Starting phenix.real_space_refine (version: dev) on Thu Feb 23 23:00:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cna_7529/02_2023/6cna_7529.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cna_7529/02_2023/6cna_7529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cna_7529/02_2023/6cna_7529.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cna_7529/02_2023/6cna_7529.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cna_7529/02_2023/6cna_7529.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cna_7529/02_2023/6cna_7529.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 1.443 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 Process input model Symmetric amino acids flipped Residue "A ARG 174": "NH1" <-> "NH2" Residue "C ARG 174": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 21426 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5381 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 795, 5381 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 247} Link IDs: {'CIS': 1, 'PTRANS': 32, 'TRANS': 761} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 923 Unresolved non-hydrogen angles: 1130 Unresolved non-hydrogen dihedrals: 774 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 4, 'TYR:plan': 8, 'ASN:plan1': 7, 'ASP:plan': 12, 'PHE:plan': 11, 'GLU:plan': 26, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 481 Chain: "B" Number of atoms: 5178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5178 Classifications: {'peptide': 785} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 281} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 755} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 1050 Unresolved non-hydrogen angles: 1297 Unresolved non-hydrogen dihedrals: 896 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 15, 'TYR:plan': 7, 'ASN:plan1': 12, 'TRP:plan': 3, 'HIS:plan': 6, 'PHE:plan': 17, 'GLU:plan': 34, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 567 Chain: "C" Number of atoms: 5381 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 795, 5381 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 247} Link IDs: {'CIS': 1, 'PTRANS': 32, 'TRANS': 761} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 923 Unresolved non-hydrogen angles: 1130 Unresolved non-hydrogen dihedrals: 774 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 4, 'TYR:plan': 8, 'ASN:plan1': 7, 'ASP:plan': 12, 'PHE:plan': 11, 'GLU:plan': 26, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 481 Chain: "D" Number of atoms: 5178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5178 Classifications: {'peptide': 785} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 281} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 755} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 1050 Unresolved non-hydrogen angles: 1297 Unresolved non-hydrogen dihedrals: 896 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 15, 'TYR:plan': 7, 'ASN:plan1': 12, 'TRP:plan': 3, 'HIS:plan': 6, 'PHE:plan': 17, 'GLU:plan': 34, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 567 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 12.40, per 1000 atoms: 0.58 Number of scatterers: 21426 At special positions: 0 Unit cell: (116.59, 142.79, 174.23, 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 104 16.00 O 4176 8.00 N 3632 7.00 C 13514 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 476 " distance=2.02 Simple disulfide: pdb=" SG CYS A 765 " - pdb=" SG CYS A 819 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.04 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.02 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.04 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 329 " distance=2.03 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 457 " - pdb=" SG CYS C 476 " distance=2.02 Simple disulfide: pdb=" SG CYS C 765 " - pdb=" SG CYS C 819 " distance=2.03 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.04 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.02 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " 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 BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 904 " - " ASN A 297 " " NAG A 905 " - " ASN A 321 " " NAG B 903 " - " ASN B 74 " " NAG B 904 " - " ASN B 341 " " NAG C 904 " - " ASN C 297 " " NAG C 905 " - " ASN C 321 " " NAG D 903 " - " ASN D 74 " " NAG D 904 " - " ASN D 341 " " NAG E 1 " - " ASN A 389 " " NAG F 1 " - " ASN A 224 " " NAG G 1 " - " ASN B 688 " " NAG H 1 " - " ASN C 389 " " NAG I 1 " - " ASN C 224 " " NAG J 1 " - " ASN D 688 " Time building additional restraints: 9.86 Conformation dependent library (CDL) restraints added in 4.0 seconds 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5896 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 32 sheets defined 44.1% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 35 through 51 removed outlier: 3.548A pdb=" N GLU A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 80 Processing helix chain 'A' and resid 82 through 86 Processing helix chain 'A' and resid 105 through 114 Processing helix chain 'A' and resid 125 through 129 removed outlier: 3.801A pdb=" N TYR A 128 " --> pdb=" O MET A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 146 through 159 removed outlier: 3.693A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 225 through 235 removed outlier: 3.728A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU A 234 " --> pdb=" O MET A 230 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 235 " --> pdb=" O GLU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 259 Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.700A pdb=" N TYR A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 318 removed outlier: 3.760A pdb=" N GLU A 318 " --> pdb=" O HIS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 349 Processing helix chain 'A' and resid 478 through 491 Processing helix chain 'A' and resid 521 through 528 Processing helix chain 'A' and resid 543 through 546 Processing helix chain 'A' and resid 580 through 605 removed outlier: 4.387A pdb=" N SER A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 637 removed outlier: 3.860A pdb=" N MET A 628 " --> pdb=" O LEU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 677 Processing helix chain 'A' and resid 690 through 695 Processing helix chain 'A' and resid 708 through 716 removed outlier: 4.217A pdb=" N ARG A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 728 removed outlier: 3.763A pdb=" N GLU A 728 " --> pdb=" O TYR A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 744 Processing helix chain 'A' and resid 754 through 764 Processing helix chain 'A' and resid 788 through 802 removed outlier: 3.998A pdb=" N GLN A 792 " --> pdb=" O PRO A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 813 Processing helix chain 'A' and resid 832 through 862 Processing helix chain 'B' and resid 46 through 57 removed outlier: 3.534A pdb=" N ILE B 50 " --> pdb=" O ASP B 46 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 removed outlier: 3.768A pdb=" N ARG B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 120 Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 149 through 165 removed outlier: 4.109A pdb=" N TYR B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 192 removed outlier: 4.028A pdb=" N ASN B 192 " --> pdb=" O SER B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 221 Processing helix chain 'B' and resid 233 through 248 removed outlier: 3.667A pdb=" N TYR B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 264 removed outlier: 4.251A pdb=" N ALA B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 311 Processing helix chain 'B' and resid 322 through 326 removed outlier: 3.508A pdb=" N HIS B 325 " --> pdb=" O TYR B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 341 removed outlier: 4.460A pdb=" N TYR B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN B 341 " --> pdb=" O ARG B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 473 Processing helix chain 'B' and resid 496 through 503 Processing helix chain 'B' and resid 519 through 523 removed outlier: 3.612A pdb=" N VAL B 522 " --> pdb=" O ARG B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 556 Processing helix chain 'B' and resid 556 through 578 removed outlier: 4.041A pdb=" N VAL B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL B 574 " --> pdb=" O SER B 570 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU B 578 " --> pdb=" O VAL B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 613 Processing helix chain 'B' and resid 625 through 655 Processing helix chain 'B' and resid 673 through 677 removed outlier: 3.973A pdb=" N PHE B 677 " --> pdb=" O PRO B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 699 removed outlier: 4.410A pdb=" N ASN B 697 " --> pdb=" O ARG B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 707 removed outlier: 3.715A pdb=" N HIS B 703 " --> pdb=" O TYR B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 710 No H-bonds generated for 'chain 'B' and resid 708 through 710' Processing helix chain 'B' and resid 713 through 724 removed outlier: 3.850A pdb=" N ALA B 717 " --> pdb=" O GLY B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 742 Processing helix chain 'B' and resid 771 through 786 removed outlier: 4.036A pdb=" N GLN B 775 " --> pdb=" O GLY B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 796 removed outlier: 4.199A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 843 removed outlier: 3.774A pdb=" N ALA B 819 " --> pdb=" O ILE B 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 51 removed outlier: 3.549A pdb=" N GLU C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS C 51 " --> pdb=" O ASN C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 80 Processing helix chain 'C' and resid 82 through 86 Processing helix chain 'C' and resid 105 through 114 Processing helix chain 'C' and resid 125 through 129 removed outlier: 3.803A pdb=" N TYR C 128 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 146 through 159 removed outlier: 3.693A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 185 Processing helix chain 'C' and resid 225 through 235 removed outlier: 3.728A pdb=" N LEU C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU C 234 " --> pdb=" O MET C 230 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 235 " --> pdb=" O GLU C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 259 Processing helix chain 'C' and resid 278 through 283 removed outlier: 3.701A pdb=" N TYR C 282 " --> pdb=" O ASN C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 318 removed outlier: 3.760A pdb=" N GLU C 318 " --> pdb=" O HIS C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 349 Processing helix chain 'C' and resid 478 through 491 Processing helix chain 'C' and resid 521 through 528 Processing helix chain 'C' and resid 543 through 546 Processing helix chain 'C' and resid 580 through 605 removed outlier: 4.387A pdb=" N SER C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 637 removed outlier: 3.860A pdb=" N MET C 628 " --> pdb=" O LEU C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 677 Processing helix chain 'C' and resid 690 through 695 Processing helix chain 'C' and resid 708 through 716 removed outlier: 4.217A pdb=" N ARG C 716 " --> pdb=" O ILE C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 728 removed outlier: 3.763A pdb=" N GLU C 728 " --> pdb=" O TYR C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 744 Processing helix chain 'C' and resid 754 through 764 Processing helix chain 'C' and resid 788 through 802 removed outlier: 3.997A pdb=" N GLN C 792 " --> pdb=" O PRO C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 813 Processing helix chain 'C' and resid 832 through 862 Processing helix chain 'D' and resid 46 through 57 removed outlier: 3.533A pdb=" N ILE D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 92 removed outlier: 3.769A pdb=" N ARG D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 120 Processing helix chain 'D' and resid 128 through 132 Processing helix chain 'D' and resid 149 through 165 removed outlier: 4.110A pdb=" N TYR D 164 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 192 removed outlier: 4.028A pdb=" N ASN D 192 " --> pdb=" O SER D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 221 Processing helix chain 'D' and resid 233 through 248 removed outlier: 3.667A pdb=" N TYR D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 264 removed outlier: 4.251A pdb=" N ALA D 263 " --> pdb=" O PRO D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 311 Processing helix chain 'D' and resid 322 through 326 removed outlier: 3.508A pdb=" N HIS D 325 " --> pdb=" O TYR D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 341 removed outlier: 4.460A pdb=" N TYR D 338 " --> pdb=" O MET D 334 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN D 341 " --> pdb=" O ARG D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 473 Processing helix chain 'D' and resid 496 through 503 Processing helix chain 'D' and resid 519 through 523 removed outlier: 3.611A pdb=" N VAL D 522 " --> pdb=" O ARG D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 556 Processing helix chain 'D' and resid 556 through 578 removed outlier: 4.042A pdb=" N VAL D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL D 574 " --> pdb=" O SER D 570 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU D 578 " --> pdb=" O VAL D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 613 Processing helix chain 'D' and resid 625 through 655 Processing helix chain 'D' and resid 673 through 677 removed outlier: 3.972A pdb=" N PHE D 677 " --> pdb=" O PRO D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 699 removed outlier: 4.411A pdb=" N ASN D 697 " --> pdb=" O ARG D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 707 removed outlier: 3.714A pdb=" N HIS D 703 " --> pdb=" O TYR D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 710 No H-bonds generated for 'chain 'D' and resid 708 through 710' Processing helix chain 'D' and resid 713 through 724 removed outlier: 3.850A pdb=" N ALA D 717 " --> pdb=" O GLY D 713 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 771 through 786 removed outlier: 4.037A pdb=" N GLN D 775 " --> pdb=" O GLY D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 796 removed outlier: 4.199A pdb=" N GLU D 791 " --> pdb=" O GLY D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 815 through 843 removed outlier: 3.775A pdb=" N ALA D 819 " --> pdb=" O ILE D 815 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 29 removed outlier: 5.523A pdb=" N VAL A 27 " --> pdb=" O GLN A 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 215 through 216 removed outlier: 3.525A pdb=" N VAL A 167 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU A 166 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 288 through 292 removed outlier: 6.549A pdb=" N TYR A 372 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE A 387 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE A 374 " --> pdb=" O VAL A 385 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 494 through 499 removed outlier: 8.552A pdb=" N MET A 533 " --> pdb=" O ARG A 418 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LYS A 420 " --> pdb=" O MET A 533 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N MET A 783 " --> pdb=" O GLU A 549 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 431 through 433 Processing sheet with id=AA6, first strand: chain 'A' and resid 508 through 510 removed outlier: 3.533A pdb=" N GLU A 509 " --> pdb=" O GLU A 518 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 702 through 704 removed outlier: 6.742A pdb=" N ALA A 703 " --> pdb=" O ILE A 751 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N ASP A 753 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TRP A 752 " --> pdb=" O THR A 560 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL A 563 " --> pdb=" O VAL A 768 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 768 " --> pdb=" O VAL A 563 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 702 through 704 removed outlier: 6.742A pdb=" N ALA A 703 " --> pdb=" O ILE A 751 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N ASP A 753 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TRP A 752 " --> pdb=" O THR A 560 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LYS A 555 " --> pdb=" O GLY A 778 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY A 778 " --> pdb=" O LYS A 555 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLN A 557 " --> pdb=" O ARG A 776 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ARG A 776 " --> pdb=" O GLN A 557 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE A 774 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 73 removed outlier: 5.833A pdb=" N ILE B 35 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLU B 69 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE B 37 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N VAL B 71 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL B 39 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N MET B 73 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU B 41 " --> pdb=" O MET B 73 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLY B 36 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N VAL B 98 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ALA B 38 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ALA B 100 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ILE B 40 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL B 97 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ILE B 126 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N PHE B 99 " --> pdb=" O ILE B 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 202 through 204 removed outlier: 6.411A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL B 172 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE B 257 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU B 230 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL B 280 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 366 " --> pdb=" O GLU B 374 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU B 374 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 351 through 352 removed outlier: 3.832A pdb=" N TYR B 356 " --> pdb=" O SER B 352 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 377 through 380 removed outlier: 3.770A pdb=" N LYS B 378 " --> pdb=" O GLN B 385 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN B 385 " --> pdb=" O LYS B 378 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 408 through 409 removed outlier: 3.641A pdb=" N VAL B 409 " --> pdb=" O MET B 508 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 434 through 436 Processing sheet with id=AB6, first strand: chain 'B' and resid 683 through 684 removed outlier: 6.239A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N ASP B 732 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 749 " --> pdb=" O VAL B 538 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 683 through 684 removed outlier: 6.239A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N ASP B 732 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE B 530 " --> pdb=" O GLY B 761 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY B 761 " --> pdb=" O ILE B 530 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N THR B 532 " --> pdb=" O SER B 759 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N SER B 759 " --> pdb=" O THR B 532 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 26 through 29 removed outlier: 5.523A pdb=" N VAL C 27 " --> pdb=" O GLN C 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 215 through 216 removed outlier: 3.525A pdb=" N VAL C 167 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU C 166 " --> pdb=" O SER C 243 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 288 through 292 removed outlier: 6.549A pdb=" N TYR C 372 " --> pdb=" O ILE C 387 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE C 387 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE C 374 " --> pdb=" O VAL C 385 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 494 through 499 removed outlier: 8.551A pdb=" N MET C 533 " --> pdb=" O ARG C 418 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LYS C 420 " --> pdb=" O MET C 533 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N MET C 783 " --> pdb=" O GLU C 549 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 431 through 433 Processing sheet with id=AC4, first strand: chain 'C' and resid 508 through 510 removed outlier: 3.532A pdb=" N GLU C 509 " --> pdb=" O GLU C 518 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 702 through 704 removed outlier: 6.743A pdb=" N ALA C 703 " --> pdb=" O ILE C 751 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N ASP C 753 " --> pdb=" O ALA C 703 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TRP C 752 " --> pdb=" O THR C 560 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL C 563 " --> pdb=" O VAL C 768 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL C 768 " --> pdb=" O VAL C 563 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 702 through 704 removed outlier: 6.743A pdb=" N ALA C 703 " --> pdb=" O ILE C 751 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N ASP C 753 " --> pdb=" O ALA C 703 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TRP C 752 " --> pdb=" O THR C 560 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LYS C 555 " --> pdb=" O GLY C 778 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY C 778 " --> pdb=" O LYS C 555 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLN C 557 " --> pdb=" O ARG C 776 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ARG C 776 " --> pdb=" O GLN C 557 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE C 774 " --> pdb=" O LEU C 559 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 66 through 73 removed outlier: 5.834A pdb=" N ILE D 35 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLU D 69 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE D 37 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N VAL D 71 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL D 39 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N MET D 73 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU D 41 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLY D 36 " --> pdb=" O GLY D 96 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N VAL D 98 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ALA D 38 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ALA D 100 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ILE D 40 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ILE D 126 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N PHE D 99 " --> pdb=" O ILE D 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 202 through 204 removed outlier: 6.412A pdb=" N ILE D 171 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL D 172 " --> pdb=" O TYR D 231 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE D 257 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU D 230 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL D 280 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU D 366 " --> pdb=" O GLU D 374 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU D 374 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 351 through 352 removed outlier: 3.831A pdb=" N TYR D 356 " --> pdb=" O SER D 352 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 377 through 380 removed outlier: 3.770A pdb=" N LYS D 378 " --> pdb=" O GLN D 385 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN D 385 " --> pdb=" O LYS D 378 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 408 through 409 removed outlier: 3.641A pdb=" N VAL D 409 " --> pdb=" O MET D 508 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 434 through 436 Processing sheet with id=AD4, first strand: chain 'D' and resid 683 through 684 removed outlier: 6.240A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL D 749 " --> pdb=" O VAL D 538 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 683 through 684 removed outlier: 6.240A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE D 530 " --> pdb=" O GLY D 761 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLY D 761 " --> pdb=" O ILE D 530 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N THR D 532 " --> pdb=" O SER D 759 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N SER D 759 " --> pdb=" O THR D 532 " (cutoff:3.500A) 1022 hydrogen bonds defined for protein. 2946 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: 7.60 Time building geometry restraints manager: 10.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7266 1.34 - 1.46: 5171 1.46 - 1.58: 9218 1.58 - 1.70: 1 1.70 - 1.82: 166 Bond restraints: 21822 Sorted by residual: bond pdb=" C VAL C 472 " pdb=" N PRO C 473 " ideal model delta sigma weight residual 1.334 1.588 -0.254 2.34e-02 1.83e+03 1.18e+02 bond pdb=" C VAL A 472 " pdb=" N PRO A 473 " ideal model delta sigma weight residual 1.334 1.395 -0.062 2.34e-02 1.83e+03 6.93e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.426 1.492 -0.066 3.20e-02 9.77e+02 4.28e+00 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.426 1.491 -0.065 3.20e-02 9.77e+02 4.17e+00 bond pdb=" CB PHE A 550 " pdb=" CG PHE A 550 " ideal model delta sigma weight residual 1.502 1.457 0.045 2.30e-02 1.89e+03 3.85e+00 ... (remaining 21817 not shown) Histogram of bond angle deviations from ideal: 91.74 - 104.40: 379 104.40 - 117.06: 15692 117.06 - 129.73: 13794 129.73 - 142.39: 141 142.39 - 155.05: 2 Bond angle restraints: 30008 Sorted by residual: angle pdb=" O PRO A 473 " pdb=" C PRO A 473 " pdb=" N GLN A 474 " ideal model delta sigma weight residual 122.73 105.59 17.14 7.10e-01 1.98e+00 5.83e+02 angle pdb=" C VAL A 472 " pdb=" N PRO A 473 " pdb=" CA PRO A 473 " ideal model delta sigma weight residual 120.79 91.74 29.05 1.30e+00 5.92e-01 4.99e+02 angle pdb=" O VAL A 472 " pdb=" C VAL A 472 " pdb=" N PRO A 473 " ideal model delta sigma weight residual 121.10 139.13 -18.03 1.14e+00 7.69e-01 2.50e+02 angle pdb=" C VAL C 472 " pdb=" N PRO C 473 " pdb=" CA PRO C 473 " ideal model delta sigma weight residual 120.79 101.64 19.15 1.30e+00 5.92e-01 2.17e+02 angle pdb=" CA PRO A 473 " pdb=" C PRO A 473 " pdb=" N GLN A 474 " ideal model delta sigma weight residual 116.09 128.04 -11.95 9.20e-01 1.18e+00 1.69e+02 ... (remaining 30003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.15: 12476 22.15 - 44.29: 142 44.29 - 66.44: 16 66.44 - 88.58: 6 88.58 - 110.73: 14 Dihedral angle restraints: 12654 sinusoidal: 3532 harmonic: 9122 Sorted by residual: dihedral pdb=" CA PRO D 415 " pdb=" C PRO D 415 " pdb=" N PHE D 416 " pdb=" CA PHE D 416 " ideal model delta harmonic sigma weight residual -180.00 -144.20 -35.80 0 5.00e+00 4.00e-02 5.13e+01 dihedral pdb=" CA PRO B 415 " pdb=" C PRO B 415 " pdb=" N PHE B 416 " pdb=" CA PHE B 416 " ideal model delta harmonic sigma weight residual -180.00 -144.21 -35.79 0 5.00e+00 4.00e-02 5.12e+01 dihedral pdb=" CA GLU D 449 " pdb=" C GLU D 449 " pdb=" N PRO D 450 " pdb=" CA PRO D 450 " ideal model delta harmonic sigma weight residual 180.00 150.04 29.96 0 5.00e+00 4.00e-02 3.59e+01 ... (remaining 12651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 3634 0.120 - 0.241: 62 0.241 - 0.361: 4 0.361 - 0.482: 0 0.482 - 0.602: 2 Chirality restraints: 3702 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.37e+01 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 2.12e+01 chirality pdb=" C1 NAG B 904 " pdb=" ND2 ASN B 341 " pdb=" C2 NAG B 904 " pdb=" O5 NAG B 904 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 9.06e+00 ... (remaining 3699 not shown) Planarity restraints: 3944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO C 473 " 0.045 2.00e-02 2.50e+03 8.99e-02 8.09e+01 pdb=" C PRO C 473 " -0.155 2.00e-02 2.50e+03 pdb=" O PRO C 473 " 0.060 2.00e-02 2.50e+03 pdb=" N GLN C 474 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 473 " -0.039 2.00e-02 2.50e+03 6.74e-02 4.55e+01 pdb=" C PRO A 473 " 0.117 2.00e-02 2.50e+03 pdb=" O PRO A 473 " -0.039 2.00e-02 2.50e+03 pdb=" N GLN A 474 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 269 " -0.047 5.00e-02 4.00e+02 7.13e-02 8.14e+00 pdb=" N PRO B 270 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 270 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 270 " -0.039 5.00e-02 4.00e+02 ... (remaining 3941 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 433 2.60 - 3.17: 22753 3.17 - 3.75: 32598 3.75 - 4.32: 43694 4.32 - 4.90: 63974 Nonbonded interactions: 163452 Sorted by model distance: nonbonded pdb=" O HIS D 127 " pdb=" OG SER D 130 " model vdw 2.021 2.440 nonbonded pdb=" O HIS B 127 " pdb=" OG SER B 130 " model vdw 2.021 2.440 nonbonded pdb=" O GLU C 758 " pdb=" OG SER C 762 " model vdw 2.047 2.440 nonbonded pdb=" O GLU A 758 " pdb=" OG SER A 762 " model vdw 2.048 2.440 nonbonded pdb=" OD2 ASP D 138 " pdb=" OG SER D 140 " model vdw 2.060 2.440 ... (remaining 163447 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints Number of NCS constrained groups: 3 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' } pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set refine NCS operators NCS operators will be refined. Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 104 5.16 5 C 13514 2.51 5 N 3632 2.21 5 O 4176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.830 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: 0.020 Extract box with map and model: 5.950 Check model and map are aligned: 0.280 Process input model: 58.310 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.170 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.254 21822 Z= 0.423 Angle : 0.913 30.052 30008 Z= 0.549 Chirality : 0.051 0.602 3702 Planarity : 0.006 0.090 3930 Dihedral : 10.187 110.725 6710 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 26.49 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.65 % Favored : 90.09 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.80 (0.11), residues: 3128 helix: -3.86 (0.09), residues: 1220 sheet: -2.67 (0.21), residues: 336 loop : -2.67 (0.12), residues: 1572 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1455 time to fit residues: 41.8670 Evaluate side-chains 144 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.595 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8680 Evaluate side-chains 200 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.1211 time to fit residues: 33.1436 Evaluate side-chains 144 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.557 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7799 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0023 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 265 optimal weight: 20.0000 chunk 237 optimal weight: 30.0000 chunk 132 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 160 optimal weight: 0.0570 chunk 127 optimal weight: 8.9990 chunk 246 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 149 optimal weight: 0.0270 chunk 183 optimal weight: 8.9990 chunk 285 optimal weight: 2.9990 overall best weight: 3.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 118 GLN D 483 ASN D 486 HIS Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 21822 Z= 0.330 Angle : 0.799 22.080 30008 Z= 0.429 Chirality : 0.056 0.840 3702 Planarity : 0.006 0.106 3930 Dihedral : 9.363 109.115 3408 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 22.91 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.18 % Favored : 91.62 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.13 % Twisted Proline : 1.67 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.12), residues: 3128 helix: -2.09 (0.12), residues: 1228 sheet: -2.41 (0.24), residues: 284 loop : -2.25 (0.14), residues: 1616 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 184 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.1466 time to fit residues: 36.1752 Evaluate side-chains 131 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.680 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8584 Evaluate side-chains 187 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 185 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 185 average time/residue: 0.1294 time to fit residues: 32.7296 Evaluate side-chains 158 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.603 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8216 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0024 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 158 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 237 optimal weight: 0.8980 chunk 194 optimal weight: 0.4980 chunk 78 optimal weight: 30.0000 chunk 285 optimal weight: 8.9990 chunk 308 optimal weight: 0.0970 chunk 254 optimal weight: 20.0000 chunk 283 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 229 optimal weight: 1.9990 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 ASN C 474 GLN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 110 GLN D 153 GLN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.241 21822 Z= 0.580 Angle : 1.157 31.285 30008 Z= 0.617 Chirality : 0.067 0.851 3702 Planarity : 0.014 0.375 3930 Dihedral : 9.504 108.931 3408 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 26.65 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.65 % Favored : 90.09 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.13 % Twisted Proline : 1.67 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.12), residues: 3128 helix: -2.19 (0.11), residues: 1254 sheet: -2.61 (0.23), residues: 318 loop : -2.35 (0.14), residues: 1556 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 168 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 170 average time/residue: 0.1288 time to fit residues: 30.4776 Evaluate side-chains 141 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 138 time to evaluate : 0.654 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0612 time to fit residues: 1.1849 Evaluate side-chains 180 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1296 time to fit residues: 31.9147 Evaluate side-chains 151 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 0.536 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7484 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0026 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 282 optimal weight: 0.3980 chunk 214 optimal weight: 6.9990 chunk 148 optimal weight: 0.1980 chunk 31 optimal weight: 7.9990 chunk 136 optimal weight: 10.0000 chunk 191 optimal weight: 20.0000 chunk 286 optimal weight: 50.0000 chunk 303 optimal weight: 0.0980 chunk 149 optimal weight: 0.0270 chunk 271 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 ASN ** C 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.241 21822 Z= 0.580 Angle : 1.157 31.285 30008 Z= 0.617 Chirality : 0.067 0.851 3702 Planarity : 0.014 0.375 3930 Dihedral : 9.504 108.931 3408 Min Nonbonded Distance : 1.323 Molprobity Statistics. All-atom Clashscore : 41.87 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.65 % Favored : 90.09 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.13 % Twisted Proline : 1.67 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.12), residues: 3128 helix: -2.19 (0.11), residues: 1254 sheet: -2.61 (0.23), residues: 318 loop : -2.35 (0.14), residues: 1556 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1410 time to fit residues: 33.3682 Evaluate side-chains 137 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.581 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8525 Evaluate side-chains 173 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1260 time to fit residues: 29.9225 Evaluate side-chains 146 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.584 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8028 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0028 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 252 optimal weight: 0.8980 chunk 172 optimal weight: 50.0000 chunk 4 optimal weight: 0.5980 chunk 225 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 259 optimal weight: 0.5980 chunk 209 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 154 optimal weight: 20.0000 chunk 272 optimal weight: 0.0010 chunk 76 optimal weight: 0.0980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 ASN ** A 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 110 GLN ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.307 21822 Z= 0.563 Angle : 1.086 28.745 30008 Z= 0.562 Chirality : 0.065 0.808 3702 Planarity : 0.011 0.264 3930 Dihedral : 9.425 108.807 3408 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 26.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.40 % Favored : 90.41 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.13 % Twisted Proline : 1.67 % 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: -3.52 (0.12), residues: 3128 helix: -2.17 (0.12), residues: 1256 sheet: -2.62 (0.23), residues: 330 loop : -2.37 (0.14), residues: 1542 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1324 time to fit residues: 30.2563 Evaluate side-chains 133 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.643 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8803 Evaluate side-chains 177 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 176 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 0.1247 time to fit residues: 30.5694 Evaluate side-chains 152 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.579 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8332 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0023 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 102 optimal weight: 0.0270 chunk 273 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 178 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 303 optimal weight: 1.9990 chunk 252 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 25 optimal weight: 0.4980 chunk 100 optimal weight: 8.9990 chunk 159 optimal weight: 7.9990 overall best weight: 3.1044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 ASN ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6610 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.307 21822 Z= 0.563 Angle : 1.086 28.745 30008 Z= 0.562 Chirality : 0.096 3.106 3702 Planarity : 0.011 0.264 3930 Dihedral : 9.425 108.807 3408 Min Nonbonded Distance : 1.305 Molprobity Statistics. All-atom Clashscore : 36.78 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.40 % Favored : 90.41 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.13 % Twisted Proline : 1.67 % 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: -3.52 (0.12), residues: 3128 helix: -2.17 (0.12), residues: 1256 sheet: -2.62 (0.23), residues: 330 loop : -2.37 (0.14), residues: 1542 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1188 time to fit residues: 26.6479 Evaluate side-chains 127 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.578 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8218 Evaluate side-chains 173 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1305 time to fit residues: 31.3046 Evaluate side-chains 149 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.618 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8604 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0024 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 292 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 173 optimal weight: 20.0000 chunk 221 optimal weight: 0.6980 chunk 171 optimal weight: 0.7980 chunk 255 optimal weight: 8.9990 chunk 169 optimal weight: 1.9990 chunk 302 optimal weight: 4.9990 chunk 189 optimal weight: 0.4980 chunk 184 optimal weight: 0.1980 chunk 139 optimal weight: 20.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 ASN ** C 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 153 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.136 21822 Z= 0.435 Angle : 0.990 20.859 30008 Z= 0.521 Chirality : 0.069 1.377 3702 Planarity : 0.012 0.285 3930 Dihedral : 9.418 108.621 3408 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 26.63 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.97 % Favored : 89.83 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.13 % Twisted Proline : 1.67 % 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: -3.52 (0.12), residues: 3128 helix: -2.18 (0.12), residues: 1254 sheet: -2.63 (0.24), residues: 318 loop : -2.36 (0.14), residues: 1556 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1229 time to fit residues: 27.8050 Evaluate side-chains 136 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.651 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9341 Evaluate side-chains 172 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1330 time to fit residues: 31.3261 Evaluate side-chains 139 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.639 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8764 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0023 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 675, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 770, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/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-4877/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: 72.0453 > 50: distance: 0 - 1: 56.796 distance: 1 - 2: 70.746 distance: 1 - 4: 39.070 distance: 2 - 3: 55.614 distance: 2 - 8: 68.833 distance: 4 - 5: 41.194 distance: 9 - 12: 56.189 distance: 10 - 16: 40.304 distance: 12 - 14: 55.532 distance: 13 - 15: 41.206 distance: 17 - 18: 15.141 distance: 18 - 19: 44.510 distance: 18 - 30: 44.991 distance: 20 - 21: 34.887 distance: 21 - 22: 40.872 distance: 21 - 23: 34.467 distance: 23 - 25: 69.613 distance: 24 - 25: 39.955 distance: 26 - 28: 41.050 distance: 28 - 29: 56.347 distance: 30 - 36: 40.330 distance: 31 - 32: 40.624 distance: 31 - 34: 40.522 distance: 32 - 33: 38.919 distance: 32 - 37: 41.069 distance: 37 - 38: 39.165 distance: 38 - 39: 38.667 distance: 39 - 40: 40.249 distance: 39 - 41: 57.830 distance: 42 - 43: 56.446 distance: 43 - 45: 40.683 distance: 45 - 46: 36.848 distance: 46 - 47: 3.363 distance: 46 - 49: 66.573 distance: 47 - 50: 39.091 distance: 51 - 52: 40.684 distance: 51 - 54: 38.593 distance: 52 - 53: 40.994 distance: 52 - 55: 49.932 distance: 55 - 56: 9.256 distance: 56 - 57: 54.759 distance: 57 - 58: 4.311 distance: 57 - 60: 35.396 distance: 60 - 61: 56.776 distance: 61 - 64: 56.101 distance: 62 - 63: 40.139