Starting phenix.real_space_refine on Wed Jul 24 03:12:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dev_27400/07_2024/8dev_27400.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dev_27400/07_2024/8dev_27400.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dev_27400/07_2024/8dev_27400.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dev_27400/07_2024/8dev_27400.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dev_27400/07_2024/8dev_27400.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dev_27400/07_2024/8dev_27400.cif" } resolution = 3.08 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= -0.000 sd= 0.044 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: 5 Type Number sf(0) Gaussians P 19 5.49 5 S 135 5.16 5 C 15631 2.51 5 N 3920 2.21 5 O 4540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 99": "OD1" <-> "OD2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "A GLU 168": "OE1" <-> "OE2" Residue "A GLU 312": "OE1" <-> "OE2" Residue "A PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 565": "OD1" <-> "OD2" Residue "A ASP 775": "OD1" <-> "OD2" Residue "A ASP 846": "OD1" <-> "OD2" Residue "A GLU 855": "OE1" <-> "OE2" Residue "A GLU 862": "OE1" <-> "OE2" Residue "A GLU 863": "OE1" <-> "OE2" Residue "A PHE 919": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 956": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 697": "OE1" <-> "OE2" Residue "B GLU 823": "OE1" <-> "OE2" Residue "B TYR 874": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 890": "OE1" <-> "OE2" Residue "C GLU 242": "OE1" <-> "OE2" Residue "C GLU 271": "OE1" <-> "OE2" Residue "C ASP 272": "OD1" <-> "OD2" Residue "C PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 421": "OE1" <-> "OE2" Residue "C PHE 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 862": "OE1" <-> "OE2" Residue "C GLU 863": "OE1" <-> "OE2" Residue "C TYR 889": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 24245 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 7761 Classifications: {'peptide': 1037} Link IDs: {'PTRANS': 39, 'TRANS': 997} Chain breaks: 1 Chain: "B" Number of atoms: 7813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1043, 7813 Classifications: {'peptide': 1043} Link IDs: {'PTRANS': 40, 'TRANS': 1002} Chain: "C" Number of atoms: 7806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 7806 Classifications: {'peptide': 1042} Link IDs: {'PTRANS': 40, 'TRANS': 1001} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'RE6': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="RE6 D 1 " pdbres="DAB D 2 " Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'DAB:plan-1': 4, 'RE6:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 37 Classifications: {'peptide': 5} Modifications used: {'PEPT-D': 1} Link IDs: {'CIS': 1, 'TRANS': 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'DAB:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 242 Unusual residues: {'PTY': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 304 Unusual residues: {'PTY': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 96 Chain: "C" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 238 Unusual residues: {'PTY': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PTY:plan-2': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 13.19, per 1000 atoms: 0.54 Number of scatterers: 24245 At special positions: 0 Unit cell: (130.152, 158.202, 126.786, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 135 16.00 P 19 15.00 O 4540 8.00 N 3920 7.00 C 15631 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.92 Conformation dependent library (CDL) restraints added in 4.4 seconds 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DLE D 7 " Number of C-beta restraints generated: 5706 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 23 sheets defined 56.6% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.00 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 61 through 68 removed outlier: 3.944A pdb=" N ASN A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 113 removed outlier: 3.787A pdb=" N GLU A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 118 removed outlier: 3.533A pdb=" N LEU A 118 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 148 through 160 Processing helix chain 'A' and resid 160 through 165 Processing helix chain 'A' and resid 197 through 207 Processing helix chain 'A' and resid 240 through 246 Processing helix chain 'A' and resid 296 through 312 removed outlier: 3.678A pdb=" N THR A 300 " --> pdb=" O ASN A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 328 through 358 Processing helix chain 'A' and resid 363 through 385 removed outlier: 3.518A pdb=" N THR A 367 " --> pdb=" O THR A 363 " (cutoff:3.500A) Proline residue: A 371 - end of helix Processing helix chain 'A' and resid 390 through 421 removed outlier: 3.921A pdb=" N MET A 396 " --> pdb=" O THR A 392 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 452 removed outlier: 5.443A pdb=" N GLY A 438 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ALA A 439 " --> pdb=" O GLN A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 456 removed outlier: 3.628A pdb=" N MET A 456 " --> pdb=" O PRO A 453 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 453 through 456' Processing helix chain 'A' and resid 461 through 494 removed outlier: 3.921A pdb=" N TYR A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Proline residue: A 488 - end of helix Processing helix chain 'A' and resid 509 through 532 removed outlier: 3.793A pdb=" N LYS A 530 " --> pdb=" O GLY A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 555 Processing helix chain 'A' and resid 580 through 598 removed outlier: 3.724A pdb=" N THR A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER A 597 " --> pdb=" O GLN A 593 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE A 598 " --> pdb=" O LEU A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 632 Processing helix chain 'A' and resid 634 through 637 removed outlier: 3.983A pdb=" N SER A 637 " --> pdb=" O ALA A 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 634 through 637' Processing helix chain 'A' and resid 638 through 654 Processing helix chain 'A' and resid 687 through 704 removed outlier: 3.741A pdb=" N LEU A 691 " --> pdb=" O GLY A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 734 Processing helix chain 'A' and resid 740 through 752 removed outlier: 4.232A pdb=" N LEU A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER A 752 " --> pdb=" O ALA A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 778 removed outlier: 4.250A pdb=" N MET A 778 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 783 removed outlier: 3.607A pdb=" N ILE A 783 " --> pdb=" O PRO A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 801 Processing helix chain 'A' and resid 833 through 848 removed outlier: 3.517A pdb=" N LEU A 848 " --> pdb=" O MET A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 865 removed outlier: 3.878A pdb=" N GLU A 863 " --> pdb=" O GLN A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 890 removed outlier: 3.688A pdb=" N LEU A 876 " --> pdb=" O ALA A 872 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 878 " --> pdb=" O TYR A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 900 removed outlier: 3.920A pdb=" N VAL A 898 " --> pdb=" O ILE A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 924 removed outlier: 4.071A pdb=" N GLY A 905 " --> pdb=" O VAL A 901 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 906 " --> pdb=" O MET A 902 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY A 924 " --> pdb=" O GLU A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 958 removed outlier: 3.669A pdb=" N ALA A 947 " --> pdb=" O MET A 943 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS A 948 " --> pdb=" O GLY A 944 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 998 removed outlier: 3.807A pdb=" N LEU A 972 " --> pdb=" O VAL A 968 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ARG A 980 " --> pdb=" O ARG A 976 " (cutoff:3.500A) Proline residue: A 981 - end of helix Proline residue: A 995 - end of helix removed outlier: 3.556A pdb=" N ILE A 998 " --> pdb=" O VAL A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1041 removed outlier: 4.127A pdb=" N GLN A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR A1022 " --> pdb=" O MET A1018 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A1023 " --> pdb=" O LEU A1019 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE A1027 " --> pdb=" O LEU A1023 " (cutoff:3.500A) Proline residue: A1030 - end of helix removed outlier: 3.778A pdb=" N LYS A1041 " --> pdb=" O ARG A1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 28 removed outlier: 3.515A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 68 removed outlier: 3.972A pdb=" N ASN B 68 " --> pdb=" O VAL B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 112 Processing helix chain 'B' and resid 113 through 118 removed outlier: 5.494A pdb=" N SER B 116 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU B 118 " --> pdb=" O LEU B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 148 through 160 Processing helix chain 'B' and resid 160 through 165 Processing helix chain 'B' and resid 187 through 195 Processing helix chain 'B' and resid 197 through 209 Processing helix chain 'B' and resid 240 through 246 Processing helix chain 'B' and resid 296 through 312 removed outlier: 3.616A pdb=" N THR B 300 " --> pdb=" O ASN B 296 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 315 No H-bonds generated for 'chain 'B' and resid 313 through 315' Processing helix chain 'B' and resid 328 through 358 removed outlier: 3.797A pdb=" N GLU B 332 " --> pdb=" O SER B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 385 Proline residue: B 371 - end of helix removed outlier: 3.532A pdb=" N GLY B 385 " --> pdb=" O ILE B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 422 removed outlier: 4.279A pdb=" N GLY B 401 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE B 402 " --> pdb=" O LEU B 398 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASP B 405 " --> pdb=" O GLY B 401 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASP B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA B 407 " --> pdb=" O VAL B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 452 removed outlier: 5.447A pdb=" N GLY B 438 " --> pdb=" O GLY B 434 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ALA B 439 " --> pdb=" O GLN B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 457 removed outlier: 4.195A pdb=" N PHE B 457 " --> pdb=" O LEU B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 495 removed outlier: 3.971A pdb=" N GLN B 467 " --> pdb=" O ASN B 463 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE B 468 " --> pdb=" O ILE B 464 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N THR B 487 " --> pdb=" O ALA B 483 " (cutoff:3.500A) Proline residue: B 488 - end of helix removed outlier: 3.609A pdb=" N LEU B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 533 removed outlier: 3.717A pdb=" N ARG B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 555 removed outlier: 3.516A pdb=" N ARG B 555 " --> pdb=" O PHE B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 595 removed outlier: 3.902A pdb=" N THR B 584 " --> pdb=" O THR B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 598 No H-bonds generated for 'chain 'B' and resid 596 through 598' Processing helix chain 'B' and resid 628 through 633 removed outlier: 3.669A pdb=" N THR B 633 " --> pdb=" O ASN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 652 removed outlier: 3.679A pdb=" N GLY B 652 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 704 removed outlier: 3.749A pdb=" N LEU B 691 " --> pdb=" O GLY B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 736 removed outlier: 3.705A pdb=" N GLN B 736 " --> pdb=" O ALA B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 751 removed outlier: 3.658A pdb=" N ARG B 744 " --> pdb=" O PHE B 740 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU B 751 " --> pdb=" O LEU B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 777 removed outlier: 3.668A pdb=" N ARG B 777 " --> pdb=" O GLY B 774 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 774 through 777' Processing helix chain 'B' and resid 779 through 783 removed outlier: 3.624A pdb=" N ILE B 783 " --> pdb=" O PRO B 780 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 848 removed outlier: 3.500A pdb=" N LEU B 848 " --> pdb=" O MET B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 865 removed outlier: 3.905A pdb=" N LYS B 865 " --> pdb=" O ARG B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 890 Processing helix chain 'B' and resid 893 through 900 removed outlier: 3.774A pdb=" N ALA B 897 " --> pdb=" O SER B 893 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 922 removed outlier: 3.677A pdb=" N GLY B 905 " --> pdb=" O VAL B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 962 Processing helix chain 'B' and resid 966 through 994 removed outlier: 4.914A pdb=" N ARG B 980 " --> pdb=" O ARG B 976 " (cutoff:3.500A) Proline residue: B 981 - end of helix Processing helix chain 'B' and resid 995 through 998 removed outlier: 3.547A pdb=" N ILE B 998 " --> pdb=" O PRO B 995 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 995 through 998' Processing helix chain 'B' and resid 1005 through 1040 removed outlier: 3.970A pdb=" N THR B1013 " --> pdb=" O ALA B1009 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N PHE B1027 " --> pdb=" O LEU B1023 " (cutoff:3.500A) Proline residue: B1030 - end of helix Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 8 through 28 removed outlier: 3.538A pdb=" N ALA C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 61 through 69 removed outlier: 3.536A pdb=" N ILE C 65 " --> pdb=" O VAL C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 113 Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 148 through 166 removed outlier: 4.601A pdb=" N VAL C 161 " --> pdb=" O GLN C 157 " (cutoff:3.500A) Proline residue: C 162 - end of helix removed outlier: 3.648A pdb=" N ARG C 166 " --> pdb=" O PRO C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 194 Processing helix chain 'C' and resid 197 through 207 Processing helix chain 'C' and resid 240 through 245 Processing helix chain 'C' and resid 296 through 312 Processing helix chain 'C' and resid 329 through 358 Processing helix chain 'C' and resid 363 through 385 Proline residue: C 371 - end of helix Processing helix chain 'C' and resid 389 through 400 Processing helix chain 'C' and resid 404 through 422 Processing helix chain 'C' and resid 424 through 436 removed outlier: 3.673A pdb=" N LYS C 430 " --> pdb=" O LYS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 452 removed outlier: 3.767A pdb=" N VAL C 450 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE C 451 " --> pdb=" O LEU C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 456 Processing helix chain 'C' and resid 459 through 494 removed outlier: 3.869A pdb=" N THR C 471 " --> pdb=" O GLN C 467 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR C 487 " --> pdb=" O ALA C 483 " (cutoff:3.500A) Proline residue: C 488 - end of helix Processing helix chain 'C' and resid 508 through 532 removed outlier: 3.502A pdb=" N LYS C 530 " --> pdb=" O GLY C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 555 Processing helix chain 'C' and resid 580 through 596 removed outlier: 3.812A pdb=" N THR C 584 " --> pdb=" O THR C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 654 Processing helix chain 'C' and resid 687 through 703 removed outlier: 4.058A pdb=" N LEU C 691 " --> pdb=" O GLY C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 736 Processing helix chain 'C' and resid 740 through 751 removed outlier: 4.389A pdb=" N LEU C 751 " --> pdb=" O LEU C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 780 through 785 Processing helix chain 'C' and resid 833 through 849 removed outlier: 3.860A pdb=" N ALA C 837 " --> pdb=" O SER C 833 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY C 849 " --> pdb=" O VAL C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 866 removed outlier: 4.330A pdb=" N GLU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 890 removed outlier: 3.840A pdb=" N ALA C 872 " --> pdb=" O SER C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 899 Processing helix chain 'C' and resid 901 through 924 removed outlier: 3.517A pdb=" N GLY C 905 " --> pdb=" O VAL C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 932 through 962 removed outlier: 3.829A pdb=" N ILE C 953 " --> pdb=" O ASN C 949 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 998 removed outlier: 5.254A pdb=" N ARG C 980 " --> pdb=" O ARG C 976 " (cutoff:3.500A) Proline residue: C 981 - end of helix removed outlier: 3.559A pdb=" N PHE C 989 " --> pdb=" O THR C 985 " (cutoff:3.500A) Proline residue: C 995 - end of helix Processing helix chain 'C' and resid 1003 through 1040 removed outlier: 4.302A pdb=" N GLN C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR C1013 " --> pdb=" O ALA C1009 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE C1027 " --> pdb=" O LEU C1023 " (cutoff:3.500A) Proline residue: C1030 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 130 removed outlier: 8.070A pdb=" N SER A 87 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ALA A 82 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N SER A 89 " --> pdb=" O THR A 80 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N THR A 80 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N SER A 91 " --> pdb=" O MET A 78 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N MET A 78 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR A 93 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 12.325A pdb=" N GLN A 812 " --> pdb=" O GLU A 823 " (cutoff:3.500A) removed outlier: 9.352A pdb=" N GLU A 823 " --> pdb=" O GLN A 812 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL A 814 " --> pdb=" O ALA A 821 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A 714 " --> pdb=" O SER A 825 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 130 removed outlier: 8.070A pdb=" N SER A 87 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ALA A 82 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N SER A 89 " --> pdb=" O THR A 80 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N THR A 80 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N SER A 91 " --> pdb=" O MET A 78 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N MET A 78 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR A 93 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 12.325A pdb=" N GLN A 812 " --> pdb=" O GLU A 823 " (cutoff:3.500A) removed outlier: 9.352A pdb=" N GLU A 823 " --> pdb=" O GLN A 812 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL A 814 " --> pdb=" O ALA A 821 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 676 " --> pdb=" O GLY A 826 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 175 removed outlier: 6.497A pdb=" N MET A 287 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ILE A 139 " --> pdb=" O MET A 287 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL A 289 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N LEU A 137 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASP A 326 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ILE A 139 " --> pdb=" O PRO A 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 264 through 270 removed outlier: 7.987A pdb=" N ARG A 180 " --> pdb=" O ARG A 767 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N MET A 769 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N MET A 182 " --> pdb=" O MET A 769 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N GLN A 771 " --> pdb=" O MET A 182 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ILE A 184 " --> pdb=" O GLN A 771 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLN A 766 " --> pdb=" O ASP A 758 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP A 758 " --> pdb=" O GLN A 766 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL A 768 " --> pdb=" O VAL A 756 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 215 through 217 removed outlier: 4.144A pdb=" N GLY A 215 " --> pdb=" O VAL A 232 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 248 through 250 removed outlier: 6.661A pdb=" N ILE A 258 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 282 through 283 Processing sheet with id=AA8, first strand: chain 'A' and resid 805 through 809 removed outlier: 9.136A pdb=" N THR C 233 " --> pdb=" O PRO A 722 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU A 724 " --> pdb=" O THR C 233 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 47 through 48 removed outlier: 7.762A pdb=" N SER B 87 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ALA B 82 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N SER B 89 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N THR B 80 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER B 91 " --> pdb=" O MET B 78 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N MET B 78 " --> pdb=" O SER B 91 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR B 93 " --> pdb=" O ASP B 76 " (cutoff:3.500A) removed outlier: 12.642A pdb=" N GLN B 812 " --> pdb=" O GLU B 823 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N GLU B 823 " --> pdb=" O GLN B 812 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL B 814 " --> pdb=" O ALA B 821 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA B 821 " --> pdb=" O VAL B 814 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 130 through 131 removed outlier: 7.762A pdb=" N SER B 87 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ALA B 82 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N SER B 89 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N THR B 80 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER B 91 " --> pdb=" O MET B 78 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N MET B 78 " --> pdb=" O SER B 91 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR B 93 " --> pdb=" O ASP B 76 " (cutoff:3.500A) removed outlier: 12.642A pdb=" N GLN B 812 " --> pdb=" O GLU B 823 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N GLU B 823 " --> pdb=" O GLN B 812 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL B 814 " --> pdb=" O ALA B 821 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA B 821 " --> pdb=" O VAL B 814 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 170 through 175 removed outlier: 3.568A pdb=" N MET B 138 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LEU B 291 " --> pdb=" O PHE B 136 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N PHE B 136 " --> pdb=" O LEU B 291 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 170 through 175 removed outlier: 3.540A pdb=" N THR B 284 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N THR B 277 " --> pdb=" O THR B 284 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 276 " --> pdb=" O SER B 608 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 264 through 269 removed outlier: 3.668A pdb=" N ARG B 764 " --> pdb=" O ASN B 761 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 757 " --> pdb=" O VAL B 768 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B 770 " --> pdb=" O TYR B 755 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N TYR B 755 " --> pdb=" O VAL B 770 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 215 through 217 removed outlier: 4.148A pdb=" N GLY B 215 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 232 " --> pdb=" O GLY B 215 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N THR B 231 " --> pdb=" O LEU C 724 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ILE C 726 " --> pdb=" O THR B 231 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR B 233 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ILE C 728 " --> pdb=" O THR B 233 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 248 through 250 removed outlier: 6.780A pdb=" N ILE B 258 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 721 through 723 Processing sheet with id=AB8, first strand: chain 'B' and resid 726 through 728 Processing sheet with id=AB9, first strand: chain 'B' and resid 788 through 789 Processing sheet with id=AC1, first strand: chain 'C' and resid 128 through 130 removed outlier: 3.953A pdb=" N SER C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 12.019A pdb=" N GLN C 812 " --> pdb=" O GLU C 823 " (cutoff:3.500A) removed outlier: 9.542A pdb=" N GLU C 823 " --> pdb=" O GLN C 812 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL C 814 " --> pdb=" O ALA C 821 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 821 " --> pdb=" O VAL C 814 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY C 826 " --> pdb=" O LEU C 676 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 170 through 173 removed outlier: 6.603A pdb=" N THR C 285 " --> pdb=" O MET C 141 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N MET C 141 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N MET C 287 " --> pdb=" O ILE C 139 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE C 139 " --> pdb=" O MET C 287 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL C 289 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N LEU C 137 " --> pdb=" O ASP C 326 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ASP C 326 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ILE C 139 " --> pdb=" O PRO C 324 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 264 through 270 removed outlier: 8.614A pdb=" N ARG C 180 " --> pdb=" O LEU C 765 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ARG C 767 " --> pdb=" O ARG C 180 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER C 757 " --> pdb=" O VAL C 768 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL C 770 " --> pdb=" O TYR C 755 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N TYR C 755 " --> pdb=" O VAL C 770 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 248 through 251 removed outlier: 6.558A pdb=" N ILE C 258 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 282 through 283 removed outlier: 3.514A pdb=" N SER C 608 " --> pdb=" O SER C 276 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN C 603 " --> pdb=" O ILE C 625 " (cutoff:3.500A) 1467 hydrogen bonds defined for protein. 4263 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: 10.31 Time building geometry restraints manager: 10.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3893 1.31 - 1.43: 5929 1.43 - 1.56: 14515 1.56 - 1.68: 38 1.68 - 1.81: 267 Bond restraints: 24642 Sorted by residual: bond pdb=" C DAB D 4 " pdb=" N DAB D 5 " ideal model delta sigma weight residual 1.329 1.457 -0.128 1.40e-02 5.10e+03 8.38e+01 bond pdb=" C DAB D 9 " pdb=" N DAB D 10 " ideal model delta sigma weight residual 1.329 1.456 -0.127 1.40e-02 5.10e+03 8.21e+01 bond pdb=" C LEU D 8 " pdb=" N DAB D 9 " ideal model delta sigma weight residual 1.329 1.456 -0.127 1.40e-02 5.10e+03 8.19e+01 bond pdb=" C DAB D 10 " pdb=" N THR D 11 " ideal model delta sigma weight residual 1.329 1.454 -0.125 1.40e-02 5.10e+03 7.93e+01 bond pdb=" C THR D 3 " pdb=" N DAB D 4 " ideal model delta sigma weight residual 1.329 1.453 -0.124 1.40e-02 5.10e+03 7.88e+01 ... (remaining 24637 not shown) Histogram of bond angle deviations from ideal: 100.05 - 106.84: 639 106.84 - 113.63: 14165 113.63 - 120.42: 9164 120.42 - 127.20: 9102 127.20 - 133.99: 178 Bond angle restraints: 33248 Sorted by residual: angle pdb=" O11 PTY A1106 " pdb=" P1 PTY A1106 " pdb=" O14 PTY A1106 " ideal model delta sigma weight residual 92.90 110.48 -17.58 3.00e+00 1.11e-01 3.43e+01 angle pdb=" N VAL A 968 " pdb=" CA VAL A 968 " pdb=" C VAL A 968 " ideal model delta sigma weight residual 113.53 107.83 5.70 9.80e-01 1.04e+00 3.38e+01 angle pdb=" O11 PTY C1103 " pdb=" P1 PTY C1103 " pdb=" O14 PTY C1103 " ideal model delta sigma weight residual 92.90 109.91 -17.01 3.00e+00 1.11e-01 3.21e+01 angle pdb=" O11 PTY C1102 " pdb=" P1 PTY C1102 " pdb=" O14 PTY C1102 " ideal model delta sigma weight residual 92.90 109.67 -16.77 3.00e+00 1.11e-01 3.12e+01 angle pdb=" O11 PTY B1105 " pdb=" P1 PTY B1105 " pdb=" O14 PTY B1105 " ideal model delta sigma weight residual 92.90 109.61 -16.71 3.00e+00 1.11e-01 3.10e+01 ... (remaining 33243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.46: 14401 33.46 - 66.92: 395 66.92 - 100.38: 55 100.38 - 133.84: 14 133.84 - 167.29: 8 Dihedral angle restraints: 14873 sinusoidal: 5969 harmonic: 8904 Sorted by residual: dihedral pdb=" CA PRO C 221 " pdb=" C PRO C 221 " pdb=" N ALA C 222 " pdb=" CA ALA C 222 " ideal model delta harmonic sigma weight residual 180.00 155.03 24.97 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" C3 PTY C1101 " pdb=" O11 PTY C1101 " pdb=" P1 PTY C1101 " pdb=" O12 PTY C1101 " ideal model delta sinusoidal sigma weight residual 300.23 132.94 167.29 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C3 PTY C1106 " pdb=" O11 PTY C1106 " pdb=" P1 PTY C1106 " pdb=" O12 PTY C1106 " ideal model delta sinusoidal sigma weight residual -59.77 107.25 -167.02 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 14870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2525 0.031 - 0.062: 921 0.062 - 0.094: 266 0.094 - 0.125: 146 0.125 - 0.156: 4 Chirality restraints: 3862 Sorted by residual: chirality pdb=" CA DAB D 9 " pdb=" N DAB D 9 " pdb=" C DAB D 9 " pdb=" CB DAB D 9 " both_signs ideal model delta sigma weight residual False 2.48 2.64 -0.16 2.00e-01 2.50e+01 6.09e-01 chirality pdb=" CA LEU C 220 " pdb=" N LEU C 220 " pdb=" C LEU C 220 " pdb=" CB LEU C 220 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CA ILE B 498 " pdb=" N ILE B 498 " pdb=" C ILE B 498 " pdb=" CB ILE B 498 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 3859 not shown) Planarity restraints: 4158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 994 " 0.067 5.00e-02 4.00e+02 1.00e-01 1.60e+01 pdb=" N PRO C 995 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO C 995 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 995 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 796 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.05e+00 pdb=" N PRO B 797 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 797 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 797 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 220 " -0.031 5.00e-02 4.00e+02 4.70e-02 3.54e+00 pdb=" N PRO C 221 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 221 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 221 " -0.026 5.00e-02 4.00e+02 ... (remaining 4155 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 156 2.57 - 3.15: 20201 3.15 - 3.74: 34068 3.74 - 4.32: 47898 4.32 - 4.90: 84440 Nonbonded interactions: 186763 Sorted by model distance: nonbonded pdb=" OE1 GLU B 58 " pdb=" OG SER B 813 " model vdw 1.991 2.440 nonbonded pdb=" O LYS B 627 " pdb=" NH1 ARG B 632 " model vdw 2.043 2.520 nonbonded pdb=" OG SER A 148 " pdb=" OE1 GLU A 151 " model vdw 2.055 2.440 nonbonded pdb=" OH TYR A 542 " pdb=" O LEU A 900 " model vdw 2.055 2.440 nonbonded pdb=" OH TYR B 465 " pdb=" OE1 GLN B 936 " model vdw 2.056 2.440 ... (remaining 186758 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' and (resid 1 through 1042 or (resid 1101 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C2 or name C5 or name C6 or name C8 or name N1 or name O10 \ or name O11 or name O12 or name O13 or name O14 or name O30 or name O4 or name O \ 7 or name P1 )) or (resid 1102 and (name C1 or name C11 or name C12 or name C13 \ or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name \ C2 or name C20 or name C5 or name C6 or name C8 or name N1 or name O10 or name O \ 11 or name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name \ P1 )) or resid 1103 or (resid 1104 and (name C1 or name C11 or name C12 or name \ C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C5 or nam \ e C6 or name C8 or name N1 or name O10 or name O11 or name O12 or name O13 or na \ me O14 or name O30 or name O4 or name O7 or name P1 )) or (resid 1105 and (name \ C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or na \ me C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name C3 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C5 or name C6 o \ r name C8 or name N1 or name O10 or name O11 or name O12 or name O13 or name O14 \ or name O30 or name O4 or name O7 or name P1 )) or (resid 1107 and (name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C1 \ 8 or name C19 or name C20 or name C21 or name C22 or name C8 or name O10 or name \ O7 )))) selection = (chain 'B' and (resid 1 through 498 or resid 508 through 1042 or (resid 1102 and \ (name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C1 \ 6 or name C17 or name C18 or name C19 or name C2 or name C5 or name C6 or name C \ 8 or name N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name \ O30 or name O4 or name O7 or name P1 )) or (resid 1103 and (name C1 or name C11 \ or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name \ C18 or name C19 or name C2 or name C20 or name C5 or name C6 or name C8 or name \ N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or n \ ame O4 or name O7 or name P1 )) or (resid 1104 and (name C11 or name C12 or name \ C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or \ name C8 )) or (resid 1105 and (name C1 or name C11 or name C12 or name C2 or nam \ e C3 or name C30 or name C31 or name C32 or name C33 or name C5 or name C6 or na \ me C8 or name N1 or name O10 or name O11 or name O12 or name O13 or name O14 or \ name O30 or name O4 or name O7 or name P1 )) or (resid 1106 and (name C1 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or \ name C18 or name C19 or name C2 or name C20 or name C21 or name C3 or name C30 o \ r name C31 or name C32 or name C33 or name C34 or name C5 or name C6 or name C8 \ or name N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O \ 30 or name O4 or name O7 or name P1 )) or (resid 1108 and (name C11 or name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19 or name C20 or name C21 or name C22 or name C8 or name O10 or name O7 )))) selection = (chain 'C' and (resid 1 through 498 or resid 508 through 1042 or (resid 1102 and \ (name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C1 \ 6 or name C17 or name C18 or name C19 or name C2 or name C5 or name C6 or name C \ 8 or name N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name \ O30 or name O4 or name O7 or name P1 )) or (resid 1103 and (name C1 or name C11 \ or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name \ C18 or name C19 or name C2 or name C20 or name C5 or name C6 or name C8 or name \ N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or n \ ame O4 or name O7 or name P1 )) or (resid 1104 and (name C11 or name C12 or name \ C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or \ name C8 )) or (resid 1105 and (name C1 or name C11 or name C12 or name C20 or na \ me C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 o \ r name C30 or name C31 or name C32 or name C33 or name C5 or name C6 or name C8 \ or name O10 or name O30 or name O4 or name O7 )) or resid 1106 or resid 1108)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.910 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 65.940 Find NCS groups from input model: 1.860 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.128 24642 Z= 0.345 Angle : 0.905 17.576 33248 Z= 0.390 Chirality : 0.039 0.156 3862 Planarity : 0.004 0.100 4158 Dihedral : 16.803 167.294 9167 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.16 % Allowed : 0.24 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: 0.81 (0.16), residues: 3114 helix: 2.15 (0.13), residues: 1655 sheet: -0.37 (0.26), residues: 423 loop : -1.82 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1016 HIS 0.002 0.001 HIS A 688 PHE 0.011 0.001 PHE C1015 TYR 0.015 0.001 TYR B 49 ARG 0.006 0.000 ARG C 767 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 309 time to evaluate : 2.775 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 521 THR cc_start: 0.8620 (t) cc_final: 0.8362 (m) REVERT: B 984 MET cc_start: 0.8874 (mtp) cc_final: 0.8654 (mtp) REVERT: D 8 LEU cc_start: 0.3480 (OUTLIER) cc_final: 0.3153 (mp) outliers start: 4 outliers final: 0 residues processed: 312 average time/residue: 0.3775 time to fit residues: 191.5738 Evaluate side-chains 259 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 258 time to evaluate : 2.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 8 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.7499 > 50: distance: 1 - 15: 13.160 distance: 5 - 22: 28.578 distance: 9 - 33: 28.500 distance: 13 - 15: 14.195 distance: 14 - 41: 27.852 distance: 15 - 16: 20.593 distance: 16 - 17: 27.834 distance: 16 - 19: 22.614 distance: 17 - 18: 9.877 distance: 17 - 22: 25.287 distance: 18 - 52: 42.189 distance: 19 - 21: 7.189 distance: 22 - 23: 10.477 distance: 23 - 24: 16.650 distance: 24 - 25: 13.222 distance: 24 - 33: 14.272 distance: 25 - 60: 21.376 distance: 26 - 27: 22.467 distance: 27 - 28: 7.088 distance: 27 - 29: 17.474 distance: 28 - 30: 12.328 distance: 29 - 31: 18.062 distance: 30 - 32: 9.714 distance: 31 - 32: 8.745 distance: 33 - 34: 22.673 distance: 34 - 35: 26.259 distance: 34 - 37: 10.413 distance: 35 - 36: 8.977 distance: 35 - 41: 7.632 distance: 37 - 38: 11.333 distance: 38 - 39: 8.301 distance: 38 - 40: 16.052 distance: 41 - 42: 26.438 distance: 42 - 43: 53.531 distance: 42 - 45: 18.825 distance: 43 - 44: 14.247 distance: 43 - 52: 29.276 distance: 45 - 46: 10.997 distance: 46 - 47: 38.469 distance: 46 - 48: 11.691 distance: 47 - 49: 7.960 distance: 48 - 50: 16.306 distance: 49 - 51: 40.818 distance: 50 - 51: 8.726 distance: 52 - 53: 10.881 distance: 53 - 54: 18.090 distance: 53 - 56: 13.458 distance: 54 - 55: 29.071 distance: 54 - 60: 15.493 distance: 56 - 57: 3.179 distance: 57 - 58: 15.764 distance: 58 - 59: 9.614 distance: 60 - 61: 18.475 distance: 61 - 62: 27.736 distance: 61 - 64: 33.518 distance: 62 - 63: 42.399 distance: 62 - 71: 31.584 distance: 64 - 65: 32.468 distance: 65 - 66: 40.834 distance: 66 - 67: 25.001 distance: 67 - 68: 12.120 distance: 68 - 69: 17.523 distance: 68 - 70: 21.537 distance: 71 - 72: 18.918 distance: 72 - 73: 25.797 distance: 72 - 75: 16.766 distance: 73 - 74: 4.542 distance: 73 - 79: 40.753 distance: 75 - 76: 13.653 distance: 76 - 77: 6.860 distance: 76 - 78: 43.997 distance: 79 - 80: 33.718 distance: 79 - 85: 32.585 distance: 80 - 81: 39.968 distance: 80 - 83: 35.682 distance: 81 - 82: 41.078 distance: 84 - 85: 36.774 distance: 86 - 87: 37.984 distance: 90 - 92: 11.795 distance: 93 - 94: 57.005 distance: 94 - 95: 12.769 distance: 94 - 97: 4.617 distance: 95 - 96: 6.485 distance: 95 - 99: 30.770 distance: 97 - 98: 28.845