Starting phenix.real_space_refine on Tue Aug 6 11:18:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mts_23996/08_2024/7mts_23996.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mts_23996/08_2024/7mts_23996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mts_23996/08_2024/7mts_23996.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mts_23996/08_2024/7mts_23996.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mts_23996/08_2024/7mts_23996.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mts_23996/08_2024/7mts_23996.cif" } resolution = 3.2 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= 0.004 sd= 0.038 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: 4 Type Number sf(0) Gaussians S 109 5.16 5 C 10258 2.51 5 N 2787 2.21 5 O 2914 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 225": "OE1" <-> "OE2" Residue "C GLU 25": "OE1" <-> "OE2" Residue "C GLU 318": "OE1" <-> "OE2" Residue "E GLU 22": "OE1" <-> "OE2" Residue "A GLU 902": "OE1" <-> "OE2" Residue "B GLU 901": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 16068 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6003 Classifications: {'peptide': 783} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 38, 'TRANS': 744} Chain breaks: 2 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 8, 'ARG:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 79 Chain: "B" Number of atoms: 5773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 763, 5773 Classifications: {'peptide': 763} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 37, 'TRANS': 725} Chain breaks: 4 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 110 Chain: "C" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1412 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 1, 'TRANS': 205} Chain breaks: 3 Unresolved non-hydrogen bonds: 263 Unresolved non-hydrogen angles: 315 Unresolved non-hydrogen dihedrals: 220 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 10, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 138 Chain: "D" Number of atoms: 2438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2438 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 7, 'ASN:plan1': 5, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 127 Chain: "E" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 364 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {'NAG': 1, 'ZQY': 1} Inner-chain residues flagged as termini: ['pdbres="GLU A 902 "'] Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.83, per 1000 atoms: 0.61 Number of scatterers: 16068 At special positions: 0 Unit cell: (109.33, 123.213, 252.501, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 109 16.00 O 2914 8.00 N 2787 7.00 C 10258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 92 " distance=2.04 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 518 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 362 " distance=2.03 Simple disulfide: pdb=" SG CYS A 400 " - pdb=" SG CYS A 407 " distance=2.02 Simple disulfide: pdb=" SG CYS A 500 " - pdb=" SG CYS A 519 " distance=2.03 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 525 " - pdb=" SG CYS A 537 " distance=2.03 Simple disulfide: pdb=" SG CYS A 540 " - pdb=" SG CYS A 553 " distance=2.03 Simple disulfide: pdb=" SG CYS A 632 " - pdb=" SG CYS A 721 " distance=2.03 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 234 " - pdb=" SG CYS B 518 " distance=2.04 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 362 " distance=2.03 Simple disulfide: pdb=" SG CYS B 400 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 500 " - pdb=" SG CYS B 519 " distance=2.05 Simple disulfide: pdb=" SG CYS B 504 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 525 " - pdb=" SG CYS B 537 " distance=2.04 Simple disulfide: pdb=" SG CYS B 540 " - pdb=" SG CYS B 553 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 903 " - " ASN A 203 " " NAG B 902 " - " ASN B 203 " Time building additional restraints: 5.83 Conformation dependent library (CDL) restraints added in 2.8 seconds 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4020 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 24 sheets defined 43.3% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 58 through 74 removed outlier: 3.797A pdb=" N LEU A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 102 Processing helix chain 'A' and resid 102 through 107 removed outlier: 3.941A pdb=" N VAL A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 156 Processing helix chain 'A' and resid 170 through 174 Processing helix chain 'A' and resid 188 through 202 removed outlier: 3.841A pdb=" N ALA A 192 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS A 193 " --> pdb=" O PHE A 189 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE A 202 " --> pdb=" O ILE A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 230 removed outlier: 3.554A pdb=" N GLU A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 259 Processing helix chain 'A' and resid 271 through 286 Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 324 through 332 removed outlier: 3.905A pdb=" N ALA A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 354 Processing helix chain 'A' and resid 377 through 400 removed outlier: 3.559A pdb=" N VAL A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N CYS A 400 " --> pdb=" O HIS A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 565 through 592 removed outlier: 4.408A pdb=" N GLY A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) Proline residue: A 571 - end of helix Processing helix chain 'A' and resid 595 through 601 removed outlier: 3.734A pdb=" N SER A 601 " --> pdb=" O VAL A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 625 removed outlier: 4.714A pdb=" N THR A 620 " --> pdb=" O CYS A 616 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N PHE A 621 " --> pdb=" O TYR A 617 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE A 622 " --> pdb=" O CYS A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 663 removed outlier: 4.063A pdb=" N LEU A 639 " --> pdb=" O ARG A 635 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLY A 640 " --> pdb=" O ARG A 636 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE A 657 " --> pdb=" O LYS A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 666 No H-bonds generated for 'chain 'A' and resid 664 through 666' Processing helix chain 'A' and resid 677 through 701 removed outlier: 3.841A pdb=" N GLN A 690 " --> pdb=" O LEU A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 749 removed outlier: 3.595A pdb=" N THR A 749 " --> pdb=" O TYR A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 757 Processing helix chain 'A' and resid 758 through 783 Proline residue: A 778 - end of helix Processing helix chain 'A' and resid 786 through 819 removed outlier: 3.867A pdb=" N GLN A 790 " --> pdb=" O ASP A 786 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER A 797 " --> pdb=" O THR A 793 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA A 811 " --> pdb=" O GLY A 807 " (cutoff:3.500A) Proline residue: A 812 - end of helix Processing helix chain 'A' and resid 820 through 824 Processing helix chain 'B' and resid 58 through 73 Processing helix chain 'B' and resid 94 through 107 removed outlier: 5.037A pdb=" N ASP B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N PHE B 105 " --> pdb=" O GLN B 101 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 156 removed outlier: 3.624A pdb=" N LEU B 154 " --> pdb=" O GLN B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 174 removed outlier: 3.791A pdb=" N LEU B 172 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 202 removed outlier: 3.658A pdb=" N PHE B 202 " --> pdb=" O ILE B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 230 removed outlier: 3.554A pdb=" N ALA B 230 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 258 Processing helix chain 'B' and resid 271 through 285 Processing helix chain 'B' and resid 307 through 312 Processing helix chain 'B' and resid 324 through 332 removed outlier: 4.182A pdb=" N ALA B 328 " --> pdb=" O ILE B 324 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER B 329 " --> pdb=" O SER B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 354 removed outlier: 3.528A pdb=" N PHE B 348 " --> pdb=" O TRP B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 400 removed outlier: 3.716A pdb=" N VAL B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 422 removed outlier: 3.757A pdb=" N TYR B 419 " --> pdb=" O GLY B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 426 removed outlier: 3.734A pdb=" N VAL B 426 " --> pdb=" O VAL B 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 423 through 426' Processing helix chain 'B' and resid 565 through 592 removed outlier: 4.590A pdb=" N GLY B 570 " --> pdb=" O ALA B 566 " (cutoff:3.500A) Proline residue: B 571 - end of helix Processing helix chain 'B' and resid 595 through 601 removed outlier: 3.574A pdb=" N SER B 601 " --> pdb=" O VAL B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 624 removed outlier: 4.316A pdb=" N THR B 620 " --> pdb=" O CYS B 616 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE B 621 " --> pdb=" O TYR B 617 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE B 622 " --> pdb=" O CYS B 618 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE B 624 " --> pdb=" O THR B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 660 removed outlier: 4.198A pdb=" N LEU B 639 " --> pdb=" O ARG B 635 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N GLY B 640 " --> pdb=" O ARG B 636 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS B 646 " --> pdb=" O ALA B 642 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE B 660 " --> pdb=" O ARG B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 701 removed outlier: 3.680A pdb=" N GLN B 690 " --> pdb=" O LEU B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 727 No H-bonds generated for 'chain 'B' and resid 725 through 727' Processing helix chain 'B' and resid 728 through 749 removed outlier: 3.690A pdb=" N LEU B 732 " --> pdb=" O MET B 728 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR B 734 " --> pdb=" O GLY B 730 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN B 735 " --> pdb=" O SER B 731 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU B 744 " --> pdb=" O ALA B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 783 removed outlier: 4.163A pdb=" N PHE B 761 " --> pdb=" O ASN B 757 " (cutoff:3.500A) Proline residue: B 778 - end of helix removed outlier: 4.144A pdb=" N TYR B 781 " --> pdb=" O LEU B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 819 removed outlier: 3.576A pdb=" N GLN B 790 " --> pdb=" O ASP B 786 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL B 805 " --> pdb=" O SER B 801 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 811 " --> pdb=" O GLY B 807 " (cutoff:3.500A) Proline residue: B 812 - end of helix Processing helix chain 'C' and resid 6 through 31 Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.687A pdb=" N MET C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 removed outlier: 4.132A pdb=" N TRP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 216 Processing helix chain 'C' and resid 242 through 256 Processing helix chain 'C' and resid 270 through 281 removed outlier: 4.158A pdb=" N GLU C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 309 Processing helix chain 'C' and resid 330 through 351 removed outlier: 3.650A pdb=" N ASP C 341 " --> pdb=" O ASP C 337 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS C 351 " --> pdb=" O ASN C 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 26 removed outlier: 3.647A pdb=" N ALA D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'E' and resid 8 through 23 Processing helix chain 'E' and resid 29 through 44 removed outlier: 3.535A pdb=" N CYS E 41 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU E 42 " --> pdb=" O MET E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 59 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.507A pdb=" N LEU A 32 " --> pdb=" O GLY A 85 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N HIS A 87 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU A 34 " --> pdb=" O HIS A 87 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LEU A 89 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLY A 36 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL A 33 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ILE A 140 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY A 35 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N ILE A 163 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL A 139 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 234 through 241 removed outlier: 7.523A pdb=" N VAL A 207 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N SER A 238 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR A 209 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LYS A 240 " --> pdb=" O THR A 209 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ALA A 211 " --> pdb=" O LYS A 240 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N VAL A 265 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N TRP A 291 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ILE A 317 " --> pdb=" O TRP A 291 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ALA A 293 " --> pdb=" O ILE A 317 " (cutoff:3.500A) removed outlier: 9.333A pdb=" N LEU A 319 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TYR A 453 " --> pdb=" O TYR A 473 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N TYR A 473 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE A 455 " --> pdb=" O VAL A 471 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 428 through 429 removed outlier: 3.670A pdb=" N PHE A 428 " --> pdb=" O VAL A 441 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 508 through 512 Processing sheet with id=AA6, first strand: chain 'A' and resid 529 through 533 removed outlier: 3.514A pdb=" N LEU A 532 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N THR A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 544 through 546 Processing sheet with id=AA8, first strand: chain 'A' and resid 705 through 708 Processing sheet with id=AA9, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.620A pdb=" N LEU B 32 " --> pdb=" O GLY B 85 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N HIS B 87 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU B 34 " --> pdb=" O HIS B 87 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N LEU B 89 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLY B 36 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY B 138 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 37 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL B 139 " --> pdb=" O ILE B 163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 41 through 43 removed outlier: 4.688A pdb=" N GLN B 42 " --> pdb=" O GLY B 51 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 234 through 241 removed outlier: 6.042A pdb=" N VAL B 207 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR B 237 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N TYR B 206 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N VAL B 267 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N SER B 208 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N PHE B 269 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL B 210 " --> pdb=" O PHE B 269 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N TRP B 291 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N ILE B 317 " --> pdb=" O TRP B 291 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ALA B 293 " --> pdb=" O ILE B 317 " (cutoff:3.500A) removed outlier: 9.295A pdb=" N LEU B 319 " --> pdb=" O ALA B 293 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TYR B 453 " --> pdb=" O TYR B 473 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TYR B 473 " --> pdb=" O TYR B 453 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE B 455 " --> pdb=" O VAL B 471 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 428 through 429 removed outlier: 3.720A pdb=" N PHE B 428 " --> pdb=" O VAL B 441 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 508 through 511 Processing sheet with id=AB5, first strand: chain 'B' and resid 529 through 533 removed outlier: 6.824A pdb=" N THR B 536 " --> pdb=" O LEU B 532 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 544 through 546 Processing sheet with id=AB7, first strand: chain 'B' and resid 705 through 708 Processing sheet with id=AB8, first strand: chain 'C' and resid 185 through 190 removed outlier: 6.236A pdb=" N VAL C 34 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N PHE C 199 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU C 36 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LYS C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ILE C 222 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N CYS C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N LEU C 39 " --> pdb=" O CYS C 224 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N ALA C 226 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 46 through 51 removed outlier: 5.703A pdb=" N THR D 47 " --> pdb=" O ASN D 340 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ASN D 340 " --> pdb=" O THR D 47 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE D 338 " --> pdb=" O ARG D 49 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 58 through 63 removed outlier: 7.350A pdb=" N ALA D 73 " --> pdb=" O TYR D 59 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N MET D 61 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL D 71 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N TRP D 63 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU D 69 " --> pdb=" O TRP D 63 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER D 74 " --> pdb=" O LYS D 78 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU D 79 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ALA D 92 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE D 81 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN D 88 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 102 through 105 removed outlier: 6.230A pdb=" N ASN D 125 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL D 135 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 146 through 151 removed outlier: 6.830A pdb=" N SER D 160 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N CYS D 149 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL D 158 " --> pdb=" O CYS D 149 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N PHE D 151 " --> pdb=" O GLN D 156 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N GLN D 156 " --> pdb=" O PHE D 151 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR D 178 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ASP D 170 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLN D 176 " --> pdb=" O ASP D 170 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 187 through 192 removed outlier: 6.537A pdb=" N ALA D 208 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N THR D 221 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU D 210 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 229 through 234 removed outlier: 6.944A pdb=" N GLY D 244 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ILE D 232 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA D 242 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N PHE D 234 " --> pdb=" O ALA D 240 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ALA D 240 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N CYS D 250 " --> pdb=" O THR D 263 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR D 263 " --> pdb=" O CYS D 250 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU D 252 " --> pdb=" O LEU D 261 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 273 through 278 removed outlier: 3.876A pdb=" N SER D 275 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASN D 293 " --> pdb=" O TYR D 289 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY D 306 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ASP D 298 " --> pdb=" O ARG D 304 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ARG D 304 " --> pdb=" O ASP D 298 " (cutoff:3.500A) 762 hydrogen bonds defined for protein. 2220 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.44 Time building geometry restraints manager: 6.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5051 1.34 - 1.46: 3879 1.46 - 1.58: 7363 1.58 - 1.71: 0 1.71 - 1.83: 141 Bond restraints: 16434 Sorted by residual: bond pdb=" C1 ZQY A 901 " pdb=" C2 ZQY A 901 " ideal model delta sigma weight residual 1.390 1.528 -0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" C5 ZQY A 901 " pdb=" C6 ZQY A 901 " ideal model delta sigma weight residual 1.392 1.519 -0.127 2.00e-02 2.50e+03 4.06e+01 bond pdb=" C3 ZQY A 901 " pdb=" C4 ZQY A 901 " ideal model delta sigma weight residual 1.394 1.519 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" C9 ZQY A 901 " pdb=" N1 ZQY A 901 " ideal model delta sigma weight residual 1.337 1.446 -0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" N5 ZQY A 901 " pdb=" N6 ZQY A 901 " ideal model delta sigma weight residual 1.274 1.371 -0.097 2.00e-02 2.50e+03 2.34e+01 ... (remaining 16429 not shown) Histogram of bond angle deviations from ideal: 89.46 - 98.42: 3 98.42 - 107.38: 578 107.38 - 116.33: 10206 116.33 - 125.29: 11319 125.29 - 134.24: 287 Bond angle restraints: 22393 Sorted by residual: angle pdb=" N GLU A 712 " pdb=" CA GLU A 712 " pdb=" C GLU A 712 " ideal model delta sigma weight residual 109.15 99.20 9.95 1.44e+00 4.82e-01 4.78e+01 angle pdb=" CA PRO B 711 " pdb=" N PRO B 711 " pdb=" CD PRO B 711 " ideal model delta sigma weight residual 112.00 104.31 7.69 1.40e+00 5.10e-01 3.01e+01 angle pdb=" C GLU A 712 " pdb=" CA GLU A 712 " pdb=" CB GLU A 712 " ideal model delta sigma weight residual 110.67 118.62 -7.95 1.52e+00 4.33e-01 2.73e+01 angle pdb=" C ALA A 710 " pdb=" N PRO A 711 " pdb=" CA PRO A 711 " ideal model delta sigma weight residual 119.28 124.70 -5.42 1.10e+00 8.26e-01 2.42e+01 angle pdb=" CA ARG A 714 " pdb=" C ARG A 714 " pdb=" O ARG A 714 " ideal model delta sigma weight residual 120.55 115.53 5.02 1.06e+00 8.90e-01 2.24e+01 ... (remaining 22388 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 8900 17.93 - 35.85: 656 35.85 - 53.78: 109 53.78 - 71.70: 15 71.70 - 89.63: 18 Dihedral angle restraints: 9698 sinusoidal: 3480 harmonic: 6218 Sorted by residual: dihedral pdb=" CB CYS A 400 " pdb=" SG CYS A 400 " pdb=" SG CYS A 407 " pdb=" CB CYS A 407 " ideal model delta sinusoidal sigma weight residual 93.00 -177.37 -89.63 1 1.00e+01 1.00e-02 9.54e+01 dihedral pdb=" CB CYS B 540 " pdb=" SG CYS B 540 " pdb=" SG CYS B 553 " pdb=" CB CYS B 553 " ideal model delta sinusoidal sigma weight residual -86.00 -168.46 82.46 1 1.00e+01 1.00e-02 8.34e+01 dihedral pdb=" CB CYS A 234 " pdb=" SG CYS A 234 " pdb=" SG CYS A 518 " pdb=" CB CYS A 518 " ideal model delta sinusoidal sigma weight residual -86.00 -156.23 70.23 1 1.00e+01 1.00e-02 6.35e+01 ... (remaining 9695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2457 0.105 - 0.211: 108 0.211 - 0.316: 8 0.316 - 0.421: 0 0.421 - 0.526: 1 Chirality restraints: 2574 Sorted by residual: chirality pdb=" C1 NAG A 903 " pdb=" ND2 ASN A 203 " pdb=" C2 NAG A 903 " pdb=" O5 NAG A 903 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 6.92e+00 chirality pdb=" CA GLU B 516 " pdb=" N GLU B 516 " pdb=" C GLU B 516 " pdb=" CB GLU B 516 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA PRO B 711 " pdb=" N PRO B 711 " pdb=" C PRO B 711 " pdb=" CB PRO B 711 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 2571 not shown) Planarity restraints: 2878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 903 " -0.164 2.00e-02 2.50e+03 1.36e-01 2.30e+02 pdb=" C7 NAG A 903 " 0.046 2.00e-02 2.50e+03 pdb=" C8 NAG A 903 " -0.121 2.00e-02 2.50e+03 pdb=" N2 NAG A 903 " 0.220 2.00e-02 2.50e+03 pdb=" O7 NAG A 903 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 902 " 0.073 2.00e-02 2.50e+03 5.99e-02 4.49e+01 pdb=" C7 NAG B 902 " -0.021 2.00e-02 2.50e+03 pdb=" C8 NAG B 902 " 0.055 2.00e-02 2.50e+03 pdb=" N2 NAG B 902 " -0.095 2.00e-02 2.50e+03 pdb=" O7 NAG B 902 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 710 " 0.097 5.00e-02 4.00e+02 1.43e-01 3.25e+01 pdb=" N PRO B 711 " -0.246 5.00e-02 4.00e+02 pdb=" CA PRO B 711 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO B 711 " 0.076 5.00e-02 4.00e+02 ... (remaining 2875 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2266 2.75 - 3.29: 14941 3.29 - 3.83: 24828 3.83 - 4.36: 28588 4.36 - 4.90: 51302 Nonbonded interactions: 121925 Sorted by model distance: nonbonded pdb=" OH TYR C 320 " pdb=" OD2 ASP C 341 " model vdw 2.213 3.040 nonbonded pdb=" O LEU B 686 " pdb=" OH TYR B 734 " model vdw 2.213 3.040 nonbonded pdb=" ND1 HIS D 142 " pdb=" OG SER D 161 " model vdw 2.233 3.120 nonbonded pdb=" O ALA A 630 " pdb=" OG1 THR A 633 " model vdw 2.235 3.040 nonbonded pdb=" O GLU B 508 " pdb=" NH1 ARG B 531 " model vdw 2.242 3.120 ... (remaining 121920 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 47 or (resid 48 and (name N or name CA or name \ C or name O or name CB )) or resid 49 through 358 or resid 360 through 419 or (r \ esid 420 and (name N or name CA or name C or name O or name CB )) or resid 421 t \ hrough 462 or resid 465 through 504 or (resid 505 through 506 and (name N or nam \ e CA or name C or name O or name CB )) or resid 507 through 512 or (resid 513 an \ d (name N or name CA or name C or name O or name CB )) or resid 514 through 549 \ or (resid 550 through 551 and (name N or name CA or name C or name O or name CB \ )) or resid 552 through 557 or (resid 558 through 559 and (name N or name CA or \ name C or name O or name CB )) or resid 560 or (resid 561 through 562 and (name \ N or name CA or name C or name O or name CB )) or resid 563 through 589 or (resi \ d 590 through 591 and (name N or name CA or name C or name O or name CB )) or re \ sid 592 through 598 or (resid 599 through 600 and (name N or name CA or name C o \ r name O or name CB )) or resid 601 through 602 or (resid 603 through 604 and (n \ ame N or name CA or name C or name O or name CB )) or resid 605 through 607 or ( \ resid 608 and (name N or name CA or name C or name O or name CB )) or resid 609 \ through 625 or (resid 626 and (name N or name CA or name C or name O or name CB \ )) or resid 627 through 640 or (resid 641 through 642 and (name N or name CA or \ name C or name O or name CB )) or resid 643 through 647 or (resid 648 through 64 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 650 through \ 654 or (resid 655 through 656 and (name N or name CA or name C or name O or name \ CB )) or resid 657 through 658 or (resid 659 through 661 and (name N or name CA \ or name C or name O or name CB )) or (resid 673 through 675 and (name N or name \ CA or name C or name O or name CB )) or resid 676 through 677 or (resid 678 and \ (name N or name CA or name C or name O or name CB )) or resid 679 through 681 o \ r (resid 682 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 83 through 687 or (resid 688 and (name N or name CA or name C or name O or name \ CB )) or resid 689 through 708 or (resid 709 through 710 and (name N or name CA \ or name C or name O or name CB )) or resid 711 through 713 or (resid 714 through \ 716 and (name N or name CA or name C or name O or name CB )) or resid 717 throu \ gh 721 or (resid 722 and (name N or name CA or name C or name O or name CB )) or \ resid 723 through 757 or (resid 758 through 759 and (name N or name CA or name \ C or name O or name CB )) or resid 760 through 765 or (resid 766 and (name N or \ name CA or name C or name O or name CB )) or resid 767 through 784 or (resid 785 \ and (name N or name CA or name C or name O or name CB )) or resid 786 through 8 \ 02 or (resid 803 and (name N or name CA or name C or name O or name CB )) or res \ id 804 through 817 or (resid 818 through 820 and (name N or name CA or name C or \ name O or name CB )) or resid 821 through 823 or resid 902 through 903)) selection = (chain 'B' and (resid 23 through 435 or (resid 436 and (name N or name CA or nam \ e C or name O or name CB )) or resid 437 through 475 or (resid 476 and (name N o \ r name CA or name C or name O or name CB )) or resid 477 through 505 or (resid 5 \ 06 and (name N or name CA or name C or name O or name CB )) or resid 507 through \ 590 or (resid 591 and (name N or name CA or name C or name O or name CB )) or r \ esid 592 through 714 or (resid 715 through 716 and (name N or name CA or name C \ or name O or name CB )) or resid 717 through 823 or resid 901 or resid 902)) } 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: 5.490 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: 0.720 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 43.460 Find NCS groups from input model: 0.740 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: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.138 16434 Z= 0.462 Angle : 0.774 9.951 22393 Z= 0.437 Chirality : 0.052 0.526 2574 Planarity : 0.007 0.143 2876 Dihedral : 13.165 87.771 5627 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.13 % Allowed : 2.67 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.41 (0.18), residues: 2120 helix: 1.72 (0.18), residues: 842 sheet: -0.20 (0.25), residues: 394 loop : -0.91 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 339 HIS 0.008 0.002 HIS D 225 PHE 0.044 0.002 PHE A 554 TYR 0.021 0.002 TYR B 734 ARG 0.008 0.001 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 143 time to evaluate : 1.780 Fit side-chains REVERT: D 102 THR cc_start: 0.8355 (m) cc_final: 0.8038 (p) REVERT: D 110 ASN cc_start: 0.8098 (m-40) cc_final: 0.7729 (m110) outliers start: 2 outliers final: 1 residues processed: 145 average time/residue: 0.2825 time to fit residues: 62.2044 Evaluate side-chains 133 residues out of total 1791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 0.6980 chunk 160 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 123 optimal weight: 4.9990 chunk 192 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN D 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16434 Z= 0.187 Angle : 0.512 7.202 22393 Z= 0.276 Chirality : 0.042 0.139 2574 Planarity : 0.005 0.080 2876 Dihedral : 5.434 88.938 2369 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.64 % Allowed : 4.64 % Favored : 94.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.71 (0.18), residues: 2120 helix: 2.15 (0.18), residues: 855 sheet: -0.30 (0.26), residues: 364 loop : -0.84 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 339 HIS 0.005 0.001 HIS D 183 PHE 0.017 0.001 PHE C 189 TYR 0.012 0.001 TYR D 124 ARG 0.004 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 138 time to evaluate : 1.863 Fit side-chains REVERT: B 623 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.7240 (t80) outliers start: 10 outliers final: 5 residues processed: 140 average time/residue: 0.2733 time to fit residues: 58.6578 Evaluate side-chains 131 residues out of total 1791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 125 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 307 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 208 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 154 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 GLN ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN D 88 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 16434 Z= 0.395 Angle : 0.607 8.442 22393 Z= 0.325 Chirality : 0.045 0.152 2574 Planarity : 0.005 0.067 2876 Dihedral : 5.543 85.702 2368 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.14 % Allowed : 6.99 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.39 (0.18), residues: 2120 helix: 1.90 (0.18), residues: 866 sheet: -0.45 (0.26), residues: 389 loop : -1.10 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 339 HIS 0.007 0.001 HIS D 225 PHE 0.032 0.002 PHE A 554 TYR 0.017 0.002 TYR D 111 ARG 0.004 0.000 ARG B 713 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 134 time to evaluate : 1.756 Fit side-chains REVERT: B 623 PHE cc_start: 0.8896 (OUTLIER) cc_final: 0.7938 (t80) REVERT: D 127 LYS cc_start: 0.8491 (mtmm) cc_final: 0.8260 (mtmm) REVERT: D 212 ASP cc_start: 0.6963 (p0) cc_final: 0.6760 (p0) outliers start: 18 outliers final: 12 residues processed: 142 average time/residue: 0.2815 time to fit residues: 60.4239 Evaluate side-chains 141 residues out of total 1791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 128 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain B residue 438 HIS Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 307 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 129 optimal weight: 8.9990 chunk 193 optimal weight: 0.6980 chunk 204 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 16434 Z= 0.312 Angle : 0.560 7.611 22393 Z= 0.301 Chirality : 0.043 0.157 2574 Planarity : 0.005 0.061 2876 Dihedral : 5.338 77.743 2368 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.53 % Allowed : 8.96 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.41 (0.18), residues: 2120 helix: 1.99 (0.18), residues: 865 sheet: -0.50 (0.26), residues: 379 loop : -1.13 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 339 HIS 0.006 0.001 HIS D 225 PHE 0.033 0.002 PHE A 554 TYR 0.014 0.002 TYR B 734 ARG 0.005 0.000 ARG B 713 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 127 time to evaluate : 1.922 Fit side-chains REVERT: B 623 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.7737 (t80) REVERT: D 188 MET cc_start: 0.8463 (mtp) cc_final: 0.8070 (mtt) REVERT: D 212 ASP cc_start: 0.6941 (p0) cc_final: 0.6675 (p0) outliers start: 24 outliers final: 17 residues processed: 142 average time/residue: 0.2524 time to fit residues: 55.7117 Evaluate side-chains 146 residues out of total 1791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 128 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 438 HIS Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 307 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 5.9990 chunk 116 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16434 Z= 0.337 Angle : 0.572 7.952 22393 Z= 0.307 Chirality : 0.044 0.169 2574 Planarity : 0.005 0.060 2876 Dihedral : 5.275 71.418 2368 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.72 % Allowed : 10.36 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.31 (0.18), residues: 2120 helix: 1.96 (0.18), residues: 864 sheet: -0.59 (0.25), residues: 399 loop : -1.24 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 349 HIS 0.006 0.001 HIS D 142 PHE 0.033 0.002 PHE A 554 TYR 0.014 0.002 TYR B 734 ARG 0.003 0.000 ARG D 137 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 132 time to evaluate : 1.776 Fit side-chains REVERT: A 375 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7938 (tm-30) REVERT: B 623 PHE cc_start: 0.8869 (OUTLIER) cc_final: 0.7830 (t80) REVERT: D 212 ASP cc_start: 0.6993 (OUTLIER) cc_final: 0.6740 (p0) outliers start: 27 outliers final: 19 residues processed: 148 average time/residue: 0.2519 time to fit residues: 57.8191 Evaluate side-chains 150 residues out of total 1791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 128 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 438 HIS Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 307 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.5855 > 50: distance: 28 - 101: 10.358 distance: 43 - 105: 21.516 distance: 46 - 102: 16.205 distance: 54 - 59: 4.274 distance: 59 - 60: 9.964 distance: 60 - 61: 21.032 distance: 60 - 63: 20.034 distance: 61 - 62: 27.120 distance: 61 - 67: 26.409 distance: 63 - 64: 13.942 distance: 64 - 65: 19.923 distance: 64 - 66: 12.764 distance: 67 - 68: 28.782 distance: 68 - 69: 36.090 distance: 68 - 71: 23.540 distance: 69 - 70: 31.587 distance: 69 - 72: 17.175 distance: 72 - 73: 8.667 distance: 73 - 74: 17.470 distance: 73 - 76: 19.372 distance: 74 - 75: 4.637 distance: 74 - 77: 27.441 distance: 77 - 78: 3.730 distance: 78 - 79: 14.749 distance: 78 - 81: 4.103 distance: 79 - 80: 11.556 distance: 79 - 85: 11.626 distance: 81 - 82: 4.613 distance: 82 - 83: 8.780 distance: 82 - 84: 12.505 distance: 85 - 86: 4.233 distance: 86 - 87: 6.380 distance: 87 - 88: 5.902 distance: 87 - 92: 6.529 distance: 89 - 90: 11.574 distance: 92 - 93: 7.256 distance: 93 - 94: 5.446 distance: 94 - 95: 7.561 distance: 94 - 96: 7.445 distance: 96 - 97: 22.731 distance: 97 - 98: 32.760 distance: 97 - 100: 19.762 distance: 98 - 99: 30.680 distance: 98 - 102: 33.008 distance: 102 - 103: 19.461 distance: 103 - 104: 11.029 distance: 103 - 106: 7.949 distance: 104 - 105: 28.603 distance: 104 - 113: 14.977 distance: 106 - 107: 15.325 distance: 107 - 108: 7.928 distance: 107 - 109: 13.580 distance: 108 - 110: 3.507 distance: 109 - 111: 4.332 distance: 110 - 112: 6.290 distance: 111 - 112: 5.689 distance: 113 - 114: 20.471 distance: 114 - 115: 28.791 distance: 114 - 117: 16.462 distance: 115 - 116: 12.785 distance: 115 - 118: 18.238 distance: 118 - 119: 27.414 distance: 119 - 120: 15.514 distance: 119 - 122: 14.993 distance: 120 - 121: 15.942 distance: 120 - 126: 22.224 distance: 122 - 123: 22.341 distance: 123 - 124: 28.859 distance: 123 - 125: 40.887