Starting phenix.real_space_refine on Thu Jun 27 06:23:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj7_16907/06_2024/8oj7_16907_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj7_16907/06_2024/8oj7_16907.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj7_16907/06_2024/8oj7_16907_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj7_16907/06_2024/8oj7_16907_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj7_16907/06_2024/8oj7_16907_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj7_16907/06_2024/8oj7_16907.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj7_16907/06_2024/8oj7_16907.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj7_16907/06_2024/8oj7_16907_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj7_16907/06_2024/8oj7_16907_updated.pdb" } resolution = 2.46 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= 0.002 sd= 0.039 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: 6 Type Number sf(0) Gaussians P 70 5.49 5 Mg 2 5.21 5 S 47 5.16 5 C 7457 2.51 5 N 2117 2.21 5 O 2333 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 64": "NH1" <-> "NH2" Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A ARG 101": "NH1" <-> "NH2" Residue "A ARG 112": "NH1" <-> "NH2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A ARG 125": "NH1" <-> "NH2" Residue "A ARG 126": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 163": "NH1" <-> "NH2" Residue "A ARG 170": "NH1" <-> "NH2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A ARG 227": "NH1" <-> "NH2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A ARG 241": "NH1" <-> "NH2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A ARG 274": "NH1" <-> "NH2" Residue "A ARG 277": "NH1" <-> "NH2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A ARG 430": "NH1" <-> "NH2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A ARG 500": "NH1" <-> "NH2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "A ARG 558": "NH1" <-> "NH2" Residue "A ARG 571": "NH1" <-> "NH2" Residue "A ARG 603": "NH1" <-> "NH2" Residue "A ARG 611": "NH1" <-> "NH2" Residue "A ARG 620": "NH1" <-> "NH2" Residue "A ARG 627": "NH1" <-> "NH2" Residue "A ARG 642": "NH1" <-> "NH2" Residue "A ARG 692": "NH1" <-> "NH2" Residue "A ARG 700": "NH1" <-> "NH2" Residue "A ARG 739": "NH1" <-> "NH2" Residue "A ARG 760": "NH1" <-> "NH2" Residue "A ARG 761": "NH1" <-> "NH2" Residue "A ARG 770": "NH1" <-> "NH2" Residue "A ARG 779": "NH1" <-> "NH2" Residue "A ARG 785": "NH1" <-> "NH2" Residue "A ARG 789": "NH1" <-> "NH2" Residue "A ARG 791": "NH1" <-> "NH2" Residue "A PHE 820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 842": "NH1" <-> "NH2" Residue "A ARG 849": "NH1" <-> "NH2" Residue "A ARG 855": "NH1" <-> "NH2" Residue "A ARG 873": "NH1" <-> "NH2" Residue "A ARG 881": "NH1" <-> "NH2" Residue "A ARG 895": "NH1" <-> "NH2" Residue "A ARG 915": "NH1" <-> "NH2" Residue "A TYR 941": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 959": "NH1" <-> "NH2" Residue "A PHE 965": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 968": "NH1" <-> "NH2" Residue "A ARG 971": "NH1" <-> "NH2" Residue "A ARG 993": "NH1" <-> "NH2" Residue "A ARG 1001": "NH1" <-> "NH2" Residue "A ARG 1019": "NH1" <-> "NH2" Residue "A ARG 1020": "NH1" <-> "NH2" Residue "A ARG 1026": "NH1" <-> "NH2" Residue "A ARG 1039": "NH1" <-> "NH2" Residue "A ARG 1042": "NH1" <-> "NH2" Residue "A ARG 1048": "NH1" <-> "NH2" Residue "A ARG 1061": "NH1" <-> "NH2" Residue "A ARG 1062": "NH1" <-> "NH2" Residue "A ARG 1071": "NH1" <-> "NH2" Residue "A ARG 1081": "NH1" <-> "NH2" Residue "A ARG 1089": "NH1" <-> "NH2" Residue "A ARG 1190": "NH1" <-> "NH2" Residue "A ARG 1205": "NH1" <-> "NH2" Residue "A ARG 1207": "NH1" <-> "NH2" Residue "A ARG 1224": "NH1" <-> "NH2" Residue "A ARG 1225": "NH1" <-> "NH2" Residue "A ARG 1229": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "B ARG 64": "NH1" <-> "NH2" Residue "B PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B ARG 90": "NH1" <-> "NH2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "B ARG 106": "NH1" <-> "NH2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B ARG 121": "NH1" <-> "NH2" Residue "B ARG 122": "NH1" <-> "NH2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "B ARG 160": "NH1" <-> "NH2" Residue "B ARG 179": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 224": "NH1" <-> "NH2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B ARG 275": "NH1" <-> "NH2" Residue "B ARG 279": "NH1" <-> "NH2" Residue "B ARG 280": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 12026 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1089, 8577 Classifications: {'peptide': 1089} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 52, 'TRANS': 1034} Chain breaks: 2 Chain: "B" Number of atoms: 2049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2049 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 14, 'TRANS': 251} Chain breaks: 1 Chain: "C" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 586 Unusual residues: {'DOC': 1} Classifications: {'DNA': 28, 'undetermined': 1} Link IDs: {'rna3p': 27, None: 1} Not linked: pdbres=" DA C 52 " pdbres="DOC C 53 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "D" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 782 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 2, 'DTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.56, per 1000 atoms: 0.63 Number of scatterers: 12026 At special positions: 0 Unit cell: (113.05, 125.8, 144.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 47 16.00 P 70 15.00 Mg 2 11.99 O 2333 8.00 N 2117 7.00 C 7457 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.55 Conformation dependent library (CDL) restraints added in 1.7 seconds 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2516 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 14 sheets defined 35.4% alpha, 17.9% beta 26 base pairs and 59 stacking pairs defined. Time for finding SS restraints: 5.95 Creating SS restraints... Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 169 through 175 removed outlier: 3.708A pdb=" N ALA A 174 " --> pdb=" O ARG A 170 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A 175 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 221 through 233 Processing helix chain 'A' and resid 245 through 247 No H-bonds generated for 'chain 'A' and resid 245 through 247' Processing helix chain 'A' and resid 276 through 285 Processing helix chain 'A' and resid 299 through 306 Processing helix chain 'A' and resid 332 through 334 No H-bonds generated for 'chain 'A' and resid 332 through 334' Processing helix chain 'A' and resid 347 through 349 No H-bonds generated for 'chain 'A' and resid 347 through 349' Processing helix chain 'A' and resid 421 through 429 Processing helix chain 'A' and resid 443 through 457 Processing helix chain 'A' and resid 471 through 481 Processing helix chain 'A' and resid 525 through 531 removed outlier: 3.543A pdb=" N ASP A 531 " --> pdb=" O GLY A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 557 through 566 Proline residue: A 561 - end of helix removed outlier: 3.512A pdb=" N ALA A 565 " --> pdb=" O PRO A 561 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 592 Processing helix chain 'A' and resid 594 through 605 Processing helix chain 'A' and resid 609 through 614 Processing helix chain 'A' and resid 618 through 632 removed outlier: 3.569A pdb=" N GLN A 631 " --> pdb=" O ARG A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 733 through 735 No H-bonds generated for 'chain 'A' and resid 733 through 735' Processing helix chain 'A' and resid 741 through 743 No H-bonds generated for 'chain 'A' and resid 741 through 743' Processing helix chain 'A' and resid 773 through 791 removed outlier: 3.773A pdb=" N ARG A 779 " --> pdb=" O SER A 775 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASP A 780 " --> pdb=" O ILE A 776 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N TRP A 781 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG A 791 " --> pdb=" O GLN A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 822 removed outlier: 3.977A pdb=" N TYR A 818 " --> pdb=" O CYS A 814 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR A 821 " --> pdb=" O VAL A 817 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY A 822 " --> pdb=" O TYR A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 855 Processing helix chain 'A' and resid 859 through 865 Processing helix chain 'A' and resid 867 through 872 removed outlier: 3.604A pdb=" N ALA A 870 " --> pdb=" O PRO A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 917 removed outlier: 4.040A pdb=" N THR A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ALA A 904 " --> pdb=" O ALA A 900 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS A 908 " --> pdb=" O ALA A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 958 No H-bonds generated for 'chain 'A' and resid 956 through 958' Processing helix chain 'A' and resid 964 through 979 Processing helix chain 'A' and resid 981 through 992 removed outlier: 4.248A pdb=" N ALA A 991 " --> pdb=" O ALA A 987 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLU A 992 " --> pdb=" O ALA A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1000 Processing helix chain 'A' and resid 1005 through 1022 removed outlier: 4.198A pdb=" N ALA A1009 " --> pdb=" O GLY A1006 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP A1016 " --> pdb=" O VAL A1013 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE A1021 " --> pdb=" O HIS A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1031 Processing helix chain 'A' and resid 1050 through 1060 Processing helix chain 'A' and resid 1081 through 1091 Processing helix chain 'A' and resid 1139 through 1141 No H-bonds generated for 'chain 'A' and resid 1139 through 1141' Processing helix chain 'A' and resid 1146 through 1151 Processing helix chain 'A' and resid 1158 through 1177 removed outlier: 5.539A pdb=" N ALA A1175 " --> pdb=" O VAL A1171 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N LEU A1176 " --> pdb=" O THR A1172 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE A1177 " --> pdb=" O PHE A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1181 through 1191 removed outlier: 4.075A pdb=" N PHE A1191 " --> pdb=" O LEU A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1208 removed outlier: 4.578A pdb=" N THR A1208 " --> pdb=" O ALA A1204 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1234 removed outlier: 3.624A pdb=" N ASP A1232 " --> pdb=" O HIS A1228 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N THR A1233 " --> pdb=" O ARG A1229 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 47 removed outlier: 3.877A pdb=" N ASN B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N GLY B 42 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 43 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA B 46 " --> pdb=" O GLY B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 85 No H-bonds generated for 'chain 'B' and resid 83 through 85' Processing helix chain 'B' and resid 108 through 112 removed outlier: 3.873A pdb=" N VAL B 111 " --> pdb=" O LEU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 155 No H-bonds generated for 'chain 'B' and resid 153 through 155' Processing helix chain 'B' and resid 182 through 190 Processing helix chain 'B' and resid 274 through 280 Processing sheet with id= A, first strand: chain 'A' and resid 74 through 79 Processing sheet with id= B, first strand: chain 'A' and resid 104 through 107 Processing sheet with id= C, first strand: chain 'A' and resid 350 through 352 removed outlier: 6.987A pdb=" N LEU A 185 " --> pdb=" O TYR A 150 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE A 152 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR A 183 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU A 154 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL A 181 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL A 156 " --> pdb=" O GLY A 179 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLY A 179 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL A 341 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N HIS A 197 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE A 343 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N TYR A 199 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N CYS A 345 " --> pdb=" O TYR A 199 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 203 through 208 Processing sheet with id= E, first strand: chain 'A' and resid 521 through 524 removed outlier: 3.857A pdb=" N GLY A 464 " --> pdb=" O ILE A 523 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LYS A 372 " --> pdb=" O VAL A 391 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N VAL A 391 " --> pdb=" O LYS A 372 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE A 392 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASP A 400 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU A 406 " --> pdb=" O ASP A 400 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL A 436 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N SER A 413 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU A 438 " --> pdb=" O SER A 413 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 499 through 502 Processing sheet with id= G, first strand: chain 'A' and resid 707 through 709 removed outlier: 6.870A pdb=" N VAL A 944 " --> pdb=" O THR A 931 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU A 933 " --> pdb=" O ILE A 942 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE A 942 " --> pdb=" O LEU A 933 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 924 through 930 removed outlier: 6.913A pdb=" N VAL A 715 " --> pdb=" O GLU A 927 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THR A 929 " --> pdb=" O VAL A 713 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL A 713 " --> pdb=" O THR A 929 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR A 884 " --> pdb=" O PHE A 891 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU A 893 " --> pdb=" O ILE A 882 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ILE A 882 " --> pdb=" O LEU A 893 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 752 through 757 Processing sheet with id= J, first strand: chain 'A' and resid 1033 through 1036 Processing sheet with id= K, first strand: chain 'B' and resid 88 through 90 removed outlier: 3.658A pdb=" N ARG B 88 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N CYS B 31 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG B 122 " --> pdb=" O TRP B 141 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.503A pdb=" N GLY B 62 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY B 65 " --> pdb=" O GLY B 62 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN B 76 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N VAL B 309 " --> pdb=" O ALA B 303 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL B 176 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR B 257 " --> pdb=" O ARG B 179 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ALA B 222 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLY B 258 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ARG B 224 " --> pdb=" O GLY B 258 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 141 through 143 Processing sheet with id= N, first strand: chain 'B' and resid 201 through 204 413 hydrogen bonds defined for protein. 1125 hydrogen bond angles defined for protein. Warning, Cannot make NA restraints for OD residue (no planarity definition) Restraints generated for nucleic acids: 64 hydrogen bonds 128 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 6.30 Time building geometry restraints manager: 4.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1944 1.32 - 1.45: 4088 1.45 - 1.58: 6197 1.58 - 1.72: 130 1.72 - 1.85: 70 Bond restraints: 12429 Sorted by residual: bond pdb=" C4 DOC C 53 " pdb=" N4 DOC C 53 " ideal model delta sigma weight residual 1.494 1.322 0.172 2.00e-02 2.50e+03 7.39e+01 bond pdb=" C5 DOC C 53 " pdb=" C6 DOC C 53 " ideal model delta sigma weight residual 1.494 1.329 0.165 2.00e-02 2.50e+03 6.78e+01 bond pdb=" C4' DOC C 53 " pdb=" O4' DOC C 53 " ideal model delta sigma weight residual 1.609 1.448 0.161 2.00e-02 2.50e+03 6.51e+01 bond pdb=" C2 DOC C 53 " pdb=" N3 DOC C 53 " ideal model delta sigma weight residual 1.492 1.335 0.157 2.00e-02 2.50e+03 6.17e+01 bond pdb=" C4' DOC C 53 " pdb=" C3' DOC C 53 " ideal model delta sigma weight residual 1.334 1.490 -0.156 2.00e-02 2.50e+03 6.09e+01 ... (remaining 12424 not shown) Histogram of bond angle deviations from ideal: 95.34 - 103.20: 318 103.20 - 111.06: 4457 111.06 - 118.91: 5695 118.91 - 126.77: 6451 126.77 - 134.63: 228 Bond angle restraints: 17149 Sorted by residual: angle pdb=" PB DTP A1303 " pdb=" O3B DTP A1303 " pdb=" PG DTP A1303 " ideal model delta sigma weight residual 139.87 123.19 16.68 1.00e+00 1.00e+00 2.78e+02 angle pdb=" O2G DTP A1303 " pdb=" PG DTP A1303 " pdb=" O3B DTP A1303 " ideal model delta sigma weight residual 104.48 112.79 -8.31 1.14e+00 7.76e-01 5.36e+01 angle pdb=" PA DTP A1303 " pdb=" O3A DTP A1303 " pdb=" PB DTP A1303 " ideal model delta sigma weight residual 136.83 130.09 6.74 1.00e+00 1.00e+00 4.54e+01 angle pdb=" N PRO A 875 " pdb=" CA PRO A 875 " pdb=" C PRO A 875 " ideal model delta sigma weight residual 113.57 121.92 -8.35 1.31e+00 5.83e-01 4.06e+01 angle pdb=" C PRO A 87 " pdb=" CA PRO A 87 " pdb=" CB PRO A 87 " ideal model delta sigma weight residual 111.39 105.92 5.47 9.40e-01 1.13e+00 3.38e+01 ... (remaining 17144 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.39: 6291 19.39 - 38.77: 599 38.77 - 58.16: 285 58.16 - 77.55: 59 77.55 - 96.93: 9 Dihedral angle restraints: 7243 sinusoidal: 3328 harmonic: 3915 Sorted by residual: dihedral pdb=" CA VAL A 517 " pdb=" C VAL A 517 " pdb=" N ASN A 518 " pdb=" CA ASN A 518 " ideal model delta harmonic sigma weight residual -180.00 -152.44 -27.56 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA SER A 119 " pdb=" C SER A 119 " pdb=" N GLY A 120 " pdb=" CA GLY A 120 " ideal model delta harmonic sigma weight residual -180.00 -155.94 -24.06 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA GLY A 321 " pdb=" C GLY A 321 " pdb=" N ARG A 322 " pdb=" CA ARG A 322 " ideal model delta harmonic sigma weight residual -180.00 -157.10 -22.90 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 7240 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 1728 0.127 - 0.254: 188 0.254 - 0.381: 9 0.381 - 0.508: 4 0.508 - 0.635: 2 Chirality restraints: 1931 Sorted by residual: chirality pdb=" P DC C 25 " pdb=" OP1 DC C 25 " pdb=" OP2 DC C 25 " pdb=" O5' DC C 25 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" P DC D 6 " pdb=" OP1 DC D 6 " pdb=" OP2 DC D 6 " pdb=" O5' DC D 6 " both_signs ideal model delta sigma weight residual True 2.35 -2.91 -0.57 2.00e-01 2.50e+01 8.00e+00 chirality pdb=" P DA C 51 " pdb=" OP1 DA C 51 " pdb=" OP2 DA C 51 " pdb=" O5' DA C 51 " both_signs ideal model delta sigma weight residual True 2.35 -1.91 0.44 2.00e-01 2.50e+01 4.80e+00 ... (remaining 1928 not shown) Planarity restraints: 1973 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 692 " 0.575 9.50e-02 1.11e+02 2.58e-01 4.48e+01 pdb=" NE ARG A 692 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A 692 " -0.042 2.00e-02 2.50e+03 pdb=" NH1 ARG A 692 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 692 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1031 " -0.052 2.00e-02 2.50e+03 3.40e-02 2.02e+01 pdb=" CG PHE A1031 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE A1031 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 PHE A1031 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A1031 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE A1031 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE A1031 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA C 45 " 0.005 2.00e-02 2.50e+03 2.71e-02 2.01e+01 pdb=" N9 DA C 45 " 0.016 2.00e-02 2.50e+03 pdb=" C8 DA C 45 " -0.029 2.00e-02 2.50e+03 pdb=" N7 DA C 45 " -0.039 2.00e-02 2.50e+03 pdb=" C5 DA C 45 " 0.028 2.00e-02 2.50e+03 pdb=" C6 DA C 45 " 0.016 2.00e-02 2.50e+03 pdb=" N6 DA C 45 " 0.010 2.00e-02 2.50e+03 pdb=" N1 DA C 45 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DA C 45 " -0.042 2.00e-02 2.50e+03 pdb=" N3 DA C 45 " -0.010 2.00e-02 2.50e+03 pdb=" C4 DA C 45 " 0.049 2.00e-02 2.50e+03 ... (remaining 1970 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.31: 8 2.31 - 2.96: 5278 2.96 - 3.61: 16938 3.61 - 4.25: 29647 4.25 - 4.90: 47022 Nonbonded interactions: 98893 Sorted by model distance: nonbonded pdb=" OE2 GLU A 370 " pdb=" CD1 ILE A 560 " model vdw 1.665 3.460 nonbonded pdb="MG MG A1301 " pdb=" O1B DTP A1303 " model vdw 2.024 2.170 nonbonded pdb="MG MG A1301 " pdb=" O1G DTP A1303 " model vdw 2.041 2.170 nonbonded pdb=" O PHE A 718 " pdb="MG MG A1301 " model vdw 2.078 2.170 nonbonded pdb=" OD2 ASP A 888 " pdb="MG MG A1301 " model vdw 2.080 2.170 ... (remaining 98888 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: 0.010 Normalize map: mean=0, sd=1: 7.300 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: 0.010 Extract box with map and model: 16.320 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 38.400 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 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:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 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 : 0.011 0.172 12429 Z= 0.697 Angle : 1.423 16.677 17149 Z= 0.928 Chirality : 0.084 0.635 1931 Planarity : 0.017 0.258 1973 Dihedral : 18.839 96.933 4727 Min Nonbonded Distance : 1.665 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.12 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.20), residues: 1345 helix: -1.06 (0.21), residues: 434 sheet: 0.01 (0.31), residues: 254 loop : -0.90 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.011 TRP B 91 HIS 0.022 0.004 HIS A 709 PHE 0.056 0.008 PHE A 450 TYR 0.061 0.011 TYR A 490 ARG 0.035 0.004 ARG A 692 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 ASP cc_start: 0.8382 (m-30) cc_final: 0.8062 (t70) REVERT: A 166 GLN cc_start: 0.8023 (mm110) cc_final: 0.7632 (mp10) REVERT: A 207 MET cc_start: 0.9016 (mtm) cc_final: 0.8798 (mtm) REVERT: A 214 ARG cc_start: 0.7268 (ttm-80) cc_final: 0.7040 (ttp80) REVERT: A 228 MET cc_start: 0.7786 (mtm) cc_final: 0.7419 (mtp) REVERT: A 324 ASN cc_start: 0.7045 (t0) cc_final: 0.6616 (t0) REVERT: A 421 GLU cc_start: 0.8219 (tp30) cc_final: 0.7791 (mp0) REVERT: A 426 GLU cc_start: 0.8256 (tt0) cc_final: 0.7711 (tp30) REVERT: A 439 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8315 (tm-30) REVERT: A 451 MET cc_start: 0.8948 (mmm) cc_final: 0.8699 (mmm) REVERT: A 496 ARG cc_start: 0.8263 (mtm-85) cc_final: 0.7940 (mtm110) REVERT: A 525 MET cc_start: 0.8795 (mmm) cc_final: 0.8443 (mmm) REVERT: A 531 ASP cc_start: 0.8749 (m-30) cc_final: 0.8291 (t70) REVERT: A 539 LYS cc_start: 0.9082 (mmtm) cc_final: 0.8804 (mmpt) REVERT: A 580 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8599 (mm110) REVERT: A 747 GLU cc_start: 0.8287 (tp30) cc_final: 0.8017 (tp30) REVERT: A 799 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7745 (tp30) REVERT: A 928 LYS cc_start: 0.8371 (pttt) cc_final: 0.8099 (ptpp) REVERT: A 949 LYS cc_start: 0.8478 (tttm) cc_final: 0.8196 (ttpt) REVERT: A 994 PRO cc_start: 0.8231 (Cg_exo) cc_final: 0.7899 (Cg_endo) REVERT: A 1042 ARG cc_start: 0.8358 (ttm110) cc_final: 0.8141 (mtp-110) REVERT: A 1046 ASN cc_start: 0.7797 (m-40) cc_final: 0.7589 (m110) REVERT: A 1048 ARG cc_start: 0.8203 (mmm-85) cc_final: 0.7466 (mmp80) REVERT: A 1062 ARG cc_start: 0.8591 (mtt180) cc_final: 0.7911 (mmm160) REVERT: A 1182 LYS cc_start: 0.8759 (mtpt) cc_final: 0.8206 (mmpt) REVERT: A 1185 GLU cc_start: 0.8126 (tp30) cc_final: 0.7678 (tt0) REVERT: A 1189 LYS cc_start: 0.8628 (mttm) cc_final: 0.8128 (mtmm) REVERT: B 45 GLN cc_start: 0.6669 (tp-100) cc_final: 0.6289 (mm-40) REVERT: B 60 VAL cc_start: 0.7929 (t) cc_final: 0.7694 (m) REVERT: B 108 LEU cc_start: 0.5773 (pp) cc_final: 0.5427 (mt) REVERT: B 116 GLN cc_start: 0.4844 (tp40) cc_final: 0.4518 (tp40) REVERT: B 152 LEU cc_start: 0.5951 (tp) cc_final: 0.5713 (pt) REVERT: B 182 ARG cc_start: 0.6991 (tmm-80) cc_final: 0.6724 (tpp-160) REVERT: B 261 THR cc_start: 0.6639 (p) cc_final: 0.6184 (p) REVERT: B 279 ARG cc_start: 0.5126 (ptt180) cc_final: 0.4790 (mmt90) REVERT: B 282 GLN cc_start: 0.6357 (tm-30) cc_final: 0.5859 (tm-30) REVERT: B 283 VAL cc_start: 0.6748 (t) cc_final: 0.6457 (t) outliers start: 0 outliers final: 1 residues processed: 195 average time/residue: 1.4139 time to fit residues: 295.8709 Evaluate side-chains 144 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 143 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1226 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 81 optimal weight: 0.0470 chunk 126 optimal weight: 20.0000 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN A 323 ASN A 787 GLN A1008 GLN B 36 GLN ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12429 Z= 0.233 Angle : 0.670 8.959 17149 Z= 0.368 Chirality : 0.043 0.159 1931 Planarity : 0.005 0.047 1973 Dihedral : 20.060 80.774 2254 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.64 % Favored : 98.29 % Rotamer: Outliers : 1.69 % Allowed : 9.26 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.22), residues: 1345 helix: 0.41 (0.25), residues: 449 sheet: 0.12 (0.30), residues: 263 loop : -0.35 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 502 HIS 0.013 0.001 HIS B 69 PHE 0.020 0.002 PHE A 444 TYR 0.021 0.002 TYR A 490 ARG 0.004 0.001 ARG A 959 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 162 time to evaluate : 1.144 Fit side-chains revert: symmetry clash REVERT: A 110 ASP cc_start: 0.8249 (m-30) cc_final: 0.7990 (t70) REVERT: A 166 GLN cc_start: 0.7867 (mm110) cc_final: 0.7429 (mp10) REVERT: A 227 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7135 (mtt-85) REVERT: A 228 MET cc_start: 0.7845 (mtm) cc_final: 0.7382 (mtp) REVERT: A 324 ASN cc_start: 0.6855 (t0) cc_final: 0.6465 (t0) REVERT: A 421 GLU cc_start: 0.8143 (tp30) cc_final: 0.7721 (mp0) REVERT: A 426 GLU cc_start: 0.8273 (tt0) cc_final: 0.7742 (tp30) REVERT: A 451 MET cc_start: 0.8895 (mmm) cc_final: 0.8645 (mmm) REVERT: A 496 ARG cc_start: 0.8130 (mtm-85) cc_final: 0.7835 (mtm110) REVERT: A 531 ASP cc_start: 0.8778 (m-30) cc_final: 0.8367 (t70) REVERT: A 539 LYS cc_start: 0.9112 (mmtm) cc_final: 0.8797 (mmpt) REVERT: A 747 GLU cc_start: 0.8250 (tp30) cc_final: 0.7905 (tp30) REVERT: A 799 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7679 (tp30) REVERT: A 928 LYS cc_start: 0.8352 (pttt) cc_final: 0.7972 (ptpp) REVERT: A 949 LYS cc_start: 0.8337 (tttm) cc_final: 0.8075 (ttpt) REVERT: A 994 PRO cc_start: 0.8045 (Cg_exo) cc_final: 0.7682 (Cg_endo) REVERT: A 1046 ASN cc_start: 0.7745 (m-40) cc_final: 0.7485 (m-40) REVERT: A 1048 ARG cc_start: 0.8178 (mmm-85) cc_final: 0.7440 (mmp80) REVERT: A 1062 ARG cc_start: 0.8559 (mtt180) cc_final: 0.7976 (mmm160) REVERT: A 1182 LYS cc_start: 0.8674 (mtpt) cc_final: 0.8140 (mmpt) REVERT: A 1185 GLU cc_start: 0.8020 (tp30) cc_final: 0.7615 (tt0) REVERT: A 1189 LYS cc_start: 0.8554 (mttm) cc_final: 0.8060 (mtmm) REVERT: B 61 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.6054 (mtm) REVERT: B 76 GLN cc_start: 0.7045 (mm110) cc_final: 0.6683 (mm-40) REVERT: B 108 LEU cc_start: 0.5773 (pp) cc_final: 0.5489 (mt) REVERT: B 152 LEU cc_start: 0.5898 (tp) cc_final: 0.5603 (pt) REVERT: B 182 ARG cc_start: 0.7012 (tmm-80) cc_final: 0.6760 (tpp-160) REVERT: B 282 GLN cc_start: 0.6175 (tm-30) cc_final: 0.5648 (tm-30) REVERT: B 283 VAL cc_start: 0.6804 (t) cc_final: 0.6424 (t) outliers start: 19 outliers final: 3 residues processed: 172 average time/residue: 1.3789 time to fit residues: 254.9807 Evaluate side-chains 146 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 141 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 260 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 105 optimal weight: 0.0010 chunk 85 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 126 optimal weight: 20.0000 chunk 136 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 215 HIS A 285 ASN A 323 ASN A 425 ASN A 541 ASN A 787 GLN A1008 GLN B 69 HIS B 76 GLN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12429 Z= 0.250 Angle : 0.625 6.940 17149 Z= 0.343 Chirality : 0.043 0.160 1931 Planarity : 0.005 0.061 1973 Dihedral : 19.784 81.500 2251 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.93 % Favored : 97.99 % Rotamer: Outliers : 2.14 % Allowed : 10.69 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.22), residues: 1345 helix: 0.70 (0.25), residues: 455 sheet: 0.13 (0.30), residues: 255 loop : -0.27 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 130 HIS 0.009 0.001 HIS A 65 PHE 0.023 0.002 PHE A 820 TYR 0.020 0.002 TYR A 399 ARG 0.006 0.001 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 148 time to evaluate : 1.239 Fit side-chains REVERT: A 64 ARG cc_start: 0.7322 (tpp-160) cc_final: 0.6957 (ttt180) REVERT: A 110 ASP cc_start: 0.8254 (m-30) cc_final: 0.7993 (t70) REVERT: A 143 THR cc_start: 0.7974 (OUTLIER) cc_final: 0.7673 (t) REVERT: A 166 GLN cc_start: 0.7855 (mm110) cc_final: 0.7457 (mp10) REVERT: A 227 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7114 (mtt-85) REVERT: A 228 MET cc_start: 0.7917 (mtm) cc_final: 0.7397 (mtp) REVERT: A 259 TYR cc_start: 0.8208 (OUTLIER) cc_final: 0.6581 (m-80) REVERT: A 324 ASN cc_start: 0.6891 (t0) cc_final: 0.6468 (t0) REVERT: A 421 GLU cc_start: 0.8110 (tp30) cc_final: 0.7703 (mp0) REVERT: A 426 GLU cc_start: 0.8271 (tt0) cc_final: 0.7759 (tp30) REVERT: A 496 ARG cc_start: 0.8213 (mtm-85) cc_final: 0.7882 (mtm110) REVERT: A 531 ASP cc_start: 0.8771 (m-30) cc_final: 0.8403 (t70) REVERT: A 533 ILE cc_start: 0.8571 (mm) cc_final: 0.8358 (mm) REVERT: A 539 LYS cc_start: 0.9069 (mmtm) cc_final: 0.8754 (mmpt) REVERT: A 545 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8003 (tm-30) REVERT: A 799 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7693 (tp30) REVERT: A 850 GLU cc_start: 0.8324 (mm-30) cc_final: 0.8071 (pp20) REVERT: A 860 GLU cc_start: 0.8397 (mt-10) cc_final: 0.7917 (mm-30) REVERT: A 928 LYS cc_start: 0.8320 (pttt) cc_final: 0.7968 (ptpp) REVERT: A 949 LYS cc_start: 0.8308 (tttm) cc_final: 0.8038 (ttpt) REVERT: A 994 PRO cc_start: 0.7824 (Cg_exo) cc_final: 0.7351 (Cg_endo) REVERT: A 1046 ASN cc_start: 0.7689 (m-40) cc_final: 0.7381 (m-40) REVERT: A 1048 ARG cc_start: 0.8059 (mmm-85) cc_final: 0.7333 (mmp80) REVERT: A 1062 ARG cc_start: 0.8557 (mtt180) cc_final: 0.7964 (mmm160) REVERT: A 1182 LYS cc_start: 0.8616 (mtpt) cc_final: 0.8096 (mmtt) REVERT: A 1185 GLU cc_start: 0.7993 (tp30) cc_final: 0.7728 (tt0) REVERT: B 36 GLN cc_start: 0.5913 (mm-40) cc_final: 0.5666 (mp-120) REVERT: B 108 LEU cc_start: 0.5829 (pp) cc_final: 0.5440 (mt) REVERT: B 165 PHE cc_start: 0.7260 (p90) cc_final: 0.6949 (p90) REVERT: B 182 ARG cc_start: 0.7001 (tmm-80) cc_final: 0.6673 (tpt170) REVERT: B 282 GLN cc_start: 0.5919 (tm-30) cc_final: 0.5425 (tm-30) REVERT: B 283 VAL cc_start: 0.6891 (t) cc_final: 0.6461 (t) outliers start: 24 outliers final: 10 residues processed: 166 average time/residue: 1.3815 time to fit residues: 247.3655 Evaluate side-chains 148 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 134 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 700 ARG Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 260 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 20.0000 chunk 95 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 126 optimal weight: 10.0000 chunk 134 optimal weight: 30.0000 chunk 66 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 36 optimal weight: 0.7980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS A 285 ASN A 323 ASN A 425 ASN A 541 ASN A 787 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12429 Z= 0.318 Angle : 0.671 7.451 17149 Z= 0.365 Chirality : 0.046 0.178 1931 Planarity : 0.005 0.061 1973 Dihedral : 19.817 84.363 2251 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.86 % Favored : 98.07 % Rotamer: Outliers : 2.23 % Allowed : 12.11 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.22), residues: 1345 helix: 0.55 (0.25), residues: 454 sheet: 0.10 (0.30), residues: 255 loop : -0.30 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 472 HIS 0.006 0.001 HIS A 158 PHE 0.026 0.003 PHE A 820 TYR 0.022 0.003 TYR A 399 ARG 0.006 0.001 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 139 time to evaluate : 1.167 Fit side-chains REVERT: A 64 ARG cc_start: 0.7429 (tpp-160) cc_final: 0.7110 (ttt-90) REVERT: A 110 ASP cc_start: 0.8345 (m-30) cc_final: 0.8060 (t70) REVERT: A 116 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7794 (ttm-80) REVERT: A 166 GLN cc_start: 0.7878 (mm110) cc_final: 0.7480 (mp10) REVERT: A 227 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7164 (mtt-85) REVERT: A 228 MET cc_start: 0.7917 (mtm) cc_final: 0.7630 (mtp) REVERT: A 259 TYR cc_start: 0.8218 (OUTLIER) cc_final: 0.6622 (m-80) REVERT: A 324 ASN cc_start: 0.6957 (t0) cc_final: 0.6519 (t0) REVERT: A 356 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7158 (mtp) REVERT: A 421 GLU cc_start: 0.8132 (tp30) cc_final: 0.7690 (mp0) REVERT: A 426 GLU cc_start: 0.8285 (tt0) cc_final: 0.7780 (tp30) REVERT: A 496 ARG cc_start: 0.8207 (mtm-85) cc_final: 0.7862 (mtm110) REVERT: A 531 ASP cc_start: 0.8774 (m-30) cc_final: 0.8392 (t0) REVERT: A 539 LYS cc_start: 0.9040 (mmtm) cc_final: 0.8726 (mmpt) REVERT: A 545 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8007 (tm-30) REVERT: A 799 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7747 (tp30) REVERT: A 850 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8096 (pp20) REVERT: A 860 GLU cc_start: 0.8418 (mt-10) cc_final: 0.7952 (mm-30) REVERT: A 928 LYS cc_start: 0.8289 (pttt) cc_final: 0.7960 (ptpp) REVERT: A 949 LYS cc_start: 0.8265 (tttm) cc_final: 0.7999 (ttpt) REVERT: A 994 PRO cc_start: 0.7766 (Cg_exo) cc_final: 0.7259 (Cg_endo) REVERT: A 1048 ARG cc_start: 0.7969 (mmm-85) cc_final: 0.7312 (mmp80) REVERT: A 1062 ARG cc_start: 0.8551 (mtt180) cc_final: 0.7916 (mmm160) REVERT: A 1182 LYS cc_start: 0.8628 (mtpt) cc_final: 0.8107 (mmtt) REVERT: A 1185 GLU cc_start: 0.7995 (tp30) cc_final: 0.7707 (tp30) REVERT: B 61 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.6232 (mtm) REVERT: B 182 ARG cc_start: 0.7033 (tmm-80) cc_final: 0.6765 (tpp-160) REVERT: B 282 GLN cc_start: 0.5902 (tm-30) cc_final: 0.5351 (tm-30) REVERT: B 283 VAL cc_start: 0.6876 (t) cc_final: 0.6445 (t) outliers start: 25 outliers final: 11 residues processed: 156 average time/residue: 1.4366 time to fit residues: 241.2928 Evaluate side-chains 149 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 700 ARG Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 1079 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 260 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 1 optimal weight: 0.0670 chunk 100 optimal weight: 0.4980 chunk 55 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 120 optimal weight: 20.0000 chunk 33 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS A 285 ASN A 323 ASN A 425 ASN A1046 ASN B 36 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12429 Z= 0.207 Angle : 0.569 6.532 17149 Z= 0.312 Chirality : 0.041 0.157 1931 Planarity : 0.004 0.062 1973 Dihedral : 19.601 88.973 2251 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.71 % Favored : 98.22 % Rotamer: Outliers : 2.05 % Allowed : 13.00 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.22), residues: 1345 helix: 0.76 (0.25), residues: 459 sheet: 0.18 (0.31), residues: 255 loop : -0.27 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 472 HIS 0.005 0.001 HIS A 215 PHE 0.021 0.002 PHE A 820 TYR 0.021 0.002 TYR A 399 ARG 0.004 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 140 time to evaluate : 1.198 Fit side-chains REVERT: A 64 ARG cc_start: 0.7411 (tpp-160) cc_final: 0.7118 (ttt180) REVERT: A 110 ASP cc_start: 0.8301 (m-30) cc_final: 0.8035 (t70) REVERT: A 116 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7588 (ttp-110) REVERT: A 166 GLN cc_start: 0.7826 (mm110) cc_final: 0.7428 (mp10) REVERT: A 227 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7111 (mtt-85) REVERT: A 228 MET cc_start: 0.7871 (mtm) cc_final: 0.7618 (mtp) REVERT: A 259 TYR cc_start: 0.8214 (OUTLIER) cc_final: 0.6653 (m-80) REVERT: A 324 ASN cc_start: 0.6869 (t0) cc_final: 0.6474 (t0) REVERT: A 421 GLU cc_start: 0.8108 (tp30) cc_final: 0.7671 (mp0) REVERT: A 426 GLU cc_start: 0.8275 (tt0) cc_final: 0.7774 (tp30) REVERT: A 496 ARG cc_start: 0.8160 (mtm-85) cc_final: 0.7863 (mtm110) REVERT: A 531 ASP cc_start: 0.8719 (m-30) cc_final: 0.8360 (t0) REVERT: A 539 LYS cc_start: 0.9033 (mmtm) cc_final: 0.8729 (mmpt) REVERT: A 545 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7980 (tm-30) REVERT: A 799 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7769 (mm-30) REVERT: A 850 GLU cc_start: 0.8283 (mm-30) cc_final: 0.8062 (pp20) REVERT: A 860 GLU cc_start: 0.8402 (mt-10) cc_final: 0.7937 (mm-30) REVERT: A 923 LYS cc_start: 0.8867 (tttt) cc_final: 0.8406 (tptt) REVERT: A 928 LYS cc_start: 0.8272 (pttt) cc_final: 0.7959 (ptpp) REVERT: A 949 LYS cc_start: 0.8257 (tttm) cc_final: 0.7997 (ttpt) REVERT: A 1048 ARG cc_start: 0.7950 (mmm-85) cc_final: 0.7327 (mmp80) REVERT: A 1062 ARG cc_start: 0.8543 (mtt180) cc_final: 0.7937 (mmm160) REVERT: A 1182 LYS cc_start: 0.8608 (mtpt) cc_final: 0.8094 (mmtt) REVERT: A 1185 GLU cc_start: 0.7946 (tp30) cc_final: 0.7686 (tp30) REVERT: B 36 GLN cc_start: 0.5978 (mm-40) cc_final: 0.5542 (mp-120) REVERT: B 182 ARG cc_start: 0.6975 (tmm-80) cc_final: 0.6721 (tpp-160) REVERT: B 282 GLN cc_start: 0.5781 (tm-30) cc_final: 0.5247 (tm-30) REVERT: B 283 VAL cc_start: 0.6939 (t) cc_final: 0.6541 (t) outliers start: 23 outliers final: 10 residues processed: 158 average time/residue: 1.4501 time to fit residues: 246.2486 Evaluate side-chains 152 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 138 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 700 ARG Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 260 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 0.6980 chunk 120 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 134 optimal weight: 30.0000 chunk 111 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS A 285 ASN A 323 ASN A 425 ASN A1046 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12429 Z= 0.254 Angle : 0.607 6.613 17149 Z= 0.331 Chirality : 0.043 0.162 1931 Planarity : 0.005 0.062 1973 Dihedral : 19.617 89.468 2251 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.93 % Favored : 97.99 % Rotamer: Outliers : 2.67 % Allowed : 12.91 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.22), residues: 1345 helix: 0.69 (0.25), residues: 459 sheet: 0.17 (0.31), residues: 255 loop : -0.28 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 130 HIS 0.005 0.001 HIS A1051 PHE 0.024 0.002 PHE A 820 TYR 0.019 0.002 TYR A 399 ARG 0.006 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 141 time to evaluate : 1.241 Fit side-chains REVERT: A 64 ARG cc_start: 0.7441 (tpp-160) cc_final: 0.7141 (ttt-90) REVERT: A 110 ASP cc_start: 0.8367 (m-30) cc_final: 0.8086 (t70) REVERT: A 116 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7612 (ttp-110) REVERT: A 166 GLN cc_start: 0.7817 (mm110) cc_final: 0.7420 (mp10) REVERT: A 227 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7109 (mtt-85) REVERT: A 228 MET cc_start: 0.7908 (mtm) cc_final: 0.7643 (mtp) REVERT: A 259 TYR cc_start: 0.8193 (OUTLIER) cc_final: 0.6625 (m-80) REVERT: A 324 ASN cc_start: 0.6895 (t0) cc_final: 0.6486 (t0) REVERT: A 356 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.7207 (mtp) REVERT: A 421 GLU cc_start: 0.8089 (tp30) cc_final: 0.7669 (mp0) REVERT: A 426 GLU cc_start: 0.8270 (tt0) cc_final: 0.7759 (tp30) REVERT: A 496 ARG cc_start: 0.8161 (mtm-85) cc_final: 0.7867 (mtm110) REVERT: A 531 ASP cc_start: 0.8770 (m-30) cc_final: 0.8436 (t70) REVERT: A 539 LYS cc_start: 0.9052 (mmtm) cc_final: 0.8748 (mmpt) REVERT: A 545 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8002 (tm-30) REVERT: A 799 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7576 (tp30) REVERT: A 850 GLU cc_start: 0.8318 (mm-30) cc_final: 0.8101 (pp20) REVERT: A 860 GLU cc_start: 0.8416 (mt-10) cc_final: 0.7953 (mm-30) REVERT: A 923 LYS cc_start: 0.8915 (tttt) cc_final: 0.8472 (tptt) REVERT: A 928 LYS cc_start: 0.8289 (pttt) cc_final: 0.7983 (ptpp) REVERT: A 949 LYS cc_start: 0.8286 (tttm) cc_final: 0.8019 (ttpt) REVERT: A 994 PRO cc_start: 0.7594 (Cg_exo) cc_final: 0.7054 (Cg_endo) REVERT: A 1048 ARG cc_start: 0.7942 (mmm-85) cc_final: 0.7345 (mmp80) REVERT: A 1062 ARG cc_start: 0.8533 (mtt180) cc_final: 0.7936 (mmm160) REVERT: A 1182 LYS cc_start: 0.8610 (mtpt) cc_final: 0.8103 (mmtt) REVERT: A 1185 GLU cc_start: 0.7928 (tp30) cc_final: 0.7665 (tp30) REVERT: B 125 LEU cc_start: 0.4478 (mp) cc_final: 0.4157 (mt) REVERT: B 182 ARG cc_start: 0.6999 (tmm-80) cc_final: 0.6757 (tpp-160) REVERT: B 282 GLN cc_start: 0.5771 (tm-30) cc_final: 0.5268 (tm-30) REVERT: B 283 VAL cc_start: 0.6922 (t) cc_final: 0.6513 (t) outliers start: 30 outliers final: 11 residues processed: 163 average time/residue: 1.4327 time to fit residues: 252.7861 Evaluate side-chains 153 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 137 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 700 ARG Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 260 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 7.9990 chunk 15 optimal weight: 0.0050 chunk 76 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 113 optimal weight: 0.9990 chunk 75 optimal weight: 0.3980 chunk 133 optimal weight: 0.0970 chunk 83 optimal weight: 1.9990 chunk 81 optimal weight: 0.0470 chunk 61 optimal weight: 0.5980 chunk 82 optimal weight: 0.3980 overall best weight: 0.1890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS A 285 ASN A 323 ASN A1046 ASN B 36 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12429 Z= 0.136 Angle : 0.503 6.620 17149 Z= 0.275 Chirality : 0.039 0.157 1931 Planarity : 0.004 0.063 1973 Dihedral : 19.208 79.242 2251 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.71 % Favored : 98.22 % Rotamer: Outliers : 1.51 % Allowed : 14.16 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.23), residues: 1345 helix: 1.18 (0.25), residues: 452 sheet: 0.22 (0.31), residues: 255 loop : -0.07 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 502 HIS 0.004 0.001 HIS A 215 PHE 0.023 0.001 PHE B 221 TYR 0.014 0.001 TYR A 399 ARG 0.004 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 147 time to evaluate : 1.124 Fit side-chains REVERT: A 64 ARG cc_start: 0.7348 (tpp-160) cc_final: 0.7087 (ttt180) REVERT: A 104 LYS cc_start: 0.8795 (mtmm) cc_final: 0.8586 (mtpt) REVERT: A 110 ASP cc_start: 0.8302 (m-30) cc_final: 0.8040 (t70) REVERT: A 116 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7581 (ttp-110) REVERT: A 166 GLN cc_start: 0.7778 (mm110) cc_final: 0.7363 (mp10) REVERT: A 227 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.7086 (mtt-85) REVERT: A 228 MET cc_start: 0.7868 (mtm) cc_final: 0.7614 (mtp) REVERT: A 324 ASN cc_start: 0.6728 (t0) cc_final: 0.6353 (t0) REVERT: A 421 GLU cc_start: 0.8117 (tp30) cc_final: 0.7681 (mp0) REVERT: A 426 GLU cc_start: 0.8250 (tt0) cc_final: 0.7741 (tp30) REVERT: A 496 ARG cc_start: 0.8118 (mtm-85) cc_final: 0.7828 (mtm110) REVERT: A 531 ASP cc_start: 0.8718 (m-30) cc_final: 0.8396 (t0) REVERT: A 539 LYS cc_start: 0.9030 (mmtm) cc_final: 0.8732 (mmpt) REVERT: A 545 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7965 (tm-30) REVERT: A 799 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7735 (mm-30) REVERT: A 850 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7987 (pp20) REVERT: A 860 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7930 (mm-30) REVERT: A 923 LYS cc_start: 0.8773 (tttt) cc_final: 0.8352 (tptt) REVERT: A 928 LYS cc_start: 0.8257 (pttt) cc_final: 0.7954 (ptpp) REVERT: A 949 LYS cc_start: 0.8275 (tttm) cc_final: 0.7999 (ttpt) REVERT: A 1048 ARG cc_start: 0.8001 (mmm-85) cc_final: 0.7366 (mmp80) REVERT: A 1062 ARG cc_start: 0.8534 (mtt180) cc_final: 0.7898 (mmm160) REVERT: A 1185 GLU cc_start: 0.7889 (tp30) cc_final: 0.7645 (tp30) REVERT: B 125 LEU cc_start: 0.4462 (mp) cc_final: 0.4132 (mt) REVERT: B 158 MET cc_start: 0.5286 (ttm) cc_final: 0.5064 (ttp) REVERT: B 182 ARG cc_start: 0.7042 (tmm-80) cc_final: 0.6797 (tpt170) REVERT: B 282 GLN cc_start: 0.5655 (tm-30) cc_final: 0.5239 (tm-30) REVERT: B 283 VAL cc_start: 0.6864 (t) cc_final: 0.6565 (t) outliers start: 17 outliers final: 7 residues processed: 157 average time/residue: 1.4444 time to fit residues: 243.5405 Evaluate side-chains 152 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 142 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 700 ARG Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 260 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 0.0980 chunk 80 optimal weight: 0.7980 chunk 40 optimal weight: 0.1980 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS A 285 ASN A 323 ASN A1046 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12429 Z= 0.184 Angle : 0.538 5.926 17149 Z= 0.294 Chirality : 0.040 0.150 1931 Planarity : 0.004 0.064 1973 Dihedral : 19.274 83.727 2251 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.56 % Favored : 98.36 % Rotamer: Outliers : 2.32 % Allowed : 13.71 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.22), residues: 1345 helix: 1.11 (0.25), residues: 452 sheet: 0.28 (0.31), residues: 255 loop : -0.07 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 502 HIS 0.005 0.001 HIS A1051 PHE 0.018 0.002 PHE A 820 TYR 0.019 0.002 TYR A 399 ARG 0.007 0.000 ARG A1019 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 139 time to evaluate : 1.174 Fit side-chains REVERT: A 64 ARG cc_start: 0.7354 (tpp-160) cc_final: 0.7100 (ttt180) REVERT: A 110 ASP cc_start: 0.8313 (m-30) cc_final: 0.8035 (t70) REVERT: A 116 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7604 (ttp-110) REVERT: A 143 THR cc_start: 0.7954 (OUTLIER) cc_final: 0.7656 (t) REVERT: A 166 GLN cc_start: 0.7784 (mm110) cc_final: 0.7400 (mp10) REVERT: A 227 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.7087 (mtt-85) REVERT: A 228 MET cc_start: 0.7891 (mtm) cc_final: 0.7616 (mtp) REVERT: A 259 TYR cc_start: 0.8226 (OUTLIER) cc_final: 0.6628 (m-80) REVERT: A 324 ASN cc_start: 0.6770 (t0) cc_final: 0.6384 (t0) REVERT: A 421 GLU cc_start: 0.8125 (tp30) cc_final: 0.7683 (mp0) REVERT: A 426 GLU cc_start: 0.8264 (tt0) cc_final: 0.7750 (tp30) REVERT: A 496 ARG cc_start: 0.8147 (mtm-85) cc_final: 0.7854 (mtm110) REVERT: A 531 ASP cc_start: 0.8749 (m-30) cc_final: 0.8412 (t0) REVERT: A 539 LYS cc_start: 0.9034 (mmtm) cc_final: 0.8732 (mmpt) REVERT: A 545 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7978 (tm-30) REVERT: A 799 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7534 (tp30) REVERT: A 860 GLU cc_start: 0.8427 (mt-10) cc_final: 0.7951 (mm-30) REVERT: A 923 LYS cc_start: 0.8845 (tttt) cc_final: 0.8405 (tptt) REVERT: A 928 LYS cc_start: 0.8279 (pttt) cc_final: 0.7977 (ptpp) REVERT: A 949 LYS cc_start: 0.8288 (tttm) cc_final: 0.8008 (ttpt) REVERT: A 1048 ARG cc_start: 0.8009 (mmm-85) cc_final: 0.7385 (mmp80) REVERT: A 1062 ARG cc_start: 0.8525 (mtt180) cc_final: 0.7875 (mmm160) REVERT: A 1185 GLU cc_start: 0.7886 (tp30) cc_final: 0.7586 (tp30) REVERT: B 125 LEU cc_start: 0.4534 (mp) cc_final: 0.4186 (mt) REVERT: B 158 MET cc_start: 0.5369 (ttm) cc_final: 0.5134 (ttp) REVERT: B 165 PHE cc_start: 0.7246 (p90) cc_final: 0.6986 (p90) REVERT: B 282 GLN cc_start: 0.5664 (tm-30) cc_final: 0.5255 (tm-30) REVERT: B 283 VAL cc_start: 0.6861 (t) cc_final: 0.6394 (m) outliers start: 26 outliers final: 10 residues processed: 156 average time/residue: 1.3594 time to fit residues: 228.7647 Evaluate side-chains 153 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 138 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 1021 ILE Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 260 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.7965 > 50: distance: 82 - 108: 34.463 distance: 88 - 119: 19.031 distance: 97 - 124: 8.204 distance: 104 - 108: 34.646 distance: 108 - 109: 48.087 distance: 109 - 110: 24.354 distance: 109 - 112: 10.009 distance: 110 - 111: 50.546 distance: 110 - 119: 39.978 distance: 112 - 113: 20.319 distance: 113 - 114: 16.486 distance: 114 - 115: 22.716 distance: 115 - 116: 11.212 distance: 116 - 117: 15.978 distance: 116 - 118: 21.686 distance: 119 - 120: 15.480 distance: 120 - 121: 26.008 distance: 120 - 123: 21.722 distance: 121 - 122: 29.766 distance: 121 - 124: 14.309 distance: 124 - 125: 5.442 distance: 125 - 126: 17.109 distance: 125 - 128: 8.565 distance: 126 - 127: 15.216 distance: 126 - 132: 13.448 distance: 129 - 130: 6.908 distance: 129 - 131: 9.330 distance: 132 - 133: 11.846 distance: 133 - 134: 18.766 distance: 133 - 136: 6.248 distance: 134 - 135: 34.190 distance: 134 - 143: 21.523 distance: 136 - 137: 5.076 distance: 137 - 138: 13.695 distance: 137 - 139: 11.362 distance: 138 - 140: 3.429 distance: 139 - 141: 5.980 distance: 140 - 142: 4.605 distance: 141 - 142: 5.427 distance: 144 - 145: 6.432 distance: 144 - 147: 14.958 distance: 145 - 146: 20.567 distance: 145 - 151: 21.182 distance: 147 - 148: 16.044 distance: 148 - 149: 27.983 distance: 148 - 150: 16.835 distance: 151 - 152: 23.450 distance: 151 - 157: 9.702 distance: 152 - 153: 28.391 distance: 152 - 155: 33.868 distance: 153 - 154: 26.372 distance: 153 - 158: 12.684 distance: 155 - 156: 15.419 distance: 156 - 157: 5.315 distance: 158 - 159: 12.271 distance: 158 - 164: 16.037 distance: 159 - 160: 17.706 distance: 159 - 162: 7.340 distance: 160 - 161: 18.003 distance: 160 - 165: 18.730 distance: 162 - 163: 23.882 distance: 163 - 164: 5.450 distance: 165 - 166: 22.821 distance: 166 - 167: 15.543 distance: 166 - 169: 5.350 distance: 167 - 168: 16.481 distance: 167 - 173: 25.063 distance: 169 - 170: 18.093 distance: 169 - 171: 15.954 distance: 170 - 172: 24.422 distance: 173 - 174: 43.672 distance: 174 - 175: 10.675 distance: 174 - 177: 33.208 distance: 175 - 176: 18.777 distance: 175 - 182: 34.104 distance: 177 - 178: 18.761 distance: 178 - 179: 15.579 distance: 179 - 180: 14.472 distance: 180 - 181: 12.450 distance: 182 - 183: 36.642 distance: 183 - 184: 9.529 distance: 183 - 186: 16.475 distance: 184 - 185: 17.429 distance: 184 - 190: 23.890 distance: 186 - 187: 24.822 distance: 187 - 188: 3.942 distance: 187 - 189: 11.167