Starting phenix.real_space_refine on Sat Aug 10 16:29:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfn_37497/08_2024/8wfn_37497.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfn_37497/08_2024/8wfn_37497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfn_37497/08_2024/8wfn_37497.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfn_37497/08_2024/8wfn_37497.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfn_37497/08_2024/8wfn_37497.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfn_37497/08_2024/8wfn_37497.cif" } resolution = 4.48 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= 0.001 sd= 0.094 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 111 5.16 5 C 19101 2.51 5 N 4763 2.21 5 O 5557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 877": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 996": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 29532 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 963, 8016 Classifications: {'peptide': 963} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 944} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 8117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 976, 8117 Classifications: {'peptide': 976} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 956} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 851 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain breaks: 4 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 837 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain breaks: 4 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 5585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 666, 5585 Classifications: {'peptide': 666} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 652} Chain breaks: 13 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 5492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5492 Classifications: {'peptide': 659} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 646} Chain breaks: 14 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 312 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain breaks: 5 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 5, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 76 Chain: "H" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain breaks: 4 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 1, 'PHE:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 41 Time building chain proxies: 14.73, per 1000 atoms: 0.50 Number of scatterers: 29532 At special positions: 0 Unit cell: (105.4, 132.6, 243.1, 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 111 16.00 O 5557 8.00 N 4763 7.00 C 19101 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.63 Conformation dependent library (CDL) restraints added in 5.2 seconds 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6836 Finding SS restraints... Secondary structure from input PDB file: 208 helices and 14 sheets defined 66.6% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.96 Creating SS restraints... Processing helix chain 'A' and resid 23 through 39 Processing helix chain 'A' and resid 48 through 54 removed outlier: 3.587A pdb=" N THR A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 72 removed outlier: 3.735A pdb=" N LEU A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR A 71 " --> pdb=" O HIS A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 95 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 96 through 106 removed outlier: 3.696A pdb=" N PHE A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.661A pdb=" N ASP A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 145 Processing helix chain 'A' and resid 154 through 158 removed outlier: 4.050A pdb=" N VAL A 158 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 183 Processing helix chain 'A' and resid 186 through 192 removed outlier: 3.791A pdb=" N TYR A 190 " --> pdb=" O LYS A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 197 through 211 removed outlier: 3.591A pdb=" N SER A 201 " --> pdb=" O TYR A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 237 removed outlier: 3.517A pdb=" N ASN A 226 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 240 No H-bonds generated for 'chain 'A' and resid 238 through 240' Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 281 through 296 removed outlier: 3.780A pdb=" N LEU A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 302 Processing helix chain 'A' and resid 304 through 316 removed outlier: 3.722A pdb=" N VAL A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE A 309 " --> pdb=" O ASP A 305 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 321 removed outlier: 3.671A pdb=" N PHE A 320 " --> pdb=" O SER A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 333 Processing helix chain 'A' and resid 355 through 366 removed outlier: 3.529A pdb=" N SER A 366 " --> pdb=" O GLU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 374 through 392 Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 417 through 427 Processing helix chain 'A' and resid 431 through 446 Processing helix chain 'A' and resid 447 through 466 removed outlier: 3.689A pdb=" N ILE A 463 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ASP A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU A 465 " --> pdb=" O ASN A 461 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 493 Processing helix chain 'A' and resid 494 through 501 removed outlier: 3.857A pdb=" N LEU A 498 " --> pdb=" O GLY A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 525 through 531 removed outlier: 4.598A pdb=" N ASN A 529 " --> pdb=" O ASP A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 540 through 546 removed outlier: 3.701A pdb=" N GLU A 543 " --> pdb=" O LYS A 540 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE A 544 " --> pdb=" O ILE A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 572 removed outlier: 3.741A pdb=" N LEU A 561 " --> pdb=" O LYS A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 598 removed outlier: 3.774A pdb=" N VAL A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN A 598 " --> pdb=" O PHE A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 604 removed outlier: 3.901A pdb=" N VAL A 603 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 629 Processing helix chain 'A' and resid 648 through 658 removed outlier: 4.160A pdb=" N HIS A 658 " --> pdb=" O ASN A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 670 removed outlier: 3.629A pdb=" N SER A 670 " --> pdb=" O ASN A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 676 Processing helix chain 'A' and resid 680 through 701 removed outlier: 3.626A pdb=" N ILE A 684 " --> pdb=" O GLU A 680 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ALA A 701 " --> pdb=" O LYS A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 723 removed outlier: 4.868A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 726 No H-bonds generated for 'chain 'A' and resid 724 through 726' Processing helix chain 'A' and resid 729 through 742 Processing helix chain 'A' and resid 750 through 765 Processing helix chain 'A' and resid 768 through 786 Processing helix chain 'A' and resid 800 through 812 Processing helix chain 'A' and resid 817 through 826 Processing helix chain 'A' and resid 831 through 840 Processing helix chain 'A' and resid 841 through 845 removed outlier: 4.056A pdb=" N LEU A 844 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 856 Processing helix chain 'A' and resid 861 through 871 Processing helix chain 'A' and resid 878 through 900 Processing helix chain 'A' and resid 911 through 922 removed outlier: 3.707A pdb=" N THR A 915 " --> pdb=" O ASP A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 933 removed outlier: 3.739A pdb=" N GLU A 931 " --> pdb=" O ASN A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 945 Processing helix chain 'A' and resid 950 through 954 removed outlier: 3.538A pdb=" N LYS A 953 " --> pdb=" O ASP A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 962 removed outlier: 4.146A pdb=" N TYR A 962 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 972 Processing helix chain 'A' and resid 973 through 990 removed outlier: 3.759A pdb=" N LYS A 977 " --> pdb=" O ASN A 973 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N HIS A 979 " --> pdb=" O HIS A 975 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N GLU A 982 " --> pdb=" O HIS A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1005 removed outlier: 3.668A pdb=" N TYR A1003 " --> pdb=" O ILE A 999 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE A1005 " --> pdb=" O MET A1001 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 40 Processing helix chain 'B' and resid 48 through 54 removed outlier: 3.654A pdb=" N THR B 52 " --> pdb=" O ALA B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 72 removed outlier: 3.612A pdb=" N LEU B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 85 removed outlier: 3.688A pdb=" N LEU B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 96 Processing helix chain 'B' and resid 97 through 108 Processing helix chain 'B' and resid 115 through 123 removed outlier: 4.064A pdb=" N ASP B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 146 removed outlier: 3.539A pdb=" N GLY B 146 " --> pdb=" O CYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 159 removed outlier: 3.701A pdb=" N VAL B 158 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 197 removed outlier: 4.648A pdb=" N ASP B 194 " --> pdb=" O TYR B 190 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLN B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 222 through 237 Processing helix chain 'B' and resid 238 through 240 No H-bonds generated for 'chain 'B' and resid 238 through 240' Processing helix chain 'B' and resid 254 through 265 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 281 through 295 removed outlier: 4.197A pdb=" N MET B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 removed outlier: 3.989A pdb=" N PHE B 301 " --> pdb=" O GLN B 297 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 297 through 302' Processing helix chain 'B' and resid 304 through 317 Processing helix chain 'B' and resid 318 through 320 No H-bonds generated for 'chain 'B' and resid 318 through 320' Processing helix chain 'B' and resid 326 through 333 removed outlier: 3.966A pdb=" N LYS B 331 " --> pdb=" O ILE B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 366 Processing helix chain 'B' and resid 366 through 372 Processing helix chain 'B' and resid 374 through 392 Processing helix chain 'B' and resid 417 through 427 Processing helix chain 'B' and resid 431 through 445 Processing helix chain 'B' and resid 447 through 462 Processing helix chain 'B' and resid 463 through 465 No H-bonds generated for 'chain 'B' and resid 463 through 465' Processing helix chain 'B' and resid 467 through 494 removed outlier: 4.443A pdb=" N TYR B 471 " --> pdb=" O ASN B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 501 removed outlier: 4.045A pdb=" N LEU B 498 " --> pdb=" O GLY B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 519 removed outlier: 3.957A pdb=" N LEU B 512 " --> pdb=" O THR B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 531 removed outlier: 4.048A pdb=" N ASN B 529 " --> pdb=" O ASP B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 540 Processing helix chain 'B' and resid 541 through 546 removed outlier: 4.245A pdb=" N PHE B 544 " --> pdb=" O ILE B 541 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B 545 " --> pdb=" O LEU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 570 Processing helix chain 'B' and resid 579 through 598 removed outlier: 3.686A pdb=" N ASN B 598 " --> pdb=" O PHE B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.748A pdb=" N VAL B 603 " --> pdb=" O LEU B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 629 removed outlier: 3.592A pdb=" N HIS B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 638 Processing helix chain 'B' and resid 648 through 658 removed outlier: 3.705A pdb=" N HIS B 658 " --> pdb=" O ASN B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 671 Processing helix chain 'B' and resid 672 through 676 removed outlier: 3.795A pdb=" N LYS B 675 " --> pdb=" O SER B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 701 removed outlier: 4.062A pdb=" N ALA B 701 " --> pdb=" O LYS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 723 removed outlier: 4.967A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLU B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 726 No H-bonds generated for 'chain 'B' and resid 724 through 726' Processing helix chain 'B' and resid 729 through 743 Processing helix chain 'B' and resid 750 through 765 removed outlier: 4.024A pdb=" N CYS B 764 " --> pdb=" O ARG B 760 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN B 765 " --> pdb=" O LEU B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 786 Processing helix chain 'B' and resid 801 through 812 removed outlier: 4.010A pdb=" N GLY B 805 " --> pdb=" O SER B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 825 Processing helix chain 'B' and resid 833 through 841 Processing helix chain 'B' and resid 848 through 857 removed outlier: 3.759A pdb=" N HIS B 852 " --> pdb=" O ASN B 848 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B 853 " --> pdb=" O ALA B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 871 Processing helix chain 'B' and resid 878 through 900 Processing helix chain 'B' and resid 911 through 922 Processing helix chain 'B' and resid 937 through 945 Processing helix chain 'B' and resid 950 through 954 removed outlier: 3.543A pdb=" N LYS B 953 " --> pdb=" O ASP B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 961 removed outlier: 3.941A pdb=" N LEU B 959 " --> pdb=" O ILE B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 972 removed outlier: 3.626A pdb=" N GLY B 972 " --> pdb=" O GLY B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 974 through 991 removed outlier: 4.280A pdb=" N HIS B 978 " --> pdb=" O LYS B 974 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N HIS B 979 " --> pdb=" O HIS B 975 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N VAL B 980 " --> pdb=" O MET B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1004 removed outlier: 4.003A pdb=" N TYR B1003 " --> pdb=" O ILE B 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 74 Processing helix chain 'D' and resid 70 through 74 removed outlier: 3.660A pdb=" N LEU D 73 " --> pdb=" O LEU D 70 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA D 74 " --> pdb=" O GLU D 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 70 through 74' Processing helix chain 'E' and resid 23 through 39 Processing helix chain 'E' and resid 48 through 54 removed outlier: 3.553A pdb=" N THR E 52 " --> pdb=" O ALA E 48 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER E 54 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 71 removed outlier: 3.515A pdb=" N LEU E 62 " --> pdb=" O GLN E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 94 removed outlier: 3.740A pdb=" N LEU E 85 " --> pdb=" O SER E 81 " (cutoff:3.500A) Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 96 through 108 Processing helix chain 'E' and resid 115 through 125 Processing helix chain 'E' and resid 136 through 145 Processing helix chain 'E' and resid 186 through 192 Processing helix chain 'E' and resid 192 through 197 removed outlier: 3.810A pdb=" N TYR E 197 " --> pdb=" O TYR E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 211 removed outlier: 3.796A pdb=" N SER E 201 " --> pdb=" O TYR E 197 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA E 209 " --> pdb=" O LYS E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 237 removed outlier: 3.702A pdb=" N LEU E 235 " --> pdb=" O TRP E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 240 No H-bonds generated for 'chain 'E' and resid 238 through 240' Processing helix chain 'E' and resid 254 through 265 removed outlier: 3.749A pdb=" N GLY E 265 " --> pdb=" O TYR E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 275 Processing helix chain 'E' and resid 278 through 280 No H-bonds generated for 'chain 'E' and resid 278 through 280' Processing helix chain 'E' and resid 281 through 295 removed outlier: 4.204A pdb=" N ASP E 291 " --> pdb=" O SER E 287 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LEU E 292 " --> pdb=" O ALA E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 317 Processing helix chain 'E' and resid 318 through 322 Processing helix chain 'E' and resid 328 through 332 removed outlier: 3.779A pdb=" N LYS E 331 " --> pdb=" O ILE E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 366 Processing helix chain 'E' and resid 367 through 372 Processing helix chain 'E' and resid 376 through 392 Processing helix chain 'E' and resid 411 through 416 Processing helix chain 'E' and resid 417 through 425 Processing helix chain 'E' and resid 432 through 444 Processing helix chain 'E' and resid 448 through 457 removed outlier: 4.852A pdb=" N TYR E 455 " --> pdb=" O SER E 451 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER E 456 " --> pdb=" O TYR E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 467 through 491 removed outlier: 3.808A pdb=" N ILE E 481 " --> pdb=" O ASN E 477 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLN E 483 " --> pdb=" O TYR E 479 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER E 484 " --> pdb=" O ARG E 480 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR E 486 " --> pdb=" O TYR E 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 499 removed outlier: 3.991A pdb=" N THR E 499 " --> pdb=" O LEU E 495 " (cutoff:3.500A) Processing helix chain 'E' and resid 534 through 539 Processing helix chain 'E' and resid 541 through 545 removed outlier: 3.555A pdb=" N PHE E 544 " --> pdb=" O ILE E 541 " (cutoff:3.500A) Processing helix chain 'E' and resid 551 through 572 Processing helix chain 'E' and resid 579 through 598 removed outlier: 4.078A pdb=" N VAL E 583 " --> pdb=" O SER E 579 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN E 598 " --> pdb=" O PHE E 594 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 604 removed outlier: 3.771A pdb=" N VAL E 603 " --> pdb=" O LEU E 600 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 626 Processing helix chain 'E' and resid 648 through 658 Processing helix chain 'E' and resid 660 through 670 Processing helix chain 'E' and resid 680 through 689 removed outlier: 3.510A pdb=" N ILE E 684 " --> pdb=" O GLU E 680 " (cutoff:3.500A) Processing helix chain 'E' and resid 692 through 698 Processing helix chain 'E' and resid 707 through 724 Processing helix chain 'E' and resid 730 through 742 Processing helix chain 'E' and resid 750 through 764 Processing helix chain 'E' and resid 768 through 777 removed outlier: 3.581A pdb=" N ILE E 772 " --> pdb=" O PRO E 768 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE E 774 " --> pdb=" O SER E 770 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 40 Processing helix chain 'G' and resid 48 through 54 removed outlier: 3.608A pdb=" N THR G 52 " --> pdb=" O ALA G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 72 Processing helix chain 'G' and resid 81 through 94 Proline residue: G 88 - end of helix Processing helix chain 'G' and resid 96 through 108 removed outlier: 4.386A pdb=" N ILE G 103 " --> pdb=" O ALA G 99 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU G 104 " --> pdb=" O PHE G 100 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP G 106 " --> pdb=" O GLY G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 124 removed outlier: 4.055A pdb=" N LYS G 120 " --> pdb=" O PRO G 116 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE G 121 " --> pdb=" O ILE G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 146 Processing helix chain 'G' and resid 157 through 161 removed outlier: 3.736A pdb=" N ALA G 161 " --> pdb=" O VAL G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 192 Processing helix chain 'G' and resid 192 through 197 removed outlier: 3.538A pdb=" N TYR G 197 " --> pdb=" O TYR G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 211 Processing helix chain 'G' and resid 223 through 237 Processing helix chain 'G' and resid 254 through 264 Processing helix chain 'G' and resid 272 through 274 No H-bonds generated for 'chain 'G' and resid 272 through 274' Processing helix chain 'G' and resid 281 through 296 Processing helix chain 'G' and resid 316 through 322 removed outlier: 4.264A pdb=" N ALA G 321 " --> pdb=" O PRO G 318 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU G 322 " --> pdb=" O LEU G 319 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 333 removed outlier: 3.706A pdb=" N LYS G 331 " --> pdb=" O ILE G 328 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N HIS G 332 " --> pdb=" O ASP G 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 355 through 366 Processing helix chain 'G' and resid 366 through 373 Processing helix chain 'G' and resid 374 through 391 Processing helix chain 'G' and resid 411 through 416 Processing helix chain 'G' and resid 417 through 426 Processing helix chain 'G' and resid 433 through 445 Processing helix chain 'G' and resid 447 through 462 Processing helix chain 'G' and resid 463 through 465 No H-bonds generated for 'chain 'G' and resid 463 through 465' Processing helix chain 'G' and resid 467 through 494 removed outlier: 4.245A pdb=" N TYR G 471 " --> pdb=" O ASN G 467 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY G 494 " --> pdb=" O THR G 490 " (cutoff:3.500A) Processing helix chain 'G' and resid 513 through 519 Processing helix chain 'G' and resid 525 through 531 removed outlier: 4.004A pdb=" N ASN G 529 " --> pdb=" O ASP G 525 " (cutoff:3.500A) Processing helix chain 'G' and resid 532 through 539 Processing helix chain 'G' and resid 540 through 544 Processing helix chain 'G' and resid 551 through 552 No H-bonds generated for 'chain 'G' and resid 551 through 552' Processing helix chain 'G' and resid 554 through 554 No H-bonds generated for 'chain 'G' and resid 554 through 554' Processing helix chain 'G' and resid 555 through 569 Processing helix chain 'G' and resid 580 through 596 Processing helix chain 'G' and resid 600 through 604 removed outlier: 4.038A pdb=" N VAL G 603 " --> pdb=" O LEU G 600 " (cutoff:3.500A) Processing helix chain 'G' and resid 605 through 628 removed outlier: 3.738A pdb=" N ALA G 623 " --> pdb=" O LEU G 619 " (cutoff:3.500A) Processing helix chain 'G' and resid 650 through 658 removed outlier: 4.159A pdb=" N HIS G 658 " --> pdb=" O ASN G 654 " (cutoff:3.500A) Processing helix chain 'G' and resid 660 through 671 removed outlier: 3.593A pdb=" N ILE G 664 " --> pdb=" O LYS G 660 " (cutoff:3.500A) Processing helix chain 'G' and resid 683 through 701 removed outlier: 3.834A pdb=" N ALA G 701 " --> pdb=" O LYS G 697 " (cutoff:3.500A) Processing helix chain 'G' and resid 707 through 723 removed outlier: 4.286A pdb=" N GLN G 711 " --> pdb=" O VAL G 707 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE G 713 " --> pdb=" O TYR G 709 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER G 714 " --> pdb=" O THR G 710 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA G 716 " --> pdb=" O PHE G 712 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA G 718 " --> pdb=" O SER G 714 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA G 723 " --> pdb=" O ALA G 719 " (cutoff:3.500A) Processing helix chain 'G' and resid 731 through 743 Processing helix chain 'G' and resid 750 through 765 Processing helix chain 'G' and resid 770 through 786 Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.070A pdb=" N SER A 150 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LYS A 169 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE A 152 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL A 129 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N HIS A 128 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 44 " --> pdb=" O HIS A 128 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE A 130 " --> pdb=" O PHE A 44 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE A 213 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ILE A 246 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N PHE A 215 " --> pdb=" O ILE A 246 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 340 Processing sheet with id=AA3, first strand: chain 'A' and resid 574 through 575 removed outlier: 6.803A pdb=" N THR C 62 " --> pdb=" O GLN C 28 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA C 30 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASN C 60 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE C 32 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLU C 58 " --> pdb=" O PHE C 32 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE C 59 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN C 197 " --> pdb=" O TYR C 171 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TYR C 171 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL C 11 " --> pdb=" O THR C 24 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N THR C 24 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N PHE C 13 " --> pdb=" O VAL C 22 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 574 through 575 removed outlier: 6.803A pdb=" N THR C 62 " --> pdb=" O GLN C 28 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA C 30 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASN C 60 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE C 32 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLU C 58 " --> pdb=" O PHE C 32 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE C 59 " --> pdb=" O ALA C 222 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 150 through 152 removed outlier: 6.290A pdb=" N SER B 150 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LYS B 169 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE B 152 " --> pdb=" O LYS B 169 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU B 42 " --> pdb=" O HIS B 128 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N ILE B 130 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE B 44 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE B 244 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 246 " --> pdb=" O PHE B 215 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE B 245 " --> pdb=" O ILE B 269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AA7, first strand: chain 'D' and resid 67 through 68 removed outlier: 4.232A pdb=" N PHE D 67 " --> pdb=" O THR D 24 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR D 24 " --> pdb=" O PHE D 67 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU D 21 " --> pdb=" O ARG D 15 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ARG D 15 " --> pdb=" O LEU D 21 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N TYR D 171 " --> pdb=" O ASN D 197 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN D 197 " --> pdb=" O TYR D 171 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 67 through 68 removed outlier: 4.232A pdb=" N PHE D 67 " --> pdb=" O THR D 24 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR D 24 " --> pdb=" O PHE D 67 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 42 through 46 removed outlier: 3.527A pdb=" N PHE E 244 " --> pdb=" O ILE E 213 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N PHE E 245 " --> pdb=" O ILE E 269 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 574 through 575 removed outlier: 3.716A pdb=" N TYR E 574 " --> pdb=" O ALA F 30 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA F 30 " --> pdb=" O TYR E 574 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'G' and resid 150 through 152 removed outlier: 5.976A pdb=" N SER G 150 " --> pdb=" O LEU G 167 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LYS G 169 " --> pdb=" O SER G 150 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE G 152 " --> pdb=" O LYS G 169 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL G 129 " --> pdb=" O TYR G 166 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N HIS G 128 " --> pdb=" O LEU G 42 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ILE G 213 " --> pdb=" O PHE G 244 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N ILE G 246 " --> pdb=" O ILE G 213 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N PHE G 215 " --> pdb=" O ILE G 246 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 338 through 340 Processing sheet with id=AB4, first strand: chain 'F' and resid 67 through 68 removed outlier: 4.320A pdb=" N PHE F 67 " --> pdb=" O THR F 24 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR F 24 " --> pdb=" O PHE F 67 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N TYR F 171 " --> pdb=" O ASN F 197 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ASN F 197 " --> pdb=" O TYR F 171 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR F 192 " --> pdb=" O ILE F 235 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL F 233 " --> pdb=" O GLN F 194 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 23 through 26 1578 hydrogen bonds defined for protein. 4536 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: 10.92 Time building geometry restraints manager: 12.72 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: 9078 1.34 - 1.46: 5564 1.46 - 1.57: 15333 1.57 - 1.69: 0 1.69 - 1.81: 184 Bond restraints: 30159 Sorted by residual: bond pdb=" CA ILE G 87 " pdb=" CB ILE G 87 " ideal model delta sigma weight residual 1.534 1.547 -0.012 6.80e-03 2.16e+04 3.24e+00 bond pdb=" C ILE G 87 " pdb=" N PRO G 88 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.36e-02 5.41e+03 3.02e+00 bond pdb=" CA ILE G 87 " pdb=" C ILE G 87 " ideal model delta sigma weight residual 1.520 1.535 -0.015 8.80e-03 1.29e+04 2.97e+00 bond pdb=" C ILE B 87 " pdb=" N PRO B 88 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.25e-02 6.40e+03 2.10e+00 bond pdb=" C ASP E 281 " pdb=" N TYR E 282 " ideal model delta sigma weight residual 1.335 1.352 -0.017 1.27e-02 6.20e+03 1.84e+00 ... (remaining 30154 not shown) Histogram of bond angle deviations from ideal: 98.25 - 105.89: 321 105.89 - 113.53: 15970 113.53 - 121.17: 16906 121.17 - 128.81: 7245 128.81 - 136.45: 148 Bond angle restraints: 40590 Sorted by residual: angle pdb=" C ARG G 86 " pdb=" N ILE G 87 " pdb=" CA ILE G 87 " ideal model delta sigma weight residual 120.24 125.76 -5.52 6.30e-01 2.52e+00 7.68e+01 angle pdb=" C PRO B 74 " pdb=" N LYS B 75 " pdb=" CA LYS B 75 " ideal model delta sigma weight residual 121.54 130.03 -8.49 1.91e+00 2.74e-01 1.98e+01 angle pdb=" C ARG E 247 " pdb=" N THR E 248 " pdb=" CA THR E 248 " ideal model delta sigma weight residual 121.54 129.88 -8.34 1.91e+00 2.74e-01 1.91e+01 angle pdb=" C MET G 124 " pdb=" N ASN G 125 " pdb=" CA ASN G 125 " ideal model delta sigma weight residual 121.80 132.22 -10.42 2.44e+00 1.68e-01 1.82e+01 angle pdb=" CA TYR B 282 " pdb=" CB TYR B 282 " pdb=" CG TYR B 282 " ideal model delta sigma weight residual 113.90 121.40 -7.50 1.80e+00 3.09e-01 1.73e+01 ... (remaining 40585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 15884 17.22 - 34.43: 1536 34.43 - 51.65: 416 51.65 - 68.86: 99 68.86 - 86.08: 10 Dihedral angle restraints: 17945 sinusoidal: 7369 harmonic: 10576 Sorted by residual: dihedral pdb=" CA PHE B 921 " pdb=" C PHE B 921 " pdb=" N LEU B 922 " pdb=" CA LEU B 922 " ideal model delta harmonic sigma weight residual 180.00 150.60 29.40 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA SER B 287 " pdb=" C SER B 287 " pdb=" N ALA B 288 " pdb=" CA ALA B 288 " ideal model delta harmonic sigma weight residual 180.00 -151.49 -28.51 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA PHE E 550 " pdb=" C PHE E 550 " pdb=" N LEU E 551 " pdb=" CA LEU E 551 " ideal model delta harmonic sigma weight residual 180.00 157.77 22.23 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 17942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2940 0.043 - 0.086: 1106 0.086 - 0.129: 247 0.129 - 0.171: 56 0.171 - 0.214: 2 Chirality restraints: 4351 Sorted by residual: chirality pdb=" CB THR E 562 " pdb=" CA THR E 562 " pdb=" OG1 THR E 562 " pdb=" CG2 THR E 562 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA THR E 248 " pdb=" N THR E 248 " pdb=" C THR E 248 " pdb=" CB THR E 248 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB ILE G 275 " pdb=" CA ILE G 275 " pdb=" CG1 ILE G 275 " pdb=" CG2 ILE G 275 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.28e-01 ... (remaining 4348 not shown) Planarity restraints: 5159 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 317 " 0.051 5.00e-02 4.00e+02 7.58e-02 9.20e+00 pdb=" N PRO B 318 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO B 318 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 318 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 317 " -0.047 5.00e-02 4.00e+02 7.01e-02 7.86e+00 pdb=" N PRO E 318 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO E 318 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 318 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN G 115 " 0.040 5.00e-02 4.00e+02 6.13e-02 6.02e+00 pdb=" N PRO G 116 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO G 116 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO G 116 " 0.034 5.00e-02 4.00e+02 ... (remaining 5156 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4497 2.76 - 3.30: 29167 3.30 - 3.83: 52789 3.83 - 4.37: 60079 4.37 - 4.90: 96199 Nonbonded interactions: 242731 Sorted by model distance: nonbonded pdb=" OH TYR E 436 " pdb=" O VAL E 470 " model vdw 2.228 3.040 nonbonded pdb=" O GLU B 516 " pdb=" OG1 THR B 520 " model vdw 2.258 3.040 nonbonded pdb=" OH TYR E 472 " pdb=" O LEU E 542 " model vdw 2.260 3.040 nonbonded pdb=" OH TYR E 218 " pdb=" O ASP E 222 " model vdw 2.269 3.040 nonbonded pdb=" O VAL G 707 " pdb=" OG1 THR G 710 " model vdw 2.269 3.040 ... (remaining 242726 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 546 or resid 548 through 638 or resid 642 throu \ gh 830 or resid 832 through 843 or resid 847 through 1005)) selection = (chain 'B' and (resid 23 through 73 or resid 81 through 110 or (resid 111 throug \ h 113 and (name N or name CA or name C or name O or name CB )) or resid 114 thro \ ugh 160 or resid 165 through 269 or resid 279 through 801 or (resid 802 and (nam \ e N or name CA or name C or name O or name CB )) or resid 803 through 1005)) } ncs_group { reference = (chain 'C' and (resid 5 through 33 or resid 52 through 177 or resid 190 through \ 236)) selection = (chain 'D' and (resid 5 through 209 or resid 217 through 227 or (resid 228 throu \ gh 229 and (name N or name CA or name C or name O or name CB )) or resid 230 thr \ ough 235 or (resid 236 and (name N or name CA or name C or name O or name CB ))) \ ) } ncs_group { reference = (chain 'E' and (resid 22 through 179 or resid 186 through 217 or resid 222 throu \ gh 297 or resid 316 through 396 or resid 409 through 426 or resid 432 through 49 \ 8 or resid 502 or resid 507 through 553 or resid 555 through 573 or resid 580 th \ rough 627 or resid 649 through 672 or resid 682 through 727 or resid 730 through \ 766 or resid 769 through 777)) selection = (chain 'G' and (resid 22 through 71 or resid 80 through 110 or resid 112 through \ 125 or resid 130 through 145 or resid 165 through 343 or resid 347 through 353 \ or resid 355 through 372 or resid 375 through 498 or resid 517 or resid 522 or r \ esid 527 through 627 or resid 649 through 689 or resid 691 through 700 or resid \ 706 through 777)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.050 Extract box with map and model: 0.980 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 76.160 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.120 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 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 : 0.003 0.052 30159 Z= 0.214 Angle : 0.700 11.453 40590 Z= 0.395 Chirality : 0.046 0.214 4351 Planarity : 0.005 0.076 5159 Dihedral : 14.999 86.081 11109 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.73 % Favored : 96.12 % Rotamer: Outliers : 5.17 % Allowed : 12.04 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.12), residues: 3455 helix: -1.17 (0.10), residues: 2022 sheet: -0.37 (0.37), residues: 218 loop : -1.60 (0.16), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 601 HIS 0.008 0.001 HIS B 128 PHE 0.022 0.002 PHE A 559 TYR 0.018 0.002 TYR D 175 ARG 0.011 0.001 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 468 time to evaluate : 3.424 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 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 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 revert: symmetry clash REVERT: A 124 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8183 (tpp) REVERT: A 204 MET cc_start: 0.9637 (tmm) cc_final: 0.9191 (tmm) REVERT: A 226 ASN cc_start: 0.9077 (OUTLIER) cc_final: 0.8663 (p0) REVERT: A 260 TYR cc_start: 0.8024 (OUTLIER) cc_final: 0.6924 (m-80) REVERT: A 290 MET cc_start: 0.9604 (ttt) cc_final: 0.9347 (ttt) REVERT: A 421 MET cc_start: 0.9381 (ppp) cc_final: 0.9059 (ppp) REVERT: A 504 TYR cc_start: 0.7366 (t80) cc_final: 0.6997 (t80) REVERT: A 519 MET cc_start: 0.9134 (mmp) cc_final: 0.8387 (mmm) REVERT: A 524 ILE cc_start: 0.9515 (pt) cc_final: 0.8855 (mp) REVERT: A 527 LEU cc_start: 0.9509 (mt) cc_final: 0.9186 (mt) REVERT: A 557 LYS cc_start: 0.9464 (mtmm) cc_final: 0.9063 (mtmm) REVERT: A 588 LEU cc_start: 0.9723 (OUTLIER) cc_final: 0.9448 (tt) REVERT: A 660 LYS cc_start: 0.9377 (tptp) cc_final: 0.9052 (tptp) REVERT: A 662 ASP cc_start: 0.9146 (p0) cc_final: 0.8796 (p0) REVERT: A 693 GLU cc_start: 0.9403 (tp30) cc_final: 0.8652 (tp30) REVERT: A 704 MET cc_start: 0.7364 (ptp) cc_final: 0.6931 (ptp) REVERT: A 712 PHE cc_start: 0.9342 (t80) cc_final: 0.9009 (t80) REVERT: A 866 MET cc_start: 0.9488 (tmm) cc_final: 0.9256 (tmm) REVERT: A 913 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7931 (ppp) REVERT: A 938 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.8241 (p0) REVERT: B 100 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.7916 (m-80) REVERT: B 105 LYS cc_start: 0.9358 (mmtt) cc_final: 0.9105 (mmmm) REVERT: B 183 VAL cc_start: 0.8515 (OUTLIER) cc_final: 0.8008 (p) REVERT: B 315 LYS cc_start: 0.9308 (tttt) cc_final: 0.9014 (tttt) REVERT: B 331 LYS cc_start: 0.9571 (pttp) cc_final: 0.9353 (mtmm) REVERT: B 361 PHE cc_start: 0.9474 (m-80) cc_final: 0.8788 (m-10) REVERT: B 396 MET cc_start: 0.9002 (mpp) cc_final: 0.8749 (mpp) REVERT: B 412 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.8764 (tp) REVERT: B 441 PHE cc_start: 0.9498 (m-10) cc_final: 0.9222 (m-80) REVERT: B 448 TRP cc_start: 0.9121 (m-10) cc_final: 0.8879 (m-10) REVERT: B 525 ASP cc_start: 0.9426 (p0) cc_final: 0.9124 (p0) REVERT: B 540 LYS cc_start: 0.9196 (tmmt) cc_final: 0.8979 (tmtt) REVERT: B 553 ASP cc_start: 0.9544 (p0) cc_final: 0.9320 (p0) REVERT: B 616 MET cc_start: 0.9192 (ttm) cc_final: 0.8856 (ttm) REVERT: B 618 LEU cc_start: 0.9636 (OUTLIER) cc_final: 0.9216 (mm) REVERT: B 759 GLU cc_start: 0.9677 (OUTLIER) cc_final: 0.9263 (mm-30) REVERT: B 915 THR cc_start: 0.9643 (OUTLIER) cc_final: 0.9361 (p) REVERT: B 959 LEU cc_start: 0.9724 (tp) cc_final: 0.9516 (tp) REVERT: B 975 HIS cc_start: 0.8770 (OUTLIER) cc_final: 0.7406 (p90) REVERT: B 976 MET cc_start: 0.8872 (mpp) cc_final: 0.8668 (mmt) REVERT: B 994 LYS cc_start: 0.9197 (mppt) cc_final: 0.8974 (mmtm) REVERT: B 997 LEU cc_start: 0.9719 (mt) cc_final: 0.9471 (tt) REVERT: C 67 PHE cc_start: 0.8892 (m-80) cc_final: 0.8593 (m-80) REVERT: D 63 VAL cc_start: 0.9131 (OUTLIER) cc_final: 0.8814 (p) REVERT: D 192 TYR cc_start: 0.8700 (m-80) cc_final: 0.8456 (m-80) REVERT: D 231 MET cc_start: 0.8201 (pmm) cc_final: 0.7856 (pmm) REVERT: E 197 TYR cc_start: 0.7635 (OUTLIER) cc_final: 0.7307 (m-80) REVERT: E 202 ASN cc_start: 0.9070 (t0) cc_final: 0.8800 (t0) REVERT: E 282 TYR cc_start: 0.8917 (OUTLIER) cc_final: 0.8493 (m-10) REVERT: G 91 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.7744 (t80) REVERT: G 202 ASN cc_start: 0.8846 (m110) cc_final: 0.8538 (t0) REVERT: G 396 MET cc_start: 0.6287 (mtt) cc_final: 0.6047 (mmt) REVERT: G 471 TYR cc_start: 0.7109 (t80) cc_final: 0.6725 (t80) REVERT: G 587 ARG cc_start: 0.9295 (tpp80) cc_final: 0.9051 (mmp80) REVERT: G 697 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8609 (ptmm) outliers start: 166 outliers final: 28 residues processed: 606 average time/residue: 0.3927 time to fit residues: 380.6914 Evaluate side-chains 355 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 309 time to evaluate : 3.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 298 optimal weight: 7.9990 chunk 267 optimal weight: 20.0000 chunk 148 optimal weight: 0.0970 chunk 91 optimal weight: 0.9980 chunk 180 optimal weight: 9.9990 chunk 142 optimal weight: 1.9990 chunk 276 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 320 optimal weight: 5.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 192 ASN A 351 ASN A 493 ASN A 591 ASN A 910 ASN ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 HIS B 78 ASN B 226 ASN B 461 ASN B 477 ASN B 563 ASN B 591 ASN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 323 GLN E 332 HIS E 591 ASN ** E 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 521 ASN G 666 ASN G 765 ASN G 782 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 30159 Z= 0.198 Angle : 0.572 8.963 40590 Z= 0.314 Chirality : 0.041 0.188 4351 Planarity : 0.004 0.053 5159 Dihedral : 4.976 24.152 3886 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.88 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.14), residues: 3455 helix: 0.01 (0.11), residues: 2091 sheet: 0.08 (0.37), residues: 198 loop : -1.46 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 143 HIS 0.008 0.001 HIS A 606 PHE 0.039 0.002 PHE G 91 TYR 0.032 0.002 TYR G 92 ARG 0.012 0.001 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 399 time to evaluate : 3.392 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 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 REVERT: A 124 MET cc_start: 0.8618 (tpp) cc_final: 0.7906 (tpp) REVERT: A 202 ASN cc_start: 0.9378 (t0) cc_final: 0.9171 (t0) REVERT: A 204 MET cc_start: 0.9608 (tmm) cc_final: 0.9296 (tmm) REVERT: A 290 MET cc_start: 0.9479 (ttt) cc_final: 0.8863 (ttm) REVERT: A 435 ASP cc_start: 0.9258 (m-30) cc_final: 0.8850 (t0) REVERT: A 493 ASN cc_start: 0.9464 (m110) cc_final: 0.9092 (p0) REVERT: A 519 MET cc_start: 0.9172 (mmp) cc_final: 0.8903 (mmm) REVERT: A 524 ILE cc_start: 0.9566 (pt) cc_final: 0.8951 (mm) REVERT: A 527 LEU cc_start: 0.9574 (mt) cc_final: 0.9255 (mt) REVERT: A 557 LYS cc_start: 0.9542 (mtmm) cc_final: 0.9217 (mtmm) REVERT: A 620 ILE cc_start: 0.9934 (pt) cc_final: 0.9699 (pt) REVERT: A 647 MET cc_start: 0.9153 (mmp) cc_final: 0.8779 (mmm) REVERT: A 693 GLU cc_start: 0.9420 (tp30) cc_final: 0.8882 (tp30) REVERT: A 704 MET cc_start: 0.7178 (ptp) cc_final: 0.6697 (ptp) REVERT: A 712 PHE cc_start: 0.9391 (t80) cc_final: 0.9090 (t80) REVERT: A 866 MET cc_start: 0.9369 (tmm) cc_final: 0.8945 (tmm) REVERT: B 315 LYS cc_start: 0.9441 (tttt) cc_final: 0.9060 (tttt) REVERT: B 361 PHE cc_start: 0.9417 (m-80) cc_final: 0.8995 (m-80) REVERT: B 375 LYS cc_start: 0.8859 (mmpt) cc_final: 0.8390 (mmmt) REVERT: B 434 ASP cc_start: 0.9588 (m-30) cc_final: 0.9046 (t70) REVERT: B 441 PHE cc_start: 0.9644 (m-10) cc_final: 0.9046 (m-80) REVERT: B 448 TRP cc_start: 0.9060 (m-10) cc_final: 0.8852 (m-10) REVERT: B 531 MET cc_start: 0.8810 (mmm) cc_final: 0.8503 (mmt) REVERT: B 553 ASP cc_start: 0.9637 (p0) cc_final: 0.9269 (p0) REVERT: B 759 GLU cc_start: 0.9850 (mm-30) cc_final: 0.9600 (mm-30) REVERT: B 776 ASP cc_start: 0.9140 (t70) cc_final: 0.8795 (t0) REVERT: B 887 GLU cc_start: 0.9335 (pp20) cc_final: 0.9095 (pp20) REVERT: C 61 LEU cc_start: 0.9505 (mp) cc_final: 0.9242 (mt) REVERT: C 67 PHE cc_start: 0.8995 (m-80) cc_final: 0.8659 (m-80) REVERT: C 219 LYS cc_start: 0.9066 (tptp) cc_final: 0.8847 (tppt) REVERT: D 231 MET cc_start: 0.8553 (pmm) cc_final: 0.8078 (pmm) REVERT: E 197 TYR cc_start: 0.8068 (m-80) cc_final: 0.7861 (m-80) REVERT: E 202 ASN cc_start: 0.8867 (t0) cc_final: 0.8581 (t0) REVERT: E 261 TYR cc_start: 0.8181 (m-10) cc_final: 0.7715 (m-80) REVERT: E 290 MET cc_start: 0.8826 (ptt) cc_final: 0.8316 (ppp) REVERT: G 202 ASN cc_start: 0.8679 (m110) cc_final: 0.8347 (t0) REVERT: G 471 TYR cc_start: 0.7157 (t80) cc_final: 0.6833 (t80) REVERT: G 495 LEU cc_start: 0.8853 (tp) cc_final: 0.8594 (tt) REVERT: G 587 ARG cc_start: 0.9334 (tpp80) cc_final: 0.9114 (mmp80) REVERT: G 594 PHE cc_start: 0.9164 (t80) cc_final: 0.8842 (t80) outliers start: 0 outliers final: 0 residues processed: 399 average time/residue: 0.4077 time to fit residues: 257.9236 Evaluate side-chains 271 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 3.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 178 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 266 optimal weight: 3.9990 chunk 218 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 chunk 321 optimal weight: 0.0980 chunk 346 optimal weight: 40.0000 chunk 286 optimal weight: 0.7980 chunk 318 optimal weight: 8.9990 chunk 109 optimal weight: 0.9980 chunk 257 optimal weight: 8.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN A 658 HIS A 852 HIS A 939 GLN B 563 ASN ** B 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 810 HIS ** B 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 487 GLN E 503 HIS ** E 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30159 Z= 0.172 Angle : 0.532 8.588 40590 Z= 0.291 Chirality : 0.041 0.216 4351 Planarity : 0.004 0.060 5159 Dihedral : 4.738 21.826 3886 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.91 % Favored : 95.98 % Rotamer: Outliers : 0.06 % Allowed : 2.58 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.14), residues: 3455 helix: 0.47 (0.11), residues: 2102 sheet: -0.12 (0.36), residues: 208 loop : -1.37 (0.18), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 448 HIS 0.013 0.001 HIS B 810 PHE 0.020 0.001 PHE D 195 TYR 0.030 0.001 TYR E 721 ARG 0.004 0.000 ARG E 233 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 374 time to evaluate : 3.369 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.8688 (tpp) cc_final: 0.7644 (tpp) REVERT: A 168 LEU cc_start: 0.9074 (tp) cc_final: 0.8726 (mm) REVERT: A 202 ASN cc_start: 0.9335 (t0) cc_final: 0.9015 (t0) REVERT: A 204 MET cc_start: 0.9642 (tmm) cc_final: 0.9259 (tmm) REVERT: A 290 MET cc_start: 0.9481 (ttt) cc_final: 0.8899 (ttm) REVERT: A 421 MET cc_start: 0.9322 (ppp) cc_final: 0.9110 (ppp) REVERT: A 519 MET cc_start: 0.9257 (mmp) cc_final: 0.8889 (mmm) REVERT: A 524 ILE cc_start: 0.9526 (pt) cc_final: 0.8847 (mm) REVERT: A 578 MET cc_start: 0.8944 (ppp) cc_final: 0.8700 (ppp) REVERT: A 587 ARG cc_start: 0.8781 (ttp80) cc_final: 0.8545 (ttp80) REVERT: A 647 MET cc_start: 0.9190 (mmp) cc_final: 0.8965 (mmm) REVERT: A 693 GLU cc_start: 0.9409 (tp30) cc_final: 0.8867 (tp30) REVERT: A 704 MET cc_start: 0.7224 (ptp) cc_final: 0.6789 (ptp) REVERT: A 712 PHE cc_start: 0.9379 (t80) cc_final: 0.9109 (t80) REVERT: A 866 MET cc_start: 0.9386 (tmm) cc_final: 0.8940 (tmm) REVERT: B 168 LEU cc_start: 0.9511 (tp) cc_final: 0.9148 (tp) REVERT: B 315 LYS cc_start: 0.9507 (tttt) cc_final: 0.9120 (tttt) REVERT: B 361 PHE cc_start: 0.9372 (m-80) cc_final: 0.8754 (m-80) REVERT: B 375 LYS cc_start: 0.8875 (mmpt) cc_final: 0.8401 (mmmt) REVERT: B 434 ASP cc_start: 0.9580 (m-30) cc_final: 0.8982 (t70) REVERT: B 441 PHE cc_start: 0.9644 (m-10) cc_final: 0.9051 (m-80) REVERT: B 448 TRP cc_start: 0.9064 (m-10) cc_final: 0.8858 (m-10) REVERT: B 531 MET cc_start: 0.9291 (mmm) cc_final: 0.8612 (mmt) REVERT: B 553 ASP cc_start: 0.9635 (p0) cc_final: 0.9247 (p0) REVERT: B 595 LEU cc_start: 0.9506 (mt) cc_final: 0.9298 (mt) REVERT: B 759 GLU cc_start: 0.9856 (mm-30) cc_final: 0.9625 (mm-30) REVERT: B 776 ASP cc_start: 0.9132 (t70) cc_final: 0.8700 (t0) REVERT: C 67 PHE cc_start: 0.8976 (m-80) cc_final: 0.8707 (m-80) REVERT: C 219 LYS cc_start: 0.9032 (tptp) cc_final: 0.8760 (tptp) REVERT: D 231 MET cc_start: 0.8713 (pmm) cc_final: 0.8177 (pmm) REVERT: E 202 ASN cc_start: 0.8734 (t0) cc_final: 0.8433 (t0) REVERT: E 261 TYR cc_start: 0.8201 (m-10) cc_final: 0.7746 (m-80) REVERT: E 290 MET cc_start: 0.8857 (ptt) cc_final: 0.8430 (ppp) REVERT: G 202 ASN cc_start: 0.8661 (m110) cc_final: 0.8307 (t0) REVERT: G 227 MET cc_start: 0.8921 (tmm) cc_final: 0.8660 (tmm) REVERT: G 471 TYR cc_start: 0.7227 (t80) cc_final: 0.6884 (t80) REVERT: G 594 PHE cc_start: 0.9135 (t80) cc_final: 0.8663 (t80) REVERT: H 193 ILE cc_start: 0.7698 (tp) cc_final: 0.7492 (tp) outliers start: 2 outliers final: 1 residues processed: 375 average time/residue: 0.4033 time to fit residues: 242.5755 Evaluate side-chains 255 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 254 time to evaluate : 3.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.4098 > 50: distance: 44 - 53: 29.874 distance: 53 - 54: 50.715 distance: 53 - 59: 22.168 distance: 54 - 55: 32.631 distance: 54 - 57: 7.198 distance: 55 - 56: 22.786 distance: 55 - 60: 24.190 distance: 57 - 58: 24.541 distance: 58 - 59: 34.689 distance: 60 - 61: 52.248 distance: 61 - 62: 15.225 distance: 61 - 64: 58.876 distance: 62 - 63: 11.381 distance: 62 - 69: 42.581 distance: 64 - 65: 67.969 distance: 65 - 66: 20.033 distance: 66 - 67: 42.394 distance: 66 - 68: 44.169 distance: 69 - 70: 10.689 distance: 70 - 71: 47.446 distance: 70 - 73: 59.118 distance: 71 - 72: 54.795 distance: 71 - 80: 20.746 distance: 73 - 74: 61.140 distance: 74 - 75: 31.321 distance: 75 - 76: 6.328 distance: 76 - 77: 30.048 distance: 77 - 78: 13.263 distance: 77 - 79: 13.173 distance: 80 - 81: 43.400 distance: 81 - 84: 40.941 distance: 82 - 83: 67.579 distance: 82 - 88: 20.450 distance: 84 - 85: 29.539 distance: 85 - 86: 57.334 distance: 85 - 87: 44.045 distance: 88 - 89: 37.063 distance: 89 - 90: 46.628 distance: 89 - 92: 31.630 distance: 90 - 91: 57.200 distance: 90 - 96: 56.509 distance: 92 - 93: 38.463 distance: 93 - 94: 26.997 distance: 93 - 95: 34.693 distance: 96 - 97: 32.861 distance: 97 - 98: 17.100 distance: 97 - 100: 37.626 distance: 98 - 99: 43.847 distance: 98 - 104: 52.217 distance: 99 - 125: 52.020 distance: 100 - 101: 34.896 distance: 101 - 102: 13.672 distance: 101 - 103: 32.269 distance: 104 - 105: 40.052 distance: 105 - 106: 54.986 distance: 105 - 108: 43.541 distance: 106 - 107: 47.422 distance: 106 - 112: 26.740 distance: 107 - 136: 29.563 distance: 108 - 109: 50.237 distance: 108 - 110: 51.483 distance: 109 - 111: 21.362 distance: 112 - 113: 28.190 distance: 113 - 114: 43.022 distance: 114 - 115: 41.569 distance: 114 - 116: 28.035 distance: 115 - 143: 32.211 distance: 116 - 117: 43.113 distance: 117 - 118: 31.238 distance: 117 - 120: 48.212 distance: 118 - 119: 43.229 distance: 118 - 125: 41.781 distance: 119 - 150: 27.721 distance: 120 - 121: 59.199 distance: 121 - 122: 31.090 distance: 122 - 123: 23.161 distance: 123 - 124: 11.761 distance: 125 - 126: 51.416 distance: 126 - 127: 53.081 distance: 126 - 129: 39.693 distance: 127 - 128: 53.085 distance: 127 - 136: 31.837 distance: 128 - 162: 28.892 distance: 129 - 130: 67.898 distance: 130 - 131: 57.856 distance: 131 - 132: 58.120 distance: 132 - 133: 22.983 distance: 133 - 134: 36.583 distance: 133 - 135: 43.198