Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 16 23:55:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh5_14724/08_2023/7zh5_14724.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh5_14724/08_2023/7zh5_14724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh5_14724/08_2023/7zh5_14724.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh5_14724/08_2023/7zh5_14724.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh5_14724/08_2023/7zh5_14724.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh5_14724/08_2023/7zh5_14724.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 13796 2.51 5 N 3586 2.21 5 O 4096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 268": "OE1" <-> "OE2" Residue "A GLU 730": "OE1" <-> "OE2" Residue "B GLU 972": "OE1" <-> "OE2" Residue "B GLU 1054": "OE1" <-> "OE2" Residue "C GLU 569": "OE1" <-> "OE2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 21592 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 904, 6920 Classifications: {'peptide': 904} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 40, 'TRANS': 863} Chain breaks: 15 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 82 Chain: "B" Number of atoms: 7018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 926, 7018 Classifications: {'peptide': 926} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 45, 'TRANS': 880} Chain breaks: 8 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 9, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 111 Chain: "C" Number of atoms: 7332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 962, 7332 Classifications: {'peptide': 962} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 41, 'TRANS': 920} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 227 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 104 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 11.00, per 1000 atoms: 0.51 Number of scatterers: 21592 At special positions: 0 Unit cell: (134.4, 149.1, 178.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 4096 8.00 N 3586 7.00 C 13796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.04 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.04 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.04 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.03 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.04 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.05 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.04 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.03 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.04 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.03 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 65 " " NAG A1302 " - " ASN A 158 " " NAG A1303 " - " ASN A 227 " " NAG A1304 " - " ASN A 269 " " NAG A1305 " - " ASN A 691 " " NAG A1306 " - " ASN A 699 " " NAG A1307 " - " ASN A 783 " " NAG A1308 " - " ASN A1056 " " NAG A1309 " - " ASN A1080 " " NAG B1301 " - " ASN B 318 " " NAG B1302 " - " ASN B 602 " " NAG B1303 " - " ASN B 691 " " NAG B1304 " - " ASN B 699 " " NAG B1305 " - " ASN B 783 " " NAG B1306 " - " ASN B1056 " " NAG B1307 " - " ASN B1080 " " NAG C1301 " - " ASN C 227 " " NAG C1302 " - " ASN C 269 " " NAG C1303 " - " ASN C 602 " " NAG C1304 " - " ASN C 691 " " NAG C1305 " - " ASN C 699 " " NAG C1306 " - " ASN C 783 " " NAG C1307 " - " ASN C1056 " Time building additional restraints: 7.86 Conformation dependent library (CDL) restraints added in 3.2 seconds 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5234 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 46 sheets defined 23.4% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 370 through 377 removed outlier: 4.662A pdb=" N ASN A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP A 376 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 377 " --> pdb=" O LEU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 397 removed outlier: 3.539A pdb=" N VAL A 394 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ARG A 395 " --> pdb=" O ASP A 392 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A 397 " --> pdb=" O VAL A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 613 removed outlier: 3.526A pdb=" N HIS A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 724 Processing helix chain 'A' and resid 729 through 736 removed outlier: 3.800A pdb=" N LEU A 734 " --> pdb=" O GLU A 730 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 765 removed outlier: 3.836A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 758 " --> pdb=" O ALA A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 804 removed outlier: 3.610A pdb=" N LEU A 804 " --> pdb=" O ILE A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 865 removed outlier: 3.633A pdb=" N ALA A 854 " --> pdb=" O ASP A 850 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR A 856 " --> pdb=" O ILE A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 891 removed outlier: 3.505A pdb=" N ALA A 885 " --> pdb=" O ALA A 881 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE A 891 " --> pdb=" O ARG A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 901 Processing helix chain 'A' and resid 901 through 922 Processing helix chain 'A' and resid 927 through 947 removed outlier: 3.516A pdb=" N VAL A 934 " --> pdb=" O LEU A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 970 through 1014 removed outlier: 4.079A pdb=" N GLN A 974 " --> pdb=" O GLU A 970 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A1003 " --> pdb=" O GLU A 999 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A1012 " --> pdb=" O ALA A1008 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 353 through 358 Processing helix chain 'B' and resid 370 through 377 removed outlier: 4.732A pdb=" N ASN B 375 " --> pdb=" O THR B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 397 Processing helix chain 'B' and resid 403 through 409 Processing helix chain 'B' and resid 604 through 612 Processing helix chain 'B' and resid 719 through 725 removed outlier: 3.600A pdb=" N ILE B 724 " --> pdb=" O CYS B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 737 removed outlier: 3.580A pdb=" N ALA B 732 " --> pdb=" O SER B 728 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN B 737 " --> pdb=" O ASN B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 765 removed outlier: 3.876A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 808 Processing helix chain 'B' and resid 848 through 865 Processing helix chain 'B' and resid 880 through 889 removed outlier: 4.234A pdb=" N MET B 884 " --> pdb=" O PHE B 880 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA B 885 " --> pdb=" O ALA B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 901 removed outlier: 3.644A pdb=" N ASN B 901 " --> pdb=" O VAL B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 922 Processing helix chain 'B' and resid 927 through 947 Processing helix chain 'B' and resid 948 through 950 No H-bonds generated for 'chain 'B' and resid 948 through 950' Processing helix chain 'B' and resid 971 through 1014 removed outlier: 3.667A pdb=" N ASP B 976 " --> pdb=" O GLU B 972 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B1006 " --> pdb=" O ALA B1002 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 390 through 394 removed outlier: 3.767A pdb=" N VAL C 394 " --> pdb=" O GLY C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 409 removed outlier: 3.781A pdb=" N TYR C 408 " --> pdb=" O ILE C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 610 removed outlier: 3.668A pdb=" N ILE C 610 " --> pdb=" O VAL C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 724 removed outlier: 3.602A pdb=" N ILE C 724 " --> pdb=" O CYS C 720 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 737 removed outlier: 3.586A pdb=" N ASN C 733 " --> pdb=" O THR C 729 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU C 734 " --> pdb=" O GLU C 730 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN C 737 " --> pdb=" O ASN C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 765 removed outlier: 3.630A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 808 removed outlier: 3.660A pdb=" N VAL C 808 " --> pdb=" O LEU C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 865 Processing helix chain 'C' and resid 880 through 890 removed outlier: 3.665A pdb=" N MET C 884 " --> pdb=" O PHE C 880 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN C 889 " --> pdb=" O ALA C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 901 Processing helix chain 'C' and resid 901 through 923 removed outlier: 3.683A pdb=" N THR C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 947 removed outlier: 3.629A pdb=" N VAL C 933 " --> pdb=" O LYS C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 968 through 1014 removed outlier: 3.681A pdb=" N GLN C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER C1003 " --> pdb=" O GLU C 999 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 removed outlier: 3.761A pdb=" N SER A 64 " --> pdb=" O SER A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 41 removed outlier: 7.003A pdb=" N VAL A 40 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR A 215 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N TYR A 200 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 59 removed outlier: 3.867A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA5, first strand: chain 'A' and resid 124 through 127 removed outlier: 4.360A pdb=" N PHE A 161 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 298 through 306 removed outlier: 4.302A pdb=" N VAL A 581 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ASN A 304 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLY A 579 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 312 through 314 removed outlier: 4.053A pdb=" N VAL A 537 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER A 568 " --> pdb=" O ASP A 564 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 343 through 345 Processing sheet with id=AA9, first strand: chain 'A' and resid 551 through 552 removed outlier: 7.234A pdb=" N PHE A 551 " --> pdb=" O PHE C 47 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 640 through 646 removed outlier: 5.290A pdb=" N THR A 678 " --> pdb=" O VAL A 642 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N THR A 644 " --> pdb=" O THR A 678 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 694 through 710 removed outlier: 6.955A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 716 through 718 Processing sheet with id=AB4, first strand: chain 'A' and resid 769 through 771 Processing sheet with id=AB5, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AB6, first strand: chain 'A' and resid 1063 through 1064 Processing sheet with id=AB7, first strand: chain 'A' and resid 1076 through 1078 Processing sheet with id=AB8, first strand: chain 'B' and resid 33 through 35 removed outlier: 3.757A pdb=" N SER B 35 " --> pdb=" O SER B 64 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER B 64 " --> pdb=" O SER B 35 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 46 through 47 removed outlier: 6.543A pdb=" N GLY C 552 " --> pdb=" O ASP C 560 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL C 562 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR C 539 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE C 529 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY C 534 " --> pdb=" O PHE C 527 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN C 526 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG C 315 " --> pdb=" O ASN C 528 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 52 through 59 removed outlier: 3.993A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 81 through 82 removed outlier: 3.518A pdb=" N ILE B 81 " --> pdb=" O PHE B 231 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 87 through 91 Processing sheet with id=AC4, first strand: chain 'B' and resid 298 through 306 removed outlier: 4.605A pdb=" N VAL B 581 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASN B 304 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY B 579 " --> pdb=" O ASN B 304 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLY B 580 " --> pdb=" O GLN B 599 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.659A pdb=" N GLU B 341 " --> pdb=" O SER B 386 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 525 through 527 Processing sheet with id=AC7, first strand: chain 'B' and resid 562 through 564 removed outlier: 3.553A pdb=" N VAL B 562 " --> pdb=" O ILE B 570 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER B 568 " --> pdb=" O ASP B 564 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 640 through 641 removed outlier: 6.182A pdb=" N GLU B 640 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N THR B 678 " --> pdb=" O GLU B 640 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 694 through 697 Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 710 removed outlier: 3.506A pdb=" N MET B1032 " --> pdb=" O VAL B1047 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 715 through 718 removed outlier: 4.602A pdb=" N LYS B 715 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 769 through 771 removed outlier: 3.641A pdb=" N SER C 685 " --> pdb=" O MET B 770 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 778 through 779 Processing sheet with id=AD5, first strand: chain 'B' and resid 1102 through 1107 removed outlier: 4.642A pdb=" N ALA B1069 " --> pdb=" O SER B1105 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS B1064 " --> pdb=" O ILE B1115 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1076 through 1078 Processing sheet with id=AD7, first strand: chain 'C' and resid 32 through 35 removed outlier: 3.707A pdb=" N SER C 64 " --> pdb=" O SER C 35 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 52 through 59 removed outlier: 7.590A pdb=" N THR C 261 " --> pdb=" O ASP C 277 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ASP C 277 " --> pdb=" O THR C 261 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N MET C 263 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA C 275 " --> pdb=" O MET C 263 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LYS C 265 " --> pdb=" O THR C 273 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 217 through 222 removed outlier: 7.167A pdb=" N LYS C 198 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE C 220 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA C 90 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 123 through 128 removed outlier: 3.793A pdb=" N ARG C 126 " --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS C 128 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 298 through 306 removed outlier: 4.398A pdb=" N VAL C 581 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ASN C 304 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLY C 579 " --> pdb=" O ASN C 304 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 343 through 345 removed outlier: 3.941A pdb=" N VAL C 382 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AE5, first strand: chain 'C' and resid 640 through 641 removed outlier: 6.276A pdb=" N GLU C 640 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N THR C 678 " --> pdb=" O GLU C 640 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 693 through 695 Processing sheet with id=AE7, first strand: chain 'C' and resid 700 through 710 removed outlier: 7.189A pdb=" N GLY C1041 " --> pdb=" O ALA C1037 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ALA C1037 " --> pdb=" O GLY C1041 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL C1043 " --> pdb=" O PRO C1035 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU C1045 " --> pdb=" O SER C1033 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER C1033 " --> pdb=" O LEU C1045 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL C1047 " --> pdb=" O LEU C1031 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 716 through 718 Processing sheet with id=AE9, first strand: chain 'C' and resid 1102 through 1107 removed outlier: 4.325A pdb=" N ALA C1069 " --> pdb=" O SER C1105 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1076 through 1078 796 hydrogen bonds defined for protein. 2142 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.92 Time building geometry restraints manager: 8.63 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: 3482 1.31 - 1.44: 6112 1.44 - 1.57: 12294 1.57 - 1.71: 0 1.71 - 1.84: 156 Bond restraints: 22044 Sorted by residual: bond pdb=" C PHE C 62 " pdb=" O PHE C 62 " ideal model delta sigma weight residual 1.234 1.178 0.056 1.19e-02 7.06e+03 2.24e+01 bond pdb=" N GLN C 786 " pdb=" CA GLN C 786 " ideal model delta sigma weight residual 1.457 1.508 -0.051 1.29e-02 6.01e+03 1.55e+01 bond pdb=" N GLU C1054 " pdb=" CA GLU C1054 " ideal model delta sigma weight residual 1.457 1.506 -0.048 1.29e-02 6.01e+03 1.39e+01 bond pdb=" N GLN C1053 " pdb=" CA GLN C1053 " ideal model delta sigma weight residual 1.457 1.503 -0.045 1.29e-02 6.01e+03 1.23e+01 bond pdb=" N LYS C 793 " pdb=" CA LYS C 793 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.14e-02 7.69e+03 1.17e+01 ... (remaining 22039 not shown) Histogram of bond angle deviations from ideal: 100.00 - 106.85: 585 106.85 - 113.70: 12272 113.70 - 120.55: 8314 120.55 - 127.40: 8632 127.40 - 134.25: 176 Bond angle restraints: 29979 Sorted by residual: angle pdb=" CA PHE C 62 " pdb=" C PHE C 62 " pdb=" O PHE C 62 " ideal model delta sigma weight residual 121.19 109.63 11.56 1.10e+00 8.26e-01 1.10e+02 angle pdb=" O PHE C 62 " pdb=" C PHE C 62 " pdb=" N TYR C 63 " ideal model delta sigma weight residual 122.87 129.41 -6.54 1.23e+00 6.61e-01 2.82e+01 angle pdb=" N GLN C 786 " pdb=" CA GLN C 786 " pdb=" CB GLN C 786 " ideal model delta sigma weight residual 110.49 119.37 -8.88 1.69e+00 3.50e-01 2.76e+01 angle pdb=" N VAL C1110 " pdb=" CA VAL C1110 " pdb=" C VAL C1110 " ideal model delta sigma weight residual 106.21 111.57 -5.36 1.07e+00 8.73e-01 2.51e+01 angle pdb=" C GLN C1053 " pdb=" N GLU C1054 " pdb=" CA GLU C1054 " ideal model delta sigma weight residual 121.54 131.03 -9.49 1.91e+00 2.74e-01 2.47e+01 ... (remaining 29974 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 11628 17.85 - 35.71: 1057 35.71 - 53.56: 177 53.56 - 71.42: 32 71.42 - 89.27: 27 Dihedral angle restraints: 12921 sinusoidal: 4815 harmonic: 8106 Sorted by residual: dihedral pdb=" CB CYS C 725 " pdb=" SG CYS C 725 " pdb=" SG CYS C 731 " pdb=" CB CYS C 731 " ideal model delta sinusoidal sigma weight residual -86.00 -156.89 70.89 1 1.00e+01 1.00e-02 6.46e+01 dihedral pdb=" CB CYS A 725 " pdb=" SG CYS A 725 " pdb=" SG CYS A 731 " pdb=" CB CYS A 731 " ideal model delta sinusoidal sigma weight residual -86.00 -149.61 63.61 1 1.00e+01 1.00e-02 5.33e+01 dihedral pdb=" CB CYS B 524 " pdb=" SG CYS B 524 " pdb=" SG CYS B 576 " pdb=" CB CYS B 576 " ideal model delta sinusoidal sigma weight residual -86.00 -26.48 -59.52 1 1.00e+01 1.00e-02 4.73e+01 ... (remaining 12918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 3193 0.083 - 0.166: 330 0.166 - 0.248: 3 0.248 - 0.331: 4 0.331 - 0.414: 1 Chirality restraints: 3531 Sorted by residual: chirality pdb=" C1 NAG C1306 " pdb=" ND2 ASN C 783 " pdb=" C2 NAG C1306 " pdb=" O5 NAG C1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.29e+00 chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 691 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 158 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 3528 not shown) Planarity restraints: 3850 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 62 " -0.017 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C PHE C 62 " 0.065 2.00e-02 2.50e+03 pdb=" O PHE C 62 " -0.025 2.00e-02 2.50e+03 pdb=" N TYR C 63 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C1052 " -0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C SER C1052 " 0.059 2.00e-02 2.50e+03 pdb=" O SER C1052 " -0.022 2.00e-02 2.50e+03 pdb=" N GLN C1053 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 786 " 0.016 2.00e-02 2.50e+03 3.35e-02 1.13e+01 pdb=" C GLN C 786 " -0.058 2.00e-02 2.50e+03 pdb=" O GLN C 786 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE C 787 " 0.020 2.00e-02 2.50e+03 ... (remaining 3847 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 166 2.59 - 3.17: 17652 3.17 - 3.75: 28795 3.75 - 4.32: 41876 4.32 - 4.90: 71268 Nonbonded interactions: 159757 Sorted by model distance: nonbonded pdb=" O3 NAG C1306 " pdb=" O7 NAG C1306 " model vdw 2.018 2.440 nonbonded pdb=" O3 NAG B1307 " pdb=" O7 NAG B1307 " model vdw 2.061 2.440 nonbonded pdb=" O3 NAG A1307 " pdb=" O7 NAG A1307 " model vdw 2.062 2.440 nonbonded pdb=" O LEU B 959 " pdb=" OD1 ASN B 960 " model vdw 2.184 3.040 nonbonded pdb=" O GLY A 587 " pdb=" OG1 THR A 588 " model vdw 2.197 2.440 ... (remaining 159752 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 32 through 43 or (resid 44 through 45 and (name N or name \ CA or name C or name O or name CB )) or resid 46 through 49 or (resid 50 and (na \ me N or name CA or name C or name O or name CB )) or resid 51 through 70 or (res \ id 81 and (name N or name CA or name C or name O or name CB )) or resid 82 throu \ gh 83 or (resid 84 through 85 and (name N or name CA or name C or name O or name \ CB )) or resid 86 through 91 or (resid 92 and (name N or name CA or name C or n \ ame O or name CB )) or resid 113 or resid 115 or resid 121 or (resid 122 and (na \ me N or name CA or name C or name O or name CB )) or resid 123 through 125 or (r \ esid 126 through 127 and (name N or name CA or name C or name O or name CB )) or \ resid 128 through 131 or resid 193 or resid 196 or resid 198 or resid 209 or (r \ esid 210 through 211 and (name N or name CA or name C or name O or name CB )) or \ resid 212 through 223 or (resid 224 and (name N or name CA or name C or name O \ or name CB )) or resid 225 through 228 or (resid 229 and (name N or name CA or n \ ame C or name O or name CB )) or resid 230 through 231 or (resid 232 through 233 \ and (name N or name CA or name C or name O or name CB )) or resid 234 or (resid \ 235 through 251 and (name N or name CA or name C or name O or name CB )) or res \ id 252 through 317 or resid 321 or resid 325 or (resid 328 and (name N or name C \ A or name C or name O or name CB )) or resid 342 through 347 or (resid 348 and ( \ name N or name CA or name C or name O or name CB )) or resid 349 through 366 or \ (resid 367 and (name N or name CA or name C or name O or name CB )) or resid 368 \ through 369 or (resid 370 through 371 and (name N or name CA or name C or name \ O or name CB )) or resid 372 through 379 or (resid 380 through 381 and (name N o \ r name CA or name C or name O or name CB )) or resid 382 through 384 or (resid 3 \ 85 and (name N or name CA or name C or name O or name CB )) or resid 386 through \ 394 or (resid 395 and (name N or name CA or name C or name O or name CB )) or r \ esid 396 through 425 or (resid 426 through 427 and (name N or name CA or name C \ or name O or name CB )) or resid 439 through 441 or (resid 442 and (name N or na \ me CA or name C or name O or name CB )) or resid 443 or (resid 444 through 445 a \ nd (name N or name CA or name C or name O or name CB )) or resid 446 through 453 \ or resid 479 or resid 495 through 502 or (resid 503 through 506 and (name N or \ name CA or name C or name O or name CB )) or resid 507 through 511 or resid 517 \ through 549 or (resid 550 and (name N or name CA or name C or name O or name CB \ )) or resid 551 through 559 or (resid 560 and (name N or name CA or name C or na \ me O or name CB )) or resid 561 through 563 or (resid 564 and (name N or name CA \ or name C or name O or name CB )) or resid 565 or (resid 566 through 567 and (n \ ame N or name CA or name C or name O or name CB )) or resid 568 through 612 or ( \ resid 613 and (name N or name CA or name C or name O or name CB )) or resid 614 \ through 615 or (resid 616 and (name N or name CA or name C or name O or name CB \ )) or resid 617 through 630 or (resid 631 through 633 and (name N or name CA or \ name C or name O or name CB )) or resid 634 through 639 or (resid 640 and (name \ N or name CA or name C or name O or name CB )) or resid 641 through 642 or (resi \ d 643 and (name N or name CA or name C or name O or name CB )) or resid 644 thro \ ugh 662 or (resid 673 and (name N or name CA or name C or name O or name CB )) o \ r resid 674 through 767 or (resid 768 and (name N or name CA or name C or name O \ or name CB )) or resid 769 through 774 or (resid 775 and (name N or name CA or \ name C or name O or name CB )) or resid 776 through 792 or (resid 793 and (name \ N or name CA or name C or name O or name CB )) or resid 794 or (resid 795 and (n \ ame N or name CA or name C or name O or name CB )) or resid 796 through 811 or r \ esid 832 through 867 or (resid 868 and (name N or name CA or name C or name O or \ name CB )) or resid 869 through 922 or (resid 923 through 924 and (name N or na \ me CA or name C or name O or name CB )) or resid 925 through 964 or (resid 965 t \ hrough 968 and (name N or name CA or name C or name O or name CB )) or resid 969 \ or (resid 970 through 971 and (name N or name CA or name C or name O or name CB \ )) or resid 972 through 1065 or (resid 1066 and (name N or name CA or name C or \ name O or name CB )) or resid 1067 through 1073 or (resid 1074 and (name N or n \ ame CA or name C or name O or name CB )) or resid 1075 through 1104 or (resid 11 \ 05 and (name N or name CA or name C or name O or name CB )) or resid 1106 or (re \ sid 1107 and (name N or name CA or name C or name O or name CB )) or resid 1108 \ or (resid 1109 and (name N or name CA or name C or name O or name CB )) or resid \ 1110 through 1115 or (resid 1116 through 1119 and (name N or name CA or name C \ or name O or name CB )) or resid 1301 through 1307)) selection = (chain 'B' and (resid 32 through 43 or (resid 44 through 45 and (name N or name \ CA or name C or name O or name CB )) or resid 46 through 49 or (resid 50 and (na \ me N or name CA or name C or name O or name CB )) or resid 51 through 70 or resi \ d 81 through 83 or (resid 84 through 85 and (name N or name CA or name C or name \ O or name CB )) or resid 86 through 92 or resid 105 or resid 117 or resid 121 o \ r (resid 122 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 23 through 131 or resid 138 or resid 140 or resid 142 or resid 209 or (resid 210 \ through 211 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 12 through 228 or (resid 229 and (name N or name CA or name C or name O or name \ CB )) or resid 230 through 231 or (resid 232 through 233 and (name N or name CA \ or name C or name O or name CB )) or resid 234 or (resid 235 and (name N or name \ CA or name C or name O or name CB )) or resid 251 through 317 or resid 321 or r \ esid 325 or resid 328 or resid 342 through 347 or (resid 348 and (name N or name \ CA or name C or name O or name CB )) or resid 349 through 350 or (resid 351 and \ (name N or name CA or name C or name O or name CB )) or resid 352 or resid 366 \ or (resid 367 and (name N or name CA or name C or name O or name CB )) or resid \ 368 through 369 or (resid 370 through 371 and (name N or name CA or name C or na \ me O or name CB )) or resid 372 through 375 or (resid 376 and (name N or name CA \ or name C or name O or name CB )) or resid 377 through 379 or (resid 380 throug \ h 381 and (name N or name CA or name C or name O or name CB )) or resid 382 thro \ ugh 396 or (resid 397 through 398 and (name N or name CA or name C or name O or \ name CB )) or resid 399 through 400 or resid 412 through 414 or (resid 415 throu \ gh 416 and (name N or name CA or name C or name O or name CB )) or resid 417 thr \ ough 441 or (resid 442 and (name N or name CA or name C or name O or name CB )) \ or resid 443 through 453 or resid 457 or resid 495 through 511 or resid 517 thro \ ugh 542 or (resid 543 and (name N or name CA or name C or name O or name CB )) o \ r resid 544 through 563 or (resid 564 and (name N or name CA or name C or name O \ or name CB )) or resid 565 or (resid 566 through 567 and (name N or name CA or \ name C or name O or name CB )) or resid 568 through 592 or (resid 593 and (name \ N or name CA or name C or name O or name CB )) or resid 594 through 599 or (resi \ d 600 and (name N or name CA or name C or name O or name CB )) or resid 601 or ( \ resid 602 and (name N or name CA or name C or name O or name CB )) or resid 603 \ through 629 or (resid 630 through 633 and (name N or name CA or name C or name O \ or name CB )) or resid 634 through 646 or (resid 647 and (name N or name CA or \ name C or name O or name CB )) or resid 648 through 767 or (resid 768 and (name \ N or name CA or name C or name O or name CB )) or resid 769 through 792 or (resi \ d 793 and (name N or name CA or name C or name O or name CB )) or resid 794 or ( \ resid 795 and (name N or name CA or name C or name O or name CB )) or resid 796 \ through 867 or (resid 868 and (name N or name CA or name C or name O or name CB \ )) or resid 869 through 917 or (resid 918 and (name N or name CA or name C or na \ me O or name CB )) or resid 919 through 921 or (resid 922 through 924 and (name \ N or name CA or name C or name O or name CB )) or resid 925 through 1065 or (res \ id 1066 and (name N or name CA or name C or name O or name CB )) or resid 1067 t \ hrough 1073 or (resid 1074 and (name N or name CA or name C or name O or name CB \ )) or resid 1075 through 1104 or (resid 1105 and (name N or name CA or name C o \ r name O or name CB )) or resid 1106 through 1113 or (resid 1114 and (name N or \ name CA or name C or name O or name CB )) or resid 1115 or (resid 1116 through 1 \ 119 and (name N or name CA or name C or name O or name CB )) or resid 1301 throu \ gh 1307)) selection = (chain 'C' and (resid 32 through 70 or (resid 81 and (name N or name CA or name \ C or name O or name CB )) or resid 82 through 91 or (resid 92 and (name N or nam \ e CA or name C or name O or name CB )) or resid 113 or resid 115 or resid 121 th \ rough 125 or (resid 126 through 127 and (name N or name CA or name C or name O o \ r name CB )) or resid 128 through 130 or (resid 131 and (name N or name CA or na \ me C or name O or name CB )) or resid 193 or resid 196 or resid 198 or resid 209 \ through 210 or (resid 211 and (name N or name CA or name C or name O or name CB \ )) or resid 212 through 235 or resid 251 through 317 or resid 330 or resid 334 \ or (resid 337 and (name N or name CA or name C or name O or name CB )) or resid \ 342 through 352 or resid 366 through 384 or (resid 385 and (name N or name CA or \ name C or name O or name CB )) or resid 386 through 394 or (resid 395 and (name \ N or name CA or name C or name O or name CB )) or resid 396 through 400 or resi \ d 412 through 414 or (resid 415 through 416 and (name N or name CA or name C or \ name O or name CB )) or resid 417 through 425 or (resid 426 through 427 and (nam \ e N or name CA or name C or name O or name CB )) or resid 439 through 443 or (re \ sid 444 through 445 and (name N or name CA or name C or name O or name CB )) or \ resid 446 through 453 or resid 479 or resid 495 through 502 or (resid 503 throug \ h 506 and (name N or name CA or name C or name O or name CB )) or resid 507 thro \ ugh 542 or (resid 543 and (name N or name CA or name C or name O or name CB )) o \ r resid 544 through 549 or (resid 550 and (name N or name CA or name C or name O \ or name CB )) or resid 551 through 553 or (resid 554 and (name N or name CA or \ name C or name O or name CB )) or resid 555 through 559 or (resid 560 and (name \ N or name CA or name C or name O or name CB )) or resid 561 through 572 or (resi \ d 573 through 574 and (name N or name CA or name C or name O or name CB )) or re \ sid 575 through 592 or (resid 593 and (name N or name CA or name C or name O or \ name CB )) or resid 594 through 601 or (resid 602 and (name N or name CA or name \ C or name O or name CB )) or resid 603 through 612 or (resid 613 and (name N or \ name CA or name C or name O or name CB )) or resid 614 through 615 or (resid 61 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 617 through \ 629 or (resid 630 through 633 and (name N or name CA or name C or name O or name \ CB )) or resid 634 through 639 or (resid 640 and (name N or name CA or name C o \ r name O or name CB )) or resid 641 through 642 or (resid 643 and (name N or nam \ e CA or name C or name O or name CB )) or resid 644 through 660 or (resid 661 th \ rough 673 and (name N or name CA or name C or name O or name CB )) or resid 674 \ through 774 or (resid 775 and (name N or name CA or name C or name O or name CB \ )) or resid 776 through 917 or (resid 918 and (name N or name CA or name C or na \ me O or name CB )) or resid 919 through 921 or (resid 922 through 924 and (name \ N or name CA or name C or name O or name CB )) or resid 925 through 964 or (resi \ d 965 through 968 and (name N or name CA or name C or name O or name CB )) or re \ sid 969 or (resid 970 through 971 and (name N or name CA or name C or name O or \ name CB )) or resid 972 through 1081 or (resid 1082 and (name N or name CA or na \ me C or name O or name CB )) or resid 1083 through 1106 or (resid 1107 and (name \ N or name CA or name C or name O or name CB )) or resid 1108 or (resid 1109 and \ (name N or name CA or name C or name O or name CB )) or resid 1110 through 1113 \ or (resid 1114 and (name N or name CA or name C or name O or name CB )) or resi \ d 1115 through 1118 or (resid 1119 and (name N or name CA or name C or name O or \ name CB )) or resid 1301 through 1307)) } 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: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.420 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 55.900 Find NCS groups from input model: 1.830 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: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 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 : 0.004 0.056 22044 Z= 0.244 Angle : 0.597 11.561 29979 Z= 0.342 Chirality : 0.046 0.414 3531 Planarity : 0.004 0.072 3827 Dihedral : 14.134 89.270 7591 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.85 % Favored : 91.04 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.15), residues: 2724 helix: -0.72 (0.21), residues: 605 sheet: -0.50 (0.22), residues: 567 loop : -2.58 (0.14), residues: 1552 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 190 time to evaluate : 2.540 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 194 average time/residue: 0.3318 time to fit residues: 101.7539 Evaluate side-chains 159 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 156 time to evaluate : 2.492 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2324 time to fit residues: 4.6358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 234 optimal weight: 4.9990 chunk 210 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 142 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 217 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 162 optimal weight: 6.9990 chunk 252 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 GLN A 937 ASN B 692 ASN B 744 GLN C 661 HIS C1053 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 22044 Z= 0.211 Angle : 0.577 9.668 29979 Z= 0.307 Chirality : 0.047 0.447 3531 Planarity : 0.004 0.056 3827 Dihedral : 4.640 22.122 2967 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.22 % Favored : 91.67 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.16), residues: 2724 helix: 0.91 (0.22), residues: 622 sheet: -0.21 (0.22), residues: 546 loop : -2.43 (0.14), residues: 1556 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 172 time to evaluate : 2.449 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 14 residues processed: 183 average time/residue: 0.3183 time to fit residues: 94.1492 Evaluate side-chains 169 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 155 time to evaluate : 2.471 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1913 time to fit residues: 8.5432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 140 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 210 optimal weight: 0.5980 chunk 171 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 252 optimal weight: 0.0470 chunk 273 optimal weight: 10.0000 chunk 225 optimal weight: 20.0000 chunk 250 optimal weight: 0.7980 chunk 86 optimal weight: 9.9990 chunk 202 optimal weight: 6.9990 overall best weight: 1.6882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN A 915 GLN B 692 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 22044 Z= 0.185 Angle : 0.538 9.577 29979 Z= 0.284 Chirality : 0.046 0.436 3531 Planarity : 0.004 0.057 3827 Dihedral : 4.476 21.073 2967 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.89 % Favored : 92.00 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.16), residues: 2724 helix: 1.44 (0.22), residues: 623 sheet: -0.15 (0.22), residues: 551 loop : -2.35 (0.14), residues: 1550 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 168 time to evaluate : 2.561 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 182 average time/residue: 0.3178 time to fit residues: 92.7296 Evaluate side-chains 163 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 156 time to evaluate : 2.465 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1852 time to fit residues: 5.9009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 249 optimal weight: 0.7980 chunk 190 optimal weight: 20.0000 chunk 131 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 169 optimal weight: 4.9990 chunk 253 optimal weight: 10.0000 chunk 268 optimal weight: 0.0470 chunk 132 optimal weight: 7.9990 chunk 240 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 overall best weight: 1.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 692 ASN B 883 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 22044 Z= 0.201 Angle : 0.550 9.571 29979 Z= 0.289 Chirality : 0.046 0.451 3531 Planarity : 0.004 0.060 3827 Dihedral : 4.542 21.318 2967 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.48 % Favored : 91.41 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.16), residues: 2724 helix: 1.57 (0.22), residues: 623 sheet: -0.10 (0.22), residues: 552 loop : -2.35 (0.14), residues: 1549 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 160 time to evaluate : 2.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 170 average time/residue: 0.3147 time to fit residues: 87.1360 Evaluate side-chains 164 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 153 time to evaluate : 2.390 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1990 time to fit residues: 7.5036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 223 optimal weight: 7.9990 chunk 152 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 200 optimal weight: 1.9990 chunk 110 optimal weight: 8.9990 chunk 229 optimal weight: 8.9990 chunk 185 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 137 optimal weight: 1.9990 chunk 241 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN B 692 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 22044 Z= 0.286 Angle : 0.612 9.685 29979 Z= 0.321 Chirality : 0.049 0.499 3531 Planarity : 0.005 0.065 3827 Dihedral : 4.921 22.648 2967 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.96 % Favored : 90.93 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.15), residues: 2724 helix: 1.40 (0.22), residues: 621 sheet: -0.28 (0.23), residues: 472 loop : -2.37 (0.14), residues: 1631 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 163 time to evaluate : 2.348 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 16 residues processed: 191 average time/residue: 0.3155 time to fit residues: 98.1253 Evaluate side-chains 169 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 153 time to evaluate : 2.512 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1890 time to fit residues: 9.1788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 90 optimal weight: 2.9990 chunk 241 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 268 optimal weight: 0.0870 chunk 223 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 692 ASN B 917 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 22044 Z= 0.249 Angle : 0.582 9.601 29979 Z= 0.306 Chirality : 0.047 0.483 3531 Planarity : 0.004 0.062 3827 Dihedral : 4.812 22.318 2967 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.66 % Favored : 91.26 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.15), residues: 2724 helix: 1.45 (0.22), residues: 619 sheet: -0.26 (0.23), residues: 484 loop : -2.37 (0.14), residues: 1621 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 160 time to evaluate : 2.520 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 20 residues processed: 179 average time/residue: 0.3189 time to fit residues: 92.6766 Evaluate side-chains 174 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 154 time to evaluate : 2.460 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2038 time to fit residues: 11.3255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 259 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 153 optimal weight: 3.9990 chunk 196 optimal weight: 30.0000 chunk 152 optimal weight: 3.9990 chunk 226 optimal weight: 10.0000 chunk 150 optimal weight: 0.0470 chunk 267 optimal weight: 2.9990 chunk 167 optimal weight: 9.9990 chunk 163 optimal weight: 0.8980 chunk 123 optimal weight: 6.9990 overall best weight: 2.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 692 ASN B 917 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 22044 Z= 0.216 Angle : 0.562 9.586 29979 Z= 0.295 Chirality : 0.047 0.471 3531 Planarity : 0.004 0.061 3827 Dihedral : 4.685 21.915 2967 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.74 % Favored : 91.15 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.16), residues: 2724 helix: 1.55 (0.22), residues: 619 sheet: -0.22 (0.23), residues: 484 loop : -2.36 (0.14), residues: 1621 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 161 time to evaluate : 2.475 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 173 average time/residue: 0.3343 time to fit residues: 92.5817 Evaluate side-chains 163 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 155 time to evaluate : 2.671 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1973 time to fit residues: 6.5064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 165 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 chunk 170 optimal weight: 5.9990 chunk 182 optimal weight: 0.0050 chunk 132 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 210 optimal weight: 0.0770 overall best weight: 0.7154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 614 GLN B 692 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 22044 Z= 0.130 Angle : 0.490 9.428 29979 Z= 0.257 Chirality : 0.045 0.418 3531 Planarity : 0.004 0.056 3827 Dihedral : 4.138 21.023 2967 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.20 % Favored : 92.69 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.16), residues: 2724 helix: 1.96 (0.22), residues: 619 sheet: 0.02 (0.24), residues: 476 loop : -2.23 (0.14), residues: 1629 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 164 time to evaluate : 2.445 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 176 average time/residue: 0.3390 time to fit residues: 95.1672 Evaluate side-chains 158 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 152 time to evaluate : 2.618 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2250 time to fit residues: 6.0433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 243 optimal weight: 3.9990 chunk 256 optimal weight: 7.9990 chunk 234 optimal weight: 0.9990 chunk 249 optimal weight: 0.0970 chunk 150 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 196 optimal weight: 20.0000 chunk 76 optimal weight: 4.9990 chunk 225 optimal weight: 8.9990 chunk 236 optimal weight: 6.9990 chunk 248 optimal weight: 1.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 22044 Z= 0.204 Angle : 0.547 9.555 29979 Z= 0.286 Chirality : 0.046 0.452 3531 Planarity : 0.004 0.057 3827 Dihedral : 4.443 21.557 2967 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.30 % Favored : 91.63 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.16), residues: 2724 helix: 1.80 (0.22), residues: 619 sheet: -0.08 (0.24), residues: 468 loop : -2.21 (0.14), residues: 1637 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 156 time to evaluate : 2.237 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 162 average time/residue: 0.3315 time to fit residues: 86.9630 Evaluate side-chains 155 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 150 time to evaluate : 2.482 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1871 time to fit residues: 5.1238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 163 optimal weight: 7.9990 chunk 264 optimal weight: 4.9990 chunk 161 optimal weight: 7.9990 chunk 125 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 276 optimal weight: 2.9990 chunk 254 optimal weight: 5.9990 chunk 220 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 170 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 GLN B 692 ASN ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1080 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 22044 Z= 0.273 Angle : 0.601 9.612 29979 Z= 0.314 Chirality : 0.048 0.488 3531 Planarity : 0.004 0.060 3827 Dihedral : 4.806 22.027 2967 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.92 % Favored : 91.01 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.16), residues: 2724 helix: 1.58 (0.22), residues: 617 sheet: -0.14 (0.23), residues: 485 loop : -2.32 (0.14), residues: 1622 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 153 time to evaluate : 2.438 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 155 average time/residue: 0.3194 time to fit residues: 80.9974 Evaluate side-chains 154 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 2.515 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2370 time to fit residues: 3.8654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 175 optimal weight: 3.9990 chunk 234 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 203 optimal weight: 0.0050 chunk 32 optimal weight: 0.8980 chunk 61 optimal weight: 0.3980 chunk 220 optimal weight: 9.9990 chunk 92 optimal weight: 0.5980 chunk 226 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 692 ASN ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1080 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.171662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.152762 restraints weight = 28422.341| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 1.09 r_work: 0.3604 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 22044 Z= 0.129 Angle : 0.491 9.426 29979 Z= 0.257 Chirality : 0.045 0.400 3531 Planarity : 0.004 0.055 3827 Dihedral : 4.100 21.172 2967 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.16 % Favored : 92.77 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.16), residues: 2724 helix: 2.04 (0.22), residues: 616 sheet: 0.18 (0.23), residues: 513 loop : -2.21 (0.14), residues: 1595 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3581.24 seconds wall clock time: 66 minutes 18.44 seconds (3978.44 seconds total)