Starting phenix.real_space_refine on Mon Mar 18 16:22:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cna_7529/03_2024/6cna_7529.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cna_7529/03_2024/6cna_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_7529/03_2024/6cna_7529.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cna_7529/03_2024/6cna_7529.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cna_7529/03_2024/6cna_7529.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cna_7529/03_2024/6cna_7529.pdb" } resolution = 4.6 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= 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 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. 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-5265/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 11.79, per 1000 atoms: 0.55 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: 9.46 Conformation dependent library (CDL) restraints added in 5.3 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: 2.53 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: 8.15 Time building geometry restraints manager: 10.31 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=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.492 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.82e+01 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=" 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 - 24.74: 12722 24.74 - 49.47: 156 49.47 - 74.21: 46 74.21 - 98.95: 28 98.95 - 123.69: 32 Dihedral angle restraints: 12984 sinusoidal: 3862 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 12981 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. 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 4.880 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 60.780 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 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 0.254 21822 Z= 0.435 Angle : 0.927 30.052 30008 Z= 0.551 Chirality : 0.052 0.602 3702 Planarity : 0.006 0.090 3930 Dihedral : 13.747 123.685 7040 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 26.55 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.65 % Favored : 90.09 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 796 HIS 0.008 0.003 HIS D 405 PHE 0.027 0.003 PHE A 554 TYR 0.030 0.003 TYR B 179 ARG 0.006 0.001 ARG A 544 *********************** 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 : 0.529 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: A 33 LEU cc_start: 0.9229 (mt) cc_final: 0.8559 (mt) REVERT: A 41 MET cc_start: 0.8292 (tpt) cc_final: 0.7912 (mtm) REVERT: A 42 PHE cc_start: 0.9295 (t80) cc_final: 0.8999 (t80) REVERT: A 65 VAL cc_start: 0.9096 (m) cc_final: 0.8849 (m) REVERT: A 76 LEU cc_start: 0.9321 (mt) cc_final: 0.9098 (mt) REVERT: A 127 ILE cc_start: 0.9615 (tp) cc_final: 0.9391 (tp) REVERT: A 147 GLN cc_start: 0.9194 (mt0) cc_final: 0.8913 (mt0) REVERT: A 151 TRP cc_start: 0.8354 (m-10) cc_final: 0.7958 (m-10) REVERT: A 152 PHE cc_start: 0.9460 (t80) cc_final: 0.8233 (t80) REVERT: A 155 MET cc_start: 0.8232 (mtp) cc_final: 0.7536 (ttm) REVERT: A 156 ARG cc_start: 0.8081 (mtp-110) cc_final: 0.7836 (ttp-110) REVERT: A 161 ASN cc_start: 0.8546 (m-40) cc_final: 0.8279 (m-40) REVERT: A 228 LEU cc_start: 0.9512 (mp) cc_final: 0.9280 (mp) REVERT: A 301 HIS cc_start: 0.8768 (m90) cc_final: 0.8097 (m90) REVERT: A 334 ASN cc_start: 0.9504 (m-40) cc_final: 0.9277 (p0) REVERT: A 343 LYS cc_start: 0.9153 (tttm) cc_final: 0.8575 (tmtt) REVERT: A 400 ILE cc_start: 0.7994 (mt) cc_final: 0.7777 (pt) REVERT: A 474 GLN cc_start: 0.8561 (mt0) cc_final: 0.8107 (mm110) REVERT: A 482 ASP cc_start: 0.9200 (m-30) cc_final: 0.8998 (m-30) REVERT: A 498 HIS cc_start: 0.8323 (p-80) cc_final: 0.7954 (p-80) REVERT: A 554 PHE cc_start: 0.7912 (p90) cc_final: 0.7705 (p90) REVERT: A 688 ILE cc_start: 0.8407 (tt) cc_final: 0.8055 (mm) REVERT: A 689 ASN cc_start: 0.8840 (m-40) cc_final: 0.8560 (m-40) REVERT: A 799 LYS cc_start: 0.8086 (tptm) cc_final: 0.7848 (ttpp) REVERT: A 806 MET cc_start: 0.8711 (mmt) cc_final: 0.8378 (mmt) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1517 time to fit residues: 43.8442 Evaluate side-chains 146 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.706 Evaluate side-chains 200 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 0.656 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: B 75 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8386 (tt0) REVERT: B 103 THR cc_start: 0.8712 (p) cc_final: 0.8490 (p) REVERT: B 106 GLU cc_start: 0.9423 (pm20) cc_final: 0.9092 (pm20) REVERT: B 121 THR cc_start: 0.8979 (m) cc_final: 0.8659 (m) REVERT: B 126 ILE cc_start: 0.8547 (pt) cc_final: 0.8303 (pt) REVERT: B 136 ASP cc_start: 0.9384 (m-30) cc_final: 0.9125 (m-30) REVERT: B 159 ASN cc_start: 0.8937 (m110) cc_final: 0.8482 (m-40) REVERT: B 203 LEU cc_start: 0.8803 (mt) cc_final: 0.8173 (mt) REVERT: B 272 GLU cc_start: 0.9093 (mp0) cc_final: 0.8878 (pm20) REVERT: B 326 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8110 (pp20) REVERT: B 351 PHE cc_start: 0.8797 (m-80) cc_final: 0.8238 (m-80) REVERT: B 407 SER cc_start: 0.8165 (t) cc_final: 0.7779 (t) REVERT: B 426 SER cc_start: 0.8391 (t) cc_final: 0.7997 (t) REVERT: B 500 GLU cc_start: 0.9477 (mm-30) cc_final: 0.9101 (mm-30) REVERT: B 515 ILE cc_start: 0.7454 (mt) cc_final: 0.6942 (mt) REVERT: B 726 LEU cc_start: 0.8442 (tp) cc_final: 0.8164 (tp) REVERT: B 730 ILE cc_start: 0.8920 (mm) cc_final: 0.8582 (mm) REVERT: B 781 LEU cc_start: 0.9016 (mt) cc_final: 0.8781 (mt) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.1497 time to fit residues: 41.4710 Evaluate side-chains 157 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 0.617 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 : 0.002 ------------------------------------------------------------------------------- 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: 5.9990 chunk 95 optimal weight: 6.9990 chunk 149 optimal weight: 0.0270 chunk 183 optimal weight: 8.9990 chunk 285 optimal weight: 0.7980 overall best weight: 2.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.6781 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 21822 Z= 0.271 Angle : 0.735 18.641 30008 Z= 0.389 Chirality : 0.065 1.308 3702 Planarity : 0.005 0.059 3930 Dihedral : 12.667 96.032 3738 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.42 % Favored : 92.46 % Rotamer: Outliers : 0.24 % Allowed : 3.69 % Favored : 96.08 % 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: -2.93 (0.13), residues: 3128 helix: -1.66 (0.12), residues: 1256 sheet: -2.18 (0.25), residues: 262 loop : -2.12 (0.14), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 632 HIS 0.009 0.002 HIS C 134 PHE 0.024 0.002 PHE C 361 TYR 0.017 0.002 TYR C 144 ARG 0.010 0.001 ARG A 124 *********************** 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 194 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 MET cc_start: 0.8601 (tpt) cc_final: 0.8207 (mtm) REVERT: C 42 PHE cc_start: 0.9138 (t80) cc_final: 0.8863 (t80) REVERT: C 76 LEU cc_start: 0.8986 (mt) cc_final: 0.8705 (mt) REVERT: C 147 GLN cc_start: 0.9225 (mt0) cc_final: 0.8851 (mt0) REVERT: C 148 SER cc_start: 0.9718 (t) cc_final: 0.9293 (t) REVERT: C 151 TRP cc_start: 0.8342 (m-10) cc_final: 0.7803 (m-10) REVERT: C 152 PHE cc_start: 0.9365 (t80) cc_final: 0.8615 (t80) REVERT: C 161 ASN cc_start: 0.8300 (m-40) cc_final: 0.8087 (m-40) REVERT: C 174 ARG cc_start: 0.8220 (mtt90) cc_final: 0.7885 (mtt90) REVERT: C 228 LEU cc_start: 0.9464 (mp) cc_final: 0.9202 (mp) REVERT: C 266 TYR cc_start: 0.7857 (m-80) cc_final: 0.7537 (m-80) REVERT: C 301 HIS cc_start: 0.8676 (m90) cc_final: 0.7866 (m90) REVERT: C 341 LEU cc_start: 0.9373 (mp) cc_final: 0.9128 (tt) REVERT: C 343 LYS cc_start: 0.8982 (tttm) cc_final: 0.8242 (tmtt) REVERT: C 474 GLN cc_start: 0.8664 (mt0) cc_final: 0.7961 (mm110) REVERT: C 498 HIS cc_start: 0.8447 (p-80) cc_final: 0.8143 (p-80) REVERT: C 554 PHE cc_start: 0.7974 (p90) cc_final: 0.7470 (p90) REVERT: C 688 ILE cc_start: 0.8291 (tt) cc_final: 0.8034 (mm) REVERT: C 689 ASN cc_start: 0.8808 (m-40) cc_final: 0.8508 (m-40) REVERT: C 757 LEU cc_start: 0.9349 (mm) cc_final: 0.9130 (mm) REVERT: C 799 LYS cc_start: 0.8524 (tptm) cc_final: 0.8213 (ttpp) REVERT: C 806 MET cc_start: 0.8091 (mmt) cc_final: 0.7653 (mmt) outliers start: 1 outliers final: 0 residues processed: 193 average time/residue: 0.1487 time to fit residues: 38.7666 Evaluate side-chains 140 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.648 Evaluate side-chains 188 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 187 time to evaluate : 0.592 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: D 75 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8701 (tt0) REVERT: D 106 GLU cc_start: 0.9507 (pm20) cc_final: 0.9112 (pm20) REVERT: D 136 ASP cc_start: 0.9363 (m-30) cc_final: 0.9150 (m-30) REVERT: D 144 PHE cc_start: 0.8778 (m-80) cc_final: 0.8540 (m-80) REVERT: D 159 ASN cc_start: 0.8705 (m110) cc_final: 0.8254 (m-40) REVERT: D 220 LEU cc_start: 0.9133 (mt) cc_final: 0.8780 (mt) REVERT: D 224 GLN cc_start: 0.8818 (tp40) cc_final: 0.8308 (tm-30) REVERT: D 227 ILE cc_start: 0.7885 (mt) cc_final: 0.7553 (mt) REVERT: D 272 GLU cc_start: 0.9090 (mp0) cc_final: 0.8856 (pm20) REVERT: D 326 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8052 (pp20) REVERT: D 351 PHE cc_start: 0.8750 (m-80) cc_final: 0.8152 (m-80) REVERT: D 500 GLU cc_start: 0.9318 (mm-30) cc_final: 0.8978 (mm-30) REVERT: D 795 LEU cc_start: 0.8429 (tp) cc_final: 0.8119 (tp) outliers start: 1 outliers final: 0 residues processed: 187 average time/residue: 0.1160 time to fit residues: 29.9642 Evaluate side-chains 160 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 0.508 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: 0.0020 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 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 798, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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: 57.3698 > 50: distance: 0 - 1: 8.098 distance: 1 - 2: 4.272 distance: 3 - 4: 24.353 distance: 4 - 5: 16.752 distance: 4 - 7: 29.927 distance: 5 - 6: 44.955 distance: 5 - 11: 12.905 distance: 6 - 32: 23.440 distance: 7 - 8: 18.692 distance: 8 - 9: 12.844 distance: 9 - 10: 3.903 distance: 11 - 12: 25.282 distance: 12 - 13: 17.577 distance: 13 - 14: 23.529 distance: 13 - 15: 6.780 distance: 14 - 40: 19.562 distance: 15 - 16: 8.934 distance: 16 - 17: 6.762 distance: 16 - 19: 20.207 distance: 17 - 18: 4.485 distance: 17 - 24: 15.157 distance: 19 - 20: 14.080 distance: 20 - 21: 30.403 distance: 21 - 22: 30.640 distance: 21 - 23: 28.849 distance: 24 - 25: 11.143 distance: 25 - 26: 8.247 distance: 25 - 28: 18.203 distance: 26 - 27: 14.799 distance: 26 - 32: 10.217 distance: 28 - 29: 3.598 distance: 29 - 30: 20.005 distance: 29 - 31: 12.602 distance: 32 - 33: 14.111 distance: 33 - 34: 10.868 distance: 33 - 36: 9.369 distance: 34 - 35: 6.744 distance: 34 - 40: 20.221 distance: 36 - 37: 33.468 distance: 37 - 39: 34.691 distance: 40 - 41: 12.004 distance: 41 - 42: 23.799 distance: 41 - 44: 20.710 distance: 42 - 43: 22.542 distance: 42 - 46: 34.015 distance: 44 - 45: 23.842 distance: 46 - 47: 18.047 distance: 47 - 48: 8.729 distance: 48 - 49: 7.493 distance: 48 - 50: 5.223 distance: 50 - 51: 9.321 distance: 51 - 52: 9.138 distance: 51 - 54: 13.919 distance: 52 - 53: 17.078 distance: 52 - 59: 19.495 distance: 54 - 55: 14.663 distance: 55 - 56: 17.382 distance: 56 - 57: 18.573 distance: 56 - 58: 23.596 distance: 59 - 60: 27.134 distance: 60 - 61: 5.029 distance: 60 - 63: 33.078 distance: 61 - 62: 10.516 distance: 61 - 64: 6.015 distance: 64 - 65: 12.138 distance: 65 - 66: 21.299 distance: 66 - 67: 25.785 distance: 66 - 72: 31.056 distance: 68 - 69: 9.500 distance: 69 - 70: 5.339 distance: 69 - 71: 11.991