Starting phenix.real_space_refine on Fri Dec 15 09:10:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mbv_23748/12_2023/7mbv_23748.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mbv_23748/12_2023/7mbv_23748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mbv_23748/12_2023/7mbv_23748.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mbv_23748/12_2023/7mbv_23748.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mbv_23748/12_2023/7mbv_23748.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mbv_23748/12_2023/7mbv_23748.pdb" } resolution = 2.8 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= 0.002 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 Ca 8 9.91 5 S 176 5.16 5 C 20228 2.51 5 N 5180 2.21 5 O 5212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 372": "OE1" <-> "OE2" Residue "A GLU 1032": "OE1" <-> "OE2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "B GLU 1032": "OE1" <-> "OE2" Residue "C GLU 372": "OE1" <-> "OE2" Residue "C GLU 1032": "OE1" <-> "OE2" Residue "D GLU 372": "OE1" <-> "OE2" Residue "D GLU 1032": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 30804 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7570 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 138} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 952} Chain breaks: 4 Unresolved non-hydrogen bonds: 474 Unresolved non-hydrogen angles: 586 Unresolved non-hydrogen dihedrals: 370 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 28, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 29, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 325 Chain: "B" Number of atoms: 7570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7570 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 138} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 952} Chain breaks: 4 Unresolved non-hydrogen bonds: 474 Unresolved non-hydrogen angles: 586 Unresolved non-hydrogen dihedrals: 370 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 28, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 29, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 325 Chain: "C" Number of atoms: 7570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7570 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 138} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 952} Chain breaks: 4 Unresolved non-hydrogen bonds: 474 Unresolved non-hydrogen angles: 586 Unresolved non-hydrogen dihedrals: 370 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 28, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 29, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 325 Chain: "D" Number of atoms: 7570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7570 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 138} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 952} Chain breaks: 4 Unresolved non-hydrogen bonds: 474 Unresolved non-hydrogen angles: 586 Unresolved non-hydrogen dihedrals: 370 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 28, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 29, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 325 Chain: "A" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 131 Unusual residues: {' CA': 2, 'NAG': 1, 'YUS': 1, 'YUV': 1, 'YUY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 131 Unusual residues: {' CA': 2, 'NAG': 1, 'YUS': 1, 'YUV': 1, 'YUY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 131 Unusual residues: {' CA': 2, 'NAG': 1, 'YUS': 1, 'YUV': 1, 'YUY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 131 Unusual residues: {' CA': 2, 'NAG': 1, 'YUS': 1, 'YUV': 1, 'YUY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2187 SG CYS A 324 74.973 108.199 30.106 1.00 38.87 S ATOM 9757 SG CYS B 324 35.523 74.978 30.112 1.00 38.87 S ATOM 17327 SG CYS C 324 68.755 35.522 30.118 1.00 38.87 S ATOM 24897 SG CYS D 324 108.205 68.756 30.106 1.00 38.87 S Time building chain proxies: 20.84, per 1000 atoms: 0.68 Number of scatterers: 30804 At special positions: 0 Unit cell: (144.55, 144.55, 155.288, 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) Ca 8 19.99 S 176 16.00 O 5212 8.00 N 5180 7.00 C 20228 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 Links applied NAG-ASN " NAG A1501 " - " ASN A 921 " " NAG B1501 " - " ASN B 921 " " NAG C1501 " - " ASN C 921 " " NAG D3002 " - " ASN D 921 " Time building additional restraints: 13.08 Conformation dependent library (CDL) restraints added in 6.4 seconds 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7600 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 12 sheets defined 70.3% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.22 Creating SS restraints... Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.750A pdb=" N ILE A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 90 removed outlier: 3.922A pdb=" N SER A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 119 Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 139 through 144 removed outlier: 3.786A pdb=" N LEU A 143 " --> pdb=" O ASN A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 200 Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 226 through 236 Processing helix chain 'A' and resid 248 through 260 Processing helix chain 'A' and resid 263 through 275 Processing helix chain 'A' and resid 280 through 298 Processing helix chain 'A' and resid 311 through 328 Processing helix chain 'A' and resid 330 through 333 removed outlier: 3.740A pdb=" N ASP A 333 " --> pdb=" O GLU A 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 330 through 333' Processing helix chain 'A' and resid 334 through 344 Processing helix chain 'A' and resid 346 through 354 Processing helix chain 'A' and resid 362 through 376 removed outlier: 3.569A pdb=" N LEU A 366 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLU A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 388 Processing helix chain 'A' and resid 391 through 396 Processing helix chain 'A' and resid 397 through 407 Processing helix chain 'A' and resid 412 through 429 removed outlier: 3.686A pdb=" N THR A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 462 removed outlier: 3.661A pdb=" N VAL A 454 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 510 Processing helix chain 'A' and resid 513 through 523 Processing helix chain 'A' and resid 526 through 545 removed outlier: 4.109A pdb=" N HIS A 543 " --> pdb=" O LYS A 539 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU A 544 " --> pdb=" O GLU A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 556 Processing helix chain 'A' and resid 558 through 574 removed outlier: 3.638A pdb=" N PHE A 562 " --> pdb=" O LYS A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 584 Processing helix chain 'A' and resid 593 through 602 Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 609 through 622 Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 640 through 644 Processing helix chain 'A' and resid 699 through 714 Processing helix chain 'A' and resid 715 through 740 Processing helix chain 'A' and resid 751 through 774 Processing helix chain 'A' and resid 780 through 790 Processing helix chain 'A' and resid 791 through 812 Processing helix chain 'A' and resid 816 through 839 removed outlier: 4.043A pdb=" N ILE A 836 " --> pdb=" O THR A 832 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N HIS A 837 " --> pdb=" O LEU A 833 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 839 " --> pdb=" O LEU A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 842 No H-bonds generated for 'chain 'A' and resid 840 through 842' Processing helix chain 'A' and resid 845 through 882 removed outlier: 4.818A pdb=" N LYS A 857 " --> pdb=" O GLU A 853 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASP A 858 " --> pdb=" O ARG A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 902 removed outlier: 4.920A pdb=" N ARG A 898 " --> pdb=" O ARG A 894 " (cutoff:3.500A) Proline residue: A 899 - end of helix Processing helix chain 'A' and resid 903 through 905 No H-bonds generated for 'chain 'A' and resid 903 through 905' Processing helix chain 'A' and resid 908 through 912 Processing helix chain 'A' and resid 913 through 917 Processing helix chain 'A' and resid 925 through 931 Processing helix chain 'A' and resid 942 through 994 removed outlier: 3.760A pdb=" N VAL A 946 " --> pdb=" O ALA A 942 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 961 " --> pdb=" O THR A 957 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LEU A 962 " --> pdb=" O ASN A 958 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N GLU A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASN A 979 " --> pdb=" O VAL A 975 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN A 990 " --> pdb=" O PHE A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1020 removed outlier: 3.902A pdb=" N SER A1009 " --> pdb=" O PHE A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1062 Processing helix chain 'A' and resid 1063 through 1092 Processing helix chain 'B' and resid 40 through 51 removed outlier: 3.751A pdb=" N ILE B 44 " --> pdb=" O ASP B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 90 removed outlier: 3.922A pdb=" N SER B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 119 Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 139 through 144 removed outlier: 3.786A pdb=" N LEU B 143 " --> pdb=" O ASN B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 200 Processing helix chain 'B' and resid 223 through 225 No H-bonds generated for 'chain 'B' and resid 223 through 225' Processing helix chain 'B' and resid 226 through 236 Processing helix chain 'B' and resid 248 through 260 Processing helix chain 'B' and resid 263 through 275 Processing helix chain 'B' and resid 280 through 298 Processing helix chain 'B' and resid 311 through 328 Processing helix chain 'B' and resid 330 through 333 removed outlier: 3.740A pdb=" N ASP B 333 " --> pdb=" O GLU B 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 330 through 333' Processing helix chain 'B' and resid 334 through 344 Processing helix chain 'B' and resid 346 through 354 Processing helix chain 'B' and resid 362 through 376 removed outlier: 3.569A pdb=" N LEU B 366 " --> pdb=" O SER B 362 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU B 368 " --> pdb=" O GLN B 364 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL B 369 " --> pdb=" O ASP B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 388 Processing helix chain 'B' and resid 391 through 396 Processing helix chain 'B' and resid 397 through 407 Processing helix chain 'B' and resid 412 through 429 removed outlier: 3.685A pdb=" N THR B 416 " --> pdb=" O ASN B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 462 removed outlier: 3.661A pdb=" N VAL B 454 " --> pdb=" O THR B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 510 Processing helix chain 'B' and resid 513 through 523 Processing helix chain 'B' and resid 526 through 545 removed outlier: 4.109A pdb=" N HIS B 543 " --> pdb=" O LYS B 539 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU B 544 " --> pdb=" O GLU B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 556 Processing helix chain 'B' and resid 558 through 574 removed outlier: 3.638A pdb=" N PHE B 562 " --> pdb=" O LYS B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 584 Processing helix chain 'B' and resid 593 through 602 Processing helix chain 'B' and resid 603 through 608 Processing helix chain 'B' and resid 609 through 622 Processing helix chain 'B' and resid 629 through 639 Processing helix chain 'B' and resid 640 through 644 Processing helix chain 'B' and resid 699 through 714 Processing helix chain 'B' and resid 715 through 740 Processing helix chain 'B' and resid 751 through 774 Processing helix chain 'B' and resid 780 through 790 Processing helix chain 'B' and resid 791 through 812 Processing helix chain 'B' and resid 816 through 839 removed outlier: 4.042A pdb=" N ILE B 836 " --> pdb=" O THR B 832 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N HIS B 837 " --> pdb=" O LEU B 833 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE B 839 " --> pdb=" O LEU B 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 842 No H-bonds generated for 'chain 'B' and resid 840 through 842' Processing helix chain 'B' and resid 845 through 882 removed outlier: 4.817A pdb=" N LYS B 857 " --> pdb=" O GLU B 853 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASP B 858 " --> pdb=" O ARG B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 902 removed outlier: 4.919A pdb=" N ARG B 898 " --> pdb=" O ARG B 894 " (cutoff:3.500A) Proline residue: B 899 - end of helix Processing helix chain 'B' and resid 903 through 905 No H-bonds generated for 'chain 'B' and resid 903 through 905' Processing helix chain 'B' and resid 908 through 912 Processing helix chain 'B' and resid 913 through 917 Processing helix chain 'B' and resid 925 through 931 Processing helix chain 'B' and resid 942 through 994 removed outlier: 3.760A pdb=" N VAL B 946 " --> pdb=" O ALA B 942 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU B 961 " --> pdb=" O THR B 957 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LEU B 962 " --> pdb=" O ASN B 958 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N GLU B 978 " --> pdb=" O GLN B 974 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASN B 979 " --> pdb=" O VAL B 975 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN B 990 " --> pdb=" O PHE B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 1005 through 1020 removed outlier: 3.902A pdb=" N SER B1009 " --> pdb=" O PHE B1005 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1062 Processing helix chain 'B' and resid 1063 through 1092 Processing helix chain 'C' and resid 40 through 51 removed outlier: 3.750A pdb=" N ILE C 44 " --> pdb=" O ASP C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 90 removed outlier: 3.922A pdb=" N SER C 90 " --> pdb=" O LYS C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 119 Processing helix chain 'C' and resid 135 through 137 No H-bonds generated for 'chain 'C' and resid 135 through 137' Processing helix chain 'C' and resid 139 through 144 removed outlier: 3.786A pdb=" N LEU C 143 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 200 Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 226 through 236 Processing helix chain 'C' and resid 248 through 260 Processing helix chain 'C' and resid 263 through 275 Processing helix chain 'C' and resid 280 through 298 Processing helix chain 'C' and resid 311 through 328 Processing helix chain 'C' and resid 330 through 333 removed outlier: 3.740A pdb=" N ASP C 333 " --> pdb=" O GLU C 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 330 through 333' Processing helix chain 'C' and resid 334 through 344 Processing helix chain 'C' and resid 346 through 354 Processing helix chain 'C' and resid 362 through 376 removed outlier: 3.569A pdb=" N LEU C 366 " --> pdb=" O SER C 362 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU C 368 " --> pdb=" O GLN C 364 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL C 369 " --> pdb=" O ASP C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 388 Processing helix chain 'C' and resid 391 through 396 Processing helix chain 'C' and resid 397 through 407 Processing helix chain 'C' and resid 412 through 429 removed outlier: 3.686A pdb=" N THR C 416 " --> pdb=" O ASN C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 462 removed outlier: 3.661A pdb=" N VAL C 454 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 510 Processing helix chain 'C' and resid 513 through 523 Processing helix chain 'C' and resid 526 through 545 removed outlier: 4.109A pdb=" N HIS C 543 " --> pdb=" O LYS C 539 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU C 544 " --> pdb=" O GLU C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 556 Processing helix chain 'C' and resid 558 through 574 removed outlier: 3.638A pdb=" N PHE C 562 " --> pdb=" O LYS C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 584 Processing helix chain 'C' and resid 593 through 602 Processing helix chain 'C' and resid 603 through 608 Processing helix chain 'C' and resid 609 through 622 Processing helix chain 'C' and resid 629 through 639 Processing helix chain 'C' and resid 640 through 644 Processing helix chain 'C' and resid 699 through 714 Processing helix chain 'C' and resid 715 through 740 Processing helix chain 'C' and resid 751 through 774 Processing helix chain 'C' and resid 780 through 790 Processing helix chain 'C' and resid 791 through 812 Processing helix chain 'C' and resid 816 through 839 removed outlier: 4.043A pdb=" N ILE C 836 " --> pdb=" O THR C 832 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N HIS C 837 " --> pdb=" O LEU C 833 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE C 839 " --> pdb=" O LEU C 835 " (cutoff:3.500A) Processing helix chain 'C' and resid 840 through 842 No H-bonds generated for 'chain 'C' and resid 840 through 842' Processing helix chain 'C' and resid 845 through 882 removed outlier: 4.817A pdb=" N LYS C 857 " --> pdb=" O GLU C 853 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASP C 858 " --> pdb=" O ARG C 854 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 902 removed outlier: 4.920A pdb=" N ARG C 898 " --> pdb=" O ARG C 894 " (cutoff:3.500A) Proline residue: C 899 - end of helix Processing helix chain 'C' and resid 903 through 905 No H-bonds generated for 'chain 'C' and resid 903 through 905' Processing helix chain 'C' and resid 908 through 912 Processing helix chain 'C' and resid 913 through 917 Processing helix chain 'C' and resid 925 through 931 Processing helix chain 'C' and resid 942 through 994 removed outlier: 3.760A pdb=" N VAL C 946 " --> pdb=" O ALA C 942 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C 961 " --> pdb=" O THR C 957 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LEU C 962 " --> pdb=" O ASN C 958 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N GLU C 978 " --> pdb=" O GLN C 974 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASN C 979 " --> pdb=" O VAL C 975 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN C 990 " --> pdb=" O PHE C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1020 removed outlier: 3.903A pdb=" N SER C1009 " --> pdb=" O PHE C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1034 through 1062 Processing helix chain 'C' and resid 1063 through 1092 Processing helix chain 'D' and resid 40 through 51 removed outlier: 3.750A pdb=" N ILE D 44 " --> pdb=" O ASP D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 90 removed outlier: 3.922A pdb=" N SER D 90 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 119 Processing helix chain 'D' and resid 135 through 137 No H-bonds generated for 'chain 'D' and resid 135 through 137' Processing helix chain 'D' and resid 139 through 144 removed outlier: 3.786A pdb=" N LEU D 143 " --> pdb=" O ASN D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 200 Processing helix chain 'D' and resid 223 through 225 No H-bonds generated for 'chain 'D' and resid 223 through 225' Processing helix chain 'D' and resid 226 through 236 Processing helix chain 'D' and resid 248 through 260 Processing helix chain 'D' and resid 263 through 275 Processing helix chain 'D' and resid 280 through 298 Processing helix chain 'D' and resid 311 through 328 Processing helix chain 'D' and resid 330 through 333 removed outlier: 3.740A pdb=" N ASP D 333 " --> pdb=" O GLU D 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 330 through 333' Processing helix chain 'D' and resid 334 through 344 Processing helix chain 'D' and resid 346 through 354 Processing helix chain 'D' and resid 362 through 376 removed outlier: 3.569A pdb=" N LEU D 366 " --> pdb=" O SER D 362 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU D 368 " --> pdb=" O GLN D 364 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL D 369 " --> pdb=" O ASP D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 388 Processing helix chain 'D' and resid 391 through 396 Processing helix chain 'D' and resid 397 through 407 Processing helix chain 'D' and resid 412 through 429 removed outlier: 3.686A pdb=" N THR D 416 " --> pdb=" O ASN D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 462 removed outlier: 3.661A pdb=" N VAL D 454 " --> pdb=" O THR D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 510 Processing helix chain 'D' and resid 513 through 523 Processing helix chain 'D' and resid 526 through 545 removed outlier: 4.109A pdb=" N HIS D 543 " --> pdb=" O LYS D 539 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU D 544 " --> pdb=" O GLU D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 556 Processing helix chain 'D' and resid 558 through 574 removed outlier: 3.638A pdb=" N PHE D 562 " --> pdb=" O LYS D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 584 Processing helix chain 'D' and resid 593 through 602 Processing helix chain 'D' and resid 603 through 608 Processing helix chain 'D' and resid 609 through 622 Processing helix chain 'D' and resid 629 through 639 Processing helix chain 'D' and resid 640 through 644 Processing helix chain 'D' and resid 699 through 714 Processing helix chain 'D' and resid 715 through 740 Processing helix chain 'D' and resid 751 through 774 Processing helix chain 'D' and resid 780 through 790 Processing helix chain 'D' and resid 791 through 812 Processing helix chain 'D' and resid 816 through 839 removed outlier: 4.043A pdb=" N ILE D 836 " --> pdb=" O THR D 832 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N HIS D 837 " --> pdb=" O LEU D 833 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE D 839 " --> pdb=" O LEU D 835 " (cutoff:3.500A) Processing helix chain 'D' and resid 840 through 842 No H-bonds generated for 'chain 'D' and resid 840 through 842' Processing helix chain 'D' and resid 845 through 882 removed outlier: 4.817A pdb=" N LYS D 857 " --> pdb=" O GLU D 853 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASP D 858 " --> pdb=" O ARG D 854 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 902 removed outlier: 4.921A pdb=" N ARG D 898 " --> pdb=" O ARG D 894 " (cutoff:3.500A) Proline residue: D 899 - end of helix Processing helix chain 'D' and resid 903 through 905 No H-bonds generated for 'chain 'D' and resid 903 through 905' Processing helix chain 'D' and resid 908 through 912 Processing helix chain 'D' and resid 913 through 917 Processing helix chain 'D' and resid 925 through 931 Processing helix chain 'D' and resid 942 through 994 removed outlier: 3.760A pdb=" N VAL D 946 " --> pdb=" O ALA D 942 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU D 961 " --> pdb=" O THR D 957 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LEU D 962 " --> pdb=" O ASN D 958 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N GLU D 978 " --> pdb=" O GLN D 974 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASN D 979 " --> pdb=" O VAL D 975 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN D 990 " --> pdb=" O PHE D 986 " (cutoff:3.500A) Processing helix chain 'D' and resid 1005 through 1020 removed outlier: 3.902A pdb=" N SER D1009 " --> pdb=" O PHE D1005 " (cutoff:3.500A) Processing helix chain 'D' and resid 1034 through 1062 Processing helix chain 'D' and resid 1063 through 1092 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 32 removed outlier: 3.604A pdb=" N THR A 28 " --> pdb=" O PHE A 22 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE A 32 " --> pdb=" O GLY A 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 36 removed outlier: 8.789A pdb=" N HIS A 173 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA A 128 " --> pdb=" O HIS A 173 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE A 175 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLY A 130 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N VAL A 177 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA A 132 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA A 93 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ILE A 129 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ILE A 95 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE A 131 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR A 97 " --> pdb=" O ILE A 131 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N LEU A 241 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N CYS A 217 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LEU A 243 " --> pdb=" O CYS A 217 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU A 219 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TRP A 240 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N HIS A 304 " --> pdb=" O TRP A 240 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ILE A 242 " --> pdb=" O HIS A 304 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 202 through 204 Processing sheet with id=AA4, first strand: chain 'B' and resid 28 through 32 removed outlier: 3.605A pdb=" N THR B 28 " --> pdb=" O PHE B 22 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE B 32 " --> pdb=" O GLY B 18 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 34 through 36 removed outlier: 8.790A pdb=" N HIS B 173 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA B 128 " --> pdb=" O HIS B 173 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE B 175 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLY B 130 " --> pdb=" O ILE B 175 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL B 177 " --> pdb=" O GLY B 130 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA B 132 " --> pdb=" O VAL B 177 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA B 93 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE B 129 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ILE B 95 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE B 131 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR B 97 " --> pdb=" O ILE B 131 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N LEU B 241 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N CYS B 217 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LEU B 243 " --> pdb=" O CYS B 217 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU B 219 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TRP B 240 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N HIS B 304 " --> pdb=" O TRP B 240 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ILE B 242 " --> pdb=" O HIS B 304 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 202 through 204 Processing sheet with id=AA7, first strand: chain 'C' and resid 28 through 32 removed outlier: 3.605A pdb=" N THR C 28 " --> pdb=" O PHE C 22 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE C 32 " --> pdb=" O GLY C 18 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 34 through 36 removed outlier: 8.790A pdb=" N HIS C 173 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA C 128 " --> pdb=" O HIS C 173 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ILE C 175 " --> pdb=" O ALA C 128 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLY C 130 " --> pdb=" O ILE C 175 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N VAL C 177 " --> pdb=" O GLY C 130 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA C 132 " --> pdb=" O VAL C 177 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA C 93 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE C 129 " --> pdb=" O ALA C 93 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ILE C 95 " --> pdb=" O ILE C 129 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE C 131 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR C 97 " --> pdb=" O ILE C 131 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N LEU C 241 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N CYS C 217 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LEU C 243 " --> pdb=" O CYS C 217 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU C 219 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TRP C 240 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N HIS C 304 " --> pdb=" O TRP C 240 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ILE C 242 " --> pdb=" O HIS C 304 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 202 through 204 Processing sheet with id=AB1, first strand: chain 'D' and resid 28 through 32 removed outlier: 3.604A pdb=" N THR D 28 " --> pdb=" O PHE D 22 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE D 32 " --> pdb=" O GLY D 18 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 34 through 36 removed outlier: 8.790A pdb=" N HIS D 173 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA D 128 " --> pdb=" O HIS D 173 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ILE D 175 " --> pdb=" O ALA D 128 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLY D 130 " --> pdb=" O ILE D 175 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL D 177 " --> pdb=" O GLY D 130 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA D 132 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA D 93 " --> pdb=" O VAL D 127 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ILE D 129 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ILE D 95 " --> pdb=" O ILE D 129 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE D 131 " --> pdb=" O ILE D 95 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR D 97 " --> pdb=" O ILE D 131 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N LEU D 241 " --> pdb=" O VAL D 215 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N CYS D 217 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LEU D 243 " --> pdb=" O CYS D 217 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU D 219 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TRP D 240 " --> pdb=" O THR D 302 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N HIS D 304 " --> pdb=" O TRP D 240 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ILE D 242 " --> pdb=" O HIS D 304 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 202 through 204 2020 hydrogen bonds defined for protein. 5964 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: 13.64 Time building geometry restraints manager: 14.02 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: 9501 1.34 - 1.46: 4859 1.46 - 1.57: 16956 1.57 - 1.69: 4 1.69 - 1.81: 292 Bond restraints: 31612 Sorted by residual: bond pdb=" CB PRO A 746 " pdb=" CG PRO A 746 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.03e+00 bond pdb=" CB PRO B 746 " pdb=" CG PRO B 746 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.02e+00 bond pdb=" CB PRO D 746 " pdb=" CG PRO D 746 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.02e+00 bond pdb=" CB PRO C 746 " pdb=" CG PRO C 746 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.02e+00 bond pdb=" N YUS A1504 " pdb=" N1 YUS A1504 " ideal model delta sigma weight residual 1.342 1.376 -0.034 2.00e-02 2.50e+03 2.92e+00 ... (remaining 31607 not shown) Histogram of bond angle deviations from ideal: 99.64 - 106.51: 1003 106.51 - 113.39: 17815 113.39 - 120.26: 10927 120.26 - 127.14: 13063 127.14 - 134.01: 404 Bond angle restraints: 43212 Sorted by residual: angle pdb=" CA PRO A 746 " pdb=" N PRO A 746 " pdb=" CD PRO A 746 " ideal model delta sigma weight residual 112.00 104.59 7.41 1.40e+00 5.10e-01 2.80e+01 angle pdb=" CA PRO C 746 " pdb=" N PRO C 746 " pdb=" CD PRO C 746 " ideal model delta sigma weight residual 112.00 104.63 7.37 1.40e+00 5.10e-01 2.78e+01 angle pdb=" CA PRO D 746 " pdb=" N PRO D 746 " pdb=" CD PRO D 746 " ideal model delta sigma weight residual 112.00 104.63 7.37 1.40e+00 5.10e-01 2.78e+01 angle pdb=" CA PRO B 746 " pdb=" N PRO B 746 " pdb=" CD PRO B 746 " ideal model delta sigma weight residual 112.00 104.63 7.37 1.40e+00 5.10e-01 2.78e+01 angle pdb=" C ASP C 463 " pdb=" CA ASP C 463 " pdb=" CB ASP C 463 " ideal model delta sigma weight residual 110.92 116.07 -5.15 1.59e+00 3.96e-01 1.05e+01 ... (remaining 43207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 17693 16.93 - 33.85: 1290 33.85 - 50.78: 221 50.78 - 67.71: 44 67.71 - 84.63: 24 Dihedral angle restraints: 19272 sinusoidal: 7592 harmonic: 11680 Sorted by residual: dihedral pdb=" CA ASP A 610 " pdb=" CB ASP A 610 " pdb=" CG ASP A 610 " pdb=" OD1 ASP A 610 " ideal model delta sinusoidal sigma weight residual -30.00 -89.40 59.40 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP C 610 " pdb=" CB ASP C 610 " pdb=" CG ASP C 610 " pdb=" OD1 ASP C 610 " ideal model delta sinusoidal sigma weight residual -30.00 -89.36 59.36 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP D 610 " pdb=" CB ASP D 610 " pdb=" CG ASP D 610 " pdb=" OD1 ASP D 610 " ideal model delta sinusoidal sigma weight residual -30.00 -89.36 59.36 1 2.00e+01 2.50e-03 1.18e+01 ... (remaining 19269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 5029 0.100 - 0.200: 91 0.200 - 0.300: 4 0.300 - 0.401: 0 0.401 - 0.501: 4 Chirality restraints: 5128 Sorted by residual: chirality pdb=" C1 NAG B1501 " pdb=" ND2 ASN B 921 " pdb=" C2 NAG B1501 " pdb=" O5 NAG B1501 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.27e+00 chirality pdb=" C1 NAG A1501 " pdb=" ND2 ASN A 921 " pdb=" C2 NAG A1501 " pdb=" O5 NAG A1501 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.27e+00 chirality pdb=" C1 NAG C1501 " pdb=" ND2 ASN C 921 " pdb=" C2 NAG C1501 " pdb=" O5 NAG C1501 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.27e+00 ... (remaining 5125 not shown) Planarity restraints: 5288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1501 " 0.338 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C7 NAG B1501 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG B1501 " 0.136 2.00e-02 2.50e+03 pdb=" N2 NAG B1501 " -0.522 2.00e-02 2.50e+03 pdb=" O7 NAG B1501 " 0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1501 " 0.338 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C7 NAG C1501 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG C1501 " 0.136 2.00e-02 2.50e+03 pdb=" N2 NAG C1501 " -0.521 2.00e-02 2.50e+03 pdb=" O7 NAG C1501 " 0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D3002 " 0.338 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C7 NAG D3002 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG D3002 " 0.136 2.00e-02 2.50e+03 pdb=" N2 NAG D3002 " -0.521 2.00e-02 2.50e+03 pdb=" O7 NAG D3002 " 0.128 2.00e-02 2.50e+03 ... (remaining 5285 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 7733 2.80 - 3.33: 30559 3.33 - 3.85: 53168 3.85 - 4.38: 60817 4.38 - 4.90: 103372 Nonbonded interactions: 255649 Sorted by model distance: nonbonded pdb=" O GLY D 524 " pdb=" NZ LYS D1049 " model vdw 2.280 2.520 nonbonded pdb=" O GLY A 524 " pdb=" NZ LYS A1049 " model vdw 2.280 2.520 nonbonded pdb=" O GLY C 524 " pdb=" NZ LYS C1049 " model vdw 2.280 2.520 nonbonded pdb=" O GLY B 524 " pdb=" NZ LYS B1049 " model vdw 2.280 2.520 nonbonded pdb=" OD1 ASP A 463 " pdb=" N ASP A 464 " model vdw 2.301 2.520 ... (remaining 255644 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 16 through 1092 or resid 1503)) selection = (chain 'B' and (resid 16 through 1092 or resid 1503)) selection = (chain 'C' and (resid 16 through 1092 or resid 1503)) selection = (chain 'D' and (resid 16 through 1092 or resid 3003)) } 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: 2.440 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: 0.040 Extract box with map and model: 11.280 Check model and map are aligned: 0.410 Set scattering table: 0.250 Process input model: 92.020 Find NCS groups from input model: 2.610 Set up NCS constraints: 0.200 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:18.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 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 0.087 31612 Z= 0.220 Angle : 0.585 7.407 43212 Z= 0.316 Chirality : 0.041 0.501 5128 Planarity : 0.010 0.292 5284 Dihedral : 12.274 84.632 11672 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.48 (0.14), residues: 3944 helix: 1.56 (0.10), residues: 2620 sheet: 0.72 (0.32), residues: 252 loop : -0.30 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP A 760 HIS 0.003 0.001 HIS B1060 PHE 0.021 0.001 PHE A 734 TYR 0.012 0.001 TYR D 231 ARG 0.003 0.000 ARG D 448 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 4.744 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 1.4264 time to fit residues: 504.1760 Evaluate side-chains 159 residues out of total 3520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 2.743 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 334 optimal weight: 7.9990 chunk 300 optimal weight: 9.9990 chunk 166 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 202 optimal weight: 6.9990 chunk 160 optimal weight: 9.9990 chunk 310 optimal weight: 40.0000 chunk 120 optimal weight: 9.9990 chunk 188 optimal weight: 2.9990 chunk 231 optimal weight: 10.0000 chunk 359 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: