residue 60 LEU Chi-restraints excluded: chain w residue 102 ILE Chi-restraints excluded: chain w residue 149 THR Chi-restraints excluded: chain x residue 3 THR Chi-restraints excluded: chain x residue 12 ILE Chi-restraints excluded: chain x residue 24 ILE Chi-restraints excluded: chain x residue 66 VAL Chi-restraints excluded: chain x residue 71 VAL Chi-restraints excluded: chain x residue 108 ILE Chi-restraints excluded: chain x residue 121 MET Chi-restraints excluded: chain x residue 134 VAL Chi-restraints excluded: chain x residue 141 VAL Chi-restraints excluded: chain x residue 172 LEU Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 166 THR Chi-restraints excluded: chain K residue 193 SER Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 307 ILE Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 390 VAL Chi-restraints excluded: chain K residue 470 LEU Chi-restraints excluded: chain K residue 491 ILE Chi-restraints excluded: chain K residue 517 VAL Chi-restraints excluded: chain K residue 545 GLU Chi-restraints excluded: chain K residue 566 THR Chi-restraints excluded: chain K residue 638 THR Chi-restraints excluded: chain K residue 657 LEU Chi-restraints excluded: chain K residue 694 VAL Chi-restraints excluded: chain K residue 705 VAL Chi-restraints excluded: chain K residue 709 LEU Chi-restraints excluded: chain K residue 737 VAL Chi-restraints excluded: chain K residue 766 VAL Chi-restraints excluded: chain K residue 785 GLU Chi-restraints excluded: chain K residue 815 ASP Chi-restraints excluded: chain K residue 852 LEU Chi-restraints excluded: chain K residue 860 SER Chi-restraints excluded: chain K residue 919 LEU Chi-restraints excluded: chain K residue 926 VAL Chi-restraints excluded: chain K residue 930 SER Chi-restraints excluded: chain K residue 954 ILE Chi-restraints excluded: chain K residue 977 LEU Chi-restraints excluded: chain K residue 997 PHE Chi-restraints excluded: chain Z residue 17 THR Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain Z residue 74 THR Chi-restraints excluded: chain Z residue 88 LEU Chi-restraints excluded: chain Z residue 154 VAL Chi-restraints excluded: chain z residue 43 VAL Chi-restraints excluded: chain z residue 60 LEU Chi-restraints excluded: chain z residue 88 LEU Chi-restraints excluded: chain z residue 132 THR Chi-restraints excluded: chain z residue 148 ILE Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 127 LYS Chi-restraints excluded: chain H residue 153 TYR Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain H residue 242 VAL Chi-restraints excluded: chain H residue 247 LEU Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain Y residue 16 ILE Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Y residue 29 HIS Chi-restraints excluded: chain Y residue 33 ILE Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 20 VAL Chi-restraints excluded: chain y residue 108 ILE Chi-restraints excluded: chain y residue 149 THR Chi-restraints excluded: chain y residue 154 VAL Chi-restraints excluded: chain y residue 159 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 813 random chunks: chunk 654 optimal weight: 6.9990 chunk 446 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 585 optimal weight: 5.9990 chunk 324 optimal weight: 0.9990 chunk 670 optimal weight: 8.9990 chunk 543 optimal weight: 4.9990 chunk 0 optimal weight: 0.6980 chunk 401 optimal weight: 10.0000 chunk 705 optimal weight: 0.9980 chunk 198 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN D 13 HIS E 141 ASN J 337 ASN L 174 GLN ** O 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 GLN P 174 GLN Q 174 GLN ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 147 ASN ** l 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 79 GLN n 4 GLN n 14 ASN n 53 ASN o 4 GLN p 4 GLN q 29 HIS ** r 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 4 GLN ** s 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 175 HIS K 259 GLN K 845 ASN ** z 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 GLN ** H 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 69072 Z= 0.242 Angle : 0.696 11.412 93895 Z= 0.361 Chirality : 0.048 0.378 10992 Planarity : 0.005 0.067 11507 Dihedral : 11.073 174.129 10376 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.74 % Favored : 87.23 % Rotamer: Outliers : 3.99 % Allowed : 23.69 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.48 (0.09), residues: 8103 helix: -1.59 (0.10), residues: 2258 sheet: -1.52 (0.15), residues: 1266 loop : -3.05 (0.08), residues: 4579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K 240 HIS 0.009 0.001 HIS Y 29 PHE 0.029 0.001 PHE K 629 TYR 0.029 0.002 TYR n 112 ARG 0.008 0.001 ARG p 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16206 Ramachandran restraints generated. 8103 Oldfield, 0 Emsley, 8103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16206 Ramachandran restraints generated. 8103 Oldfield, 0 Emsley, 8103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1672 residues out of total 7446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 297 poor density : 1375 time to evaluate : 5.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 38 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6813 (pm20) REVERT: G 246 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.6191 (mt-10) REVERT: J 125 ASP cc_start: 0.6330 (m-30) cc_final: 0.5296 (m-30) REVERT: J 311 ASN cc_start: 0.6863 (p0) cc_final: 0.6457 (p0) REVERT: J 405 PHE cc_start: 0.7071 (OUTLIER) cc_final: 0.6094 (p90) REVERT: O 9 PHE cc_start: 0.5499 (p90) cc_final: 0.5168 (p90) REVERT: T 93 LEU cc_start: 0.7256 (mp) cc_final: 0.6985 (mp) REVERT: m 35 GLU cc_start: 0.5762 (mm-30) cc_final: 0.5397 (mm-30) REVERT: K 73 ASP cc_start: 0.4995 (OUTLIER) cc_final: 0.4618 (t0) REVERT: K 208 ILE cc_start: 0.8366 (mm) cc_final: 0.8141 (mm) REVERT: z 121 MET cc_start: 0.2950 (ptp) cc_final: 0.2635 (ptp) REVERT: z 144 LYS cc_start: 0.6163 (pttt) cc_final: 0.5609 (tptt) outliers start: 297 outliers final: 201 residues processed: 1584 average time/residue: 0.6401 time to fit residues: 1744.3154 Evaluate side-chains 1437 residues out of total 7446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 1232 time to evaluate : 5.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain G residue 66 ASP Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 168 ASP Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 182 GLU Chi-restraints excluded: chain I residue 200 PHE Chi-restraints excluded: chain I residue 252 CYS Chi-restraints excluded: chain I residue 257 ILE Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 111 CYS Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 283 SER Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 356 CYS Chi-restraints excluded: chain J residue 366 VAL Chi-restraints excluded: chain J residue 405 PHE Chi-restraints excluded: chain J residue 437 ILE Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 165 GLU Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 34 ASP Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 64 ASP Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 69 ILE Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 132 THR Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain P residue 24 ILE Chi-restraints excluded: chain P residue 77 GLN Chi-restraints excluded: chain P residue 113 SER Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 30 ILE Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 102 ILE Chi-restraints excluded: chain Q residue 132 THR Chi-restraints excluded: chain Q residue 174 GLN Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain S residue 9 PHE Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 18 ILE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 42 LEU Chi-restraints excluded: chain S residue 49 VAL Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain T residue 45 THR Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 132 THR Chi-restraints excluded: chain W residue 30 ILE Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 63 CYS Chi-restraints excluded: chain W residue 129 SER Chi-restraints excluded: chain W residue 133 ILE Chi-restraints excluded: chain X residue 16 ILE Chi-restraints excluded: chain X residue 17 THR Chi-restraints excluded: chain X residue 108 ILE Chi-restraints excluded: chain X residue 141 VAL Chi-restraints excluded: chain l residue 86 LEU Chi-restraints excluded: chain l residue 106 LEU Chi-restraints excluded: chain l residue 126 VAL Chi-restraints excluded: chain m residue 8 VAL Chi-restraints excluded: chain m residue 23 THR Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain n residue 16 ILE Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain o residue 16 ILE Chi-restraints excluded: chain o residue 59 THR Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain o residue 96 ILE Chi-restraints excluded: chain q residue 29 HIS Chi-restraints excluded: chain q residue 30 ILE Chi-restraints excluded: chain q residue 74 THR Chi-restraints excluded: chain q residue 154 VAL Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 16 ILE Chi-restraints excluded: chain r residue 42 LEU Chi-restraints excluded: chain r residue 49 VAL Chi-restraints excluded: chain r residue 57 VAL Chi-restraints excluded: chain r residue 88 LEU Chi-restraints excluded: chain s residue 8 VAL Chi-restraints excluded: chain s residue 43 VAL Chi-restraints excluded: chain s residue 60 LEU Chi-restraints excluded: chain s residue 105 ASP Chi-restraints excluded: chain t residue 120 SER Chi-restraints excluded: chain t residue 121 MET Chi-restraints excluded: chain t residue 143 ASP Chi-restraints excluded: chain t residue 149 THR Chi-restraints excluded: chain w residue 16 ILE Chi-restraints excluded: chain w residue 38 ILE Chi-restraints excluded: chain w residue 57 VAL Chi-restraints excluded: chain w residue 60 LEU Chi-restraints excluded: chain w residue 71 VAL Chi-restraints excluded: chain w residue 149 THR Chi-restraints excluded: chain x residue 12 ILE Chi-restraints excluded: chain x residue 24 ILE Chi-restraints excluded: chain x residue 108 ILE Chi-restraints excluded: chain x residue 121 MET Chi-restraints excluded: chain x residue 134 VAL Chi-restraints excluded: chain x residue 141 VAL Chi-restraints excluded: chain x residue 172 LEU Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 193 SER Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 308 ILE Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 354 LEU Chi-restraints excluded: chain K residue 491 ILE Chi-restraints excluded: chain K residue 517 VAL Chi-restraints excluded: chain K residue 545 GLU Chi-restraints excluded: chain K residue 558 THR Chi-restraints excluded: chain K residue 566 THR Chi-restraints excluded: chain K residue 638 THR Chi-restraints excluded: chain K residue 657 LEU Chi-restraints excluded: chain K residue 694 VAL Chi-restraints excluded: chain K residue 705 VAL Chi-restraints excluded: chain K residue 709 LEU Chi-restraints excluded: chain K residue 737 VAL Chi-restraints excluded: chain K residue 748 VAL Chi-restraints excluded: chain K residue 766 VAL Chi-restraints excluded: chain K residue 785 GLU Chi-restraints excluded: chain K residue 852 LEU Chi-restraints excluded: chain K residue 919 LEU Chi-restraints excluded: chain K residue 926 VAL Chi-restraints excluded: chain Z residue 17 THR Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain Z residue 88 LEU Chi-restraints excluded: chain z residue 39 HIS Chi-restraints excluded: chain z residue 43 VAL Chi-restraints excluded: chain z residue 45 THR Chi-restraints excluded: chain z residue 88 LEU Chi-restraints excluded: chain z residue 148 ILE Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain H residue 242 VAL Chi-restraints excluded: chain H residue 247 LEU Chi-restraints excluded: chain Y residue 16 ILE Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Y residue 105 ASP Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 20 VAL Chi-restraints excluded: chain y residue 38 ILE Chi-restraints excluded: chain y residue 108 ILE Chi-restraints excluded: chain y residue 149 THR Chi-restraints excluded: chain y residue 154 VAL Chi-restraints excluded: chain y residue 159 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 813 random chunks: chunk 264 optimal weight: 0.9980 chunk 707 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 461 optimal weight: 30.0000 chunk 193 optimal weight: 2.9990 chunk 786 optimal weight: 20.0000 chunk 652 optimal weight: 10.0000 chunk 364 optimal weight: 20.0000 chunk 65 optimal weight: 0.8980 chunk 260 optimal weight: 10.0000 chunk 412 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN A 128 ASN B 84 ASN B 111 GLN D 203 ASN ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 337 ASN M 150 GLN P 77 GLN P 174 GLN ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 174 GLN S 4 GLN ** T 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 53 ASN m 29 HIS ** m 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 135 ASN n 4 GLN ** n 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 79 GLN q 29 HIS r 4 GLN ** r 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 4 GLN ** s 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 175 HIS K 259 GLN ** z 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 69072 Z= 0.294 Angle : 0.701 11.592 93895 Z= 0.363 Chirality : 0.049 0.418 10992 Planarity : 0.004 0.071 11507 Dihedral : 10.977 174.265 10376 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.16 % Favored : 86.81 % Rotamer: Outliers : 4.19 % Allowed : 24.05 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.37 (0.09), residues: 8103 helix: -1.48 (0.10), residues: 2251 sheet: -1.40 (0.15), residues: 1281 loop : -3.01 (0.08), residues: 4571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 240 HIS 0.012 0.001 HIS q 29 PHE 0.039 0.002 PHE K 629 TYR 0.028 0.002 TYR W 112 ARG 0.010 0.001 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16206 Ramachandran restraints generated. 8103 Oldfield, 0 Emsley, 8103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16206 Ramachandran restraints generated. 8103 Oldfield, 0 Emsley, 8103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1639 residues out of total 7446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 312 poor density : 1327 time to evaluate : 5.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7883 (mmt90) REVERT: E 38 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6851 (pm20) REVERT: G 246 GLU cc_start: 0.6675 (OUTLIER) cc_final: 0.6258 (mt-10) REVERT: I 3 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7788 (tt) REVERT: J 311 ASN cc_start: 0.6876 (p0) cc_final: 0.6519 (p0) REVERT: J 405 PHE cc_start: 0.7059 (OUTLIER) cc_final: 0.6071 (p90) REVERT: S 65 TYR cc_start: 0.8347 (p90) cc_final: 0.7677 (p90) REVERT: T 56 LEU cc_start: 0.6992 (mt) cc_final: 0.6660 (mt) REVERT: T 93 LEU cc_start: 0.7222 (mp) cc_final: 0.6981 (mp) REVERT: m 35 GLU cc_start: 0.5710 (mm-30) cc_final: 0.5361 (mm-30) REVERT: m 86 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7598 (pp) REVERT: n 44 ILE cc_start: 0.8085 (mt) cc_final: 0.7863 (tt) REVERT: s 4 GLN cc_start: 0.6110 (mt0) cc_final: 0.5763 (mt0) REVERT: w 102 ILE cc_start: 0.6582 (OUTLIER) cc_final: 0.6207 (mm) REVERT: K 73 ASP cc_start: 0.4961 (OUTLIER) cc_final: 0.4733 (t0) REVERT: K 187 MET cc_start: 0.5142 (ppp) cc_final: 0.3887 (ppp) REVERT: K 290 ILE cc_start: 0.6367 (OUTLIER) cc_final: 0.5896 (mt) REVERT: K 835 MET cc_start: 0.4728 (mpp) cc_final: 0.4201 (mtm) REVERT: Z 164 LYS cc_start: 0.4996 (mmtt) cc_final: 0.4615 (mttt) REVERT: z 60 LEU cc_start: 0.4661 (OUTLIER) cc_final: 0.3910 (mm) REVERT: z 121 MET cc_start: 0.2946 (ptp) cc_final: 0.2744 (ptp) REVERT: z 144 LYS cc_start: 0.6161 (pttt) cc_final: 0.5578 (tptt) REVERT: H 254 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8462 (m) outliers start: 312 outliers final: 237 residues processed: 1544 average time/residue: 0.6350 time to fit residues: 1685.5625 Evaluate side-chains 1473 residues out of total 7446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 1225 time to evaluate : 5.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 114 ARG Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain G residue 66 ASP Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 256 CYS Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 182 GLU Chi-restraints excluded: chain I residue 200 PHE Chi-restraints excluded: chain I residue 252 CYS Chi-restraints excluded: chain I residue 257 ILE Chi-restraints excluded: chain I residue 263 LEU Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 111 CYS Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 283 SER Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 356 CYS Chi-restraints excluded: chain J residue 366 VAL Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain J residue 405 PHE Chi-restraints excluded: chain L residue 38 ILE Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 121 MET Chi-restraints excluded: chain L residue 165 GLU Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 34 ASP Chi-restraints excluded: chain M residue 55 ARG Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 64 ASP Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain N residue 129 SER Chi-restraints excluded: chain N residue 132 THR Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 141 VAL Chi-restraints excluded: chain N residue 172 LEU Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain P residue 24 ILE Chi-restraints excluded: chain P residue 113 SER Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 30 ILE Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 102 ILE Chi-restraints excluded: chain Q residue 119 ASN Chi-restraints excluded: chain Q residue 132 THR Chi-restraints excluded: chain Q residue 159 VAL Chi-restraints excluded: chain Q residue 168 SER Chi-restraints excluded: chain Q residue 174 GLN Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain R residue 108 ILE Chi-restraints excluded: chain S residue 8 VAL Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 18 ILE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 42 LEU Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 49 VAL Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 121 MET Chi-restraints excluded: chain T residue 9 PHE Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain T residue 45 THR Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 69 ILE Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 132 THR Chi-restraints excluded: chain W residue 19 ASP Chi-restraints excluded: chain W residue 30 ILE Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 129 SER Chi-restraints excluded: chain W residue 133 ILE Chi-restraints excluded: chain X residue 16 ILE Chi-restraints excluded: chain X residue 17 THR Chi-restraints excluded: chain X residue 33 ILE Chi-restraints excluded: chain l residue 106 LEU Chi-restraints excluded: chain l residue 126 VAL Chi-restraints excluded: chain m residue 8 VAL Chi-restraints excluded: chain m residue 23 THR Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 165 GLU Chi-restraints excluded: chain n residue 4 GLN Chi-restraints excluded: chain n residue 16 ILE Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain n residue 127 SER Chi-restraints excluded: chain o residue 16 ILE Chi-restraints excluded: chain o residue 59 THR Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain o residue 96 ILE Chi-restraints excluded: chain p residue 93 LEU Chi-restraints excluded: chain q residue 30 ILE Chi-restraints excluded: chain q residue 49 VAL Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 74 THR Chi-restraints excluded: chain q residue 113 SER Chi-restraints excluded: chain q residue 154 VAL Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 16 ILE Chi-restraints excluded: chain r residue 38 ILE Chi-restraints excluded: chain r residue 42 LEU Chi-restraints excluded: chain r residue 49 VAL Chi-restraints excluded: chain r residue 57 VAL Chi-restraints excluded: chain r residue 88 LEU Chi-restraints excluded: chain s residue 8 VAL Chi-restraints excluded: chain s residue 43 VAL Chi-restraints excluded: chain s residue 60 LEU Chi-restraints excluded: chain s residue 95 LEU Chi-restraints excluded: chain s residue 105 ASP Chi-restraints excluded: chain t residue 8 VAL Chi-restraints excluded: chain t residue 42 LEU Chi-restraints excluded: chain t residue 74 THR Chi-restraints excluded: chain t residue 120 SER Chi-restraints excluded: chain t residue 121 MET Chi-restraints excluded: chain t residue 149 THR Chi-restraints excluded: chain w residue 16 ILE Chi-restraints excluded: chain w residue 38 ILE Chi-restraints excluded: chain w residue 60 LEU Chi-restraints excluded: chain w residue 102 ILE Chi-restraints excluded: chain w residue 149 THR Chi-restraints excluded: chain x residue 12 ILE Chi-restraints excluded: chain x residue 24 ILE Chi-restraints excluded: chain x residue 66 VAL Chi-restraints excluded: chain x residue 71 VAL Chi-restraints excluded: chain x residue 81 ASN Chi-restraints excluded: chain x residue 108 ILE Chi-restraints excluded: chain x residue 121 MET Chi-restraints excluded: chain x residue 134 VAL Chi-restraints excluded: chain x residue 141 VAL Chi-restraints excluded: chain x residue 172 LEU Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain K residue 290 ILE Chi-restraints excluded: chain K residue 307 ILE Chi-restraints excluded: chain K residue 308 ILE Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 354 LEU Chi-restraints excluded: chain K residue 425 PHE Chi-restraints excluded: chain K residue 470 LEU Chi-restraints excluded: chain K residue 491 ILE Chi-restraints excluded: chain K residue 517 VAL Chi-restraints excluded: chain K residue 545 GLU Chi-restraints excluded: chain K residue 558 THR Chi-restraints excluded: chain K residue 566 THR Chi-restraints excluded: chain K residue 638 THR Chi-restraints excluded: chain K residue 694 VAL Chi-restraints excluded: chain K residue 709 LEU Chi-restraints excluded: chain K residue 737 VAL Chi-restraints excluded: chain K residue 748 VAL Chi-restraints excluded: chain K residue 785 GLU Chi-restraints excluded: chain K residue 852 LEU Chi-restraints excluded: chain K residue 886 GLU Chi-restraints excluded: chain K residue 919 LEU Chi-restraints excluded: chain K residue 926 VAL Chi-restraints excluded: chain Z residue 17 THR Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain Z residue 74 THR Chi-restraints excluded: chain Z residue 88 LEU Chi-restraints excluded: chain z residue 39 HIS Chi-restraints excluded: chain z residue 43 VAL Chi-restraints excluded: chain z residue 45 THR Chi-restraints excluded: chain z residue 60 LEU Chi-restraints excluded: chain z residue 88 LEU Chi-restraints excluded: chain z residue 132 THR Chi-restraints excluded: chain z residue 148 ILE Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain H residue 242 VAL Chi-restraints excluded: chain H residue 247 LEU Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 295 ILE Chi-restraints excluded: chain Y residue 16 ILE Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Y residue 105 ASP Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 20 VAL Chi-restraints excluded: chain y residue 38 ILE Chi-restraints excluded: chain y residue 108 ILE Chi-restraints excluded: chain y residue 149 THR Chi-restraints excluded: chain y residue 154 VAL Chi-restraints excluded: chain y residue 159 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 813 random chunks: chunk 758 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 448 optimal weight: 0.7980 chunk 574 optimal weight: 20.0000 chunk 445 optimal weight: 10.0000 chunk 662 optimal weight: 5.9990 chunk 439 optimal weight: 7.9990 chunk 783 optimal weight: 30.0000 chunk 490 optimal weight: 3.9990 chunk 477 optimal weight: 2.9990 chunk 361 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN D 203 ASN E 77 ASN E 141 ASN J 220 HIS J 337 ASN O 119 ASN ** P 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 76 GLN S 4 GLN T 4 GLN ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 29 HIS ** m 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 4 GLN ** n 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 29 HIS ** r 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 175 HIS K 503 ASN ** z 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 GLN H 130 GLN ** H 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 69072 Z= 0.323 Angle : 0.711 11.093 93895 Z= 0.368 Chirality : 0.049 0.343 10992 Planarity : 0.005 0.074 11507 Dihedral : 10.925 174.107 10372 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.88 % Favored : 87.08 % Rotamer: Outliers : 4.53 % Allowed : 24.48 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.32 (0.09), residues: 8103 helix: -1.49 (0.10), residues: 2268 sheet: -1.31 (0.15), residues: 1278 loop : -2.97 (0.08), residues: 4557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 770 HIS 0.008 0.001 HIS K 175 PHE 0.048 0.002 PHE K 629 TYR 0.027 0.002 TYR B 96 ARG 0.010 0.000 ARG p 118 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16206 Ramachandran restraints generated. 8103 Oldfield, 0 Emsley, 8103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16206 Ramachandran restraints generated. 8103 Oldfield, 0 Emsley, 8103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1626 residues out of total 7446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 337 poor density : 1289 time to evaluate : 7.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7904 (mmt90) REVERT: E 38 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6882 (pm20) REVERT: G 246 GLU cc_start: 0.6643 (OUTLIER) cc_final: 0.6259 (mt-10) REVERT: I 3 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7803 (tt) REVERT: J 311 ASN cc_start: 0.6867 (p0) cc_final: 0.6493 (p0) REVERT: J 400 GLU cc_start: 0.5556 (OUTLIER) cc_final: 0.4584 (tt0) REVERT: J 405 PHE cc_start: 0.7073 (OUTLIER) cc_final: 0.6089 (p90) REVERT: T 4 GLN cc_start: 0.4729 (OUTLIER) cc_final: 0.4083 (mp-120) REVERT: T 56 LEU cc_start: 0.6953 (mt) cc_final: 0.6620 (mt) REVERT: T 93 LEU cc_start: 0.7199 (mp) cc_final: 0.6959 (mp) REVERT: m 35 GLU cc_start: 0.5724 (mm-30) cc_final: 0.5392 (mm-30) REVERT: m 86 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7584 (pp) REVERT: n 44 ILE cc_start: 0.8104 (mt) cc_final: 0.7873 (tt) REVERT: w 102 ILE cc_start: 0.6613 (OUTLIER) cc_final: 0.6239 (mm) REVERT: K 187 MET cc_start: 0.5210 (ppp) cc_final: 0.4314 (ppp) REVERT: K 835 MET cc_start: 0.4762 (mpp) cc_final: 0.4400 (mtm) REVERT: K 974 GLU cc_start: 0.6064 (tp30) cc_final: 0.5383 (tp30) REVERT: z 60 LEU cc_start: 0.4676 (OUTLIER) cc_final: 0.3903 (mm) REVERT: z 144 LYS cc_start: 0.6148 (pttt) cc_final: 0.5571 (tptt) REVERT: H 254 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8454 (m) outliers start: 337 outliers final: 257 residues processed: 1525 average time/residue: 0.6435 time to fit residues: 1692.6562 Evaluate side-chains 1492 residues out of total 7446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 1224 time to evaluate : 5.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 114 ARG Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain G residue 66 ASP Chi-restraints excluded: chain G residue 141 ASN Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 256 CYS Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 182 GLU Chi-restraints excluded: chain I residue 200 PHE Chi-restraints excluded: chain I residue 252 CYS Chi-restraints excluded: chain I residue 257 ILE Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 111 CYS Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 283 SER Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 356 CYS Chi-restraints excluded: chain J residue 366 VAL Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain J residue 400 GLU Chi-restraints excluded: chain J residue 405 PHE Chi-restraints excluded: chain L residue 38 ILE Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 165 GLU Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 34 ASP Chi-restraints excluded: chain M residue 55 ARG Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 129 SER Chi-restraints excluded: chain N residue 132 THR Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 141 VAL Chi-restraints excluded: chain N residue 172 LEU Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 16 ILE Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain P residue 24 ILE Chi-restraints excluded: chain P residue 113 SER Chi-restraints excluded: chain P residue 121 MET Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 30 ILE Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 102 ILE Chi-restraints excluded: chain Q residue 119 ASN Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 132 THR Chi-restraints excluded: chain Q residue 168 SER Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain R residue 108 ILE Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 8 VAL Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 18 ILE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 42 LEU Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 49 VAL Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 121 MET Chi-restraints excluded: chain T residue 4 GLN Chi-restraints excluded: chain T residue 9 PHE Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain T residue 45 THR Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 69 ILE Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 132 THR Chi-restraints excluded: chain W residue 19 ASP Chi-restraints excluded: chain W residue 32 ASN Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 103 SER Chi-restraints excluded: chain W residue 129 SER Chi-restraints excluded: chain W residue 133 ILE Chi-restraints excluded: chain X residue 16 ILE Chi-restraints excluded: chain X residue 17 THR Chi-restraints excluded: chain X residue 33 ILE Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain l residue 106 LEU Chi-restraints excluded: chain l residue 121 MET Chi-restraints excluded: chain l residue 126 VAL Chi-restraints excluded: chain m residue 8 VAL Chi-restraints excluded: chain m residue 17 THR Chi-restraints excluded: chain m residue 23 THR Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 165 GLU Chi-restraints excluded: chain n residue 4 GLN Chi-restraints excluded: chain n residue 16 ILE Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain n residue 127 SER Chi-restraints excluded: chain o residue 16 ILE Chi-restraints excluded: chain o residue 59 THR Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain o residue 96 ILE Chi-restraints excluded: chain p residue 16 ILE Chi-restraints excluded: chain p residue 74 THR Chi-restraints excluded: chain p residue 93 LEU Chi-restraints excluded: chain p residue 137 ILE Chi-restraints excluded: chain q residue 29 HIS Chi-restraints excluded: chain q residue 30 ILE Chi-restraints excluded: chain q residue 49 VAL Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 113 SER Chi-restraints excluded: chain q residue 154 VAL Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 16 ILE Chi-restraints excluded: chain r residue 38 ILE Chi-restraints excluded: chain r residue 42 LEU Chi-restraints excluded: chain r residue 49 VAL Chi-restraints excluded: chain r residue 57 VAL Chi-restraints excluded: chain r residue 88 LEU Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 8 VAL Chi-restraints excluded: chain s residue 43 VAL Chi-restraints excluded: chain s residue 60 LEU Chi-restraints excluded: chain s residue 95 LEU Chi-restraints excluded: chain s residue 105 ASP Chi-restraints excluded: chain t residue 8 VAL Chi-restraints excluded: chain t residue 74 THR Chi-restraints excluded: chain t residue 120 SER Chi-restraints excluded: chain t residue 143 ASP Chi-restraints excluded: chain t residue 149 THR Chi-restraints excluded: chain w residue 16 ILE Chi-restraints excluded: chain w residue 38 ILE Chi-restraints excluded: chain w residue 57 VAL Chi-restraints excluded: chain w residue 60 LEU Chi-restraints excluded: chain w residue 102 ILE Chi-restraints excluded: chain w residue 149 THR Chi-restraints excluded: chain x residue 12 ILE Chi-restraints excluded: chain x residue 24 ILE Chi-restraints excluded: chain x residue 66 VAL Chi-restraints excluded: chain x residue 71 VAL Chi-restraints excluded: chain x residue 81 ASN Chi-restraints excluded: chain x residue 121 MET Chi-restraints excluded: chain x residue 134 VAL Chi-restraints excluded: chain x residue 141 VAL Chi-restraints excluded: chain x residue 172 LEU Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 166 THR Chi-restraints excluded: chain K residue 193 SER Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain K residue 307 ILE Chi-restraints excluded: chain K residue 308 ILE Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 354 LEU Chi-restraints excluded: chain K residue 425 PHE Chi-restraints excluded: chain K residue 491 ILE Chi-restraints excluded: chain K residue 517 VAL Chi-restraints excluded: chain K residue 545 GLU Chi-restraints excluded: chain K residue 558 THR Chi-restraints excluded: chain K residue 566 THR Chi-restraints excluded: chain K residue 633 ARG Chi-restraints excluded: chain K residue 638 THR Chi-restraints excluded: chain K residue 689 LEU Chi-restraints excluded: chain K residue 694 VAL Chi-restraints excluded: chain K residue 705 VAL Chi-restraints excluded: chain K residue 709 LEU Chi-restraints excluded: chain K residue 737 VAL Chi-restraints excluded: chain K residue 748 VAL Chi-restraints excluded: chain K residue 765 ILE Chi-restraints excluded: chain K residue 785 GLU Chi-restraints excluded: chain K residue 788 LEU Chi-restraints excluded: chain K residue 852 LEU Chi-restraints excluded: chain K residue 886 GLU Chi-restraints excluded: chain K residue 893 MET Chi-restraints excluded: chain K residue 919 LEU Chi-restraints excluded: chain K residue 926 VAL Chi-restraints excluded: chain Z residue 17 THR Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain Z residue 74 THR Chi-restraints excluded: chain Z residue 88 LEU Chi-restraints excluded: chain z residue 30 ILE Chi-restraints excluded: chain z residue 39 HIS Chi-restraints excluded: chain z residue 43 VAL Chi-restraints excluded: chain z residue 45 THR Chi-restraints excluded: chain z residue 60 LEU Chi-restraints excluded: chain z residue 88 LEU Chi-restraints excluded: chain z residue 132 THR Chi-restraints excluded: chain z residue 148 ILE Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 91 HIS Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain H residue 242 VAL Chi-restraints excluded: chain H residue 247 LEU Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 295 ILE Chi-restraints excluded: chain Y residue 16 ILE Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Y residue 105 ASP Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 20 VAL Chi-restraints excluded: chain y residue 38 ILE Chi-restraints excluded: chain y residue 108 ILE Chi-restraints excluded: chain y residue 149 THR Chi-restraints excluded: chain y residue 154 VAL Chi-restraints excluded: chain y residue 159 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 813 random chunks: chunk 484 optimal weight: 0.9980 chunk 312 optimal weight: 3.9990 chunk 468 optimal weight: 0.8980 chunk 236 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 151 optimal weight: 0.9990 chunk 498 optimal weight: 8.9990 chunk 533 optimal weight: 9.9990 chunk 387 optimal weight: 0.0270 chunk 73 optimal weight: 1.9990 chunk 615 optimal weight: 3.9990 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN D 203 ASN E 141 ASN F 166 ASN J 337 ASN N 53 ASN ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 GLN Q 39 HIS Q 76 GLN Q 150 GLN W 40 ASN ** m 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 29 HIS ** m 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 79 GLN q 29 HIS ** r 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 4 GLN ** s 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 76 GLN x 29 HIS K 175 HIS K 259 GLN K 344 ASN ** z 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 130 GLN H 187 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 69072 Z= 0.202 Angle : 0.695 14.207 93895 Z= 0.359 Chirality : 0.048 0.434 10992 Planarity : 0.004 0.075 11507 Dihedral : 10.840 175.345 10372 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.84 % Favored : 88.14 % Rotamer: Outliers : 3.76 % Allowed : 25.58 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.15 (0.09), residues: 8103 helix: -1.30 (0.11), residues: 2228 sheet: -1.39 (0.14), residues: 1449 loop : -2.85 (0.08), residues: 4426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 235 HIS 0.011 0.001 HIS K 175 PHE 0.037 0.001 PHE K 629 TYR 0.025 0.001 TYR p 112 ARG 0.012 0.001 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16206 Ramachandran restraints generated. 8103 Oldfield, 0 Emsley, 8103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16206 Ramachandran restraints generated. 8103 Oldfield, 0 Emsley, 8103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1676 residues out of total 7446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 1396 time to evaluate : 5.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ARG cc_start: 0.6839 (ttm110) cc_final: 0.6638 (ttm-80) REVERT: B 114 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7770 (mmt90) REVERT: I 156 GLU cc_start: 0.7470 (tt0) cc_final: 0.6950 (tt0) REVERT: J 311 ASN cc_start: 0.6799 (p0) cc_final: 0.6425 (p0) REVERT: J 400 GLU cc_start: 0.5116 (OUTLIER) cc_final: 0.4724 (tt0) REVERT: J 405 PHE cc_start: 0.6978 (OUTLIER) cc_final: 0.6073 (p90) REVERT: M 77 GLN cc_start: 0.6454 (mm110) cc_final: 0.6097 (mm110) REVERT: Q 53 ASN cc_start: 0.5846 (t0) cc_final: 0.5157 (m-40) REVERT: T 93 LEU cc_start: 0.7098 (mp) cc_final: 0.6892 (mp) REVERT: K 73 ASP cc_start: 0.4658 (OUTLIER) cc_final: 0.4320 (t0) REVERT: K 187 MET cc_start: 0.5082 (ppp) cc_final: 0.4444 (ppp) REVERT: K 188 MET cc_start: 0.5750 (tpp) cc_final: 0.5503 (mmm) REVERT: K 290 ILE cc_start: 0.6247 (OUTLIER) cc_final: 0.5588 (mt) REVERT: K 570 MET cc_start: 0.5876 (mmp) cc_final: 0.5490 (mmt) REVERT: K 738 ASN cc_start: 0.0714 (OUTLIER) cc_final: -0.0599 (t0) REVERT: z 60 LEU cc_start: 0.4616 (OUTLIER) cc_final: 0.3799 (mm) REVERT: z 144 LYS cc_start: 0.6095 (pttt) cc_final: 0.5544 (tptt) REVERT: H 254 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8384 (m) outliers start: 280 outliers final: 212 residues processed: 1587 average time/residue: 0.6401 time to fit residues: 1740.8974 Evaluate side-chains 1505 residues out of total 7446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 1285 time to evaluate : 5.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 114 ARG Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain G residue 66 ASP Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain G residue 256 CYS Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 200 PHE Chi-restraints excluded: chain I residue 252 CYS Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 111 CYS Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 356 CYS Chi-restraints excluded: chain J residue 366 VAL Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain J residue 400 GLU Chi-restraints excluded: chain J residue 405 PHE Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 121 MET Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 34 ASP Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain N residue 129 SER Chi-restraints excluded: chain N residue 132 THR Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 141 VAL Chi-restraints excluded: chain N residue 172 LEU Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 16 ILE Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain P residue 24 ILE Chi-restraints excluded: chain P residue 77 GLN Chi-restraints excluded: chain P residue 113 SER Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 30 ILE Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 119 ASN Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 132 THR Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 8 VAL Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 18 ILE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 42 LEU Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 49 VAL Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain T residue 45 THR Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 69 ILE Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 132 THR Chi-restraints excluded: chain W residue 19 ASP Chi-restraints excluded: chain W residue 30 ILE Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 97 ARG Chi-restraints excluded: chain W residue 162 ASP Chi-restraints excluded: chain X residue 16 ILE Chi-restraints excluded: chain X residue 17 THR Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain l residue 106 LEU Chi-restraints excluded: chain l residue 126 VAL Chi-restraints excluded: chain m residue 8 VAL Chi-restraints excluded: chain m residue 23 THR Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain m residue 165 GLU Chi-restraints excluded: chain n residue 16 ILE Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain n residue 166 LEU Chi-restraints excluded: chain o residue 16 ILE Chi-restraints excluded: chain o residue 59 THR Chi-restraints excluded: chain p residue 93 LEU Chi-restraints excluded: chain p residue 137 ILE Chi-restraints excluded: chain q residue 29 HIS Chi-restraints excluded: chain q residue 30 ILE Chi-restraints excluded: chain q residue 31 THR Chi-restraints excluded: chain q residue 49 VAL Chi-restraints excluded: chain q residue 56 LEU Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 113 SER Chi-restraints excluded: chain q residue 154 VAL Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 16 ILE Chi-restraints excluded: chain r residue 42 LEU Chi-restraints excluded: chain r residue 49 VAL Chi-restraints excluded: chain r residue 57 VAL Chi-restraints excluded: chain r residue 79 GLN Chi-restraints excluded: chain s residue 8 VAL Chi-restraints excluded: chain s residue 43 VAL Chi-restraints excluded: chain s residue 60 LEU Chi-restraints excluded: chain s residue 105 ASP Chi-restraints excluded: chain t residue 8 VAL Chi-restraints excluded: chain t residue 74 THR Chi-restraints excluded: chain t residue 120 SER Chi-restraints excluded: chain t residue 121 MET Chi-restraints excluded: chain t residue 149 THR Chi-restraints excluded: chain w residue 16 ILE Chi-restraints excluded: chain w residue 38 ILE Chi-restraints excluded: chain w residue 149 THR Chi-restraints excluded: chain x residue 12 ILE Chi-restraints excluded: chain x residue 24 ILE Chi-restraints excluded: chain x residue 71 VAL Chi-restraints excluded: chain x residue 121 MET Chi-restraints excluded: chain x residue 134 VAL Chi-restraints excluded: chain x residue 141 VAL Chi-restraints excluded: chain x residue 172 LEU Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 166 THR Chi-restraints excluded: chain K residue 193 SER Chi-restraints excluded: chain K residue 280 ASP Chi-restraints excluded: chain K residue 290 ILE Chi-restraints excluded: chain K residue 308 ILE Chi-restraints excluded: chain K residue 313 THR Chi-restraints excluded: chain K residue 354 LEU Chi-restraints excluded: chain K residue 390 VAL Chi-restraints excluded: chain K residue 425 PHE Chi-restraints excluded: chain K residue 470 LEU Chi-restraints excluded: chain K residue 491 ILE Chi-restraints excluded: chain K residue 517 VAL Chi-restraints excluded: chain K residue 528 MET Chi-restraints excluded: chain K residue 545 GLU Chi-restraints excluded: chain K residue 551 VAL Chi-restraints excluded: chain K residue 558 THR Chi-restraints excluded: chain K residue 566 THR Chi-restraints excluded: chain K residue 633 ARG Chi-restraints excluded: chain K residue 689 LEU Chi-restraints excluded: chain K residue 694 VAL Chi-restraints excluded: chain K residue 709 LEU Chi-restraints excluded: chain K residue 737 VAL Chi-restraints excluded: chain K residue 738 ASN Chi-restraints excluded: chain K residue 748 VAL Chi-restraints excluded: chain K residue 785 GLU Chi-restraints excluded: chain K residue 788 LEU Chi-restraints excluded: chain K residue 886 GLU Chi-restraints excluded: chain K residue 893 MET Chi-restraints excluded: chain K residue 919 LEU Chi-restraints excluded: chain K residue 926 VAL Chi-restraints excluded: chain Z residue 17 THR Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain Z residue 74 THR Chi-restraints excluded: chain Z residue 88 LEU Chi-restraints excluded: chain z residue 30 ILE Chi-restraints excluded: chain z residue 39 HIS Chi-restraints excluded: chain z residue 43 VAL Chi-restraints excluded: chain z residue 45 THR Chi-restraints excluded: chain z residue 60 LEU Chi-restraints excluded: chain z residue 88 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain H residue 242 VAL Chi-restraints excluded: chain H residue 247 LEU Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 295 ILE Chi-restraints excluded: chain Y residue 16 ILE Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Y residue 105 ASP Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 20 VAL Chi-restraints excluded: chain y residue 38 ILE Chi-restraints excluded: chain y residue 108 ILE Chi-restraints excluded: chain y residue 149 THR Chi-restraints excluded: chain y residue 154 VAL Chi-restraints excluded: chain y residue 159 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 813 random chunks: chunk 712 optimal weight: 5.9990 chunk 750 optimal weight: 0.9980 chunk 684 optimal weight: 9.9990 chunk 730 optimal weight: 20.0000 chunk 439 optimal weight: 7.9990 chunk 318 optimal weight: 0.3980 chunk 573 optimal weight: 9.9990 chunk 224 optimal weight: 3.9990 chunk 659 optimal weight: 3.9990 chunk 690 optimal weight: 2.9990 chunk 727 optimal weight: 8.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN D 203 ASN ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 ASN J 220 HIS J 337 ASN P 77 GLN ** R 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 29 HIS ** m 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 147 ASN n 4 GLN ** n 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 29 HIS ** r 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 4 GLN ** s 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 175 HIS ** z 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 130 GLN ** H 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 69072 Z= 0.323 Angle : 0.733 16.577 93895 Z= 0.378 Chirality : 0.049 0.409 10992 Planarity : 0.005 0.080 11507 Dihedral : 10.812 174.093 10370 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 12.83 % Favored : 87.14 % Rotamer: Outliers : 3.80 % Allowed : 26.11 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.13 (0.09), residues: 8103 helix: -1.33 (0.11), residues: 2238 sheet: -1.42 (0.14), residues: 1477 loop : -2.81 (0.08), residues: 4388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 770 HIS 0.008 0.001 HIS K 175 PHE 0.030 0.002 PHE K 629 TYR 0.031 0.002 TYR m 112 ARG 0.014 0.001 ARG F 65 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16206 Ramachandran restraints generated. 8103 Oldfield, 0 Emsley, 8103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16206 Ramachandran restraints generated. 8103 Oldfield, 0 Emsley, 8103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1556 residues out of total 7446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 1273 time to evaluate : 5.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ARG cc_start: 0.6975 (ttm110) cc_final: 0.6741 (ttm-80) REVERT: B 114 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7716 (mmt90) REVERT: I 3 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7786 (tt) REVERT: J 311 ASN cc_start: 0.6888 (p0) cc_final: 0.6550 (p0) REVERT: J 405 PHE cc_start: 0.7036 (OUTLIER) cc_final: 0.6101 (p90) REVERT: O 55 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.6346 (mmt90) REVERT: T 56 LEU cc_start: 0.6879 (mt) cc_final: 0.6533 (mt) REVERT: W 16 ILE cc_start: 0.4248 (OUTLIER) cc_final: 0.3801 (mt) REVERT: K 73 ASP cc_start: 0.4908 (OUTLIER) cc_final: 0.4549 (t0) REVERT: K 187 MET cc_start: 0.5187 (ppp) cc_final: 0.4673 (ppp) REVERT: K 570 MET cc_start: 0.5937 (mmp) cc_final: 0.5557 (mmt) REVERT: K 738 ASN cc_start: 0.0787 (OUTLIER) cc_final: -0.0624 (t0) REVERT: Z 164 LYS cc_start: 0.5164 (mmtt) cc_final: 0.4812 (mttt) REVERT: z 60 LEU cc_start: 0.4695 (OUTLIER) cc_final: 0.3900 (mm) REVERT: z 144 LYS cc_start: 0.6109 (pttt) cc_final: 0.5572 (tptt) REVERT: H 254 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.8438 (m) outliers start: 283 outliers final: 232 residues processed: 1468 average time/residue: 0.6435 time to fit residues: 1623.5795 Evaluate side-chains 1462 residues out of total 7446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1221 time to evaluate : 5.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 114 ARG Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain G residue 66 ASP Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain G residue 256 CYS Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain I residue 182 GLU Chi-restraints excluded: chain I residue 200 PHE Chi-restraints excluded: chain I residue 252 CYS Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 111 CYS Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 356 CYS Chi-restraints excluded: chain J residue 366 VAL Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain J residue 405 PHE Chi-restraints excluded: chain J residue 454 SER Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 34 ASP Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain N residue 129 SER Chi-restraints excluded: chain N residue 132 THR Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 141 VAL Chi-restraints excluded: chain N residue 172 LEU Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain P residue 16 ILE Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain P residue 24 ILE Chi-restraints excluded: chain P residue 113 SER Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 119 ASN Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 132 THR Chi-restraints excluded: chain Q residue 168 SER Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain R residue 108 ILE Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 8 VAL Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 18 ILE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 42 LEU Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 49 VAL Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 121 MET Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain T residue 45 THR Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 63 CYS Chi-restraints excluded: chain T residue 69 ILE Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 132 THR Chi-restraints excluded: chain W residue 16 ILE Chi-restraints excluded: chain W residue 19 ASP Chi-restraints excluded: chain W residue 30 ILE Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 97 ARG Chi-restraints excluded: chain W residue 103 SER Chi-restraints excluded: chain X residue 16 ILE Chi-restraints excluded: chain X residue 17 THR Chi-restraints excluded: chain X residue 33 ILE Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain l residue 86 LEU Chi-restraints excluded: chain l residue 106 LEU Chi-restraints excluded: chain l residue 126 VAL Chi-restraints excluded: chain m residue 8 VAL Chi-restraints excluded: chain m residue 23 THR Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain m residue 165 GLU Chi-restraints excluded: chain n residue 16 ILE Chi-restraints excluded: chain n residue 23 THR Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain n residue 165 GLU Chi-restraints excluded: chain o residue 16 ILE Chi-restraints excluded: chain o residue 59 THR Chi-restraints excluded: chain o residue 96 ILE Chi-restraints excluded: chain p residue 137 ILE Chi-restraints excluded: chain q residue 29 HIS Chi-restraints excluded: chain q residue 30 ILE Chi-restraints excluded: chain q residue 31 THR Chi-restraints excluded: chain q residue 49 VAL Chi-restraints excluded: chain q residue 56 LEU Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 113 SER Chi-restraints excluded: chain q residue 154 VAL Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 16 ILE Chi-restraints excluded: chain r residue 38 ILE Chi-restraints excluded: chain r residue 42 LEU Chi-restraints excluded: chain r residue 49 VAL Chi-restraints excluded: chain r residue 57 VAL Chi-restraints excluded: chain r residue 88 LEU Chi-restraints excluded: chain s residue 8 VAL Chi-restraints excluded: chain s residue 43 VAL Chi-restraints excluded: chain s residue 60 LEU Chi-restraints excluded: chain s residue 86 LEU Chi-restraints excluded: chain s residue 105 ASP Chi-restraints excluded: chain t residue 8 VAL Chi-restraints excluded: chain t residue 70 LEU Chi-restraints excluded: chain t residue 74 THR Chi-restraints excluded: chain t residue 120 SER Chi-restraints excluded: chain t residue 121 MET Chi-restraints excluded: chain t residue 149 THR Chi-restraints excluded: chain w residue 16 ILE Chi-restraints excluded: chain w residue 57 VAL Chi-restraints excluded: chain w residue 149 THR Chi-restraints excluded: chain x residue 12 ILE Chi-restraints excluded: chain x residue 24 ILE Chi-restraints excluded: chain x residue 71 VAL Chi-restraints excluded: chain x residue 121 MET Chi-restraints excluded: chain x residue 134 VAL Chi-restraints excluded: chain x residue 141 VAL Chi-restraints excluded: chain x residue 172 LEU Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 166 THR Chi-restraints excluded: chain K residue 193 SER Chi-restraints excluded: chain K residue 280 ASP Chi-restraints excluded: chain K residue 290 ILE Chi-restraints excluded: chain K residue 308 ILE Chi-restraints excluded: chain K residue 354 LEU Chi-restraints excluded: chain K residue 390 VAL Chi-restraints excluded: chain K residue 425 PHE Chi-restraints excluded: chain K residue 470 LEU Chi-restraints excluded: chain K residue 491 ILE Chi-restraints excluded: chain K residue 517 VAL Chi-restraints excluded: chain K residue 545 GLU Chi-restraints excluded: chain K residue 551 VAL Chi-restraints excluded: chain K residue 558 THR Chi-restraints excluded: chain K residue 566 THR Chi-restraints excluded: chain K residue 633 ARG Chi-restraints excluded: chain K residue 638 THR Chi-restraints excluded: chain K residue 689 LEU Chi-restraints excluded: chain K residue 694 VAL Chi-restraints excluded: chain K residue 709 LEU Chi-restraints excluded: chain K residue 737 VAL Chi-restraints excluded: chain K residue 738 ASN Chi-restraints excluded: chain K residue 748 VAL Chi-restraints excluded: chain K residue 785 GLU Chi-restraints excluded: chain K residue 788 LEU Chi-restraints excluded: chain K residue 886 GLU Chi-restraints excluded: chain K residue 893 MET Chi-restraints excluded: chain K residue 919 LEU Chi-restraints excluded: chain K residue 926 VAL Chi-restraints excluded: chain K residue 954 ILE Chi-restraints excluded: chain K residue 977 LEU Chi-restraints excluded: chain Z residue 17 THR Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain Z residue 88 LEU Chi-restraints excluded: chain z residue 30 ILE Chi-restraints excluded: chain z residue 39 HIS Chi-restraints excluded: chain z residue 43 VAL Chi-restraints excluded: chain z residue 45 THR Chi-restraints excluded: chain z residue 60 LEU Chi-restraints excluded: chain z residue 88 LEU Chi-restraints excluded: chain z residue 148 ILE Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain H residue 242 VAL Chi-restraints excluded: chain H residue 247 LEU Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain Y residue 16 ILE Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Y residue 105 ASP Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 20 VAL Chi-restraints excluded: chain y residue 38 ILE Chi-restraints excluded: chain y residue 70 LEU Chi-restraints excluded: chain y residue 108 ILE Chi-restraints excluded: chain y residue 149 THR Chi-restraints excluded: chain y residue 154 VAL Chi-restraints excluded: chain y residue 159 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 813 random chunks: chunk 479 optimal weight: 5.9990 chunk 772 optimal weight: 0.5980 chunk 471 optimal weight: 0.9980 chunk 366 optimal weight: 0.0040 chunk 536 optimal weight: 10.0000 chunk 809 optimal weight: 9.9990 chunk 745 optimal weight: 8.9990 chunk 644 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 498 optimal weight: 0.1980 chunk 395 optimal weight: 7.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 203 ASN J 337 ASN J 440 ASN O 119 ASN ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 29 HIS ** m 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 4 GLN ** n 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 53 ASN q 29 HIS ** r 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 4 GLN ** s 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 175 HIS K 420 GLN ** z 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 130 GLN Y 32 ASN ** Y 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 69072 Z= 0.199 Angle : 0.717 16.278 93895 Z= 0.368 Chirality : 0.048 0.397 10992 Planarity : 0.004 0.081 11507 Dihedral : 10.764 175.374 10370 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.69 % Favored : 88.28 % Rotamer: Outliers : 3.04 % Allowed : 26.89 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.01 (0.09), residues: 8103 helix: -1.20 (0.11), residues: 2214 sheet: -1.24 (0.14), residues: 1447 loop : -2.78 (0.08), residues: 4442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 235 HIS 0.014 0.001 HIS q 29 PHE 0.049 0.001 PHE J 123 TYR 0.052 0.001 TYR n 112 ARG 0.013 0.001 ARG F 65 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16206 Ramachandran restraints generated. 8103 Oldfield, 0 Emsley, 8103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16206 Ramachandran restraints generated. 8103 Oldfield, 0 Emsley, 8103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1581 residues out of total 7446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1355 time to evaluate : 5.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 156 GLU cc_start: 0.7482 (tt0) cc_final: 0.6957 (tt0) REVERT: J 405 PHE cc_start: 0.6888 (OUTLIER) cc_final: 0.5972 (p90) REVERT: Q 77 GLN cc_start: 0.6319 (pm20) cc_final: 0.6104 (pm20) REVERT: W 16 ILE cc_start: 0.4112 (OUTLIER) cc_final: 0.3574 (mt) REVERT: K 187 MET cc_start: 0.5429 (ppp) cc_final: 0.4546 (ppp) REVERT: K 738 ASN cc_start: 0.0271 (OUTLIER) cc_final: -0.0759 (t0) REVERT: Z 164 LYS cc_start: 0.5052 (mmtt) cc_final: 0.4801 (mttt) REVERT: z 60 LEU cc_start: 0.4601 (OUTLIER) cc_final: 0.3801 (mm) REVERT: z 144 LYS cc_start: 0.6084 (pttt) cc_final: 0.5632 (tptt) REVERT: H 254 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8361 (m) outliers start: 226 outliers final: 197 residues processed: 1515 average time/residue: 0.7009 time to fit residues: 1830.6349 Evaluate side-chains 1490 residues out of total 7446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1288 time to evaluate : 5.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain G residue 66 ASP Chi-restraints excluded: chain G residue 141 ASN Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain G residue 256 CYS Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 200 PHE Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 111 CYS Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 356 CYS Chi-restraints excluded: chain J residue 366 VAL Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain J residue 405 PHE Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 34 ASP Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain N residue 132 THR Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 141 VAL Chi-restraints excluded: chain N residue 149 THR Chi-restraints excluded: chain N residue 172 LEU Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain P residue 16 ILE Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain P residue 24 ILE Chi-restraints excluded: chain P residue 113 SER Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 119 ASN Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 132 THR Chi-restraints excluded: chain Q residue 168 SER Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain S residue 8 VAL Chi-restraints excluded: chain S residue 9 PHE Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 18 ILE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 42 LEU Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 49 VAL Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 121 MET Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain T residue 45 THR Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 63 CYS Chi-restraints excluded: chain T residue 69 ILE Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 132 THR Chi-restraints excluded: chain W residue 16 ILE Chi-restraints excluded: chain W residue 17 THR Chi-restraints excluded: chain W residue 19 ASP Chi-restraints excluded: chain W residue 30 ILE Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain X residue 16 ILE Chi-restraints excluded: chain X residue 17 THR Chi-restraints excluded: chain X residue 33 ILE Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 165 GLU Chi-restraints excluded: chain l residue 86 LEU Chi-restraints excluded: chain l residue 106 LEU Chi-restraints excluded: chain l residue 126 VAL Chi-restraints excluded: chain m residue 8 VAL Chi-restraints excluded: chain m residue 23 THR Chi-restraints excluded: chain m residue 29 HIS Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain m residue 165 GLU Chi-restraints excluded: chain n residue 16 ILE Chi-restraints excluded: chain n residue 23 THR Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain n residue 112 TYR Chi-restraints excluded: chain n residue 172 LEU Chi-restraints excluded: chain n residue 173 GLU Chi-restraints excluded: chain o residue 16 ILE Chi-restraints excluded: chain o residue 59 THR Chi-restraints excluded: chain p residue 137 ILE Chi-restraints excluded: chain q residue 29 HIS Chi-restraints excluded: chain q residue 31 THR Chi-restraints excluded: chain q residue 49 VAL Chi-restraints excluded: chain q residue 56 LEU Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 154 VAL Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 16 ILE Chi-restraints excluded: chain r residue 42 LEU Chi-restraints excluded: chain r residue 49 VAL Chi-restraints excluded: chain r residue 57 VAL Chi-restraints excluded: chain r residue 88 LEU Chi-restraints excluded: chain s residue 8 VAL Chi-restraints excluded: chain s residue 43 VAL Chi-restraints excluded: chain s residue 60 LEU Chi-restraints excluded: chain s residue 86 LEU Chi-restraints excluded: chain t residue 8 VAL Chi-restraints excluded: chain t residue 70 LEU Chi-restraints excluded: chain t residue 74 THR Chi-restraints excluded: chain t residue 120 SER Chi-restraints excluded: chain t residue 149 THR Chi-restraints excluded: chain w residue 16 ILE Chi-restraints excluded: chain w residue 44 ILE Chi-restraints excluded: chain w residue 149 THR Chi-restraints excluded: chain x residue 12 ILE Chi-restraints excluded: chain x residue 24 ILE Chi-restraints excluded: chain x residue 71 VAL Chi-restraints excluded: chain x residue 121 MET Chi-restraints excluded: chain x residue 134 VAL Chi-restraints excluded: chain x residue 141 VAL Chi-restraints excluded: chain x residue 172 LEU Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain K residue 166 THR Chi-restraints excluded: chain K residue 193 SER Chi-restraints excluded: chain K residue 280 ASP Chi-restraints excluded: chain K residue 308 ILE Chi-restraints excluded: chain K residue 390 VAL Chi-restraints excluded: chain K residue 425 PHE Chi-restraints excluded: chain K residue 470 LEU Chi-restraints excluded: chain K residue 491 ILE Chi-restraints excluded: chain K residue 517 VAL Chi-restraints excluded: chain K residue 551 VAL Chi-restraints excluded: chain K residue 566 THR Chi-restraints excluded: chain K residue 638 THR Chi-restraints excluded: chain K residue 694 VAL Chi-restraints excluded: chain K residue 709 LEU Chi-restraints excluded: chain K residue 737 VAL Chi-restraints excluded: chain K residue 738 ASN Chi-restraints excluded: chain K residue 748 VAL Chi-restraints excluded: chain K residue 785 GLU Chi-restraints excluded: chain K residue 788 LEU Chi-restraints excluded: chain K residue 886 GLU Chi-restraints excluded: chain K residue 893 MET Chi-restraints excluded: chain K residue 919 LEU Chi-restraints excluded: chain K residue 926 VAL Chi-restraints excluded: chain K residue 1013 TYR Chi-restraints excluded: chain Z residue 17 THR Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain Z residue 88 LEU Chi-restraints excluded: chain z residue 39 HIS Chi-restraints excluded: chain z residue 43 VAL Chi-restraints excluded: chain z residue 45 THR Chi-restraints excluded: chain z residue 60 LEU Chi-restraints excluded: chain z residue 88 LEU Chi-restraints excluded: chain z residue 148 ILE Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain H residue 242 VAL Chi-restraints excluded: chain H residue 247 LEU Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain Y residue 16 ILE Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Y residue 105 ASP Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 20 VAL Chi-restraints excluded: chain y residue 38 ILE Chi-restraints excluded: chain y residue 108 ILE Chi-restraints excluded: chain y residue 149 THR Chi-restraints excluded: chain y residue 154 VAL Chi-restraints excluded: chain y residue 159 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 813 random chunks: chunk 512 optimal weight: 4.9990 chunk 687 optimal weight: 7.9990 chunk 197 optimal weight: 4.9990 chunk 594 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 179 optimal weight: 0.5980 chunk 645 optimal weight: 0.9990 chunk 270 optimal weight: 8.9990 chunk 663 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN D 203 ASN E 17 HIS G 177 ASN J 337 ASN ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 4 GLN ** n 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 29 HIS ** q 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 4 GLN ** s 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 175 HIS K 387 ASN K 420 GLN ** z 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 130 GLN ** H 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 32 ASN ** Y 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.170943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.112158 restraints weight = 114893.723| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 4.18 r_work: 0.3172 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 69072 Z= 0.201 Angle : 0.712 15.919 93895 Z= 0.365 Chirality : 0.048 0.389 10992 Planarity : 0.004 0.081 11507 Dihedral : 10.687 175.904 10370 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.59 % Favored : 88.39 % Rotamer: Outliers : 2.97 % Allowed : 27.25 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.96 (0.09), residues: 8103 helix: -1.18 (0.11), residues: 2221 sheet: -1.19 (0.14), residues: 1447 loop : -2.74 (0.08), residues: 4435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 224 HIS 0.017 0.001 HIS m 29 PHE 0.048 0.001 PHE J 123 TYR 0.051 0.001 TYR n 112 ARG 0.013 0.001 ARG F 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25695.87 seconds wall clock time: 441 minutes 11.98 seconds (26471.98 seconds total)