Starting phenix.real_space_refine on Fri Sep 27 20:49:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sh8_10196/09_2024/6sh8_10196.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sh8_10196/09_2024/6sh8_10196.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sh8_10196/09_2024/6sh8_10196.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sh8_10196/09_2024/6sh8_10196.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sh8_10196/09_2024/6sh8_10196.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sh8_10196/09_2024/6sh8_10196.cif" } resolution = 3.14 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= 0.610 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 83 5.49 5 S 111 5.16 5 C 43037 2.51 5 N 11116 2.21 5 O 13126 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 391 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: 67477 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: 1235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1235 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 2, 'TRANS': 148} 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: 2258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2258 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 10, 'TRANS': 272} Chain: "H" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2528 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 302} 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: 3833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3833 Classifications: {'peptide': 467} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 461} Chain breaks: 1 Chain: "K" Number of atoms: 8418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 8418 Classifications: {'peptide': 1024} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 988} Chain breaks: 1 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: "U" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 668 Inner-chain residues flagged as termini: ['pdbres=" U U 36 "'] Classifications: {'RNA': 32} Modifications used: {'5*END': 2, 'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 11, 'rna3p_pyr': 17} Link IDs: {'rna2p': 4, 'rna3p': 27} Chain: "V" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 1025 Classifications: {'RNA': 48} Modifications used: {'5*END': 1, 'rna2p_pur': 12, 'rna2p_pyr': 7, 'rna3p_pur': 17, 'rna3p_pyr': 12} Link IDs: {'rna2p': 19, 'rna3p': 28} 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: "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 25242 SG CYS K 464 79.191 105.660 41.606 1.00 30.02 S ATOM 25261 SG CYS K 467 79.653 101.763 40.630 1.00 26.86 S ATOM 25609 SG CYS K 512 77.673 103.636 38.641 1.00 43.48 S ATOM 25636 SG CYS K 515 76.728 103.318 40.742 1.00 39.54 S Time building chain proxies: 29.41, per 1000 atoms: 0.44 Number of scatterers: 67477 At special positions: 0 Unit cell: (163.904, 172.224, 248.768, 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 83 15.00 O 13126 8.00 N 11116 7.00 C 43037 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=2.04 Simple disulfide: pdb=" SG CYS B 115 " - pdb=" SG CYS Q 63 " distance=2.04 Simple disulfide: pdb=" SG CYS C 115 " - pdb=" SG CYS S 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=2.03 Simple disulfide: pdb=" SG CYS G 256 " - pdb=" SG CYS N 63 " distance=2.03 Simple disulfide: pdb=" SG CYS H 304 " - pdb=" SG CYS x 63 " distance=2.04 Simple disulfide: pdb=" SG CYS I 252 " - pdb=" SG CYS p 63 " distance=2.03 Simple disulfide: pdb=" SG CYS J 111 " - pdb=" SG CYS t 63 " distance=2.03 Simple disulfide: pdb=" SG CYS J 262 " - pdb=" SG CYS J 268 " distance=2.01 Simple disulfide: pdb=" SG CYS J 356 " - pdb=" SG CYS J 474 " distance=2.03 Simple disulfide: pdb=" SG CYS J 396 " - pdb=" SG CYS J 399 " distance=2.03 Simple disulfide: pdb=" SG CYS J 466 " - pdb=" SG CYS w 63 " distance=2.04 Simple disulfide: pdb=" SG CYS K 578 " - pdb=" SG CYS K 587 " distance=2.03 Simple disulfide: pdb=" SG CYS K 711 " - pdb=" SG CYS K 721 " distance=2.03 Simple disulfide: pdb=" SG CYS K 836 " - pdb=" SG CYS Y 63 " distance=2.05 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: 12.58 Conformation dependent library (CDL) restraints added in 6.5 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 467 " pdb="ZN ZN K1101 " - pdb=" SG CYS K 512 " pdb="ZN ZN K1101 " - pdb=" SG CYS K 515 " Number of angles added : 6 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: 15592 Finding SS restraints... Secondary structure from input PDB file: 207 helices and 0 sheets defined 24.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.66 Creating SS restraints... Processing helix chain 'A' and resid 4 through 20 removed outlier: 3.612A pdb=" N LEU A 9 " --> pdb=" O ASP A 6 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ALA A 10 " --> pdb=" O TYR A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 44 removed outlier: 3.805A pdb=" N SER A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL A 38 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLU A 39 " --> pdb=" O ARG A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 57 removed outlier: 3.784A pdb=" N LYS A 56 " --> pdb=" O TYR A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 72 removed outlier: 3.738A pdb=" N LEU A 67 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 70 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 100 removed outlier: 3.616A pdb=" N SER A 88 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 118 through 151 Proline residue: A 131 - end of helix removed outlier: 3.654A pdb=" N ALA A 135 " --> pdb=" O PRO A 131 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ARG A 138 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N THR A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TYR A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 12 removed outlier: 3.943A pdb=" N ALA B 10 " --> pdb=" O TYR B 7 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU B 12 " --> pdb=" O LEU B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 41 Processing helix chain 'B' and resid 46 through 56 removed outlier: 3.536A pdb=" N TYR B 52 " --> pdb=" O PRO B 48 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS B 56 " --> pdb=" O TYR B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 71 removed outlier: 5.519A pdb=" N LEU B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N PHE B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 100 Processing helix chain 'B' and resid 106 through 112 Processing helix chain 'B' and resid 116 through 150 removed outlier: 3.513A pdb=" N ARG B 119 " --> pdb=" O GLU B 116 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU B 120 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA B 130 " --> pdb=" O TYR B 127 " (cutoff:3.500A) Proline residue: B 131 - end of helix removed outlier: 4.161A pdb=" N ILE B 137 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 138 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR B 139 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA B 143 " --> pdb=" O TYR B 140 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER B 148 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 150 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 18 removed outlier: 3.525A pdb=" N LYS C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 44 removed outlier: 3.771A pdb=" N ASP C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL C 38 " --> pdb=" O ALA C 34 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N GLU C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR C 42 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 56 Processing helix chain 'C' and resid 62 through 72 removed outlier: 3.506A pdb=" N SER C 66 " --> pdb=" O ASP C 62 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU C 67 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER C 72 " --> pdb=" O ILE C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 100 Processing helix chain 'C' and resid 106 through 114 removed outlier: 3.655A pdb=" N ARG C 114 " --> pdb=" O ILE C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 128 removed outlier: 4.222A 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 137 through 151 Processing helix chain 'D' and resid 46 through 60 removed outlier: 3.768A pdb=" N LYS D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 72 Processing helix chain 'D' and resid 115 through 128 Processing helix chain 'D' and resid 139 through 149 removed outlier: 4.378A pdb=" N LYS D 149 " --> pdb=" O THR D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 167 No H-bonds generated for 'chain 'D' and resid 165 through 167' Processing helix chain 'D' and resid 195 through 203 removed outlier: 4.761A pdb=" N GLU D 200 " --> pdb=" O SER D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 260 removed outlier: 4.821A pdb=" N LEU D 258 " --> pdb=" O ALA D 254 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ARG D 259 " --> pdb=" O SER D 255 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN D 260 " --> pdb=" O CYS D 256 " (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 'E' and resid 46 through 60 removed outlier: 3.880A pdb=" N LYS E 59 " --> pdb=" O SER E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 115 through 130 removed outlier: 3.847A pdb=" N LYS E 120 " --> pdb=" O GLU E 116 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN E 130 " --> pdb=" O ASP E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 149 removed outlier: 4.150A pdb=" N LYS E 149 " --> pdb=" O THR E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 167 No H-bonds generated for 'chain 'E' and resid 165 through 167' Processing helix chain 'E' and resid 195 through 205 removed outlier: 4.002A 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 270 through 272 No H-bonds generated for 'chain 'E' and resid 270 through 272' 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: 3.608A pdb=" N SER F 55 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS F 59 " --> pdb=" O SER F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 71 removed outlier: 4.058A pdb=" N ARG F 65 " --> pdb=" O PRO F 62 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASP F 66 " --> pdb=" O ASP F 63 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE F 68 " --> pdb=" O ARG F 65 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR F 69 " --> pdb=" O ASP F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 130 removed outlier: 4.127A pdb=" N LYS F 120 " --> pdb=" O GLU F 116 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU F 123 " --> pdb=" O LYS F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 149 removed outlier: 3.974A pdb=" N THR F 145 " --> pdb=" O ASN F 141 " (cutoff:3.500A) removed outlier: 3.924A 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: 3.828A pdb=" N GLU F 200 " --> pdb=" O SER F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 256 removed outlier: 3.635A pdb=" N SER F 255 " --> pdb=" O ALA F 251 " (cutoff:3.500A) 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 removed outlier: 3.627A pdb=" N LYS G 59 " --> pdb=" O SER G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 71 removed outlier: 3.715A pdb=" N ILE G 68 " --> pdb=" O ARG G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 129 removed outlier: 3.719A pdb=" N ILE G 128 " --> pdb=" O TYR G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 149 removed outlier: 4.281A pdb=" N LYS G 142 " --> pdb=" O ASN G 138 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS G 149 " --> pdb=" O THR G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 167 No H-bonds generated for 'chain 'G' and resid 165 through 167' Processing helix chain 'G' and resid 195 through 205 removed outlier: 3.598A pdb=" N ARG G 199 " --> pdb=" O ASP G 195 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN G 203 " --> pdb=" O ARG G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 253 No H-bonds generated for 'chain 'G' and resid 250 through 253' Processing helix chain 'G' and resid 257 through 260 No H-bonds generated for 'chain 'G' and resid 257 through 260' Processing helix chain 'H' and resid 39 through 49 Processing helix chain 'H' and resid 62 through 65 No H-bonds generated for 'chain 'H' and resid 62 through 65' 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 101 through 108 Proline residue: H 104 - end of helix removed outlier: 3.631A pdb=" N LEU H 107 " --> pdb=" O PRO H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 123 Processing helix chain 'H' and resid 128 through 131 No H-bonds generated for 'chain 'H' and resid 128 through 131' Processing helix chain 'H' and resid 226 through 235 removed outlier: 3.923A pdb=" N ASP H 231 " --> pdb=" O ASP H 227 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ASN H 232 " --> pdb=" O ASN H 228 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N SER H 234 " --> pdb=" O LEU H 230 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASP H 235 " --> pdb=" O ASP H 231 " (cutoff:3.500A) Processing helix chain 'H' and resid 271 through 279 removed outlier: 4.490A pdb=" N ASP H 275 " --> pdb=" O SER H 272 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE H 277 " --> pdb=" O ILE H 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 283 through 295 removed outlier: 3.874A pdb=" N LYS H 291 " --> pdb=" O TYR H 287 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 7 Processing helix chain 'I' and resid 9 through 16 Processing helix chain 'I' and resid 22 through 39 removed outlier: 3.998A pdb=" N ILE I 31 " --> pdb=" O SER I 27 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLY I 37 " --> pdb=" O TYR I 33 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLU I 38 " --> pdb=" O ASN I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 57 Processing helix chain 'I' and resid 65 through 87 removed outlier: 3.536A pdb=" N VAL I 69 " --> pdb=" O LYS I 65 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASN I 74 " --> pdb=" O GLU I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 109 Processing helix chain 'I' and resid 154 through 168 Processing helix chain 'I' and resid 170 through 178 removed outlier: 3.518A pdb=" N GLU I 175 " --> pdb=" O GLU I 171 " (cutoff:3.500A) Processing helix chain 'I' and resid 245 through 258 Proline residue: I 250 - end of helix removed outlier: 3.927A pdb=" N ASP I 253 " --> pdb=" O PRO I 250 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER I 254 " --> pdb=" O ILE I 251 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N MET I 255 " --> pdb=" O CYS I 252 " (cutoff:3.500A) 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 56 removed outlier: 3.509A pdb=" N ASN J 51 " --> pdb=" O ARG J 47 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR J 55 " --> pdb=" O ASN J 51 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 75 removed outlier: 5.252A pdb=" N ASP J 73 " --> pdb=" O ARG J 69 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N VAL J 74 " --> pdb=" O LEU J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 110 Processing helix chain 'J' and resid 150 through 158 Processing helix chain 'J' and resid 162 through 167 removed outlier: 4.539A pdb=" N LEU J 167 " --> pdb=" O SER J 163 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 200 removed outlier: 4.111A 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 279 removed outlier: 6.756A pdb=" N LYS J 270 " --> pdb=" O SER J 266 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ILE J 271 " --> pdb=" O ILE J 267 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE J 278 " --> pdb=" O LEU J 274 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU J 279 " --> pdb=" O ALA J 275 " (cutoff:3.500A) Processing helix chain 'J' and resid 284 through 297 removed outlier: 3.988A pdb=" N LYS J 288 " --> pdb=" O GLY J 284 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER J 289 " --> pdb=" O ASN J 285 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE J 294 " --> pdb=" O LYS J 290 " (cutoff:3.500A) Processing helix chain 'J' and resid 339 through 349 removed outlier: 4.743A pdb=" N TYR J 347 " --> pdb=" O LEU J 343 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LYS J 348 " --> pdb=" O ALA J 344 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA J 349 " --> pdb=" O ASN J 345 " (cutoff:3.500A) Processing helix chain 'J' and resid 355 through 358 No H-bonds generated for 'chain 'J' and resid 355 through 358' Processing helix chain 'J' and resid 367 through 373 Processing helix chain 'J' and resid 392 through 395 No H-bonds generated for 'chain 'J' and resid 392 through 395' Processing helix chain 'J' and resid 418 through 421 No H-bonds generated for 'chain 'J' and resid 418 through 421' Processing helix chain 'J' and resid 461 through 474 Processing helix chain 'K' and resid 14 through 17 No H-bonds generated for 'chain 'K' and resid 14 through 17' Processing helix chain 'K' and resid 25 through 28 No H-bonds generated for 'chain 'K' and resid 25 through 28' Processing helix chain 'K' and resid 36 through 39 No H-bonds generated for 'chain 'K' and resid 36 through 39' Processing helix chain 'K' and resid 50 through 56 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 123 through 135 removed outlier: 3.578A pdb=" N LEU K 134 " --> pdb=" O GLU K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 143 through 160 removed outlier: 3.899A pdb=" N TYR K 147 " --> pdb=" O LEU K 143 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU K 152 " --> pdb=" O GLN K 148 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N GLU K 155 " --> pdb=" O TYR K 151 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU K 156 " --> pdb=" O LEU K 152 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TRP K 158 " --> pdb=" O TYR K 154 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 195 removed outlier: 3.574A pdb=" N ASN K 189 " --> pdb=" O ALA K 185 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TRP K 190 " --> pdb=" O ALA K 186 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER K 193 " --> pdb=" O ASN K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 214 Processing helix chain 'K' and resid 220 through 244 removed outlier: 3.945A pdb=" N ILE K 225 " --> pdb=" O ARG K 221 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU K 234 " --> pdb=" O VAL K 230 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TRP K 240 " --> pdb=" O TYR K 236 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE K 241 " --> pdb=" O VAL K 237 " (cutoff:3.500A) Processing helix chain 'K' and resid 255 through 257 No H-bonds generated for 'chain 'K' and resid 255 through 257' Processing helix chain 'K' and resid 259 through 270 Processing helix chain 'K' and resid 279 through 288 removed outlier: 4.044A pdb=" N LEU K 285 " --> pdb=" O GLU K 281 " (cutoff:3.500A) Processing helix chain 'K' and resid 296 through 299 No H-bonds generated for 'chain 'K' and resid 296 through 299' Processing helix chain 'K' and resid 334 through 361 removed outlier: 3.510A pdb=" N LYS K 361 " --> pdb=" O TYR K 357 " (cutoff:3.500A) Processing helix chain 'K' and resid 366 through 374 Processing helix chain 'K' and resid 378 through 381 No H-bonds generated for 'chain 'K' and resid 378 through 381' Processing helix chain 'K' and resid 397 through 400 No H-bonds generated for 'chain 'K' and resid 397 through 400' Processing helix chain 'K' and resid 412 through 430 removed outlier: 3.570A pdb=" N SER K 423 " --> pdb=" O ARG K 419 " (cutoff:3.500A) Processing helix chain 'K' and resid 435 through 438 Processing helix chain 'K' and resid 442 through 447 Processing helix chain 'K' and resid 483 through 486 No H-bonds generated for 'chain 'K' and resid 483 through 486' Processing helix chain 'K' and resid 497 through 501 Processing helix chain 'K' and resid 513 through 523 Processing helix chain 'K' and resid 527 through 533 removed outlier: 4.482A pdb=" N LEU K 533 " --> pdb=" O ILE K 530 " (cutoff:3.500A) Processing helix chain 'K' and resid 539 through 546 Processing helix chain 'K' and resid 558 through 562 Processing helix chain 'K' and resid 564 through 571 Processing helix chain 'K' and resid 574 through 579 Processing helix chain 'K' and resid 599 through 603 Processing helix chain 'K' and resid 615 through 618 No H-bonds generated for 'chain 'K' and resid 615 through 618' Processing helix chain 'K' and resid 626 through 634 Processing helix chain 'K' and resid 654 through 658 Processing helix chain 'K' and resid 678 through 695 removed outlier: 5.195A pdb=" N GLU K 683 " --> pdb=" O GLU K 680 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL K 685 " --> pdb=" O LYS K 682 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU K 689 " --> pdb=" O ASN K 686 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL K 694 " --> pdb=" O GLU K 691 " (cutoff:3.500A) Processing helix chain 'K' and resid 702 through 712 Processing helix chain 'K' and resid 722 through 724 No H-bonds generated for 'chain 'K' and resid 722 through 724' Processing helix chain 'K' and resid 726 through 735 removed outlier: 4.660A pdb=" N LYS K 732 " --> pdb=" O ASN K 728 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET K 734 " --> pdb=" O VAL K 730 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N PHE K 735 " --> pdb=" O ALA K 731 " (cutoff:3.500A) Processing helix chain 'K' and resid 744 through 761 removed outlier: 4.142A pdb=" N VAL K 748 " --> pdb=" O VAL K 744 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LYS K 749 " --> pdb=" O GLU K 745 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU K 752 " --> pdb=" O VAL K 748 " (cutoff:3.500A) Processing helix chain 'K' and resid 768 through 792 removed outlier: 3.549A pdb=" N ALA K 777 " --> pdb=" O SER K 773 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN K 779 " --> pdb=" O SER K 775 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU K 787 " --> pdb=" O LEU K 783 " (cutoff:3.500A) Processing helix chain 'K' and resid 813 through 824 Processing helix chain 'K' and resid 870 through 886 removed outlier: 4.495A pdb=" N GLU K 886 " --> pdb=" O GLU K 882 " (cutoff:3.500A) Processing helix chain 'K' and resid 930 through 933 removed outlier: 4.031A pdb=" N ASN K 933 " --> pdb=" O SER K 930 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 930 through 933' Processing helix chain 'K' and resid 939 through 949 Processing helix chain 'K' and resid 956 through 960 Processing helix chain 'K' and resid 962 through 969 removed outlier: 5.355A pdb=" N HIS K 967 " --> pdb=" O LYS K 964 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU K 968 " --> pdb=" O TYR K 965 " (cutoff:3.500A) Processing helix chain 'K' and resid 975 through 989 removed outlier: 3.900A pdb=" N PHE K 980 " --> pdb=" O TYR K 976 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN K 989 " --> pdb=" O TRP K 985 " (cutoff:3.500A) Processing helix chain 'K' and resid 1021 through 1036 removed outlier: 3.812A pdb=" N VAL K1026 " --> pdb=" O ILE K1022 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU K1036 " --> pdb=" O ILE K1032 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 141 Processing helix chain 'L' and resid 157 through 166 removed outlier: 4.380A pdb=" N ASP L 162 " --> pdb=" O LYS L 158 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE L 163 " --> pdb=" O VAL L 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 145 removed outlier: 4.147A pdb=" N PHE M 142 " --> pdb=" O ILE M 138 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP M 143 " --> pdb=" O LYS M 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 158 through 166 removed outlier: 3.766A pdb=" N ASP M 162 " --> pdb=" O LYS M 158 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE M 163 " --> pdb=" O VAL M 159 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS M 164 " --> pdb=" O LYS M 160 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 19 No H-bonds generated for 'chain 'N' and resid 16 through 19' Processing helix chain 'N' and resid 131 through 140 removed outlier: 4.311A pdb=" N ILE N 137 " --> pdb=" O ILE N 133 " (cutoff:3.500A) Processing helix chain 'N' and resid 142 through 145 No H-bonds generated for 'chain 'N' and resid 142 through 145' Processing helix chain 'N' and resid 156 through 166 Processing helix chain 'O' and resid 131 through 140 Processing helix chain 'O' and resid 142 through 145 No H-bonds generated for 'chain 'O' and resid 142 through 145' Processing helix chain 'O' and resid 156 through 165 removed outlier: 3.889A pdb=" N LYS O 164 " --> pdb=" O LYS O 160 " (cutoff:3.500A) Processing helix chain 'P' and resid 131 through 133 No H-bonds generated for 'chain 'P' and resid 131 through 133' Processing helix chain 'P' and resid 135 through 141 removed outlier: 4.081A pdb=" N LYS P 139 " --> pdb=" O ASN P 135 " (cutoff:3.500A) Processing helix chain 'P' and resid 156 through 165 Processing helix chain 'Q' and resid 131 through 138 removed outlier: 4.059A pdb=" N ASN Q 136 " --> pdb=" O THR Q 132 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE Q 137 " --> pdb=" O ILE Q 133 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE Q 138 " --> pdb=" O VAL Q 134 " (cutoff:3.500A) Processing helix chain 'Q' and resid 156 through 165 removed outlier: 4.563A pdb=" N ILE Q 163 " --> pdb=" O VAL Q 159 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS Q 164 " --> pdb=" O LYS Q 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 138 Processing helix chain 'R' and resid 156 through 166 removed outlier: 4.791A pdb=" N ILE R 163 " --> pdb=" O LYS R 160 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU R 166 " --> pdb=" O ILE R 163 " (cutoff:3.500A) Processing helix chain 'S' and resid 131 through 145 removed outlier: 3.535A pdb=" N GLU S 140 " --> pdb=" O ASN S 136 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ASP S 143 " --> pdb=" O LYS S 139 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS S 144 " --> pdb=" O GLU S 140 " (cutoff:3.500A) Processing helix chain 'S' and resid 157 through 162 Processing helix chain 'T' and resid 134 through 141 removed outlier: 5.323A pdb=" N LYS T 139 " --> pdb=" O ASN T 135 " (cutoff:3.500A) Processing helix chain 'T' and resid 163 through 166 No H-bonds generated for 'chain 'T' and resid 163 through 166' Processing helix chain 'W' and resid 131 through 140 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 158 through 166 removed outlier: 3.896A pdb=" N ASP W 162 " --> pdb=" O LYS W 158 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE W 163 " --> pdb=" O VAL W 159 " (cutoff:3.500A) Processing helix chain 'X' and resid 131 through 138 removed outlier: 3.842A pdb=" N ILE X 137 " --> pdb=" O ILE X 133 " (cutoff:3.500A) Processing helix chain 'X' and resid 158 through 161 No H-bonds generated for 'chain 'X' and resid 158 through 161' Processing helix chain 'X' and resid 164 through 166 No H-bonds generated for 'chain 'X' and resid 164 through 166' Processing helix chain 'l' and resid 76 through 78 No H-bonds generated for 'chain 'l' and resid 76 through 78' Processing helix chain 'l' and resid 80 through 82 No H-bonds generated for 'chain 'l' and resid 80 through 82' Processing helix chain 'l' and resid 132 through 145 removed outlier: 4.216A pdb=" N ASN l 136 " --> pdb=" O THR l 132 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ASP l 143 " --> pdb=" O LYS l 139 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N LYS l 144 " --> pdb=" O GLU l 140 " (cutoff:3.500A) Processing helix chain 'l' and resid 156 through 166 removed outlier: 3.870A pdb=" N GLU l 161 " --> pdb=" O GLU l 157 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE l 163 " --> pdb=" O VAL l 159 " (cutoff:3.500A) Processing helix chain 'm' and resid 131 through 140 Processing helix chain 'm' and resid 142 through 145 No H-bonds generated for 'chain 'm' and resid 142 through 145' Processing helix chain 'm' and resid 156 through 164 Processing helix chain 'n' and resid 131 through 140 removed outlier: 3.710A pdb=" N ASN n 136 " --> pdb=" O THR n 132 " (cutoff:3.500A) Processing helix chain 'n' and resid 156 through 165 removed outlier: 3.814A pdb=" N ILE n 163 " --> pdb=" O VAL n 159 " (cutoff:3.500A) Processing helix chain 'o' and resid 131 through 140 Processing helix chain 'o' and resid 156 through 164 removed outlier: 3.690A pdb=" N ILE o 163 " --> pdb=" O VAL o 159 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS o 164 " --> pdb=" O LYS o 160 " (cutoff:3.500A) Processing helix chain 'p' and resid 131 through 142 removed outlier: 3.762A pdb=" N VAL p 141 " --> pdb=" O ILE p 137 " (cutoff:3.500A) Processing helix chain 'p' and resid 156 through 166 removed outlier: 4.981A pdb=" N ILE p 163 " --> pdb=" O LYS p 160 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU p 166 " --> pdb=" O ILE p 163 " (cutoff:3.500A) Processing helix chain 'q' and resid 132 through 140 removed outlier: 3.760A pdb=" N ILE q 138 " --> pdb=" O VAL q 134 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS q 139 " --> pdb=" O ASN q 135 " (cutoff:3.500A) Processing helix chain 'q' and resid 162 through 166 Processing helix chain 'r' and resid 80 through 82 No H-bonds generated for 'chain 'r' and resid 80 through 82' Processing helix chain 'r' and resid 131 through 141 removed outlier: 3.705A pdb=" N ASN r 135 " --> pdb=" O THR r 132 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASN r 136 " --> pdb=" O ILE r 133 " (cutoff:3.500A) Processing helix chain 'r' and resid 156 through 160 Processing helix chain 'r' and resid 162 through 165 No H-bonds generated for 'chain 'r' and resid 162 through 165' Processing helix chain 's' and resid 134 through 140 removed outlier: 4.857A pdb=" N LYS s 139 " --> pdb=" O ASN s 135 " (cutoff:3.500A) Processing helix chain 's' and resid 157 through 161 Processing helix chain 't' and resid 136 through 141 Processing helix chain 't' and resid 155 through 165 removed outlier: 4.241A pdb=" N GLU t 161 " --> pdb=" O LYS t 158 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP t 162 " --> pdb=" O VAL t 159 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE t 163 " --> pdb=" O LYS t 160 " (cutoff:3.500A) Processing helix chain 'w' and resid 132 through 145 removed outlier: 3.791A pdb=" N LYS w 139 " --> pdb=" O ASN w 135 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ASP w 143 " --> pdb=" O LYS w 139 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS w 144 " --> pdb=" O GLU w 140 " (cutoff:3.500A) Processing helix chain 'w' and resid 156 through 161 Processing helix chain 'w' and resid 163 through 166 No H-bonds generated for 'chain 'w' and resid 163 through 166' Processing helix chain 'x' and resid 131 through 140 removed outlier: 3.986A pdb=" N ASN x 135 " --> pdb=" O ASP x 131 " (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 163 through 166 No H-bonds generated for 'chain 'x' and resid 163 through 166' Processing helix chain 'Z' and resid 131 through 138 Processing helix chain 'Z' and resid 160 through 166 removed outlier: 4.085A pdb=" N LYS Z 164 " --> pdb=" O LYS Z 160 " (cutoff:3.500A) Processing helix chain 'z' and resid 17 through 19 No H-bonds generated for 'chain 'z' and resid 17 through 19' Processing helix chain 'z' and resid 132 through 138 removed outlier: 3.898A pdb=" N ASN z 136 " --> pdb=" O THR z 132 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE z 137 " --> pdb=" O ILE z 133 " (cutoff:3.500A) Processing helix chain 'z' and resid 156 through 166 Processing helix chain 'Y' and resid 131 through 140 removed outlier: 3.798A pdb=" N LYS Y 139 " --> pdb=" O ASN Y 135 " (cutoff:3.500A) Processing helix chain 'Y' and resid 156 through 166 removed outlier: 5.172A pdb=" N GLU Y 161 " --> pdb=" O LYS Y 158 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU Y 166 " --> pdb=" O ILE Y 163 " (cutoff:3.500A) Processing helix chain 'y' and resid 132 through 140 Processing helix chain 'y' and resid 156 through 165 990 hydrogen bonds defined for protein. 2658 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 16.50 Time building geometry restraints manager: 15.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 11796 1.32 - 1.45: 17008 1.45 - 1.57: 39689 1.57 - 1.70: 162 1.70 - 1.82: 162 Bond restraints: 68817 Sorted by residual: bond pdb=" N PRO K 309 " pdb=" CA PRO K 309 " ideal model delta sigma weight residual 1.468 1.683 -0.215 1.20e-02 6.94e+03 3.22e+02 bond pdb=" N3B ANP K1103 " pdb=" PG ANP K1103 " ideal model delta sigma weight residual 1.795 1.602 0.193 2.00e-02 2.50e+03 9.35e+01 bond pdb=" C ILE K 308 " pdb=" N PRO K 309 " ideal model delta sigma weight residual 1.331 1.444 -0.113 1.20e-02 6.94e+03 8.90e+01 bond pdb=" N3B ANP K1102 " pdb=" PG ANP K1102 " ideal model delta sigma weight residual 1.795 1.612 0.183 2.00e-02 2.50e+03 8.33e+01 bond pdb=" O3A ANP K1102 " pdb=" PB ANP K1102 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.60e+01 ... (remaining 68812 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.28: 93445 6.28 - 12.56: 36 12.56 - 18.83: 2 18.83 - 25.11: 0 25.11 - 31.39: 1 Bond angle restraints: 93484 Sorted by residual: angle pdb=" C ASN K 165 " pdb=" N THR K 166 " pdb=" CA THR K 166 " ideal model delta sigma weight residual 120.49 151.88 -31.39 1.42e+00 4.96e-01 4.89e+02 angle pdb=" C ILE K 308 " pdb=" N PRO K 309 " pdb=" CA PRO K 309 " ideal model delta sigma weight residual 119.83 138.17 -18.34 1.08e+00 8.57e-01 2.88e+02 angle pdb=" N PRO K 309 " pdb=" CA PRO K 309 " pdb=" C PRO K 309 " ideal model delta sigma weight residual 111.03 96.59 14.44 1.54e+00 4.22e-01 8.79e+01 angle pdb=" CA PRO K 309 " pdb=" N PRO K 309 " pdb=" CD PRO K 309 " ideal model delta sigma weight residual 112.00 100.79 11.21 1.40e+00 5.10e-01 6.41e+01 angle pdb=" N ILE Y 16 " pdb=" CA ILE Y 16 " pdb=" C ILE Y 16 " ideal model delta sigma weight residual 111.91 107.40 4.51 8.90e-01 1.26e+00 2.57e+01 ... (remaining 93479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 41474 35.58 - 71.16: 825 71.16 - 106.73: 108 106.73 - 142.31: 3 142.31 - 177.89: 4 Dihedral angle restraints: 42414 sinusoidal: 18251 harmonic: 24163 Sorted by residual: dihedral pdb=" CB CYS J 356 " pdb=" SG CYS J 356 " pdb=" SG CYS J 474 " pdb=" CB CYS J 474 " ideal model delta sinusoidal sigma weight residual 93.00 -179.88 -87.12 1 1.00e+01 1.00e-02 9.12e+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 46.59 153.41 1 1.50e+01 4.44e-03 8.08e+01 dihedral pdb=" CB CYS K 711 " pdb=" SG CYS K 711 " pdb=" SG CYS K 721 " pdb=" CB CYS K 721 " ideal model delta sinusoidal sigma weight residual -86.00 -165.31 79.31 1 1.00e+01 1.00e-02 7.82e+01 ... (remaining 42411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 10878 0.146 - 0.292: 52 0.292 - 0.438: 2 0.438 - 0.584: 1 0.584 - 0.731: 1 Chirality restraints: 10934 Sorted by residual: chirality pdb=" CA PRO K 309 " pdb=" N PRO K 309 " pdb=" C PRO K 309 " pdb=" CB PRO K 309 " both_signs ideal model delta sigma weight residual False 2.72 3.45 -0.73 2.00e-01 2.50e+01 1.33e+01 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 -2.86 0.50 2.00e-01 2.50e+01 6.27e+00 chirality pdb=" CA ILE K 205 " pdb=" N ILE K 205 " pdb=" C ILE K 205 " pdb=" CB ILE K 205 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.32 2.00e-01 2.50e+01 2.51e+00 ... (remaining 10931 not shown) Planarity restraints: 11500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE K 308 " 0.016 2.00e-02 2.50e+03 3.03e-02 9.20e+00 pdb=" C ILE K 308 " -0.052 2.00e-02 2.50e+03 pdb=" O ILE K 308 " 0.020 2.00e-02 2.50e+03 pdb=" N PRO K 309 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A V 13 " -0.035 2.00e-02 2.50e+03 1.55e-02 6.63e+00 pdb=" N9 A V 13 " 0.034 2.00e-02 2.50e+03 pdb=" C8 A V 13 " 0.003 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 " -0.005 2.00e-02 2.50e+03 pdb=" N6 A V 13 " -0.009 2.00e-02 2.50e+03 pdb=" N1 A V 13 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A V 13 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A V 13 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A V 13 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G U 12 " 0.027 2.00e-02 2.50e+03 1.31e-02 5.17e+00 pdb=" N9 G U 12 " -0.035 2.00e-02 2.50e+03 pdb=" C8 G U 12 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G U 12 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G U 12 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G U 12 " 0.005 2.00e-02 2.50e+03 pdb=" O6 G U 12 " 0.006 2.00e-02 2.50e+03 pdb=" N1 G U 12 " -0.000 2.00e-02 2.50e+03 pdb=" C2 G U 12 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G U 12 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G U 12 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G U 12 " 0.003 2.00e-02 2.50e+03 ... (remaining 11497 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 867 2.56 - 3.14: 58964 3.14 - 3.73: 105701 3.73 - 4.31: 159513 4.31 - 4.90: 253197 Nonbonded interactions: 578242 Sorted by model distance: nonbonded pdb=" O1G ANP K1102 " pdb="MN MN K1106 " model vdw 1.970 2.320 nonbonded pdb=" O1A ANP K1102 " pdb="MN MN K1106 " model vdw 1.973 2.320 nonbonded pdb=" O1G ANP K1103 " pdb="MN MN K1104 " model vdw 1.979 2.320 nonbonded pdb=" O THR B 22 " pdb=" NH1 ARG B 79 " model vdw 2.038 3.120 nonbonded pdb=" OG1 THR q 31 " pdb=" OH TYR q 146 " model vdw 2.096 3.040 ... (remaining 578237 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' and resid 3 through 152) selection = (chain 'B' and resid 3 through 152) selection = (chain 'C' and resid 3 through 152) } ncs_group { reference = (chain 'D' and resid 2 through 284) selection = (chain 'E' and resid 2 through 284) selection = (chain 'F' and resid 2 through 284) 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: 35.090 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: 0.130 Extract box with map and model: 2.150 Check model and map are aligned: 0.400 Set scattering table: 0.500 Process input model: 118.480 Find NCS groups from input model: 2.140 Set up NCS constraints: 0.680 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 162.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.215 68817 Z= 0.426 Angle : 0.740 31.389 93484 Z= 0.418 Chirality : 0.050 0.731 10934 Planarity : 0.004 0.057 11500 Dihedral : 15.445 177.888 26774 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.49 % Favored : 87.28 % Rotamer: Outliers : 0.09 % Allowed : 8.09 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -4.90 (0.07), residues: 8103 helix: -3.15 (0.08), residues: 2121 sheet: -2.51 (0.12), residues: 1319 loop : -3.68 (0.07), residues: 4663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 281 HIS 0.005 0.001 HIS q 29 PHE 0.026 0.002 PHE H 188 TYR 0.029 0.002 TYR B 42 ARG 0.006 0.001 ARG o 5 *********************** 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 1821 residues out of total 7451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1814 time to evaluate : 6.004 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: F 79 GLU cc_start: 0.6721 (mp0) cc_final: 0.6490 (mt-10) REVERT: L 173 GLU cc_start: 0.6564 (mm-30) cc_final: 0.6337 (mm-30) REVERT: M 61 ASP cc_start: 0.6912 (t0) cc_final: 0.6460 (t0) REVERT: P 47 TYR cc_start: 0.8291 (m-10) cc_final: 0.8038 (m-80) REVERT: P 109 TYR cc_start: 0.8388 (m-80) cc_final: 0.8089 (m-10) REVERT: P 137 ILE cc_start: 0.7761 (mm) cc_final: 0.7536 (mm) REVERT: S 112 TYR cc_start: 0.7992 (t80) cc_final: 0.7657 (t80) REVERT: T 30 ILE cc_start: 0.7251 (mm) cc_final: 0.6993 (mm) REVERT: X 123 THR cc_start: 0.6592 (t) cc_final: 0.6373 (t) REVERT: r 40 ASN cc_start: 0.6465 (m-40) cc_final: 0.6122 (t0) REVERT: s 7 TYR cc_start: 0.7255 (t80) cc_final: 0.7007 (t80) REVERT: s 147 ASN cc_start: 0.5792 (m110) cc_final: 0.5431 (p0) REVERT: x 52 LYS cc_start: 0.6756 (mmtm) cc_final: 0.6530 (pptt) REVERT: z 164 LYS cc_start: 0.7140 (tptp) cc_final: 0.6149 (mmtm) REVERT: y 107 LYS cc_start: 0.6526 (mttp) cc_final: 0.6090 (mtmt) outliers start: 7 outliers final: 1 residues processed: 1818 average time/residue: 0.7026 time to fit residues: 2108.9868 Evaluate side-chains 1293 residues out of total 7451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1292 time to evaluate : 5.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 206 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 813 random chunks: chunk 686 optimal weight: 5.9990 chunk 616 optimal weight: 0.8980 chunk 341 optimal weight: 0.7980 chunk 210 optimal weight: 1.9990 chunk 415 optimal weight: 6.9990 chunk 329 optimal weight: 0.7980 chunk 637 optimal weight: 0.0670 chunk 246 optimal weight: 0.0670 chunk 387 optimal weight: 0.8980 chunk 474 optimal weight: 0.0370 chunk 738 optimal weight: 3.9990 overall best weight: 0.3534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN E 13 HIS E 141 ASN E 166 ASN ** F 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 ASN F 153 ASN F 178 ASN G 13 HIS H 253 ASN I 56 HIS I 87 ASN ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 227 HIS J 51 ASN J 265 ASN J 277 ASN ** J 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 321 ASN J 327 ASN J 345 ASN J 443 ASN K 110 GLN K 165 ASN K 180 HIS K 602 ASN K 635 HIS K 771 HIS K 845 ASN K 846 ASN ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 GLN ** M 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 ASN ** N 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 GLN P 40 ASN P 53 ASN P 76 GLN P 77 GLN P 174 GLN Q 14 ASN R 76 GLN R 77 GLN R 135 ASN S 4 GLN S 40 ASN S 79 GLN T 32 ASN T 79 GLN T 119 ASN T 174 GLN W 39 HIS W 40 ASN W 77 GLN W 136 ASN W 174 GLN l 150 GLN n 53 ASN ** p 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 135 ASN p 147 ASN r 76 GLN r 79 GLN s 32 ASN s 39 HIS s 101 ASN ** s 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 147 ASN s 174 GLN t 4 GLN t 29 HIS t 40 ASN t 77 GLN t 174 GLN w 135 ASN x 77 GLN x 79 GLN x 147 ASN ** x 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 14 ASN Z 29 HIS Z 91 ASN ** z 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 76 GLN z 135 ASN z 174 GLN ** Y 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 147 ASN y 77 GLN y 135 ASN Total number of N/Q/H flips: 80 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 68817 Z= 0.176 Angle : 0.654 11.136 93484 Z= 0.344 Chirality : 0.048 0.235 10934 Planarity : 0.005 0.066 11500 Dihedral : 11.149 178.072 10192 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.01 % Allowed : 9.95 % Favored : 90.04 % Rotamer: Outliers : 1.91 % Allowed : 14.28 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.32 % 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: -3.89 (0.08), residues: 8103 helix: -2.08 (0.10), residues: 2117 sheet: -2.13 (0.13), residues: 1262 loop : -3.08 (0.08), residues: 4724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP K 770 HIS 0.006 0.001 HIS x 39 PHE 0.031 0.001 PHE B 14 TYR 0.031 0.001 TYR O 112 ARG 0.009 0.001 ARG n 5 *********************** 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 1739 residues out of total 7451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1597 time to evaluate : 7.036 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: B 114 ARG cc_start: 0.6980 (ttm170) cc_final: 0.5976 (tpt170) REVERT: D 283 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7839 (pttt) REVERT: I 82 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6779 (mt-10) REVERT: M 162 ASP cc_start: 0.7039 (p0) cc_final: 0.6692 (p0) REVERT: O 32 ASN cc_start: 0.7601 (p0) cc_final: 0.7277 (p0) REVERT: O 162 ASP cc_start: 0.7159 (t0) cc_final: 0.6943 (t0) REVERT: P 16 ILE cc_start: 0.6220 (tp) cc_final: 0.5702 (mt) REVERT: P 47 TYR cc_start: 0.8109 (m-10) cc_final: 0.7899 (m-80) REVERT: P 137 ILE cc_start: 0.8069 (mm) cc_final: 0.7622 (mm) REVERT: R 86 LEU cc_start: 0.6739 (mt) cc_final: 0.6533 (mt) REVERT: S 112 TYR cc_start: 0.7752 (t80) cc_final: 0.7540 (t80) REVERT: W 116 ASP cc_start: 0.5667 (p0) cc_final: 0.5175 (t0) REVERT: W 163 ILE cc_start: 0.8962 (tp) cc_final: 0.8485 (mm) REVERT: l 34 ASP cc_start: 0.6536 (t0) cc_final: 0.6206 (t0) REVERT: m 130 ASP cc_start: 0.6611 (m-30) cc_final: 0.5991 (m-30) REVERT: n 157 GLU cc_start: 0.7327 (pm20) cc_final: 0.6943 (pm20) REVERT: o 140 GLU cc_start: 0.6191 (pt0) cc_final: 0.5895 (pt0) REVERT: o 173 GLU cc_start: 0.6541 (tp30) cc_final: 0.6329 (tp30) REVERT: r 160 LYS cc_start: 0.6026 (ttmt) cc_final: 0.5693 (tptm) REVERT: x 108 ILE cc_start: 0.6971 (OUTLIER) cc_final: 0.6749 (tp) REVERT: Z 156 ILE cc_start: 0.6457 (OUTLIER) cc_final: 0.5996 (pt) REVERT: z 164 LYS cc_start: 0.7199 (tptp) cc_final: 0.6215 (mmtm) outliers start: 142 outliers final: 66 residues processed: 1663 average time/residue: 0.6554 time to fit residues: 1856.0433 Evaluate side-chains 1410 residues out of total 7451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1341 time to evaluate : 5.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain I residue 166 GLU Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 283 SER Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain K residue 206 ASP Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 282 ILE Chi-restraints excluded: chain K residue 415 ASP Chi-restraints excluded: chain K residue 517 VAL Chi-restraints excluded: chain K residue 594 VAL Chi-restraints excluded: chain K residue 652 ASP Chi-restraints excluded: chain K residue 752 LEU Chi-restraints excluded: chain K residue 836 CYS Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain M residue 4 GLN Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain Q residue 168 SER Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 119 ASN Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain W residue 96 ILE Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain l residue 22 ILE Chi-restraints excluded: chain l residue 134 VAL Chi-restraints excluded: chain m residue 51 GLU Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain p residue 136 ASN Chi-restraints excluded: chain r residue 8 VAL Chi-restraints excluded: chain r residue 38 ILE Chi-restraints excluded: chain r residue 141 VAL Chi-restraints excluded: chain s residue 140 GLU Chi-restraints excluded: chain s residue 161 GLU Chi-restraints excluded: chain w residue 13 THR Chi-restraints excluded: chain w residue 35 GLU Chi-restraints excluded: chain w residue 57 VAL Chi-restraints excluded: chain w residue 106 LEU Chi-restraints excluded: chain w residue 134 VAL Chi-restraints excluded: chain x residue 8 VAL Chi-restraints excluded: chain x residue 108 ILE Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain Z residue 102 ILE Chi-restraints excluded: chain Z residue 156 ILE Chi-restraints excluded: chain Y residue 16 ILE Chi-restraints excluded: chain Y residue 31 THR Chi-restraints excluded: chain Y residue 41 VAL Chi-restraints excluded: chain Y residue 141 VAL Chi-restraints excluded: chain y residue 86 LEU Chi-restraints excluded: chain y residue 88 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 813 random chunks: chunk 410 optimal weight: 3.9990 chunk 229 optimal weight: 8.9990 chunk 614 optimal weight: 10.0000 chunk 502 optimal weight: 8.9990 chunk 203 optimal weight: 3.9990 chunk 739 optimal weight: 5.9990 chunk 799 optimal weight: 6.9990 chunk 658 optimal weight: 10.0000 chunk 733 optimal weight: 10.0000 chunk 252 optimal weight: 8.9990 chunk 593 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 166 ASN F 17 HIS F 35 GLN F 77 ASN H 28 HIS H 192 ASN I 44 GLN ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 345 ASN ** K 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 299 ASN K 382 GLN K 728 ASN L 79 GLN ** M 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 ASN R 147 ASN R 174 GLN ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 135 ASN m 40 ASN ** m 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 29 HIS r 32 ASN r 91 ASN t 4 GLN ** w 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 79 GLN x 91 ASN ** x 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 77 GLN ** Y 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 76 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.091 68817 Z= 0.621 Angle : 0.801 10.227 93484 Z= 0.414 Chirality : 0.052 0.338 10934 Planarity : 0.005 0.077 11500 Dihedral : 11.048 178.447 10192 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.51 % Favored : 87.45 % Rotamer: Outliers : 4.03 % Allowed : 17.66 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.32 % 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: -3.78 (0.08), residues: 8103 helix: -1.93 (0.10), residues: 2116 sheet: -2.10 (0.13), residues: 1320 loop : -3.04 (0.08), residues: 4667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 281 HIS 0.009 0.002 HIS L 39 PHE 0.026 0.002 PHE C 51 TYR 0.040 0.002 TYR O 112 ARG 0.007 0.001 ARG n 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 1622 residues out of total 7451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 1322 time to evaluate : 5.841 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: B 149 GLU cc_start: 0.7345 (mt-10) cc_final: 0.7034 (mt-10) REVERT: C 12 GLU cc_start: 0.6677 (mm-30) cc_final: 0.6309 (mm-30) REVERT: C 114 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7536 (ptm160) REVERT: F 30 ILE cc_start: 0.9106 (mm) cc_final: 0.8905 (mm) REVERT: F 100 GLU cc_start: 0.6826 (tt0) cc_final: 0.6604 (tt0) REVERT: J 218 ARG cc_start: 0.7244 (mtt90) cc_final: 0.6885 (mtt-85) REVERT: K 199 LYS cc_start: 0.6556 (OUTLIER) cc_final: 0.5914 (mmmt) REVERT: K 272 GLU cc_start: 0.5369 (OUTLIER) cc_final: 0.5132 (pm20) REVERT: O 32 ASN cc_start: 0.7901 (p0) cc_final: 0.7491 (p0) REVERT: P 109 TYR cc_start: 0.8356 (m-80) cc_final: 0.8151 (m-80) REVERT: P 137 ILE cc_start: 0.8117 (mm) cc_final: 0.7905 (mm) REVERT: S 112 TYR cc_start: 0.7906 (t80) cc_final: 0.7588 (t80) REVERT: m 130 ASP cc_start: 0.6572 (OUTLIER) cc_final: 0.5653 (m-30) REVERT: p 86 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8391 (pp) REVERT: r 160 LYS cc_start: 0.5874 (ttmt) cc_final: 0.5281 (tptt) REVERT: s 7 TYR cc_start: 0.7161 (t80) cc_final: 0.6941 (t80) REVERT: s 147 ASN cc_start: 0.6037 (m-40) cc_final: 0.5642 (p0) REVERT: t 67 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7873 (ptpp) REVERT: w 44 ILE cc_start: 0.7591 (mm) cc_final: 0.7234 (mm) REVERT: Z 156 ILE cc_start: 0.6522 (mp) cc_final: 0.6070 (pt) REVERT: z 164 LYS cc_start: 0.7324 (tptp) cc_final: 0.6251 (mmtt) REVERT: y 107 LYS cc_start: 0.6621 (mttp) cc_final: 0.6129 (mtmt) outliers start: 300 outliers final: 201 residues processed: 1503 average time/residue: 0.7159 time to fit residues: 1849.9133 Evaluate side-chains 1443 residues out of total 7451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1236 time to evaluate : 6.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain G residue 217 ASP Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 166 GLU Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain J residue 6 MET Chi-restraints excluded: chain J residue 72 GLU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 122 ASP Chi-restraints excluded: chain J residue 125 ASP Chi-restraints excluded: chain J residue 283 SER Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain J residue 396 CYS Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 459 ILE Chi-restraints excluded: chain J residue 475 VAL Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 113 ILE Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain K residue 168 SER Chi-restraints excluded: chain K residue 199 LYS Chi-restraints excluded: chain K residue 206 ASP Chi-restraints excluded: chain K residue 212 ASP Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 272 GLU Chi-restraints excluded: chain K residue 282 ILE Chi-restraints excluded: chain K residue 379 ASP Chi-restraints excluded: chain K residue 384 THR Chi-restraints excluded: chain K residue 386 LEU Chi-restraints excluded: chain K residue 395 VAL Chi-restraints excluded: chain K residue 415 ASP Chi-restraints excluded: chain K residue 433 VAL Chi-restraints excluded: chain K residue 436 GLU Chi-restraints excluded: chain K residue 535 ASP Chi-restraints excluded: chain K residue 571 ILE Chi-restraints excluded: chain K residue 652 ASP Chi-restraints excluded: chain K residue 702 VAL Chi-restraints excluded: chain K residue 705 VAL Chi-restraints excluded: chain K residue 752 LEU Chi-restraints excluded: chain K residue 758 ILE Chi-restraints excluded: chain K residue 764 ILE Chi-restraints excluded: chain K residue 836 CYS Chi-restraints excluded: chain K residue 876 ASP Chi-restraints excluded: chain K residue 981 LEU Chi-restraints excluded: chain K residue 1026 VAL Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain L residue 127 SER Chi-restraints excluded: chain L residue 166 LEU Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 145 ILE Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 135 ASN Chi-restraints excluded: chain Q residue 23 THR Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 148 ILE Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain S residue 42 LEU Chi-restraints excluded: chain S residue 45 THR Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 143 ASP Chi-restraints excluded: chain T residue 157 GLU Chi-restraints excluded: chain T residue 166 LEU Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 96 ILE Chi-restraints excluded: chain W residue 141 VAL Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain W residue 166 LEU Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 114 SER Chi-restraints excluded: chain X residue 126 VAL Chi-restraints excluded: chain X residue 166 LEU Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 22 ILE Chi-restraints excluded: chain l residue 30 ILE Chi-restraints excluded: chain l residue 56 LEU Chi-restraints excluded: chain l residue 134 VAL Chi-restraints excluded: chain l residue 159 VAL Chi-restraints excluded: chain m residue 10 ILE Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 110 ILE Chi-restraints excluded: chain m residue 130 ASP Chi-restraints excluded: chain m residue 165 GLU Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 93 LEU Chi-restraints excluded: chain n residue 102 ILE Chi-restraints excluded: chain n residue 149 THR Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain o residue 106 LEU Chi-restraints excluded: chain p residue 16 ILE Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain p residue 77 GLN Chi-restraints excluded: chain p residue 86 LEU Chi-restraints excluded: chain p residue 123 THR Chi-restraints excluded: chain p residue 132 THR Chi-restraints excluded: chain p residue 136 ASN Chi-restraints excluded: chain q residue 3 THR Chi-restraints excluded: chain q residue 13 THR Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 123 THR Chi-restraints excluded: chain r residue 8 VAL Chi-restraints excluded: chain r residue 38 ILE Chi-restraints excluded: chain r residue 44 ILE Chi-restraints excluded: chain r residue 141 VAL Chi-restraints excluded: chain r residue 149 THR Chi-restraints excluded: chain s residue 69 ILE Chi-restraints excluded: chain s residue 140 GLU Chi-restraints excluded: chain s residue 161 GLU Chi-restraints excluded: chain t residue 4 GLN Chi-restraints excluded: chain t residue 67 LYS Chi-restraints excluded: chain w residue 35 GLU Chi-restraints excluded: chain w residue 57 VAL Chi-restraints excluded: chain w residue 106 LEU Chi-restraints excluded: chain w residue 134 VAL Chi-restraints excluded: chain x residue 8 VAL Chi-restraints excluded: chain x residue 113 SER Chi-restraints excluded: chain x residue 114 SER Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain Z residue 102 ILE Chi-restraints excluded: chain Z residue 138 ILE Chi-restraints excluded: chain z residue 8 VAL Chi-restraints excluded: chain Y residue 16 ILE Chi-restraints excluded: chain Y residue 41 VAL Chi-restraints excluded: chain Y residue 63 CYS Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 113 SER Chi-restraints excluded: chain Y residue 137 ILE Chi-restraints excluded: chain Y residue 141 VAL Chi-restraints excluded: chain Y residue 148 ILE Chi-restraints excluded: chain y residue 20 VAL Chi-restraints excluded: chain y residue 86 LEU Chi-restraints excluded: chain y residue 88 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 813 random chunks: chunk 730 optimal weight: 7.9990 chunk 556 optimal weight: 1.9990 chunk 383 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 352 optimal weight: 2.9990 chunk 496 optimal weight: 6.9990 chunk 742 optimal weight: 0.5980 chunk 785 optimal weight: 0.1980 chunk 387 optimal weight: 0.9990 chunk 703 optimal weight: 9.9990 chunk 211 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 185 ASN E 203 ASN F 77 ASN H 192 ASN ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 285 ASN J 327 ASN ** K 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1024 ASN ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 GLN R 174 GLN ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 39 HIS l 76 GLN l 79 GLN m 4 GLN m 53 ASN ** o 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 29 HIS s 135 ASN t 4 GLN x 174 GLN z 39 HIS ** Y 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 68817 Z= 0.184 Angle : 0.637 9.955 93484 Z= 0.332 Chirality : 0.047 0.260 10934 Planarity : 0.004 0.066 11500 Dihedral : 10.728 176.505 10192 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.01 % Allowed : 9.42 % Favored : 90.57 % Rotamer: Outliers : 2.80 % Allowed : 20.40 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.33 (0.08), residues: 8103 helix: -1.47 (0.11), residues: 2090 sheet: -1.88 (0.14), residues: 1320 loop : -2.76 (0.08), residues: 4693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 60 HIS 0.003 0.001 HIS P 29 PHE 0.035 0.001 PHE B 14 TYR 0.039 0.001 TYR O 112 ARG 0.008 0.001 ARG A 79 *********************** 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 1672 residues out of total 7451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1463 time to evaluate : 5.801 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: B 114 ARG cc_start: 0.7035 (ttm170) cc_final: 0.6087 (tpt170) REVERT: C 113 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8124 (mp) REVERT: H 227 ASP cc_start: 0.6894 (m-30) cc_final: 0.6638 (m-30) REVERT: I 82 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6923 (mt-10) REVERT: K 199 LYS cc_start: 0.6467 (OUTLIER) cc_final: 0.5979 (mmmt) REVERT: O 32 ASN cc_start: 0.7789 (p0) cc_final: 0.7353 (p0) REVERT: P 16 ILE cc_start: 0.6216 (tp) cc_final: 0.5756 (mt) REVERT: P 47 TYR cc_start: 0.8181 (m-10) cc_final: 0.7969 (m-80) REVERT: P 109 TYR cc_start: 0.8253 (m-80) cc_final: 0.7988 (m-80) REVERT: S 29 HIS cc_start: 0.4838 (OUTLIER) cc_final: 0.3980 (m90) REVERT: W 93 LEU cc_start: 0.6565 (mp) cc_final: 0.6139 (mp) REVERT: l 161 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7187 (mm-30) REVERT: m 130 ASP cc_start: 0.6711 (m-30) cc_final: 0.5918 (m-30) REVERT: r 160 LYS cc_start: 0.5918 (ttmt) cc_final: 0.5328 (tptt) REVERT: s 147 ASN cc_start: 0.5854 (m-40) cc_final: 0.5588 (p0) REVERT: w 84 LEU cc_start: 0.5522 (mm) cc_final: 0.5275 (mm) REVERT: x 108 ILE cc_start: 0.6897 (OUTLIER) cc_final: 0.6329 (tp) REVERT: x 128 ILE cc_start: 0.6931 (mm) cc_final: 0.6730 (mm) outliers start: 209 outliers final: 119 residues processed: 1585 average time/residue: 0.6972 time to fit residues: 1908.4999 Evaluate side-chains 1433 residues out of total 7451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1310 time to evaluate : 5.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 166 GLU Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 283 SER Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain J residue 396 CYS Chi-restraints excluded: chain J residue 474 CYS Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 113 ILE Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 199 LYS Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 251 LEU Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 282 ILE Chi-restraints excluded: chain K residue 415 ASP Chi-restraints excluded: chain K residue 436 GLU Chi-restraints excluded: chain K residue 571 ILE Chi-restraints excluded: chain K residue 594 VAL Chi-restraints excluded: chain K residue 652 ASP Chi-restraints excluded: chain K residue 752 LEU Chi-restraints excluded: chain K residue 758 ILE Chi-restraints excluded: chain K residue 764 ILE Chi-restraints excluded: chain K residue 836 CYS Chi-restraints excluded: chain K residue 876 ASP Chi-restraints excluded: chain K residue 981 LEU Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain N residue 124 LYS Chi-restraints excluded: chain O residue 6 GLU Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain P residue 12 ILE Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain S residue 29 HIS Chi-restraints excluded: chain S residue 42 LEU Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 157 GLU Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 96 ILE Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain X residue 114 SER Chi-restraints excluded: chain X residue 126 VAL Chi-restraints excluded: chain l residue 22 ILE Chi-restraints excluded: chain l residue 56 LEU Chi-restraints excluded: chain m residue 110 ILE Chi-restraints excluded: chain m residue 165 GLU Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 93 LEU Chi-restraints excluded: chain n residue 102 ILE Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain o residue 98 LYS Chi-restraints excluded: chain p residue 16 ILE Chi-restraints excluded: chain p residue 123 THR Chi-restraints excluded: chain p residue 132 THR Chi-restraints excluded: chain p residue 136 ASN Chi-restraints excluded: chain p residue 155 LYS Chi-restraints excluded: chain q residue 13 THR Chi-restraints excluded: chain q residue 56 LEU Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain r residue 38 ILE Chi-restraints excluded: chain r residue 141 VAL Chi-restraints excluded: chain s residue 140 GLU Chi-restraints excluded: chain s residue 154 VAL Chi-restraints excluded: chain t residue 4 GLN Chi-restraints excluded: chain t residue 108 ILE Chi-restraints excluded: chain w residue 57 VAL Chi-restraints excluded: chain w residue 106 LEU Chi-restraints excluded: chain w residue 134 VAL Chi-restraints excluded: chain x residue 8 VAL Chi-restraints excluded: chain x residue 57 VAL Chi-restraints excluded: chain x residue 108 ILE Chi-restraints excluded: chain x residue 113 SER Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain Z residue 102 ILE Chi-restraints excluded: chain z residue 8 VAL Chi-restraints excluded: chain z residue 141 VAL Chi-restraints excluded: chain Y residue 16 ILE Chi-restraints excluded: chain Y residue 30 ILE Chi-restraints excluded: chain Y residue 31 THR Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 113 SER Chi-restraints excluded: chain Y residue 141 VAL Chi-restraints excluded: chain y residue 86 LEU Chi-restraints excluded: chain y residue 145 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 813 random chunks: chunk 654 optimal weight: 0.9980 chunk 446 optimal weight: 0.0020 chunk 11 optimal weight: 0.0470 chunk 585 optimal weight: 8.9990 chunk 324 optimal weight: 0.9990 chunk 670 optimal weight: 7.9990 chunk 543 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 401 optimal weight: 2.9990 chunk 705 optimal weight: 30.0000 chunk 198 optimal weight: 4.9990 overall best weight: 1.0090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 77 ASN ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 49 HIS K 368 ASN K1024 ASN N 4 GLN ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 174 GLN ** W 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 77 GLN ** l 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 4 GLN m 76 GLN ** p 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 136 ASN s 29 HIS s 174 GLN t 4 GLN x 79 GLN z 150 GLN ** Y 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 68817 Z= 0.193 Angle : 0.631 10.864 93484 Z= 0.327 Chirality : 0.047 0.235 10934 Planarity : 0.004 0.070 11500 Dihedral : 10.534 178.934 10190 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.01 % Allowed : 9.81 % Favored : 90.18 % Rotamer: Outliers : 3.21 % Allowed : 20.91 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.10 (0.09), residues: 8103 helix: -1.29 (0.11), residues: 2100 sheet: -1.70 (0.14), residues: 1325 loop : -2.63 (0.08), residues: 4678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 60 HIS 0.005 0.001 HIS O 29 PHE 0.032 0.001 PHE B 14 TYR 0.041 0.001 TYR W 112 ARG 0.009 0.000 ARG A 138 *********************** 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 1623 residues out of total 7451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 1384 time to evaluate : 5.838 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: B 114 ARG cc_start: 0.7002 (ttm170) cc_final: 0.6054 (tpt170) REVERT: F 30 ILE cc_start: 0.8942 (mm) cc_final: 0.8740 (mm) REVERT: G 66 ASP cc_start: 0.6939 (p0) cc_final: 0.6729 (p0) REVERT: H 227 ASP cc_start: 0.6876 (m-30) cc_final: 0.6579 (m-30) REVERT: I 16 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7682 (mtmt) REVERT: K 199 LYS cc_start: 0.6500 (OUTLIER) cc_final: 0.6044 (mmmt) REVERT: K 726 TYR cc_start: 0.5464 (OUTLIER) cc_final: 0.5205 (m-80) REVERT: O 32 ASN cc_start: 0.7732 (p0) cc_final: 0.7173 (p0) REVERT: P 16 ILE cc_start: 0.6091 (tp) cc_final: 0.5656 (mt) REVERT: P 47 TYR cc_start: 0.8135 (m-10) cc_final: 0.7922 (m-80) REVERT: P 157 GLU cc_start: 0.7238 (pm20) cc_final: 0.7033 (mp0) REVERT: S 29 HIS cc_start: 0.4807 (OUTLIER) cc_final: 0.3819 (m90) REVERT: W 67 LYS cc_start: 0.7326 (mtmm) cc_final: 0.7115 (mttp) REVERT: W 93 LEU cc_start: 0.6656 (mp) cc_final: 0.6349 (mp) REVERT: X 172 LEU cc_start: 0.6148 (OUTLIER) cc_final: 0.5747 (mt) REVERT: l 161 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7282 (mm-30) REVERT: m 130 ASP cc_start: 0.6646 (m-30) cc_final: 0.5839 (m-30) REVERT: r 160 LYS cc_start: 0.5917 (ttmt) cc_final: 0.5474 (tptm) REVERT: r 168 SER cc_start: 0.7803 (m) cc_final: 0.7534 (p) REVERT: s 109 TYR cc_start: 0.6872 (m-10) cc_final: 0.6433 (m-10) REVERT: w 84 LEU cc_start: 0.5729 (OUTLIER) cc_final: 0.5459 (mm) REVERT: z 164 LYS cc_start: 0.7336 (tmtt) cc_final: 0.6238 (mmtm) REVERT: y 107 LYS cc_start: 0.6514 (mttp) cc_final: 0.6136 (mttt) outliers start: 239 outliers final: 151 residues processed: 1524 average time/residue: 0.6471 time to fit residues: 1684.6293 Evaluate side-chains 1440 residues out of total 7451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1283 time to evaluate : 5.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 166 GLU Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 260 ILE Chi-restraints excluded: chain J residue 72 GLU Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 283 SER Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain J residue 396 CYS Chi-restraints excluded: chain J residue 402 VAL Chi-restraints excluded: chain J residue 474 CYS Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 115 ASN Chi-restraints excluded: chain K residue 199 LYS Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain K residue 251 LEU Chi-restraints excluded: chain K residue 282 ILE Chi-restraints excluded: chain K residue 415 ASP Chi-restraints excluded: chain K residue 436 GLU Chi-restraints excluded: chain K residue 539 VAL Chi-restraints excluded: chain K residue 571 ILE Chi-restraints excluded: chain K residue 594 VAL Chi-restraints excluded: chain K residue 726 TYR Chi-restraints excluded: chain K residue 752 LEU Chi-restraints excluded: chain K residue 758 ILE Chi-restraints excluded: chain K residue 764 ILE Chi-restraints excluded: chain K residue 836 CYS Chi-restraints excluded: chain K residue 929 VAL Chi-restraints excluded: chain K residue 981 LEU Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 124 LYS Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 76 GLN Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain P residue 12 ILE Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 132 THR Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain S residue 29 HIS Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 96 ILE Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain W residue 166 LEU Chi-restraints excluded: chain X residue 114 SER Chi-restraints excluded: chain X residue 126 VAL Chi-restraints excluded: chain X residue 172 LEU Chi-restraints excluded: chain l residue 22 ILE Chi-restraints excluded: chain l residue 56 LEU Chi-restraints excluded: chain l residue 134 VAL Chi-restraints excluded: chain m residue 51 GLU Chi-restraints excluded: chain m residue 110 ILE Chi-restraints excluded: chain m residue 165 GLU Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 93 LEU Chi-restraints excluded: chain n residue 149 THR Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 83 PHE Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain o residue 98 LYS Chi-restraints excluded: chain p residue 13 THR Chi-restraints excluded: chain p residue 16 ILE Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain p residue 123 THR Chi-restraints excluded: chain p residue 132 THR Chi-restraints excluded: chain p residue 136 ASN Chi-restraints excluded: chain p residue 155 LYS Chi-restraints excluded: chain q residue 56 LEU Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain q residue 136 ASN Chi-restraints excluded: chain r residue 8 VAL Chi-restraints excluded: chain s residue 140 GLU Chi-restraints excluded: chain s residue 149 THR Chi-restraints excluded: chain s residue 154 VAL Chi-restraints excluded: chain s residue 161 GLU Chi-restraints excluded: chain t residue 4 GLN Chi-restraints excluded: chain t residue 49 VAL Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 108 ILE Chi-restraints excluded: chain w residue 13 THR Chi-restraints excluded: chain w residue 57 VAL Chi-restraints excluded: chain w residue 84 LEU Chi-restraints excluded: chain w residue 106 LEU Chi-restraints excluded: chain w residue 134 VAL Chi-restraints excluded: chain w residue 136 ASN Chi-restraints excluded: chain x residue 8 VAL Chi-restraints excluded: chain x residue 108 ILE Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain Z residue 60 LEU Chi-restraints excluded: chain Z residue 102 ILE Chi-restraints excluded: chain z residue 8 VAL Chi-restraints excluded: chain z residue 141 VAL Chi-restraints excluded: chain Y residue 16 ILE Chi-restraints excluded: chain Y residue 30 ILE Chi-restraints excluded: chain Y residue 31 THR Chi-restraints excluded: chain Y residue 41 VAL Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 141 VAL Chi-restraints excluded: chain Y residue 148 ILE Chi-restraints excluded: chain y residue 86 LEU Chi-restraints excluded: chain y residue 145 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 813 random chunks: chunk 264 optimal weight: 0.5980 chunk 707 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 461 optimal weight: 0.0980 chunk 193 optimal weight: 0.0670 chunk 786 optimal weight: 0.0570 chunk 652 optimal weight: 1.9990 chunk 364 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 260 optimal weight: 4.9990 chunk 412 optimal weight: 20.0000 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 185 ASN F 77 ASN G 133 ASN I 42 ASN ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 39 HIS l 79 GLN m 4 GLN ** m 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 14 ASN q 136 ASN s 29 HIS s 32 ASN s 147 ASN t 4 GLN Y 29 HIS Y 39 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 68817 Z= 0.167 Angle : 0.627 12.460 93484 Z= 0.322 Chirality : 0.046 0.232 10934 Planarity : 0.004 0.068 11500 Dihedral : 10.365 179.111 10190 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.01 % Allowed : 9.22 % Favored : 90.77 % Rotamer: Outliers : 2.90 % Allowed : 22.02 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.84 (0.09), residues: 8103 helix: -1.04 (0.11), residues: 2046 sheet: -1.53 (0.14), residues: 1309 loop : -2.48 (0.08), residues: 4748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 60 HIS 0.004 0.001 HIS P 29 PHE 0.034 0.001 PHE B 14 TYR 0.034 0.001 TYR W 112 ARG 0.009 0.000 ARG x 5 *********************** 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 1641 residues out of total 7451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 1425 time to evaluate : 6.250 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: A 79 ARG cc_start: 0.6244 (mmm160) cc_final: 0.5863 (mmt180) REVERT: B 114 ARG cc_start: 0.7063 (ttm170) cc_final: 0.6036 (tpt170) REVERT: G 66 ASP cc_start: 0.6872 (p0) cc_final: 0.6636 (p0) REVERT: G 83 LEU cc_start: 0.8357 (pp) cc_final: 0.8120 (pp) REVERT: H 227 ASP cc_start: 0.6730 (m-30) cc_final: 0.6429 (m-30) REVERT: H 259 MET cc_start: 0.7486 (mmm) cc_final: 0.7137 (mtt) REVERT: I 16 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7616 (mtmt) REVERT: K 199 LYS cc_start: 0.6461 (OUTLIER) cc_final: 0.6105 (mmmt) REVERT: K 726 TYR cc_start: 0.5353 (OUTLIER) cc_final: 0.5089 (m-10) REVERT: O 32 ASN cc_start: 0.7610 (p0) cc_final: 0.7273 (p0) REVERT: X 172 LEU cc_start: 0.6229 (OUTLIER) cc_final: 0.5775 (mt) REVERT: m 130 ASP cc_start: 0.6522 (m-30) cc_final: 0.5765 (m-30) REVERT: n 61 ASP cc_start: 0.6147 (t0) cc_final: 0.5077 (t0) REVERT: r 160 LYS cc_start: 0.5911 (ttmt) cc_final: 0.5653 (tptm) REVERT: r 168 SER cc_start: 0.7812 (m) cc_final: 0.7486 (p) REVERT: w 84 LEU cc_start: 0.5721 (OUTLIER) cc_final: 0.5441 (mm) REVERT: z 164 LYS cc_start: 0.7341 (tmtt) cc_final: 0.6213 (mmtm) REVERT: y 107 LYS cc_start: 0.6525 (mttp) cc_final: 0.6125 (mttt) outliers start: 216 outliers final: 143 residues processed: 1563 average time/residue: 0.6538 time to fit residues: 1755.1276 Evaluate side-chains 1441 residues out of total 7451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1293 time to evaluate : 5.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 166 GLU Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain J residue 72 GLU Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 283 SER Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain J residue 297 CYS Chi-restraints excluded: chain J residue 396 CYS Chi-restraints excluded: chain J residue 467 ILE Chi-restraints excluded: chain J residue 474 CYS Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 115 ASN Chi-restraints excluded: chain K residue 199 LYS Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 251 LEU Chi-restraints excluded: chain K residue 384 THR Chi-restraints excluded: chain K residue 415 ASP Chi-restraints excluded: chain K residue 436 GLU Chi-restraints excluded: chain K residue 571 ILE Chi-restraints excluded: chain K residue 594 VAL Chi-restraints excluded: chain K residue 652 ASP Chi-restraints excluded: chain K residue 726 TYR Chi-restraints excluded: chain K residue 752 LEU Chi-restraints excluded: chain K residue 758 ILE Chi-restraints excluded: chain K residue 764 ILE Chi-restraints excluded: chain K residue 836 CYS Chi-restraints excluded: chain K residue 981 LEU Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 124 LYS Chi-restraints excluded: chain O residue 6 GLU Chi-restraints excluded: chain O residue 16 ILE Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain P residue 12 ILE Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 132 THR Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 162 ASP Chi-restraints excluded: chain W residue 60 LEU Chi-restraints excluded: chain W residue 95 LEU Chi-restraints excluded: chain W residue 96 ILE Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain X residue 114 SER Chi-restraints excluded: chain X residue 172 LEU Chi-restraints excluded: chain l residue 22 ILE Chi-restraints excluded: chain l residue 134 VAL Chi-restraints excluded: chain m residue 110 ILE Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 93 LEU Chi-restraints excluded: chain n residue 102 ILE Chi-restraints excluded: chain n residue 149 THR Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 83 PHE Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain p residue 13 THR Chi-restraints excluded: chain p residue 16 ILE Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain p residue 123 THR Chi-restraints excluded: chain p residue 136 ASN Chi-restraints excluded: chain p residue 155 LYS Chi-restraints excluded: chain q residue 56 LEU Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain r residue 8 VAL Chi-restraints excluded: chain s residue 140 GLU Chi-restraints excluded: chain s residue 149 THR Chi-restraints excluded: chain s residue 154 VAL Chi-restraints excluded: chain t residue 4 GLN Chi-restraints excluded: chain t residue 49 VAL Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 84 LEU Chi-restraints excluded: chain w residue 35 GLU Chi-restraints excluded: chain w residue 57 VAL Chi-restraints excluded: chain w residue 84 LEU Chi-restraints excluded: chain w residue 106 LEU Chi-restraints excluded: chain w residue 134 VAL Chi-restraints excluded: chain w residue 136 ASN Chi-restraints excluded: chain x residue 8 VAL Chi-restraints excluded: chain x residue 57 VAL Chi-restraints excluded: chain x residue 108 ILE Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain Z residue 60 LEU Chi-restraints excluded: chain Z residue 102 ILE Chi-restraints excluded: chain z residue 8 VAL Chi-restraints excluded: chain z residue 141 VAL Chi-restraints excluded: chain Y residue 16 ILE Chi-restraints excluded: chain Y residue 30 ILE Chi-restraints excluded: chain Y residue 31 THR Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 113 SER Chi-restraints excluded: chain Y residue 141 VAL Chi-restraints excluded: chain y residue 86 LEU Chi-restraints excluded: chain y residue 102 ILE Chi-restraints excluded: chain y residue 145 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 813 random chunks: chunk 758 optimal weight: 7.9990 chunk 88 optimal weight: 7.9990 chunk 448 optimal weight: 4.9990 chunk 574 optimal weight: 2.9990 chunk 445 optimal weight: 1.9990 chunk 662 optimal weight: 7.9990 chunk 439 optimal weight: 9.9990 chunk 783 optimal weight: 0.9980 chunk 490 optimal weight: 0.9990 chunk 477 optimal weight: 8.9990 chunk 361 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 185 ASN F 77 ASN ** F 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 ASN I 172 GLN ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 ASN ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 39 HIS ** l 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 4 GLN m 76 GLN ** o 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 53 ASN q 14 ASN s 29 HIS s 135 ASN s 147 ASN t 4 GLN t 91 ASN x 79 GLN x 136 ASN ** Y 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 68817 Z= 0.305 Angle : 0.666 13.624 93484 Z= 0.342 Chirality : 0.048 0.262 10934 Planarity : 0.004 0.073 11500 Dihedral : 10.378 178.773 10190 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.01 % Allowed : 10.19 % Favored : 89.79 % Rotamer: Outliers : 3.17 % Allowed : 22.55 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.09), residues: 8103 helix: -1.03 (0.11), residues: 2091 sheet: -1.49 (0.14), residues: 1326 loop : -2.50 (0.08), residues: 4686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 60 HIS 0.006 0.001 HIS O 29 PHE 0.031 0.001 PHE s 9 TYR 0.031 0.002 TYR n 112 ARG 0.008 0.001 ARG X 97 *********************** 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 1541 residues out of total 7451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1305 time to evaluate : 6.935 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: B 28 GLN cc_start: 0.7291 (mp10) cc_final: 0.6856 (mm-40) REVERT: B 114 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6154 (tpt170) REVERT: G 66 ASP cc_start: 0.6958 (p0) cc_final: 0.6733 (p0) REVERT: H 227 ASP cc_start: 0.6774 (m-30) cc_final: 0.6499 (m-30) REVERT: J 299 LYS cc_start: 0.7209 (OUTLIER) cc_final: 0.6861 (mtmt) REVERT: K 199 LYS cc_start: 0.6528 (OUTLIER) cc_final: 0.6243 (mmmt) REVERT: K 654 LEU cc_start: 0.8689 (tt) cc_final: 0.8480 (tt) REVERT: K 726 TYR cc_start: 0.5531 (OUTLIER) cc_final: 0.5320 (m-80) REVERT: O 32 ASN cc_start: 0.7668 (p0) cc_final: 0.7245 (p0) REVERT: P 47 TYR cc_start: 0.8175 (m-80) cc_final: 0.7688 (m-80) REVERT: P 109 TYR cc_start: 0.8203 (m-80) cc_final: 0.7908 (m-80) REVERT: Q 137 ILE cc_start: 0.6199 (mp) cc_final: 0.5903 (mp) REVERT: S 29 HIS cc_start: 0.4729 (OUTLIER) cc_final: 0.3618 (m90) REVERT: X 67 LYS cc_start: 0.7467 (mptt) cc_final: 0.7209 (mptt) REVERT: X 172 LEU cc_start: 0.6450 (OUTLIER) cc_final: 0.6073 (mt) REVERT: m 130 ASP cc_start: 0.6659 (m-30) cc_final: 0.5844 (m-30) REVERT: r 160 LYS cc_start: 0.5865 (ttmt) cc_final: 0.5430 (tptm) REVERT: r 168 SER cc_start: 0.7908 (m) cc_final: 0.7577 (p) REVERT: w 84 LEU cc_start: 0.5684 (OUTLIER) cc_final: 0.5423 (mm) REVERT: z 164 LYS cc_start: 0.7449 (tmtt) cc_final: 0.6274 (mmtm) REVERT: y 107 LYS cc_start: 0.6521 (mttp) cc_final: 0.6107 (mttt) outliers start: 236 outliers final: 173 residues processed: 1449 average time/residue: 0.6958 time to fit residues: 1740.9614 Evaluate side-chains 1435 residues out of total 7451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1255 time to evaluate : 5.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 114 ARG Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 247 LEU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 166 GLU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 72 GLU Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 125 ASP Chi-restraints excluded: chain J residue 283 SER Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain J residue 297 CYS Chi-restraints excluded: chain J residue 299 LYS Chi-restraints excluded: chain J residue 396 CYS Chi-restraints excluded: chain J residue 402 VAL Chi-restraints excluded: chain J residue 474 CYS Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 199 LYS Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 251 LEU Chi-restraints excluded: chain K residue 282 ILE Chi-restraints excluded: chain K residue 384 THR Chi-restraints excluded: chain K residue 415 ASP Chi-restraints excluded: chain K residue 436 GLU Chi-restraints excluded: chain K residue 571 ILE Chi-restraints excluded: chain K residue 594 VAL Chi-restraints excluded: chain K residue 652 ASP Chi-restraints excluded: chain K residue 670 ILE Chi-restraints excluded: chain K residue 726 TYR Chi-restraints excluded: chain K residue 752 LEU Chi-restraints excluded: chain K residue 758 ILE Chi-restraints excluded: chain K residue 764 ILE Chi-restraints excluded: chain K residue 836 CYS Chi-restraints excluded: chain K residue 929 VAL Chi-restraints excluded: chain K residue 1026 VAL Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 124 LYS Chi-restraints excluded: chain O residue 16 ILE Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 76 GLN Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 123 THR Chi-restraints excluded: chain P residue 12 ILE Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 132 THR Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain S residue 29 HIS Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 162 ASP Chi-restraints excluded: chain W residue 95 LEU Chi-restraints excluded: chain W residue 96 ILE Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 141 VAL Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain W residue 166 LEU Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain X residue 172 LEU Chi-restraints excluded: chain l residue 22 ILE Chi-restraints excluded: chain l residue 56 LEU Chi-restraints excluded: chain l residue 134 VAL Chi-restraints excluded: chain m residue 51 GLU Chi-restraints excluded: chain m residue 110 ILE Chi-restraints excluded: chain m residue 165 GLU Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 93 LEU Chi-restraints excluded: chain n residue 149 THR Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain p residue 13 THR Chi-restraints excluded: chain p residue 16 ILE Chi-restraints excluded: chain p residue 23 THR Chi-restraints excluded: chain p residue 53 ASN Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain p residue 123 THR Chi-restraints excluded: chain p residue 136 ASN Chi-restraints excluded: chain p residue 155 LYS Chi-restraints excluded: chain q residue 56 LEU Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain r residue 8 VAL Chi-restraints excluded: chain r residue 141 VAL Chi-restraints excluded: chain s residue 140 GLU Chi-restraints excluded: chain s residue 149 THR Chi-restraints excluded: chain s residue 154 VAL Chi-restraints excluded: chain t residue 4 GLN Chi-restraints excluded: chain t residue 49 VAL Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 84 LEU Chi-restraints excluded: chain t residue 112 TYR Chi-restraints excluded: chain t residue 133 ILE Chi-restraints excluded: chain w residue 57 VAL Chi-restraints excluded: chain w residue 84 LEU Chi-restraints excluded: chain w residue 134 VAL Chi-restraints excluded: chain w residue 136 ASN Chi-restraints excluded: chain x residue 8 VAL Chi-restraints excluded: chain x residue 57 VAL Chi-restraints excluded: chain x residue 66 VAL Chi-restraints excluded: chain x residue 108 ILE Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain Z residue 60 LEU Chi-restraints excluded: chain Z residue 102 ILE Chi-restraints excluded: chain z residue 8 VAL Chi-restraints excluded: chain z residue 141 VAL Chi-restraints excluded: chain Y residue 16 ILE Chi-restraints excluded: chain Y residue 30 ILE Chi-restraints excluded: chain Y residue 31 THR Chi-restraints excluded: chain Y residue 41 VAL Chi-restraints excluded: chain Y residue 44 ILE Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 113 SER Chi-restraints excluded: chain Y residue 137 ILE Chi-restraints excluded: chain Y residue 141 VAL Chi-restraints excluded: chain Y residue 148 ILE Chi-restraints excluded: chain y residue 86 LEU Chi-restraints excluded: chain y residue 145 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 813 random chunks: chunk 484 optimal weight: 0.5980 chunk 312 optimal weight: 0.9990 chunk 468 optimal weight: 0.0000 chunk 236 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 151 optimal weight: 0.9980 chunk 498 optimal weight: 5.9990 chunk 533 optimal weight: 8.9990 chunk 387 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 615 optimal weight: 7.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 185 ASN F 166 ASN ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 110 GLN P 76 GLN ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 4 GLN ** p 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 136 ASN s 29 HIS t 4 GLN Y 29 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 68817 Z= 0.176 Angle : 0.636 13.867 93484 Z= 0.326 Chirality : 0.046 0.228 10934 Planarity : 0.004 0.068 11500 Dihedral : 10.299 178.261 10190 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.01 % Allowed : 9.21 % Favored : 90.78 % Rotamer: Outliers : 2.68 % Allowed : 23.31 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.69 (0.09), residues: 8103 helix: -0.94 (0.11), residues: 2078 sheet: -1.39 (0.14), residues: 1340 loop : -2.40 (0.08), residues: 4685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 60 HIS 0.005 0.001 HIS P 29 PHE 0.034 0.001 PHE B 14 TYR 0.030 0.001 TYR n 112 ARG 0.013 0.000 ARG p 55 *********************** 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 1577 residues out of total 7451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 1377 time to evaluate : 5.850 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: B 28 GLN cc_start: 0.7112 (mp10) cc_final: 0.6882 (mm-40) REVERT: B 114 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.6011 (tpt170) REVERT: G 83 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8169 (pp) REVERT: H 227 ASP cc_start: 0.6582 (m-30) cc_final: 0.6305 (m-30) REVERT: I 16 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7651 (mtmt) REVERT: I 60 LEU cc_start: 0.8657 (mt) cc_final: 0.8446 (mp) REVERT: J 299 LYS cc_start: 0.7241 (OUTLIER) cc_final: 0.6887 (mtmt) REVERT: J 414 GLU cc_start: 0.6532 (mp0) cc_final: 0.6216 (mp0) REVERT: N 96 ILE cc_start: 0.8881 (mm) cc_final: 0.8647 (mt) REVERT: P 47 TYR cc_start: 0.8119 (m-80) cc_final: 0.7689 (m-80) REVERT: S 29 HIS cc_start: 0.4536 (OUTLIER) cc_final: 0.3398 (m90) REVERT: T 35 GLU cc_start: 0.5387 (mm-30) cc_final: 0.5175 (mm-30) REVERT: W 67 LYS cc_start: 0.7205 (mtmm) cc_final: 0.6991 (mttp) REVERT: X 172 LEU cc_start: 0.6373 (OUTLIER) cc_final: 0.5915 (mt) REVERT: n 102 ILE cc_start: 0.6916 (OUTLIER) cc_final: 0.6348 (mm) REVERT: r 160 LYS cc_start: 0.5806 (ttmt) cc_final: 0.5408 (tptm) REVERT: r 165 GLU cc_start: 0.7155 (pt0) cc_final: 0.6929 (pt0) REVERT: r 168 SER cc_start: 0.7825 (m) cc_final: 0.7521 (p) REVERT: w 84 LEU cc_start: 0.5626 (OUTLIER) cc_final: 0.5366 (mm) REVERT: z 164 LYS cc_start: 0.7386 (tmtt) cc_final: 0.6110 (mmtm) REVERT: y 107 LYS cc_start: 0.6590 (mttp) cc_final: 0.6222 (mttt) outliers start: 200 outliers final: 162 residues processed: 1504 average time/residue: 0.6628 time to fit residues: 1710.1325 Evaluate side-chains 1463 residues out of total 7451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1293 time to evaluate : 5.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 114 ARG Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 166 GLU Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain J residue 72 GLU Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 283 SER Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain J residue 297 CYS Chi-restraints excluded: chain J residue 299 LYS Chi-restraints excluded: chain J residue 396 CYS Chi-restraints excluded: chain J residue 474 CYS Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 251 LEU Chi-restraints excluded: chain K residue 384 THR Chi-restraints excluded: chain K residue 415 ASP Chi-restraints excluded: chain K residue 436 GLU Chi-restraints excluded: chain K residue 571 ILE Chi-restraints excluded: chain K residue 594 VAL Chi-restraints excluded: chain K residue 652 ASP Chi-restraints excluded: chain K residue 752 LEU Chi-restraints excluded: chain K residue 758 ILE Chi-restraints excluded: chain K residue 764 ILE Chi-restraints excluded: chain K residue 836 CYS Chi-restraints excluded: chain K residue 892 VAL Chi-restraints excluded: chain K residue 929 VAL Chi-restraints excluded: chain K residue 1026 VAL Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 124 LYS Chi-restraints excluded: chain O residue 6 GLU Chi-restraints excluded: chain O residue 16 ILE Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 76 GLN Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 123 THR Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 145 ILE Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain S residue 29 HIS Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 134 VAL Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 162 ASP Chi-restraints excluded: chain W residue 60 LEU Chi-restraints excluded: chain W residue 95 LEU Chi-restraints excluded: chain W residue 96 ILE Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 141 VAL Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain W residue 166 LEU Chi-restraints excluded: chain X residue 43 VAL Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 172 LEU Chi-restraints excluded: chain l residue 22 ILE Chi-restraints excluded: chain l residue 134 VAL Chi-restraints excluded: chain m residue 51 GLU Chi-restraints excluded: chain m residue 110 ILE Chi-restraints excluded: chain m residue 165 GLU Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 93 LEU Chi-restraints excluded: chain n residue 102 ILE Chi-restraints excluded: chain n residue 149 THR Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 83 PHE Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain p residue 16 ILE Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain p residue 123 THR Chi-restraints excluded: chain p residue 132 THR Chi-restraints excluded: chain p residue 136 ASN Chi-restraints excluded: chain p residue 155 LYS Chi-restraints excluded: chain q residue 3 THR Chi-restraints excluded: chain q residue 56 LEU Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain q residue 136 ASN Chi-restraints excluded: chain q residue 149 THR Chi-restraints excluded: chain r residue 8 VAL Chi-restraints excluded: chain r residue 38 ILE Chi-restraints excluded: chain r residue 141 VAL Chi-restraints excluded: chain s residue 140 GLU Chi-restraints excluded: chain s residue 149 THR Chi-restraints excluded: chain s residue 154 VAL Chi-restraints excluded: chain t residue 4 GLN Chi-restraints excluded: chain t residue 49 VAL Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 84 LEU Chi-restraints excluded: chain t residue 85 THR Chi-restraints excluded: chain t residue 112 TYR Chi-restraints excluded: chain w residue 13 THR Chi-restraints excluded: chain w residue 57 VAL Chi-restraints excluded: chain w residue 84 LEU Chi-restraints excluded: chain w residue 134 VAL Chi-restraints excluded: chain w residue 136 ASN Chi-restraints excluded: chain x residue 8 VAL Chi-restraints excluded: chain x residue 57 VAL Chi-restraints excluded: chain x residue 66 VAL Chi-restraints excluded: chain x residue 108 ILE Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain Z residue 60 LEU Chi-restraints excluded: chain Z residue 102 ILE Chi-restraints excluded: chain z residue 8 VAL Chi-restraints excluded: chain z residue 141 VAL Chi-restraints excluded: chain Y residue 16 ILE Chi-restraints excluded: chain Y residue 29 HIS Chi-restraints excluded: chain Y residue 30 ILE Chi-restraints excluded: chain Y residue 31 THR Chi-restraints excluded: chain Y residue 41 VAL Chi-restraints excluded: chain Y residue 44 ILE Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 113 SER Chi-restraints excluded: chain Y residue 141 VAL Chi-restraints excluded: chain y residue 86 LEU Chi-restraints excluded: chain y residue 102 ILE Chi-restraints excluded: chain y residue 145 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 813 random chunks: chunk 712 optimal weight: 4.9990 chunk 750 optimal weight: 8.9990 chunk 684 optimal weight: 5.9990 chunk 730 optimal weight: 9.9990 chunk 439 optimal weight: 8.9990 chunk 318 optimal weight: 6.9990 chunk 573 optimal weight: 5.9990 chunk 224 optimal weight: 5.9990 chunk 659 optimal weight: 6.9990 chunk 690 optimal weight: 10.0000 chunk 727 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 106 GLN ** D 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 110 GLN K 172 ASN K 895 ASN L 29 HIS ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 39 HIS ** T 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 174 GLN ** l 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 136 ASN s 32 ASN s 147 ASN w 53 ASN ** Y 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.103 68817 Z= 0.603 Angle : 0.802 13.003 93484 Z= 0.412 Chirality : 0.052 0.293 10934 Planarity : 0.005 0.077 11500 Dihedral : 10.609 178.505 10190 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.01 % Allowed : 11.51 % Favored : 88.47 % Rotamer: Outliers : 3.15 % Allowed : 23.57 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.32 % 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: -2.99 (0.09), residues: 8103 helix: -1.27 (0.11), residues: 2132 sheet: -1.52 (0.14), residues: 1326 loop : -2.56 (0.08), residues: 4645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP G 281 HIS 0.023 0.002 HIS Y 29 PHE 0.028 0.002 PHE H 188 TYR 0.040 0.002 TYR r 112 ARG 0.012 0.001 ARG r 118 *********************** 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 1470 residues out of total 7451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1235 time to evaluate : 5.873 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: A 111 GLN cc_start: 0.7658 (tm-30) cc_final: 0.7319 (tt0) REVERT: B 79 ARG cc_start: 0.1902 (OUTLIER) cc_final: 0.0823 (tmm160) REVERT: G 83 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8291 (pp) REVERT: H 227 ASP cc_start: 0.6890 (m-30) cc_final: 0.6655 (m-30) REVERT: J 299 LYS cc_start: 0.7257 (OUTLIER) cc_final: 0.6918 (mtmt) REVERT: J 414 GLU cc_start: 0.6577 (mp0) cc_final: 0.6301 (mp0) REVERT: P 16 ILE cc_start: 0.6334 (tp) cc_final: 0.6038 (mp) REVERT: Q 146 TYR cc_start: 0.4642 (m-80) cc_final: 0.4393 (m-80) REVERT: S 29 HIS cc_start: 0.4999 (OUTLIER) cc_final: 0.3885 (m90) REVERT: W 67 LYS cc_start: 0.7344 (mtmm) cc_final: 0.7130 (mttp) REVERT: X 67 LYS cc_start: 0.7594 (mptt) cc_final: 0.7312 (mptt) REVERT: t 42 LEU cc_start: 0.7911 (tp) cc_final: 0.7623 (tp) REVERT: w 84 LEU cc_start: 0.5524 (OUTLIER) cc_final: 0.5043 (mm) REVERT: Z 18 ILE cc_start: 0.4680 (pp) cc_final: 0.4376 (pp) REVERT: z 164 LYS cc_start: 0.7510 (tmtt) cc_final: 0.6415 (mmtm) REVERT: Y 29 HIS cc_start: 0.3547 (OUTLIER) cc_final: 0.3295 (t-90) REVERT: y 107 LYS cc_start: 0.6717 (mttp) cc_final: 0.6258 (mttt) outliers start: 235 outliers final: 199 residues processed: 1378 average time/residue: 0.6868 time to fit residues: 1632.1052 Evaluate side-chains 1394 residues out of total 7451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 1189 time to evaluate : 5.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 166 GLU Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain J residue 72 GLU Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 125 ASP Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 283 SER Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain J residue 297 CYS Chi-restraints excluded: chain J residue 299 LYS Chi-restraints excluded: chain J residue 396 CYS Chi-restraints excluded: chain J residue 402 VAL Chi-restraints excluded: chain J residue 474 CYS Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 251 LEU Chi-restraints excluded: chain K residue 282 ILE Chi-restraints excluded: chain K residue 384 THR Chi-restraints excluded: chain K residue 386 LEU Chi-restraints excluded: chain K residue 415 ASP Chi-restraints excluded: chain K residue 436 GLU Chi-restraints excluded: chain K residue 571 ILE Chi-restraints excluded: chain K residue 594 VAL Chi-restraints excluded: chain K residue 652 ASP Chi-restraints excluded: chain K residue 752 LEU Chi-restraints excluded: chain K residue 758 ILE Chi-restraints excluded: chain K residue 764 ILE Chi-restraints excluded: chain K residue 836 CYS Chi-restraints excluded: chain K residue 929 VAL Chi-restraints excluded: chain K residue 1026 VAL Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain O residue 16 ILE Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain O residue 32 ASN Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 76 GLN Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain P residue 132 THR Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain S residue 29 HIS Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 134 VAL Chi-restraints excluded: chain S residue 172 LEU Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 162 ASP Chi-restraints excluded: chain W residue 60 LEU Chi-restraints excluded: chain W residue 95 LEU Chi-restraints excluded: chain W residue 96 ILE Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 141 VAL Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain W residue 166 LEU Chi-restraints excluded: chain X residue 8 VAL Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain X residue 43 VAL Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 126 VAL Chi-restraints excluded: chain l residue 22 ILE Chi-restraints excluded: chain l residue 30 ILE Chi-restraints excluded: chain l residue 134 VAL Chi-restraints excluded: chain m residue 10 ILE Chi-restraints excluded: chain m residue 51 GLU Chi-restraints excluded: chain m residue 56 LEU Chi-restraints excluded: chain m residue 110 ILE Chi-restraints excluded: chain m residue 165 GLU Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 93 LEU Chi-restraints excluded: chain n residue 149 THR Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain p residue 13 THR Chi-restraints excluded: chain p residue 16 ILE Chi-restraints excluded: chain p residue 23 THR Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain p residue 123 THR Chi-restraints excluded: chain p residue 132 THR Chi-restraints excluded: chain p residue 136 ASN Chi-restraints excluded: chain p residue 155 LYS Chi-restraints excluded: chain q residue 3 THR Chi-restraints excluded: chain q residue 56 LEU Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain q residue 136 ASN Chi-restraints excluded: chain q residue 149 THR Chi-restraints excluded: chain r residue 8 VAL Chi-restraints excluded: chain r residue 38 ILE Chi-restraints excluded: chain r residue 59 THR Chi-restraints excluded: chain r residue 141 VAL Chi-restraints excluded: chain s residue 140 GLU Chi-restraints excluded: chain s residue 149 THR Chi-restraints excluded: chain s residue 154 VAL Chi-restraints excluded: chain s residue 161 GLU Chi-restraints excluded: chain t residue 18 ILE Chi-restraints excluded: chain t residue 49 VAL Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 84 LEU Chi-restraints excluded: chain t residue 85 THR Chi-restraints excluded: chain t residue 96 ILE Chi-restraints excluded: chain t residue 112 TYR Chi-restraints excluded: chain t residue 133 ILE Chi-restraints excluded: chain t residue 159 VAL Chi-restraints excluded: chain w residue 57 VAL Chi-restraints excluded: chain w residue 84 LEU Chi-restraints excluded: chain w residue 134 VAL Chi-restraints excluded: chain w residue 136 ASN Chi-restraints excluded: chain x residue 8 VAL Chi-restraints excluded: chain x residue 57 VAL Chi-restraints excluded: chain x residue 66 VAL Chi-restraints excluded: chain x residue 108 ILE Chi-restraints excluded: chain x residue 110 ILE Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain Z residue 60 LEU Chi-restraints excluded: chain Z residue 102 ILE Chi-restraints excluded: chain z residue 8 VAL Chi-restraints excluded: chain z residue 141 VAL Chi-restraints excluded: chain Y residue 16 ILE Chi-restraints excluded: chain Y residue 29 HIS Chi-restraints excluded: chain Y residue 31 THR Chi-restraints excluded: chain Y residue 41 VAL Chi-restraints excluded: chain Y residue 93 LEU Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 113 SER Chi-restraints excluded: chain Y residue 141 VAL Chi-restraints excluded: chain Y residue 148 ILE Chi-restraints excluded: chain y residue 86 LEU Chi-restraints excluded: chain y residue 102 ILE Chi-restraints excluded: chain y residue 145 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 813 random chunks: chunk 479 optimal weight: 7.9990 chunk 772 optimal weight: 5.9990 chunk 471 optimal weight: 2.9990 chunk 366 optimal weight: 6.9990 chunk 536 optimal weight: 8.9990 chunk 809 optimal weight: 6.9990 chunk 745 optimal weight: 20.0000 chunk 644 optimal weight: 0.1980 chunk 66 optimal weight: 0.9990 chunk 498 optimal weight: 6.9990 chunk 395 optimal weight: 2.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN E 185 ASN F 138 ASN ** F 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 GLN ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 174 GLN l 39 HIS ** o 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 150 GLN ** p 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 136 ASN s 29 HIS s 135 ASN t 4 GLN Y 29 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 68817 Z= 0.329 Angle : 0.710 13.675 93484 Z= 0.365 Chirality : 0.049 0.256 10934 Planarity : 0.005 0.070 11500 Dihedral : 10.567 177.786 10190 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.01 % Allowed : 10.58 % Favored : 89.41 % Rotamer: Outliers : 2.79 % Allowed : 24.44 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.32 % 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: -2.88 (0.09), residues: 8103 helix: -1.14 (0.11), residues: 2104 sheet: -1.45 (0.14), residues: 1299 loop : -2.51 (0.08), residues: 4700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 281 HIS 0.007 0.001 HIS p 39 PHE 0.029 0.001 PHE B 14 TYR 0.038 0.002 TYR r 112 ARG 0.010 0.001 ARG A 79 ********************** 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 1467 residues out of total 7451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1259 time to evaluate : 5.843 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: A 111 GLN cc_start: 0.7624 (tm-30) cc_final: 0.7277 (tt0) REVERT: B 28 GLN cc_start: 0.7175 (mp10) cc_final: 0.6818 (mm-40) REVERT: G 83 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8233 (pp) REVERT: H 227 ASP cc_start: 0.6778 (m-30) cc_final: 0.6493 (m-30) REVERT: J 299 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6881 (mtmt) REVERT: J 414 GLU cc_start: 0.6495 (mp0) cc_final: 0.6260 (mp0) REVERT: P 16 ILE cc_start: 0.6312 (tp) cc_final: 0.6048 (mp) REVERT: S 29 HIS cc_start: 0.4736 (OUTLIER) cc_final: 0.3731 (m90) REVERT: p 7 TYR cc_start: 0.8303 (t80) cc_final: 0.8067 (t80) REVERT: r 165 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6860 (pt0) REVERT: t 42 LEU cc_start: 0.7875 (tp) cc_final: 0.7574 (tp) REVERT: w 84 LEU cc_start: 0.5515 (OUTLIER) cc_final: 0.5088 (mm) REVERT: Z 18 ILE cc_start: 0.4581 (OUTLIER) cc_final: 0.4234 (pp) REVERT: y 107 LYS cc_start: 0.6788 (mttp) cc_final: 0.6369 (mttt) outliers start: 208 outliers final: 187 residues processed: 1382 average time/residue: 0.6502 time to fit residues: 1537.2635 Evaluate side-chains 1423 residues out of total 7451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1230 time to evaluate : 5.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 114 ARG Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain I residue 166 GLU Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 72 GLU Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 283 SER Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain J residue 297 CYS Chi-restraints excluded: chain J residue 299 LYS Chi-restraints excluded: chain J residue 396 CYS Chi-restraints excluded: chain J residue 402 VAL Chi-restraints excluded: chain J residue 474 CYS Chi-restraints excluded: chain J residue 475 VAL Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 251 LEU Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain K residue 282 ILE Chi-restraints excluded: chain K residue 384 THR Chi-restraints excluded: chain K residue 415 ASP Chi-restraints excluded: chain K residue 436 GLU Chi-restraints excluded: chain K residue 571 ILE Chi-restraints excluded: chain K residue 594 VAL Chi-restraints excluded: chain K residue 617 GLU Chi-restraints excluded: chain K residue 652 ASP Chi-restraints excluded: chain K residue 705 VAL Chi-restraints excluded: chain K residue 752 LEU Chi-restraints excluded: chain K residue 758 ILE Chi-restraints excluded: chain K residue 764 ILE Chi-restraints excluded: chain K residue 836 CYS Chi-restraints excluded: chain K residue 929 VAL Chi-restraints excluded: chain K residue 1026 VAL Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 16 ILE Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 76 GLN Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain P residue 132 THR Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain S residue 29 HIS Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 134 VAL Chi-restraints excluded: chain S residue 172 LEU Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 162 ASP Chi-restraints excluded: chain W residue 60 LEU Chi-restraints excluded: chain W residue 95 LEU Chi-restraints excluded: chain W residue 96 ILE Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 141 VAL Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain W residue 166 LEU Chi-restraints excluded: chain X residue 43 VAL Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain l residue 22 ILE Chi-restraints excluded: chain l residue 30 ILE Chi-restraints excluded: chain l residue 134 VAL Chi-restraints excluded: chain m residue 51 GLU Chi-restraints excluded: chain m residue 56 LEU Chi-restraints excluded: chain m residue 110 ILE Chi-restraints excluded: chain m residue 165 GLU Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 93 LEU Chi-restraints excluded: chain n residue 149 THR Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain p residue 13 THR Chi-restraints excluded: chain p residue 16 ILE Chi-restraints excluded: chain p residue 23 THR Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain p residue 123 THR Chi-restraints excluded: chain p residue 132 THR Chi-restraints excluded: chain p residue 136 ASN Chi-restraints excluded: chain p residue 155 LYS Chi-restraints excluded: chain q residue 3 THR Chi-restraints excluded: chain q residue 56 LEU Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain q residue 136 ASN Chi-restraints excluded: chain q residue 149 THR Chi-restraints excluded: chain r residue 8 VAL Chi-restraints excluded: chain r residue 38 ILE Chi-restraints excluded: chain r residue 141 VAL Chi-restraints excluded: chain r residue 165 GLU Chi-restraints excluded: chain s residue 140 GLU Chi-restraints excluded: chain s residue 149 THR Chi-restraints excluded: chain s residue 154 VAL Chi-restraints excluded: chain s residue 161 GLU Chi-restraints excluded: chain t residue 4 GLN Chi-restraints excluded: chain t residue 18 ILE Chi-restraints excluded: chain t residue 49 VAL Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 84 LEU Chi-restraints excluded: chain t residue 85 THR Chi-restraints excluded: chain t residue 112 TYR Chi-restraints excluded: chain t residue 133 ILE Chi-restraints excluded: chain w residue 13 THR Chi-restraints excluded: chain w residue 57 VAL Chi-restraints excluded: chain w residue 84 LEU Chi-restraints excluded: chain w residue 134 VAL Chi-restraints excluded: chain w residue 136 ASN Chi-restraints excluded: chain x residue 8 VAL Chi-restraints excluded: chain x residue 57 VAL Chi-restraints excluded: chain x residue 66 VAL Chi-restraints excluded: chain x residue 74 THR Chi-restraints excluded: chain x residue 108 ILE Chi-restraints excluded: chain x residue 110 ILE Chi-restraints excluded: chain Z residue 18 ILE Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain Z residue 60 LEU Chi-restraints excluded: chain Z residue 102 ILE Chi-restraints excluded: chain z residue 8 VAL Chi-restraints excluded: chain z residue 141 VAL Chi-restraints excluded: chain Y residue 16 ILE Chi-restraints excluded: chain Y residue 29 HIS Chi-restraints excluded: chain Y residue 31 THR Chi-restraints excluded: chain Y residue 41 VAL Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 113 SER Chi-restraints excluded: chain Y residue 141 VAL Chi-restraints excluded: chain Y residue 148 ILE Chi-restraints excluded: chain y residue 86 LEU Chi-restraints excluded: chain y residue 102 ILE Chi-restraints excluded: chain y residue 145 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 813 random chunks: chunk 512 optimal weight: 0.9980 chunk 687 optimal weight: 20.0000 chunk 197 optimal weight: 0.5980 chunk 594 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 179 optimal weight: 0.9990 chunk 645 optimal weight: 3.9990 chunk 270 optimal weight: 1.9990 chunk 663 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 118 optimal weight: 7.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 13 HIS ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 ASN F 77 ASN F 166 ASN G 19 HIS I 172 GLN ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 110 GLN K 172 ASN ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 119 ASN o 4 GLN ** p 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 136 ASN s 29 HIS s 147 ASN t 4 GLN Y 29 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.168253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.107788 restraints weight = 114050.088| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.17 r_work: 0.3216 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 68817 Z= 0.196 Angle : 0.674 13.693 93484 Z= 0.346 Chirality : 0.047 0.268 10934 Planarity : 0.004 0.066 11500 Dihedral : 10.417 177.935 10190 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.01 % Allowed : 10.03 % Favored : 89.95 % Rotamer: Outliers : 2.68 % Allowed : 24.69 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.70 (0.09), residues: 8103 helix: -0.98 (0.11), residues: 2075 sheet: -1.39 (0.14), residues: 1318 loop : -2.38 (0.08), residues: 4710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 60 HIS 0.008 0.001 HIS Y 29 PHE 0.033 0.001 PHE B 14 TYR 0.043 0.001 TYR R 169 ARG 0.016 0.001 ARG t 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25992.22 seconds wall clock time: 446 minutes 38.20 seconds (26798.20 seconds total)