Starting phenix.real_space_refine on Wed Feb 21 19:23:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6q_7808/02_2024/6d6q_7808_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6q_7808/02_2024/6d6q_7808.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6q_7808/02_2024/6d6q_7808.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6q_7808/02_2024/6d6q_7808.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6q_7808/02_2024/6d6q_7808_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d6q_7808/02_2024/6d6q_7808_updated.pdb" } resolution = 3.45 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= 0.003 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 Zn 1 6.06 5 P 61 5.49 5 Mg 1 5.21 5 S 196 5.16 5 C 19695 2.51 5 N 5611 2.21 5 O 6074 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 70": "NH1" <-> "NH2" Residue "B ARG 63": "NH1" <-> "NH2" Residue "B ARG 203": "NH1" <-> "NH2" Residue "C ARG 15": "NH1" <-> "NH2" Residue "D PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 50": "NH1" <-> "NH2" Residue "E ARG 96": "NH1" <-> "NH2" Residue "E PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 167": "NH1" <-> "NH2" Residue "E TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 261": "NH1" <-> "NH2" Residue "F ARG 265": "NH1" <-> "NH2" Residue "G ARG 108": "NH1" <-> "NH2" Residue "G PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 154": "NH1" <-> "NH2" Residue "G ARG 186": "NH1" <-> "NH2" Residue "H ARG 11": "NH1" <-> "NH2" Residue "H ARG 103": "NH1" <-> "NH2" Residue "H PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 6": "NH1" <-> "NH2" Residue "I ARG 13": "NH1" <-> "NH2" Residue "I ARG 81": "NH1" <-> "NH2" Residue "I PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 100": "NH1" <-> "NH2" Residue "I ARG 109": "NH1" <-> "NH2" Residue "I ARG 123": "NH1" <-> "NH2" Residue "K ARG 86": "NH1" <-> "NH2" Residue "K ARG 407": "NH1" <-> "NH2" Residue "K ARG 467": "NH1" <-> "NH2" Residue "K ARG 557": "NH1" <-> "NH2" Residue "K PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 611": "NH1" <-> "NH2" Residue "K ARG 624": "NH1" <-> "NH2" Residue "K ARG 638": "NH1" <-> "NH2" Residue "K ARG 741": "NH1" <-> "NH2" Residue "K ARG 781": "NH1" <-> "NH2" Residue "K ARG 829": "NH1" <-> "NH2" Residue "L ARG 8": "NH1" <-> "NH2" Residue "L ARG 15": "NH1" <-> "NH2" Residue "M PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 180": "NH1" <-> "NH2" Residue "M ARG 995": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31639 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2264 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 10, 'TRANS': 276} Chain: "B" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1824 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 7, 'TRANS': 233} Chain: "C" Number of atoms: 2020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2020 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 14, 'TRANS': 250} Chain: "D" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1566 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "E" Number of atoms: 2194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2194 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain: "F" Number of atoms: 1859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1859 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 19, 'TRANS': 232} Chain breaks: 1 Chain: "G" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1806 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain breaks: 1 Chain: "H" Number of atoms: 2263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2263 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 11, 'TRANS': 277} Chain breaks: 1 Chain: "I" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1407 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain: "J" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 86 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "K" Number of atoms: 6856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 853, 6856 Classifications: {'peptide': 853} Link IDs: {'PTRANS': 40, 'TRANS': 812} Chain breaks: 6 Chain: "L" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 573 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "M" Number of atoms: 5648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 709, 5648 Classifications: {'peptide': 709} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 683} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "N" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 278 Classifications: {'RNA': 13} Modifications used: {'5*END': 1, 'rna3p_pur': 9, 'rna3p_pyr': 4} Link IDs: {'rna3p': 12} Chain: "O" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 966 Classifications: {'DNA': 13, 'RNA': 35} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 5, 'rna3p_pur': 17, 'rna3p_pyr': 11} Link IDs: {'rna2p': 6, 'rna3p': 41} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {' C%rna3p_pyr:plan': 2, ' A%rna3p_pur:plan2': 1, ' A%rna2p_pur:plan': 1, ' A%rna2p_pur:plan2': 1, ' C%rna3p_pyr:plan2': 2, ' A%rna3p_pur:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17538 SG CYS K 31 45.162 135.806 78.689 1.00 59.63 S ATOM 17564 SG CYS K 36 45.036 136.870 82.511 1.00 80.34 S ATOM 17580 SG CYS K 39 44.022 133.227 81.287 1.00 84.66 S Time building chain proxies: 17.18, per 1000 atoms: 0.54 Number of scatterers: 31639 At special positions: 0 Unit cell: (164.78, 191.53, 174.41, 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 S 196 16.00 P 61 15.00 Mg 1 11.99 O 6074 8.00 N 5611 7.00 C 19695 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.75 Conformation dependent library (CDL) restraints added in 5.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K2002 " pdb="ZN ZN K2002 " - pdb=" NE2 HIS K 159 " pdb="ZN ZN K2002 " - pdb=" SG CYS K 31 " pdb="ZN ZN K2002 " - pdb=" SG CYS K 39 " pdb="ZN ZN K2002 " - pdb=" SG CYS K 36 " Number of angles added : 3 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7264 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 109 helices and 38 sheets defined 30.3% alpha, 17.7% beta 14 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 12.01 Creating SS restraints... Processing helix chain 'A' and resid 8 through 19 Processing helix chain 'A' and resid 68 through 70 No H-bonds generated for 'chain 'A' and resid 68 through 70' Processing helix chain 'A' and resid 96 through 112 Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 200 through 202 No H-bonds generated for 'chain 'A' and resid 200 through 202' Processing helix chain 'A' and resid 211 through 215 Processing helix chain 'A' and resid 244 through 276 removed outlier: 4.143A pdb=" N VAL A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 81 No H-bonds generated for 'chain 'B' and resid 79 through 81' Processing helix chain 'B' and resid 95 through 109 removed outlier: 3.595A pdb=" N ALA B 108 " --> pdb=" O GLN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 133 through 148 removed outlier: 3.919A pdb=" N CYS B 137 " --> pdb=" O THR B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 178 Processing helix chain 'B' and resid 209 through 242 Processing helix chain 'C' and resid 10 through 19 removed outlier: 3.985A pdb=" N PHE C 17 " --> pdb=" O TYR C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 115 Processing helix chain 'C' and resid 121 through 124 Processing helix chain 'C' and resid 148 through 162 Processing helix chain 'C' and resid 212 through 216 Processing helix chain 'C' and resid 245 through 271 removed outlier: 4.194A pdb=" N GLN C 249 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ASP C 250 " --> pdb=" O LYS C 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 105 Processing helix chain 'D' and resid 130 through 143 removed outlier: 4.170A pdb=" N ASN D 135 " --> pdb=" O ALA D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 175 Processing helix chain 'D' and resid 203 through 231 Processing helix chain 'E' and resid 9 through 20 Processing helix chain 'E' and resid 71 through 73 No H-bonds generated for 'chain 'E' and resid 71 through 73' Processing helix chain 'E' and resid 99 through 111 Processing helix chain 'E' and resid 121 through 124 Processing helix chain 'E' and resid 148 through 161 Processing helix chain 'E' and resid 216 through 219 No H-bonds generated for 'chain 'E' and resid 216 through 219' Processing helix chain 'E' and resid 251 through 280 Processing helix chain 'E' and resid 282 through 284 No H-bonds generated for 'chain 'E' and resid 282 through 284' Processing helix chain 'F' and resid 18 through 20 No H-bonds generated for 'chain 'F' and resid 18 through 20' Processing helix chain 'F' and resid 119 through 130 Processing helix chain 'F' and resid 158 through 172 Processing helix chain 'F' and resid 201 through 205 Processing helix chain 'F' and resid 234 through 269 Proline residue: F 253 - end of helix Processing helix chain 'G' and resid 204 through 210 Processing helix chain 'G' and resid 217 through 224 removed outlier: 3.905A pdb=" N GLY G 222 " --> pdb=" O ILE G 218 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS G 223 " --> pdb=" O GLN G 219 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU G 224 " --> pdb=" O GLU G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 256 Processing helix chain 'G' and resid 262 through 274 Processing helix chain 'H' and resid 13 through 15 No H-bonds generated for 'chain 'H' and resid 13 through 15' Processing helix chain 'H' and resid 125 through 133 removed outlier: 4.920A pdb=" N ARG H 132 " --> pdb=" O GLU H 128 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY H 133 " --> pdb=" O LEU H 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 178 No H-bonds generated for 'chain 'H' and resid 176 through 178' Processing helix chain 'H' and resid 228 through 247 removed outlier: 4.685A pdb=" N VAL H 233 " --> pdb=" O ALA H 229 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE H 234 " --> pdb=" O ASP H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 253 through 262 Processing helix chain 'H' and resid 274 through 292 Processing helix chain 'I' and resid 17 through 19 No H-bonds generated for 'chain 'I' and resid 17 through 19' Processing helix chain 'I' and resid 58 through 60 No H-bonds generated for 'chain 'I' and resid 58 through 60' Processing helix chain 'I' and resid 118 through 121 No H-bonds generated for 'chain 'I' and resid 118 through 121' Processing helix chain 'K' and resid 70 through 75 Processing helix chain 'K' and resid 77 through 81 Processing helix chain 'K' and resid 93 through 101 Processing helix chain 'K' and resid 103 through 113 Processing helix chain 'K' and resid 141 through 163 Processing helix chain 'K' and resid 178 through 187 Processing helix chain 'K' and resid 194 through 200 Processing helix chain 'K' and resid 206 through 209 No H-bonds generated for 'chain 'K' and resid 206 through 209' Processing helix chain 'K' and resid 234 through 243 removed outlier: 3.561A pdb=" N LYS K 242 " --> pdb=" O GLN K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 426 through 436 removed outlier: 4.491A pdb=" N GLU K 431 " --> pdb=" O GLU K 427 " (cutoff:3.500A) Processing helix chain 'K' and resid 446 through 451 removed outlier: 3.517A pdb=" N PHE K 451 " --> pdb=" O ALA K 447 " (cutoff:3.500A) Processing helix chain 'K' and resid 463 through 465 No H-bonds generated for 'chain 'K' and resid 463 through 465' Processing helix chain 'K' and resid 509 through 511 No H-bonds generated for 'chain 'K' and resid 509 through 511' Processing helix chain 'K' and resid 518 through 525 Processing helix chain 'K' and resid 542 through 546 Processing helix chain 'K' and resid 590 through 598 Processing helix chain 'K' and resid 607 through 626 removed outlier: 3.781A pdb=" N LEU K 616 " --> pdb=" O GLY K 612 " (cutoff:3.500A) Processing helix chain 'K' and resid 658 through 681 Processing helix chain 'K' and resid 699 through 708 Processing helix chain 'K' and resid 718 through 725 Processing helix chain 'K' and resid 731 through 733 No H-bonds generated for 'chain 'K' and resid 731 through 733' Processing helix chain 'K' and resid 737 through 745 Processing helix chain 'K' and resid 783 through 795 Processing helix chain 'K' and resid 802 through 804 No H-bonds generated for 'chain 'K' and resid 802 through 804' Processing helix chain 'K' and resid 807 through 842 Processing helix chain 'L' and resid 11 through 14 No H-bonds generated for 'chain 'L' and resid 11 through 14' Processing helix chain 'L' and resid 17 through 20 No H-bonds generated for 'chain 'L' and resid 17 through 20' Processing helix chain 'L' and resid 64 through 67 No H-bonds generated for 'chain 'L' and resid 64 through 67' Processing helix chain 'L' and resid 82 through 91 Processing helix chain 'M' and resid 142 through 152 Processing helix chain 'M' and resid 169 through 180 Processing helix chain 'M' and resid 193 through 206 Processing helix chain 'M' and resid 230 through 238 Processing helix chain 'M' and resid 255 through 258 Processing helix chain 'M' and resid 263 through 272 removed outlier: 4.131A pdb=" N GLU M 267 " --> pdb=" O GLY M 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 289 through 300 Processing helix chain 'M' and resid 340 through 353 Processing helix chain 'M' and resid 374 through 383 Processing helix chain 'M' and resid 397 through 408 removed outlier: 5.117A pdb=" N LYS M 408 " --> pdb=" O LEU M 404 " (cutoff:3.500A) Processing helix chain 'M' and resid 415 through 430 removed outlier: 5.192A pdb=" N CYS M 430 " --> pdb=" O ASN M 426 " (cutoff:3.500A) Processing helix chain 'M' and resid 439 through 450 Proline residue: M 446 - end of helix Processing helix chain 'M' and resid 461 through 473 Processing helix chain 'M' and resid 484 through 487 No H-bonds generated for 'chain 'M' and resid 484 through 487' Processing helix chain 'M' and resid 514 through 523 removed outlier: 4.483A pdb=" N ARG M 523 " --> pdb=" O GLN M 519 " (cutoff:3.500A) Processing helix chain 'M' and resid 545 through 552 Processing helix chain 'M' and resid 567 through 574 Processing helix chain 'M' and resid 581 through 587 Processing helix chain 'M' and resid 589 through 594 removed outlier: 4.038A pdb=" N HIS M 594 " --> pdb=" O TYR M 590 " (cutoff:3.500A) Processing helix chain 'M' and resid 599 through 608 Processing helix chain 'M' and resid 832 through 839 Processing helix chain 'M' and resid 848 through 861 Processing helix chain 'M' and resid 872 through 877 Processing helix chain 'M' and resid 885 through 894 Processing helix chain 'M' and resid 902 through 913 removed outlier: 3.824A pdb=" N THR M 906 " --> pdb=" O ALA M 902 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE M 912 " --> pdb=" O LEU M 908 " (cutoff:3.500A) Processing helix chain 'M' and resid 926 through 948 Proline residue: M 931 - end of helix Processing helix chain 'M' and resid 955 through 960 Processing helix chain 'M' and resid 967 through 974 Processing helix chain 'M' and resid 979 through 981 No H-bonds generated for 'chain 'M' and resid 979 through 981' Processing helix chain 'M' and resid 990 through 1014 Processing helix chain 'M' and resid 1018 through 1030 Processing sheet with id= A, first strand: chain 'A' and resid 284 through 286 Processing sheet with id= B, first strand: chain 'A' and resid 165 through 168 Processing sheet with id= C, first strand: chain 'A' and resid 204 through 207 removed outlier: 3.747A pdb=" N MET A 225 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY A 219 " --> pdb=" O PHE A 198 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR A 233 " --> pdb=" O ALA A 224 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 24 through 28 removed outlier: 3.603A pdb=" N ALA B 49 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 40 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN B 128 " --> pdb=" O LYS B 46 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU B 48 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N VAL B 126 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N VAL B 50 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL B 124 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N TYR B 52 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ILE B 122 " --> pdb=" O TYR B 52 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU B 70 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ILE B 122 " --> pdb=" O LEU B 70 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ASN B 72 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N VAL B 124 " --> pdb=" O ASN B 72 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLN B 74 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N VAL B 126 " --> pdb=" O GLN B 74 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 167 through 170 removed outlier: 6.155A pdb=" N LEU B 189 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ILE B 195 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 35 through 39 removed outlier: 3.966A pdb=" N ASP C 143 " --> pdb=" O THR C 57 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE C 59 " --> pdb=" O CYS C 141 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N CYS C 141 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N GLY C 61 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LEU C 139 " --> pdb=" O GLY C 61 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LYS C 63 " --> pdb=" O CYS C 137 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N CYS C 137 " --> pdb=" O LYS C 63 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N GLU C 65 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N LEU C 135 " --> pdb=" O GLU C 65 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ALA C 67 " --> pdb=" O TRP C 133 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N TRP C 133 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N TYR C 78 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N CYS C 137 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL C 80 " --> pdb=" O CYS C 137 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU C 139 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASN C 82 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N CYS C 141 " --> pdb=" O ASN C 82 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASP C 84 " --> pdb=" O CYS C 141 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ASP C 143 " --> pdb=" O ASP C 84 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 206 through 208 removed outlier: 3.881A pdb=" N VAL C 194 " --> pdb=" O MET C 226 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N CYS C 234 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ASP C 227 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU C 232 " --> pdb=" O ASP C 227 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 164 through 171 removed outlier: 3.976A pdb=" N GLU C 167 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LYS C 183 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 12.521A pdb=" N THR C 169 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 11.003A pdb=" N LEU C 181 " --> pdb=" O THR C 169 " (cutoff:3.500A) removed outlier: 10.883A pdb=" N ASN C 171 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 11.245A pdb=" N VAL C 179 " --> pdb=" O ASN C 171 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 31 through 35 removed outlier: 3.751A pdb=" N SER D 53 " --> pdb=" O SER D 124 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU D 55 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N VAL D 122 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLY D 57 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LEU D 120 " --> pdb=" O GLY D 57 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N TYR D 59 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL D 118 " --> pdb=" O TYR D 59 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N THR D 75 " --> pdb=" O ILE D 116 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL D 118 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLU D 77 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N LEU D 120 " --> pdb=" O GLU D 77 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE D 79 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N VAL D 122 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ARG D 81 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N SER D 124 " --> pdb=" O ARG D 81 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 165 through 167 removed outlier: 6.839A pdb=" N ASP D 186 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU D 192 " --> pdb=" O ASP D 186 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 35 through 39 removed outlier: 6.953A pdb=" N TYR E 78 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL E 137 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU E 80 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL E 139 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE E 82 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N LEU E 141 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASP E 84 " --> pdb=" O LEU E 141 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 168 through 171 Processing sheet with id= M, first strand: chain 'E' and resid 209 through 212 removed outlier: 4.373A pdb=" N ALA E 224 " --> pdb=" O LYS E 205 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 39 through 43 removed outlier: 3.786A pdb=" N GLY F 51 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU F 63 " --> pdb=" O LEU F 150 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LEU F 150 " --> pdb=" O LEU F 63 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA F 65 " --> pdb=" O ALA F 148 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ALA F 148 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N SER F 67 " --> pdb=" O VAL F 146 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N VAL F 146 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ARG F 95 " --> pdb=" O LEU F 144 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL F 146 " --> pdb=" O ARG F 95 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU F 97 " --> pdb=" O VAL F 146 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ALA F 148 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASP F 99 " --> pdb=" O ALA F 148 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N LEU F 150 " --> pdb=" O ASP F 99 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 195 through 197 removed outlier: 4.373A pdb=" N ALA F 209 " --> pdb=" O LEU F 187 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 71 through 74 Processing sheet with id= Q, first strand: chain 'G' and resid 86 through 89 Processing sheet with id= R, first strand: chain 'G' and resid 128 through 132 removed outlier: 5.853A pdb=" N ASP G 132 " --> pdb=" O VAL G 121 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL G 121 " --> pdb=" O ASP G 132 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLU G 177 " --> pdb=" O VAL G 168 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 198 through 201 Processing sheet with id= T, first strand: chain 'H' and resid 45 through 47 Processing sheet with id= U, first strand: chain 'H' and resid 58 through 62 removed outlier: 3.797A pdb=" N SER H 59 " --> pdb=" O LYS H 70 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 106 through 109 removed outlier: 5.734A pdb=" N GLU H 99 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ILE H 88 " --> pdb=" O GLU H 99 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N SER H 155 " --> pdb=" O GLN H 146 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 170 through 173 removed outlier: 3.890A pdb=" N ALA H 193 " --> pdb=" O LEU H 189 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'I' and resid 26 through 29 Processing sheet with id= Y, first strand: chain 'I' and resid 40 through 45 removed outlier: 5.865A pdb=" N SER I 21 " --> pdb=" O VAL I 53 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N VAL I 55 " --> pdb=" O SER I 21 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N GLY I 23 " --> pdb=" O VAL I 55 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'I' and resid 131 through 134 removed outlier: 6.610A pdb=" N LEU I 143 " --> pdb=" O ILE I 133 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER I 77 " --> pdb=" O LYS I 84 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N HIS I 86 " --> pdb=" O VAL I 75 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL I 75 " --> pdb=" O HIS I 86 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL I 155 " --> pdb=" O ILE I 127 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU I 129 " --> pdb=" O VAL I 153 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N VAL I 153 " --> pdb=" O LEU I 129 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'K' and resid 2 through 10 Processing sheet with id= AB, first strand: chain 'K' and resid 87 through 90 removed outlier: 5.822A pdb=" N HIS K 119 " --> pdb=" O VAL K 88 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL K 90 " --> pdb=" O HIS K 119 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR K 121 " --> pdb=" O VAL K 90 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'K' and resid 273 through 277 removed outlier: 4.319A pdb=" N LYS K 273 " --> pdb=" O ILE K 265 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE K 251 " --> pdb=" O ASP K 290 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP K 290 " --> pdb=" O PHE K 251 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'K' and resid 383 through 385 removed outlier: 5.352A pdb=" N LEU K 360 " --> pdb=" O ARG K 396 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ARG K 396 " --> pdb=" O LEU K 360 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY K 421 " --> pdb=" O ARG K 397 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE K 399 " --> pdb=" O ASN K 419 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ASN K 419 " --> pdb=" O ILE K 399 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'K' and resid 489 through 494 removed outlier: 3.823A pdb=" N LYS K 574 " --> pdb=" O GLU K 565 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'K' and resid 688 through 691 Processing sheet with id= AG, first strand: chain 'K' and resid 862 through 864 Processing sheet with id= AH, first strand: chain 'K' and resid 886 through 888 Processing sheet with id= AI, first strand: chain 'K' and resid 925 through 928 removed outlier: 6.503A pdb=" N ILE K 911 " --> pdb=" O VAL K 846 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N VAL K 846 " --> pdb=" O ILE K 911 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'K' and resid 400 through 404 removed outlier: 6.347A pdb=" N ASN K 413 " --> pdb=" O ASP K 403 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'M' and resid 99 through 103 removed outlier: 7.195A pdb=" N SER M 156 " --> pdb=" O HIS M 305 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ILE M 307 " --> pdb=" O SER M 156 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU M 158 " --> pdb=" O ILE M 307 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N THR M 309 " --> pdb=" O LEU M 158 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N SER M 160 " --> pdb=" O THR M 309 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA M 161 " --> pdb=" O SER M 283 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ARG M 184 " --> pdb=" O ALA M 247 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL M 249 " --> pdb=" O ARG M 184 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE M 186 " --> pdb=" O VAL M 249 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N PHE M 251 " --> pdb=" O ILE M 186 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR M 188 " --> pdb=" O PHE M 251 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLY M 210 " --> pdb=" O VAL M 226 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'M' and resid 452 through 455 removed outlier: 6.488A pdb=" N ALA M 478 " --> pdb=" O GLY M 453 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N HIS M 455 " --> pdb=" O ALA M 478 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N PHE M 480 " --> pdb=" O HIS M 455 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL M 389 " --> pdb=" O LEU M 479 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ALA M 481 " --> pdb=" O VAL M 389 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ILE M 391 " --> pdb=" O ALA M 481 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR M 495 " --> pdb=" O ILE M 390 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N PHE M 392 " --> pdb=" O THR M 495 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU M 497 " --> pdb=" O PHE M 392 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE M 534 " --> pdb=" O VAL M 496 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N PHE M 498 " --> pdb=" O ILE M 534 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE M 536 " --> pdb=" O PHE M 498 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HIS M 318 " --> pdb=" O VAL M 332 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL M 332 " --> pdb=" O HIS M 318 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE M 320 " --> pdb=" O LEU M 330 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU M 330 " --> pdb=" O ILE M 320 " (cutoff:3.500A) 1115 hydrogen bonds defined for protein. 3111 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 11.33 Time building geometry restraints manager: 12.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10383 1.34 - 1.45: 4767 1.45 - 1.57: 16726 1.57 - 1.69: 121 1.69 - 1.81: 292 Bond restraints: 32289 Sorted by residual: bond pdb=" P C O 17 " pdb=" OP2 C O 17 " ideal model delta sigma weight residual 1.485 1.679 -0.194 2.00e-02 2.50e+03 9.39e+01 bond pdb=" O3A ANP M2001 " pdb=" PB ANP M2001 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.06e+01 bond pdb=" O3' DT O 16 " pdb=" P C O 17 " ideal model delta sigma weight residual 1.607 1.705 -0.098 1.50e-02 4.44e+03 4.31e+01 bond pdb=" P C O 17 " pdb=" OP1 C O 17 " ideal model delta sigma weight residual 1.485 1.591 -0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" N PRO K 648 " pdb=" CD PRO K 648 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.76e+01 ... (remaining 32284 not shown) Histogram of bond angle deviations from ideal: 91.36 - 99.90: 23 99.90 - 108.44: 2409 108.44 - 116.98: 21607 116.98 - 125.52: 19295 125.52 - 134.06: 541 Bond angle restraints: 43875 Sorted by residual: angle pdb=" O3' DT O 16 " pdb=" P C O 17 " pdb=" O5' C O 17 " ideal model delta sigma weight residual 104.00 124.84 -20.84 1.50e+00 4.44e-01 1.93e+02 angle pdb=" CA PRO K 648 " pdb=" N PRO K 648 " pdb=" CD PRO K 648 " ideal model delta sigma weight residual 112.00 99.13 12.87 1.40e+00 5.10e-01 8.46e+01 angle pdb=" C3' DT O 16 " pdb=" O3' DT O 16 " pdb=" P C O 17 " ideal model delta sigma weight residual 120.20 111.67 8.53 1.50e+00 4.44e-01 3.23e+01 angle pdb=" O3' DT O 16 " pdb=" P C O 17 " pdb=" OP2 C O 17 " ideal model delta sigma weight residual 108.00 91.36 16.64 3.00e+00 1.11e-01 3.08e+01 angle pdb=" O1B ANP M2001 " pdb=" PB ANP M2001 " pdb=" O2B ANP M2001 " ideal model delta sigma weight residual 120.08 109.41 10.67 3.00e+00 1.11e-01 1.27e+01 ... (remaining 43870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.75: 19547 33.75 - 67.50: 202 67.50 - 101.26: 31 101.26 - 135.01: 1 135.01 - 168.76: 2 Dihedral angle restraints: 19783 sinusoidal: 8558 harmonic: 11225 Sorted by residual: dihedral pdb=" CA MET K 455 " pdb=" C MET K 455 " pdb=" N PRO K 456 " pdb=" CA PRO K 456 " ideal model delta harmonic sigma weight residual 180.00 131.56 48.44 0 5.00e+00 4.00e-02 9.39e+01 dihedral pdb=" O4' C O 49 " pdb=" C1' C O 49 " pdb=" N1 C O 49 " pdb=" C2 C O 49 " ideal model delta sinusoidal sigma weight residual -128.00 32.59 -160.59 1 1.70e+01 3.46e-03 6.45e+01 dihedral pdb=" CA ASP B 201 " pdb=" C ASP B 201 " pdb=" N ALA B 202 " pdb=" CA ALA B 202 " ideal model delta harmonic sigma weight residual 180.00 148.85 31.15 0 5.00e+00 4.00e-02 3.88e+01 ... (remaining 19780 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.215: 5051 0.215 - 0.430: 2 0.430 - 0.645: 0 0.645 - 0.860: 0 0.860 - 1.075: 1 Chirality restraints: 5054 Sorted by residual: chirality pdb=" P C O 17 " pdb=" OP1 C O 17 " pdb=" OP2 C O 17 " pdb=" O5' C O 17 " both_signs ideal model delta sigma weight residual True 2.41 -3.48 -1.07 2.00e-01 2.50e+01 2.89e+01 chirality pdb=" C3' ANP M2001 " pdb=" C2' ANP M2001 " pdb=" C4' ANP M2001 " pdb=" O3' ANP M2001 " both_signs ideal model delta sigma weight residual False -2.36 -2.61 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" C1' A O 41 " pdb=" O4' A O 41 " pdb=" C2' A O 41 " pdb=" N9 A O 41 " both_signs ideal model delta sigma weight residual False 2.46 2.23 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 5051 not shown) Planarity restraints: 5456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C O 45 " -0.039 2.00e-02 2.50e+03 1.90e-02 8.08e+00 pdb=" N1 C O 45 " 0.036 2.00e-02 2.50e+03 pdb=" C2 C O 45 " 0.010 2.00e-02 2.50e+03 pdb=" O2 C O 45 " 0.003 2.00e-02 2.50e+03 pdb=" N3 C O 45 " -0.003 2.00e-02 2.50e+03 pdb=" C4 C O 45 " -0.005 2.00e-02 2.50e+03 pdb=" N4 C O 45 " -0.013 2.00e-02 2.50e+03 pdb=" C5 C O 45 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C O 45 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A O 60 " 0.036 2.00e-02 2.50e+03 1.62e-02 7.20e+00 pdb=" N9 A O 60 " -0.037 2.00e-02 2.50e+03 pdb=" C8 A O 60 " -0.006 2.00e-02 2.50e+03 pdb=" N7 A O 60 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A O 60 " 0.003 2.00e-02 2.50e+03 pdb=" C6 A O 60 " 0.006 2.00e-02 2.50e+03 pdb=" N6 A O 60 " 0.006 2.00e-02 2.50e+03 pdb=" N1 A O 60 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A O 60 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A O 60 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A O 60 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C O 42 " 0.036 2.00e-02 2.50e+03 1.77e-02 7.02e+00 pdb=" N1 C O 42 " -0.030 2.00e-02 2.50e+03 pdb=" C2 C O 42 " -0.017 2.00e-02 2.50e+03 pdb=" O2 C O 42 " 0.000 2.00e-02 2.50e+03 pdb=" N3 C O 42 " 0.006 2.00e-02 2.50e+03 pdb=" C4 C O 42 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C O 42 " 0.013 2.00e-02 2.50e+03 pdb=" C5 C O 42 " -0.001 2.00e-02 2.50e+03 pdb=" C6 C O 42 " -0.010 2.00e-02 2.50e+03 ... (remaining 5453 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 127 2.40 - 3.03: 20532 3.03 - 3.65: 44962 3.65 - 4.28: 68310 4.28 - 4.90: 114944 Nonbonded interactions: 248875 Sorted by model distance: nonbonded pdb=" OH TYR M 237 " pdb=" OE2 GLU M 268 " model vdw 1.778 2.440 nonbonded pdb=" O2' C O 42 " pdb=" O5' A O 43 " model vdw 1.823 2.440 nonbonded pdb=" OG SER B 7 " pdb=" OE1 GLN B 9 " model vdw 1.922 2.440 nonbonded pdb=" OG SER M 189 " pdb=" OG SER M 195 " model vdw 1.957 2.440 nonbonded pdb=" OE2 GLU M 267 " pdb=" OG SER M 561 " model vdw 1.963 2.440 ... (remaining 248870 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 13.450 Check model and map are aligned: 0.480 Set scattering table: 0.340 Process input model: 90.430 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.110 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: 0.000 Load rotamer database and sin/cos tables:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 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 : 0.006 0.194 32289 Z= 0.431 Angle : 0.740 20.838 43875 Z= 0.402 Chirality : 0.048 1.075 5054 Planarity : 0.004 0.052 5456 Dihedral : 10.872 168.761 12519 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 0.06 % Allowed : 2.86 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -4.46 (0.11), residues: 3839 helix: -1.96 (0.12), residues: 1237 sheet: -2.41 (0.17), residues: 776 loop : -4.01 (0.10), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 101 HIS 0.012 0.002 HIS M 305 PHE 0.029 0.003 PHE C 154 TYR 0.035 0.002 TYR M 279 ARG 0.011 0.001 ARG G 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 861 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 859 time to evaluate : 3.341 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: A 31 ASP cc_start: 0.8001 (m-30) cc_final: 0.7731 (m-30) REVERT: B 125 GLN cc_start: 0.7574 (tp40) cc_final: 0.6790 (tp40) REVERT: C 226 MET cc_start: 0.6983 (tpt) cc_final: 0.6626 (tpt) REVERT: D 72 ASN cc_start: 0.8754 (p0) cc_final: 0.8549 (p0) REVERT: D 164 THR cc_start: 0.7792 (m) cc_final: 0.6878 (p) REVERT: E 125 CYS cc_start: 0.6732 (t) cc_final: 0.6278 (p) REVERT: E 233 LYS cc_start: 0.8056 (mptp) cc_final: 0.7607 (mttp) REVERT: G 224 LEU cc_start: 0.6070 (mp) cc_final: 0.5839 (mt) REVERT: H 33 ILE cc_start: 0.8281 (mm) cc_final: 0.8025 (mm) REVERT: H 83 ILE cc_start: 0.8607 (pp) cc_final: 0.8328 (mp) REVERT: K 156 TYR cc_start: 0.7530 (OUTLIER) cc_final: 0.6020 (m-80) REVERT: K 185 ILE cc_start: 0.7990 (mp) cc_final: 0.7776 (mm) REVERT: K 566 MET cc_start: 0.6595 (mtt) cc_final: 0.6374 (mtm) REVERT: K 578 THR cc_start: 0.7655 (p) cc_final: 0.7420 (t) REVERT: K 610 LEU cc_start: 0.7965 (mt) cc_final: 0.7178 (mp) REVERT: L 91 MET cc_start: 0.7633 (mmt) cc_final: 0.7369 (mpp) outliers start: 2 outliers final: 0 residues processed: 861 average time/residue: 0.4933 time to fit residues: 638.7320 Evaluate side-chains 384 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 383 time to evaluate : 3.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 156 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 326 optimal weight: 0.9990 chunk 293 optimal weight: 1.9990 chunk 162 optimal weight: 0.0030 chunk 100 optimal weight: 0.9990 chunk 197 optimal weight: 0.5980 chunk 156 optimal weight: 6.9990 chunk 303 optimal weight: 0.0970 chunk 117 optimal weight: 0.0980 chunk 184 optimal weight: 0.4980 chunk 225 optimal weight: 0.0060 chunk 351 optimal weight: 1.9990 overall best weight: 0.1404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS E 44 ASN E 114 ASN E 131 HIS F 5 HIS ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 ASN I 178 HIS K 170 GLN K 266 HIS K 569 ASN K 902 HIS L 43 HIS M 197 GLN M 291 GLN M 300 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32289 Z= 0.177 Angle : 0.630 7.969 43875 Z= 0.321 Chirality : 0.043 0.253 5054 Planarity : 0.004 0.062 5456 Dihedral : 10.990 169.724 5045 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.78 % Allowed : 10.37 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.13), residues: 3839 helix: 0.09 (0.14), residues: 1248 sheet: -1.59 (0.18), residues: 779 loop : -2.83 (0.13), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 101 HIS 0.008 0.001 HIS K 788 PHE 0.027 0.002 PHE K 666 TYR 0.030 0.002 TYR M 279 ARG 0.007 0.001 ARG C 23 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 499 time to evaluate : 3.955 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: A 240 ILE cc_start: 0.6622 (OUTLIER) cc_final: 0.6251 (pp) REVERT: D 121 GLN cc_start: 0.8737 (tp40) cc_final: 0.8321 (tp40) REVERT: D 143 ASP cc_start: 0.7608 (t70) cc_final: 0.7320 (t0) REVERT: E 162 ASN cc_start: 0.8063 (t0) cc_final: 0.7842 (t0) REVERT: E 233 LYS cc_start: 0.8050 (mptp) cc_final: 0.7550 (mttp) REVERT: G 228 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7625 (pt0) REVERT: H 33 ILE cc_start: 0.8295 (mm) cc_final: 0.8054 (mm) REVERT: H 290 GLU cc_start: 0.6932 (pp20) cc_final: 0.6379 (pt0) REVERT: I 86 HIS cc_start: 0.7532 (m170) cc_final: 0.6748 (m-70) REVERT: K 156 TYR cc_start: 0.7552 (OUTLIER) cc_final: 0.5901 (m-80) REVERT: K 465 LYS cc_start: 0.7776 (ttpt) cc_final: 0.7170 (ttmm) REVERT: K 564 TRP cc_start: 0.4670 (m-90) cc_final: 0.4330 (m-90) REVERT: K 749 MET cc_start: 0.7531 (mmp) cc_final: 0.7293 (mmm) REVERT: K 823 MET cc_start: 0.8297 (mmp) cc_final: 0.8060 (mmt) REVERT: K 925 MET cc_start: 0.7418 (mtt) cc_final: 0.7057 (mtt) REVERT: L 43 HIS cc_start: 0.5939 (OUTLIER) cc_final: 0.4416 (p90) REVERT: L 45 TYR cc_start: 0.7961 (m-80) cc_final: 0.7683 (m-80) REVERT: M 433 ASP cc_start: 0.7168 (p0) cc_final: 0.6950 (p0) outliers start: 59 outliers final: 30 residues processed: 535 average time/residue: 0.4359 time to fit residues: 372.3646 Evaluate side-chains 388 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 354 time to evaluate : 3.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain K residue 142 ASN Chi-restraints excluded: chain K residue 156 TYR Chi-restraints excluded: chain K residue 484 THR Chi-restraints excluded: chain K residue 800 THR Chi-restraints excluded: chain K residue 838 LEU Chi-restraints excluded: chain K residue 902 HIS Chi-restraints excluded: chain L residue 43 HIS Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain M residue 1035 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 195 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 292 optimal weight: 8.9990 chunk 239 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 352 optimal weight: 0.9990 chunk 380 optimal weight: 2.9990 chunk 313 optimal weight: 2.9990 chunk 349 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 282 optimal weight: 10.0000 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 HIS ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN E 285 GLN F 5 HIS G 246 GLN H 266 HIS ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 HIS ** M 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 300 HIS M 317 GLN M 318 HIS ** M 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 898 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 32289 Z= 0.282 Angle : 0.641 11.385 43875 Z= 0.325 Chirality : 0.044 0.264 5054 Planarity : 0.004 0.054 5456 Dihedral : 10.913 170.382 5045 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.25 % Allowed : 12.15 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.13), residues: 3839 helix: 0.63 (0.15), residues: 1255 sheet: -1.16 (0.18), residues: 763 loop : -2.31 (0.13), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP M 973 HIS 0.022 0.002 HIS K 902 PHE 0.021 0.002 PHE M 411 TYR 0.019 0.002 TYR F 252 ARG 0.005 0.001 ARG H 123 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 400 time to evaluate : 3.568 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: A 77 PHE cc_start: 0.6618 (t80) cc_final: 0.6397 (t80) REVERT: A 240 ILE cc_start: 0.7004 (OUTLIER) cc_final: 0.6744 (pp) REVERT: B 72 ASN cc_start: 0.8645 (t0) cc_final: 0.8422 (t0) REVERT: B 86 LYS cc_start: 0.7090 (mmmt) cc_final: 0.6869 (mmmt) REVERT: B 186 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8179 (pt) REVERT: C 33 ARG cc_start: 0.8526 (ptt180) cc_final: 0.8306 (mtm180) REVERT: D 35 GLN cc_start: 0.8130 (mm-40) cc_final: 0.7811 (mm-40) REVERT: D 143 ASP cc_start: 0.8144 (t70) cc_final: 0.7842 (t0) REVERT: D 175 LYS cc_start: 0.8531 (ptpt) cc_final: 0.8288 (ptmm) REVERT: E 233 LYS cc_start: 0.8146 (mptp) cc_final: 0.7699 (mttp) REVERT: G 162 LEU cc_start: 0.7757 (pt) cc_final: 0.7538 (pt) REVERT: H 33 ILE cc_start: 0.8596 (mm) cc_final: 0.8252 (mt) REVERT: H 247 GLN cc_start: 0.7525 (mm-40) cc_final: 0.7290 (mm-40) REVERT: I 86 HIS cc_start: 0.7755 (m170) cc_final: 0.6965 (m-70) REVERT: K 156 TYR cc_start: 0.7510 (OUTLIER) cc_final: 0.6150 (m-80) REVERT: K 464 MET cc_start: 0.5854 (ttp) cc_final: 0.5557 (ttp) REVERT: K 465 LYS cc_start: 0.7680 (ttpt) cc_final: 0.6981 (ttmm) REVERT: K 468 GLU cc_start: 0.5954 (OUTLIER) cc_final: 0.5629 (pm20) REVERT: K 712 GLU cc_start: 0.5720 (OUTLIER) cc_final: 0.5489 (pp20) REVERT: K 925 MET cc_start: 0.7438 (mtt) cc_final: 0.7209 (mtt) REVERT: M 377 ILE cc_start: 0.7827 (mm) cc_final: 0.7619 (mm) REVERT: M 433 ASP cc_start: 0.7211 (p0) cc_final: 0.6994 (p0) REVERT: M 1007 MET cc_start: 0.8147 (mmm) cc_final: 0.7480 (mmm) outliers start: 108 outliers final: 70 residues processed: 474 average time/residue: 0.4404 time to fit residues: 332.7811 Evaluate side-chains 407 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 332 time to evaluate : 3.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain E residue 33 ARG Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 125 CYS Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 136 SER Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 43 HIS Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain H residue 277 MET Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain J residue 631 VAL Chi-restraints excluded: chain K residue 4 SER Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 156 TYR Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 468 GLU Chi-restraints excluded: chain K residue 484 THR Chi-restraints excluded: chain K residue 560 PHE Chi-restraints excluded: chain K residue 712 GLU Chi-restraints excluded: chain K residue 800 THR Chi-restraints excluded: chain K residue 838 LEU Chi-restraints excluded: chain K residue 920 HIS Chi-restraints excluded: chain L residue 43 HIS Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain M residue 121 ASP Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain M residue 143 PHE Chi-restraints excluded: chain M residue 279 TYR Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain M residue 412 ASN Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 482 THR Chi-restraints excluded: chain M residue 576 VAL Chi-restraints excluded: chain M residue 1014 ILE Chi-restraints excluded: chain M residue 1035 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 347 optimal weight: 3.9990 chunk 264 optimal weight: 9.9990 chunk 182 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 168 optimal weight: 0.6980 chunk 236 optimal weight: 0.7980 chunk 353 optimal weight: 7.9990 chunk 374 optimal weight: 0.7980 chunk 184 optimal weight: 1.9990 chunk 334 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 ASN E 285 GLN H 266 HIS K 62 GLN K 660 ASN ** K 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 HIS ** M 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 302 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32289 Z= 0.214 Angle : 0.579 8.941 43875 Z= 0.292 Chirality : 0.042 0.285 5054 Planarity : 0.004 0.058 5456 Dihedral : 10.826 170.138 5045 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.65 % Allowed : 14.10 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.13), residues: 3839 helix: 0.94 (0.15), residues: 1252 sheet: -0.86 (0.19), residues: 747 loop : -2.06 (0.13), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 457 HIS 0.009 0.001 HIS K 64 PHE 0.025 0.002 PHE M 411 TYR 0.019 0.001 TYR A 175 ARG 0.004 0.000 ARG K 471 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 361 time to evaluate : 3.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ILE cc_start: 0.7061 (OUTLIER) cc_final: 0.6675 (pp) REVERT: B 186 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8194 (pt) REVERT: D 143 ASP cc_start: 0.8308 (t70) cc_final: 0.7951 (t0) REVERT: D 175 LYS cc_start: 0.8587 (ptpt) cc_final: 0.8325 (ptmm) REVERT: E 233 LYS cc_start: 0.8203 (mptp) cc_final: 0.7764 (mttp) REVERT: G 24 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7508 (pp) REVERT: G 162 LEU cc_start: 0.7669 (pt) cc_final: 0.7336 (pt) REVERT: H 33 ILE cc_start: 0.8566 (mm) cc_final: 0.8312 (mt) REVERT: I 86 HIS cc_start: 0.7776 (m170) cc_final: 0.7110 (m-70) REVERT: K 465 LYS cc_start: 0.8064 (ttpt) cc_final: 0.7757 (ptpp) REVERT: K 662 MET cc_start: 0.7267 (ptt) cc_final: 0.6989 (ptt) REVERT: K 712 GLU cc_start: 0.5575 (OUTLIER) cc_final: 0.4940 (pp20) REVERT: K 925 MET cc_start: 0.7204 (mtt) cc_final: 0.6993 (mtt) REVERT: M 1007 MET cc_start: 0.8147 (mmm) cc_final: 0.7485 (mmm) outliers start: 88 outliers final: 65 residues processed: 420 average time/residue: 0.4169 time to fit residues: 287.0752 Evaluate side-chains 384 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 315 time to evaluate : 3.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 234 CYS Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 33 ARG Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 136 SER Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain J residue 631 VAL Chi-restraints excluded: chain K residue 62 GLN Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 156 TYR Chi-restraints excluded: chain K residue 359 MET Chi-restraints excluded: chain K residue 484 THR Chi-restraints excluded: chain K residue 560 PHE Chi-restraints excluded: chain K residue 712 GLU Chi-restraints excluded: chain K residue 838 LEU Chi-restraints excluded: chain K residue 902 HIS Chi-restraints excluded: chain K residue 920 HIS Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain M residue 121 ASP Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain M residue 143 PHE Chi-restraints excluded: chain M residue 279 TYR Chi-restraints excluded: chain M residue 331 VAL Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain M residue 573 LEU Chi-restraints excluded: chain M residue 579 ILE Chi-restraints excluded: chain M residue 1014 ILE Chi-restraints excluded: chain M residue 1035 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 311 optimal weight: 5.9990 chunk 212 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 278 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 chunk 319 optimal weight: 2.9990 chunk 258 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 191 optimal weight: 0.9990 chunk 335 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 141 HIS ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 ASN E 19 GLN ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 187 HIS I 173 GLN ** K 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 560 ASN M 593 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 32289 Z= 0.368 Angle : 0.667 10.974 43875 Z= 0.337 Chirality : 0.045 0.255 5054 Planarity : 0.005 0.055 5456 Dihedral : 10.971 169.666 5045 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.22 % Allowed : 13.98 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.13), residues: 3839 helix: 0.74 (0.15), residues: 1267 sheet: -0.77 (0.19), residues: 732 loop : -2.02 (0.13), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 96 HIS 0.008 0.001 HIS K 64 PHE 0.027 0.002 PHE B 106 TYR 0.027 0.002 TYR E 32 ARG 0.006 0.001 ARG H 238 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 353 time to evaluate : 3.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.7312 (t80) cc_final: 0.7049 (t80) REVERT: A 240 ILE cc_start: 0.7064 (OUTLIER) cc_final: 0.6764 (pt) REVERT: B 110 ILE cc_start: 0.8695 (tp) cc_final: 0.8432 (tt) REVERT: B 186 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8201 (pt) REVERT: C 15 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7307 (mtm110) REVERT: D 83 LYS cc_start: 0.8227 (pttt) cc_final: 0.7977 (pttm) REVERT: D 143 ASP cc_start: 0.8466 (t70) cc_final: 0.8025 (t0) REVERT: D 189 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6871 (tm-30) REVERT: E 233 LYS cc_start: 0.8372 (mptp) cc_final: 0.7963 (mttp) REVERT: H 107 VAL cc_start: 0.9236 (OUTLIER) cc_final: 0.8974 (m) REVERT: H 279 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7702 (pt0) REVERT: I 86 HIS cc_start: 0.7857 (m170) cc_final: 0.7137 (m-70) REVERT: K 465 LYS cc_start: 0.8016 (ttpt) cc_final: 0.7769 (ptpp) REVERT: K 662 MET cc_start: 0.7438 (ptt) cc_final: 0.7163 (ptt) REVERT: L 45 TYR cc_start: 0.8196 (OUTLIER) cc_final: 0.7911 (m-80) REVERT: M 227 MET cc_start: 0.7377 (ptt) cc_final: 0.7027 (ptt) REVERT: M 348 GLN cc_start: 0.7457 (mm110) cc_final: 0.6682 (mm-40) REVERT: M 1007 MET cc_start: 0.8176 (mmm) cc_final: 0.7802 (mmm) outliers start: 140 outliers final: 91 residues processed: 456 average time/residue: 0.4306 time to fit residues: 317.6638 Evaluate side-chains 408 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 310 time to evaluate : 3.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain C residue 15 ARG Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 234 CYS Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain E residue 33 ARG Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 125 CYS Chi-restraints excluded: chain E residue 132 CYS Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 136 SER Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 3 MET Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain H residue 279 GLU Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain J residue 631 VAL Chi-restraints excluded: chain K residue 4 SER Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 118 LYS Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 156 TYR Chi-restraints excluded: chain K residue 166 ASP Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 359 MET Chi-restraints excluded: chain K residue 560 PHE Chi-restraints excluded: chain K residue 838 LEU Chi-restraints excluded: chain K residue 885 LEU Chi-restraints excluded: chain K residue 902 HIS Chi-restraints excluded: chain K residue 920 HIS Chi-restraints excluded: chain L residue 45 TYR Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain M residue 121 ASP Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain M residue 143 PHE Chi-restraints excluded: chain M residue 279 TYR Chi-restraints excluded: chain M residue 283 SER Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain M residue 311 TYR Chi-restraints excluded: chain M residue 331 VAL Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain M residue 573 LEU Chi-restraints excluded: chain M residue 576 VAL Chi-restraints excluded: chain M residue 579 ILE Chi-restraints excluded: chain M residue 1014 ILE Chi-restraints excluded: chain M residue 1035 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 125 optimal weight: 0.5980 chunk 336 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 219 optimal weight: 6.9990 chunk 92 optimal weight: 0.5980 chunk 374 optimal weight: 0.7980 chunk 310 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 168 GLN E 131 HIS E 275 HIS E 285 GLN ** F 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 163 GLN ** M 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 405 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32289 Z= 0.210 Angle : 0.580 11.685 43875 Z= 0.290 Chirality : 0.041 0.270 5054 Planarity : 0.004 0.060 5456 Dihedral : 10.831 169.612 5045 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.04 % Allowed : 15.61 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.13), residues: 3839 helix: 1.07 (0.15), residues: 1265 sheet: -0.48 (0.19), residues: 726 loop : -1.91 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 96 HIS 0.006 0.001 HIS K 64 PHE 0.037 0.001 PHE K 666 TYR 0.015 0.001 TYR A 175 ARG 0.004 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 345 time to evaluate : 3.997 Fit side-chains revert: symmetry clash REVERT: A 240 ILE cc_start: 0.7005 (OUTLIER) cc_final: 0.6686 (pp) REVERT: B 110 ILE cc_start: 0.8698 (tp) cc_final: 0.8436 (tp) REVERT: B 186 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8302 (pt) REVERT: D 143 ASP cc_start: 0.8511 (t70) cc_final: 0.8132 (t0) REVERT: D 230 ARG cc_start: 0.7888 (ttp80) cc_final: 0.7633 (ttp80) REVERT: E 233 LYS cc_start: 0.8379 (mptp) cc_final: 0.7988 (mttp) REVERT: H 279 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7725 (pt0) REVERT: I 86 HIS cc_start: 0.7790 (m170) cc_final: 0.7142 (m-70) REVERT: K 465 LYS cc_start: 0.8070 (ttpt) cc_final: 0.7843 (ptpp) REVERT: K 662 MET cc_start: 0.7350 (ptt) cc_final: 0.7112 (ptt) REVERT: K 803 GLU cc_start: 0.6766 (mp0) cc_final: 0.6122 (tt0) REVERT: L 45 TYR cc_start: 0.8154 (OUTLIER) cc_final: 0.7946 (m-80) REVERT: L 52 LYS cc_start: 0.6983 (OUTLIER) cc_final: 0.6744 (mmmm) REVERT: M 227 MET cc_start: 0.7534 (ptt) cc_final: 0.7271 (ptt) REVERT: M 1007 MET cc_start: 0.8111 (mmm) cc_final: 0.7496 (mmm) outliers start: 101 outliers final: 69 residues processed: 420 average time/residue: 0.4096 time to fit residues: 281.9708 Evaluate side-chains 386 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 312 time to evaluate : 3.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 234 CYS Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 175 LYS Chi-restraints excluded: chain E residue 33 ARG Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 125 CYS Chi-restraints excluded: chain E residue 132 CYS Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 136 SER Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain H residue 279 GLU Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain K residue 140 ASN Chi-restraints excluded: chain K residue 156 TYR Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 359 MET Chi-restraints excluded: chain K residue 560 PHE Chi-restraints excluded: chain K residue 838 LEU Chi-restraints excluded: chain K residue 855 VAL Chi-restraints excluded: chain K residue 902 HIS Chi-restraints excluded: chain K residue 920 HIS Chi-restraints excluded: chain L residue 45 TYR Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain M residue 143 PHE Chi-restraints excluded: chain M residue 279 TYR Chi-restraints excluded: chain M residue 331 VAL Chi-restraints excluded: chain M residue 405 GLN Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain M residue 573 LEU Chi-restraints excluded: chain M residue 579 ILE Chi-restraints excluded: chain M residue 1014 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 361 optimal weight: 20.0000 chunk 42 optimal weight: 0.6980 chunk 213 optimal weight: 0.0170 chunk 273 optimal weight: 8.9990 chunk 211 optimal weight: 8.9990 chunk 315 optimal weight: 6.9990 chunk 209 optimal weight: 2.9990 chunk 373 optimal weight: 4.9990 chunk 233 optimal weight: 4.9990 chunk 227 optimal weight: 0.9990 chunk 172 optimal weight: 0.9980 overall best weight: 1.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 318 HIS M 405 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 32289 Z= 0.264 Angle : 0.600 9.423 43875 Z= 0.300 Chirality : 0.042 0.252 5054 Planarity : 0.004 0.057 5456 Dihedral : 10.826 167.816 5045 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.50 % Allowed : 15.70 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.13), residues: 3839 helix: 1.06 (0.15), residues: 1265 sheet: -0.40 (0.19), residues: 730 loop : -1.87 (0.13), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 96 HIS 0.005 0.001 HIS A 141 PHE 0.040 0.002 PHE K 666 TYR 0.018 0.001 TYR E 32 ARG 0.009 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 326 time to evaluate : 3.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 ILE cc_start: 0.7084 (OUTLIER) cc_final: 0.6805 (pp) REVERT: B 110 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8434 (tp) REVERT: B 186 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8353 (pt) REVERT: D 143 ASP cc_start: 0.8526 (t70) cc_final: 0.8072 (t0) REVERT: D 230 ARG cc_start: 0.7880 (ttp80) cc_final: 0.7654 (ttp80) REVERT: E 99 ASP cc_start: 0.7459 (m-30) cc_final: 0.7182 (m-30) REVERT: E 233 LYS cc_start: 0.8417 (mptp) cc_final: 0.7986 (mttp) REVERT: H 107 VAL cc_start: 0.9199 (OUTLIER) cc_final: 0.8967 (m) REVERT: H 279 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7790 (pt0) REVERT: I 29 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7692 (tpm170) REVERT: I 86 HIS cc_start: 0.7817 (m170) cc_final: 0.7173 (m-70) REVERT: K 465 LYS cc_start: 0.8118 (ttpt) cc_final: 0.7902 (ptpp) REVERT: K 758 MET cc_start: 0.7284 (mpp) cc_final: 0.6833 (mmt) REVERT: K 803 GLU cc_start: 0.6642 (mp0) cc_final: 0.6020 (tt0) REVERT: L 45 TYR cc_start: 0.8168 (OUTLIER) cc_final: 0.7966 (m-80) REVERT: L 52 LYS cc_start: 0.7002 (OUTLIER) cc_final: 0.6769 (mmmm) REVERT: M 227 MET cc_start: 0.7796 (ptt) cc_final: 0.7505 (ptt) REVERT: M 348 GLN cc_start: 0.7306 (mm110) cc_final: 0.7045 (mm-40) REVERT: M 956 GLU cc_start: 0.6944 (tp30) cc_final: 0.6712 (tp30) REVERT: M 1007 MET cc_start: 0.8235 (mmm) cc_final: 0.7606 (mmm) outliers start: 116 outliers final: 88 residues processed: 414 average time/residue: 0.4130 time to fit residues: 280.1738 Evaluate side-chains 407 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 311 time to evaluate : 3.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 234 CYS Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 175 LYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 33 ARG Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 125 CYS Chi-restraints excluded: chain E residue 132 CYS Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 136 SER Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 3 MET Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain H residue 279 GLU Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain I residue 29 ARG Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain K residue 4 SER Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 140 ASN Chi-restraints excluded: chain K residue 156 TYR Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 359 MET Chi-restraints excluded: chain K residue 560 PHE Chi-restraints excluded: chain K residue 799 CYS Chi-restraints excluded: chain K residue 838 LEU Chi-restraints excluded: chain K residue 842 SER Chi-restraints excluded: chain K residue 853 LEU Chi-restraints excluded: chain K residue 855 VAL Chi-restraints excluded: chain K residue 902 HIS Chi-restraints excluded: chain K residue 920 HIS Chi-restraints excluded: chain L residue 45 TYR Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain M residue 121 ASP Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain M residue 143 PHE Chi-restraints excluded: chain M residue 279 TYR Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain M residue 331 VAL Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain M residue 482 THR Chi-restraints excluded: chain M residue 573 LEU Chi-restraints excluded: chain M residue 576 VAL Chi-restraints excluded: chain M residue 579 ILE Chi-restraints excluded: chain M residue 1014 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 230 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 222 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 237 optimal weight: 3.9990 chunk 254 optimal weight: 0.9990 chunk 184 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 293 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 192 HIS F 5 HIS M 318 HIS M 405 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32289 Z= 0.227 Angle : 0.586 13.542 43875 Z= 0.292 Chirality : 0.041 0.248 5054 Planarity : 0.004 0.058 5456 Dihedral : 10.788 167.202 5045 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.25 % Allowed : 16.31 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.13), residues: 3839 helix: 1.14 (0.15), residues: 1265 sheet: -0.39 (0.19), residues: 736 loop : -1.77 (0.13), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 96 HIS 0.005 0.001 HIS A 141 PHE 0.043 0.002 PHE K 666 TYR 0.014 0.001 TYR K 106 ARG 0.012 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 333 time to evaluate : 3.870 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 ILE cc_start: 0.7037 (OUTLIER) cc_final: 0.6783 (pp) REVERT: B 110 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8395 (tp) REVERT: B 153 ARG cc_start: 0.7671 (mtt90) cc_final: 0.7257 (mtt180) REVERT: B 186 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8278 (pt) REVERT: D 143 ASP cc_start: 0.8491 (t70) cc_final: 0.8032 (t0) REVERT: E 99 ASP cc_start: 0.7468 (m-30) cc_final: 0.7220 (m-30) REVERT: E 233 LYS cc_start: 0.8439 (mptp) cc_final: 0.8004 (mttp) REVERT: H 107 VAL cc_start: 0.9191 (OUTLIER) cc_final: 0.8955 (m) REVERT: H 279 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7779 (pt0) REVERT: I 29 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7691 (tpm170) REVERT: I 86 HIS cc_start: 0.7806 (m170) cc_final: 0.7170 (m-70) REVERT: K 758 MET cc_start: 0.7283 (mpp) cc_final: 0.6804 (mmt) REVERT: K 803 GLU cc_start: 0.6726 (mp0) cc_final: 0.6145 (tt0) REVERT: L 52 LYS cc_start: 0.6995 (OUTLIER) cc_final: 0.6775 (mmmm) REVERT: M 227 MET cc_start: 0.7806 (ptt) cc_final: 0.7523 (ptt) REVERT: M 406 MET cc_start: 0.7070 (tpp) cc_final: 0.5664 (mmt) REVERT: M 1007 MET cc_start: 0.8187 (mmm) cc_final: 0.7516 (mmm) outliers start: 108 outliers final: 87 residues processed: 414 average time/residue: 0.4100 time to fit residues: 279.0924 Evaluate side-chains 409 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 315 time to evaluate : 3.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 234 CYS Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 175 LYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 33 ARG Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 125 CYS Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 136 SER Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 3 MET Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain H residue 279 GLU Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain I residue 29 ARG Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain J residue 631 VAL Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 140 ASN Chi-restraints excluded: chain K residue 156 TYR Chi-restraints excluded: chain K residue 166 ASP Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 359 MET Chi-restraints excluded: chain K residue 463 ASP Chi-restraints excluded: chain K residue 560 PHE Chi-restraints excluded: chain K residue 799 CYS Chi-restraints excluded: chain K residue 838 LEU Chi-restraints excluded: chain K residue 842 SER Chi-restraints excluded: chain K residue 853 LEU Chi-restraints excluded: chain K residue 855 VAL Chi-restraints excluded: chain K residue 902 HIS Chi-restraints excluded: chain K residue 920 HIS Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain M residue 121 ASP Chi-restraints excluded: chain M residue 143 PHE Chi-restraints excluded: chain M residue 279 TYR Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain M residue 331 VAL Chi-restraints excluded: chain M residue 390 ILE Chi-restraints excluded: chain M residue 405 GLN Chi-restraints excluded: chain M residue 412 ASN Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain M residue 573 LEU Chi-restraints excluded: chain M residue 576 VAL Chi-restraints excluded: chain M residue 579 ILE Chi-restraints excluded: chain M residue 997 MET Chi-restraints excluded: chain M residue 1014 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 339 optimal weight: 3.9990 chunk 357 optimal weight: 2.9990 chunk 326 optimal weight: 0.2980 chunk 347 optimal weight: 0.9990 chunk 209 optimal weight: 6.9990 chunk 151 optimal weight: 1.9990 chunk 272 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 314 optimal weight: 5.9990 chunk 328 optimal weight: 1.9990 chunk 346 optimal weight: 2.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 788 HIS ** M 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 207 GLN M 405 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.5250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 32289 Z= 0.284 Angle : 0.611 9.479 43875 Z= 0.307 Chirality : 0.042 0.231 5054 Planarity : 0.004 0.056 5456 Dihedral : 10.823 166.934 5045 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.38 % Allowed : 16.43 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.13), residues: 3839 helix: 1.08 (0.15), residues: 1260 sheet: -0.33 (0.19), residues: 729 loop : -1.78 (0.13), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 96 HIS 0.005 0.001 HIS A 141 PHE 0.041 0.002 PHE K 666 TYR 0.022 0.002 TYR A 175 ARG 0.007 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 317 time to evaluate : 3.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ILE cc_start: 0.7001 (OUTLIER) cc_final: 0.6737 (pp) REVERT: B 110 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8430 (tp) REVERT: B 153 ARG cc_start: 0.7712 (mtt90) cc_final: 0.7299 (mtt180) REVERT: B 186 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8285 (pt) REVERT: C 15 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7359 (mtm110) REVERT: C 75 ASP cc_start: 0.6515 (p0) cc_final: 0.6311 (p0) REVERT: D 143 ASP cc_start: 0.8511 (t70) cc_final: 0.8089 (t0) REVERT: E 99 ASP cc_start: 0.7424 (m-30) cc_final: 0.7213 (m-30) REVERT: E 233 LYS cc_start: 0.8431 (mptp) cc_final: 0.8027 (mttp) REVERT: H 107 VAL cc_start: 0.9216 (OUTLIER) cc_final: 0.8982 (m) REVERT: H 279 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7786 (pt0) REVERT: I 29 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7705 (tpm170) REVERT: I 86 HIS cc_start: 0.7858 (m170) cc_final: 0.7209 (m-70) REVERT: K 758 MET cc_start: 0.7314 (mpp) cc_final: 0.6885 (mmt) REVERT: K 803 GLU cc_start: 0.6777 (mp0) cc_final: 0.6143 (tt0) REVERT: L 45 TYR cc_start: 0.8016 (m-80) cc_final: 0.7743 (m-80) REVERT: L 52 LYS cc_start: 0.6999 (OUTLIER) cc_final: 0.6794 (mmmm) REVERT: M 227 MET cc_start: 0.7900 (ptt) cc_final: 0.7507 (ptt) REVERT: M 406 MET cc_start: 0.7070 (tpp) cc_final: 0.5588 (mmt) REVERT: M 1007 MET cc_start: 0.8099 (mmm) cc_final: 0.7739 (mmm) outliers start: 112 outliers final: 99 residues processed: 403 average time/residue: 0.4318 time to fit residues: 284.0330 Evaluate side-chains 415 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 308 time to evaluate : 3.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain C residue 15 ARG Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 234 CYS Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 175 LYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 33 ARG Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 125 CYS Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 136 SER Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 3 MET Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 168 GLN Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain H residue 279 GLU Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain I residue 29 ARG Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain J residue 631 VAL Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 118 LYS Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 140 ASN Chi-restraints excluded: chain K residue 156 TYR Chi-restraints excluded: chain K residue 166 ASP Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 359 MET Chi-restraints excluded: chain K residue 463 ASP Chi-restraints excluded: chain K residue 560 PHE Chi-restraints excluded: chain K residue 564 TRP Chi-restraints excluded: chain K residue 799 CYS Chi-restraints excluded: chain K residue 838 LEU Chi-restraints excluded: chain K residue 842 SER Chi-restraints excluded: chain K residue 853 LEU Chi-restraints excluded: chain K residue 855 VAL Chi-restraints excluded: chain K residue 862 VAL Chi-restraints excluded: chain K residue 902 HIS Chi-restraints excluded: chain K residue 920 HIS Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 121 ASP Chi-restraints excluded: chain M residue 143 PHE Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 279 TYR Chi-restraints excluded: chain M residue 283 SER Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain M residue 331 VAL Chi-restraints excluded: chain M residue 390 ILE Chi-restraints excluded: chain M residue 405 GLN Chi-restraints excluded: chain M residue 412 ASN Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain M residue 546 THR Chi-restraints excluded: chain M residue 573 LEU Chi-restraints excluded: chain M residue 576 VAL Chi-restraints excluded: chain M residue 579 ILE Chi-restraints excluded: chain M residue 887 LEU Chi-restraints excluded: chain M residue 1014 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 228 optimal weight: 20.0000 chunk 367 optimal weight: 0.6980 chunk 224 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 255 optimal weight: 2.9990 chunk 385 optimal weight: 7.9990 chunk 354 optimal weight: 2.9990 chunk 307 optimal weight: 0.0980 chunk 31 optimal weight: 1.9990 chunk 237 optimal weight: 8.9990 chunk 188 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 660 ASN ** M 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 405 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32289 Z= 0.262 Angle : 0.602 10.187 43875 Z= 0.303 Chirality : 0.042 0.226 5054 Planarity : 0.004 0.057 5456 Dihedral : 10.815 166.814 5045 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.35 % Allowed : 16.49 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.13), residues: 3839 helix: 1.11 (0.15), residues: 1259 sheet: -0.35 (0.19), residues: 736 loop : -1.73 (0.13), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 96 HIS 0.005 0.001 HIS A 141 PHE 0.042 0.002 PHE K 666 TYR 0.020 0.001 TYR A 175 ARG 0.005 0.000 ARG C 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 319 time to evaluate : 3.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ILE cc_start: 0.6993 (OUTLIER) cc_final: 0.6712 (pp) REVERT: B 110 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8443 (tp) REVERT: B 153 ARG cc_start: 0.7700 (mtt90) cc_final: 0.7273 (mtt180) REVERT: B 186 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8270 (pt) REVERT: C 15 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7375 (mtm110) REVERT: C 75 ASP cc_start: 0.6483 (p0) cc_final: 0.6283 (p0) REVERT: D 143 ASP cc_start: 0.8518 (t70) cc_final: 0.8095 (t0) REVERT: E 233 LYS cc_start: 0.8441 (mptp) cc_final: 0.8040 (mttp) REVERT: H 107 VAL cc_start: 0.9196 (OUTLIER) cc_final: 0.8952 (m) REVERT: H 279 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7772 (pt0) REVERT: I 29 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7703 (tpm170) REVERT: I 86 HIS cc_start: 0.7866 (m170) cc_final: 0.7223 (m-70) REVERT: K 758 MET cc_start: 0.7357 (mpp) cc_final: 0.6948 (mmt) REVERT: K 803 GLU cc_start: 0.6842 (mp0) cc_final: 0.6200 (tt0) REVERT: L 45 TYR cc_start: 0.8022 (m-80) cc_final: 0.7748 (m-80) REVERT: M 227 MET cc_start: 0.7914 (ptt) cc_final: 0.7609 (ptt) REVERT: M 1007 MET cc_start: 0.8172 (mmm) cc_final: 0.7652 (mmm) outliers start: 111 outliers final: 97 residues processed: 403 average time/residue: 0.4262 time to fit residues: 279.7251 Evaluate side-chains 412 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 308 time to evaluate : 3.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 15 ARG Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 234 CYS Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 175 LYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 33 ARG Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 125 CYS Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 136 SER Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 3 MET Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 168 GLN Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain H residue 279 GLU Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain I residue 29 ARG Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain J residue 631 VAL Chi-restraints excluded: chain K residue 4 SER Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 118 LYS Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 140 ASN Chi-restraints excluded: chain K residue 156 TYR Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 359 MET Chi-restraints excluded: chain K residue 463 ASP Chi-restraints excluded: chain K residue 564 TRP Chi-restraints excluded: chain K residue 799 CYS Chi-restraints excluded: chain K residue 838 LEU Chi-restraints excluded: chain K residue 842 SER Chi-restraints excluded: chain K residue 853 LEU Chi-restraints excluded: chain K residue 855 VAL Chi-restraints excluded: chain K residue 862 VAL Chi-restraints excluded: chain K residue 902 HIS Chi-restraints excluded: chain K residue 920 HIS Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 121 ASP Chi-restraints excluded: chain M residue 143 PHE Chi-restraints excluded: chain M residue 279 TYR Chi-restraints excluded: chain M residue 283 SER Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain M residue 331 VAL Chi-restraints excluded: chain M residue 390 ILE Chi-restraints excluded: chain M residue 412 ASN Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain M residue 546 THR Chi-restraints excluded: chain M residue 573 LEU Chi-restraints excluded: chain M residue 576 VAL Chi-restraints excluded: chain M residue 579 ILE Chi-restraints excluded: chain M residue 881 SER Chi-restraints excluded: chain M residue 887 LEU Chi-restraints excluded: chain M residue 1014 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 243 optimal weight: 4.9990 chunk 327 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 283 optimal weight: 0.1980 chunk 45 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 307 optimal weight: 8.9990 chunk 128 optimal weight: 1.9990 chunk 315 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 285 GLN K 517 ASN K 660 ASN M 405 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.150696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.114483 restraints weight = 51043.079| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.52 r_work: 0.3297 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.5442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32289 Z= 0.204 Angle : 0.577 10.203 43875 Z= 0.290 Chirality : 0.041 0.228 5054 Planarity : 0.004 0.066 5456 Dihedral : 10.754 166.773 5045 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.07 % Allowed : 17.09 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.13), residues: 3839 helix: 1.24 (0.15), residues: 1262 sheet: -0.37 (0.19), residues: 733 loop : -1.65 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 96 HIS 0.005 0.001 HIS K 415 PHE 0.041 0.002 PHE K 666 TYR 0.024 0.001 TYR K 735 ARG 0.006 0.000 ARG C 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8086.71 seconds wall clock time: 147 minutes 40.66 seconds (8860.66 seconds total)