Starting phenix.real_space_refine (version: dev) on Thu Apr 7 07:01:17 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bbh_12130/04_2022/7bbh_12130.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bbh_12130/04_2022/7bbh_12130.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bbh_12130/04_2022/7bbh_12130.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bbh_12130/04_2022/7bbh_12130.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bbh_12130/04_2022/7bbh_12130.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bbh_12130/04_2022/7bbh_12130.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.003 sd= 0.083 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 25827 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 8287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8287 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 49, 'TRANS': 1013} Chain breaks: 9 Chain: "B" Number of atoms: 8287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8287 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 49, 'TRANS': 1013} Chain breaks: 9 Chain: "C" Number of atoms: 8287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8287 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 49, 'TRANS': 1013} Chain breaks: 9 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 14.66, per 1000 atoms: 0.57 Number of scatterers: 25827 At special positions: 0 Unit cell: (139.062, 130.438, 176.792, 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 120 16.00 O 5103 8.00 N 4173 7.00 C 16431 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1301 " - " ASN A 17 " " NAG A1302 " - " ASN A 30 " " NAG A1303 " - " ASN A 61 " " NAG A1304 " - " ASN A 122 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 370 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A 717 " " NAG A1310 " - " ASN A1134 " " NAG A1311 " - " ASN A 616 " " NAG A1312 " - " ASN A 112 " " NAG A1313 " - " ASN A 282 " " NAG A1314 " - " ASN A 657 " " NAG A1315 " - " ASN A1074 " " NAG B1301 " - " ASN B 17 " " NAG B1302 " - " ASN B 30 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 122 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 370 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B 717 " " NAG B1310 " - " ASN B1134 " " NAG B1311 " - " ASN B 616 " " NAG B1312 " - " ASN B 112 " " NAG B1313 " - " ASN B 282 " " NAG B1314 " - " ASN B 657 " " NAG B1315 " - " ASN B1074 " " NAG C1301 " - " ASN C 17 " " NAG C1302 " - " ASN C 30 " " NAG C1303 " - " ASN C 61 " " NAG C1304 " - " ASN C 122 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 370 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C 717 " " NAG C1310 " - " ASN C1134 " " NAG C1311 " - " ASN C 616 " " NAG C1312 " - " ASN C 112 " " NAG C1313 " - " ASN C 282 " " NAG C1314 " - " ASN C 657 " " NAG C1315 " - " ASN C1074 " " NAG D 1 " - " ASN A 165 " " NAG E 1 " - " ASN A 234 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN B 165 " " NAG I 1 " - " ASN B 234 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1098 " " NAG L 1 " - " ASN C 165 " " NAG M 1 " - " ASN C 234 " " NAG N 1 " - " ASN C 801 " " NAG O 1 " - " ASN C1098 " Time building additional restraints: 10.46 Conformation dependent library (CDL) restraints added in 3.8 seconds 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5982 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 42 sheets defined 24.8% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 369 removed outlier: 4.050A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.949A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 630 through 638 removed outlier: 3.768A pdb=" N VAL A 635 " --> pdb=" O PRO A 631 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER A 637 " --> pdb=" O TRP A 633 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR A 638 " --> pdb=" O ARG A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 Processing helix chain 'A' and resid 759 through 783 removed outlier: 3.544A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.610A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.002A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY A 891 " --> pdb=" O THR A 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 891' Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.059A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.969A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.418A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 364 through 369 removed outlier: 4.050A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.948A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 630 through 638 removed outlier: 3.769A pdb=" N VAL B 635 " --> pdb=" O PRO B 631 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER B 637 " --> pdb=" O TRP B 633 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR B 638 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.544A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.609A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.002A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY B 891 " --> pdb=" O THR B 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 891' Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.060A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.969A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.419A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 369 removed outlier: 4.050A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.949A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 630 through 638 removed outlier: 3.767A pdb=" N VAL C 635 " --> pdb=" O PRO C 631 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER C 637 " --> pdb=" O TRP C 633 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR C 638 " --> pdb=" O ARG C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 Processing helix chain 'C' and resid 759 through 783 removed outlier: 3.545A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.610A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.003A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY C 891 " --> pdb=" O THR C 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 886 through 891' Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.060A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.969A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.418A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.601A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.396A pdb=" N TYR A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.862A pdb=" N LEU A 223 " --> pdb=" O TYR A 207 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.262A pdb=" N ASP A 287 " --> pdb=" O ASN A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.685A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.409A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 10.217A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.485A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASN A 132 " --> pdb=" O TYR A 163 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TYR A 163 " --> pdb=" O ASN A 132 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.887A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 356 through 358 removed outlier: 4.422A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.127A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 701 through 703 removed outlier: 7.201A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.782A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.782A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE A1095 " --> pdb=" O THR A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.526A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.602A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.396A pdb=" N TYR B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.862A pdb=" N LEU B 223 " --> pdb=" O TYR B 207 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.262A pdb=" N ASP B 287 " --> pdb=" O ASN B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.686A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.409A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.218A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.485A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN B 132 " --> pdb=" O TYR B 163 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N TYR B 163 " --> pdb=" O ASN B 132 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC2, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.886A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 356 through 358 removed outlier: 4.422A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.127A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 701 through 703 removed outlier: 7.128A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.783A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.783A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE B1095 " --> pdb=" O THR B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.526A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.601A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.396A pdb=" N TYR C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.862A pdb=" N LEU C 223 " --> pdb=" O TYR C 207 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.261A pdb=" N ASP C 287 " --> pdb=" O ASN C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.684A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 11.409A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 10.217A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.485A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASN C 132 " --> pdb=" O TYR C 163 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TYR C 163 " --> pdb=" O ASN C 132 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AD7, first strand: chain 'C' and resid 324 through 325 removed outlier: 6.886A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU C 583 " --> pdb=" O ASP C 578 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 356 through 358 removed outlier: 4.421A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.127A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.782A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.782A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE C1095 " --> pdb=" O THR C1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.526A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 1001 hydrogen bonds defined for protein. 2787 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.88 Time building geometry restraints manager: 10.91 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: 8137 1.34 - 1.47: 6639 1.47 - 1.59: 11447 1.59 - 1.71: 0 1.71 - 1.83: 150 Bond restraints: 26373 Sorted by residual: bond pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.29e-02 6.01e+03 8.04e+00 bond pdb=" N ILE B 332 " pdb=" CA ILE B 332 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.29e-02 6.01e+03 7.85e+00 bond pdb=" N ILE C 332 " pdb=" CA ILE C 332 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.29e-02 6.01e+03 7.73e+00 bond pdb=" C ALA C 271 " pdb=" N PRO C 272 " ideal model delta sigma weight residual 1.335 1.353 -0.018 8.70e-03 1.32e+04 4.38e+00 bond pdb=" C ALA A 271 " pdb=" N PRO A 272 " ideal model delta sigma weight residual 1.335 1.353 -0.018 8.70e-03 1.32e+04 4.34e+00 ... (remaining 26368 not shown) Histogram of bond angle deviations from ideal: 100.22 - 106.98: 745 106.98 - 113.74: 14865 113.74 - 120.51: 10026 120.51 - 127.27: 10071 127.27 - 134.03: 191 Bond angle restraints: 35898 Sorted by residual: angle pdb=" N PRO C1140 " pdb=" CA PRO C1140 " pdb=" C PRO C1140 " ideal model delta sigma weight residual 112.47 120.19 -7.72 2.06e+00 2.36e-01 1.41e+01 angle pdb=" N PRO B1140 " pdb=" CA PRO B1140 " pdb=" C PRO B1140 " ideal model delta sigma weight residual 112.47 120.18 -7.71 2.06e+00 2.36e-01 1.40e+01 angle pdb=" N PRO A1140 " pdb=" CA PRO A1140 " pdb=" C PRO A1140 " ideal model delta sigma weight residual 112.47 120.17 -7.70 2.06e+00 2.36e-01 1.40e+01 angle pdb=" N THR C 618 " pdb=" CA THR C 618 " pdb=" C THR C 618 " ideal model delta sigma weight residual 113.51 108.58 4.93 1.52e+00 4.33e-01 1.05e+01 angle pdb=" N THR B 618 " pdb=" CA THR B 618 " pdb=" C THR B 618 " ideal model delta sigma weight residual 113.51 108.59 4.92 1.52e+00 4.33e-01 1.05e+01 ... (remaining 35893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 14501 17.68 - 35.37: 843 35.37 - 53.05: 154 53.05 - 70.74: 42 70.74 - 88.42: 18 Dihedral angle restraints: 15558 sinusoidal: 6258 harmonic: 9300 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -122.67 36.67 1 1.00e+01 1.00e-02 1.90e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -122.65 36.65 1 1.00e+01 1.00e-02 1.90e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -122.62 36.62 1 1.00e+01 1.00e-02 1.89e+01 ... (remaining 15555 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3339 0.057 - 0.114: 846 0.114 - 0.170: 120 0.170 - 0.227: 3 0.227 - 0.284: 6 Chirality restraints: 4314 Sorted by residual: chirality pdb=" CA PRO B1140 " pdb=" N PRO B1140 " pdb=" C PRO B1140 " pdb=" CB PRO B1140 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA PRO C1140 " pdb=" N PRO C1140 " pdb=" C PRO C1140 " pdb=" CB PRO C1140 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA PRO A1140 " pdb=" N PRO A1140 " pdb=" C PRO A1140 " pdb=" CB PRO A1140 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 4311 not shown) Planarity restraints: 4590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B1139 " 0.065 5.00e-02 4.00e+02 9.84e-02 1.55e+01 pdb=" N PRO B1140 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO B1140 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO B1140 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C1139 " 0.065 5.00e-02 4.00e+02 9.83e-02 1.55e+01 pdb=" N PRO C1140 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO C1140 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO C1140 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A1139 " -0.064 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO A1140 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO A1140 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A1140 " -0.052 5.00e-02 4.00e+02 ... (remaining 4587 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 6249 2.80 - 3.32: 21591 3.32 - 3.85: 38961 3.85 - 4.37: 47162 4.37 - 4.90: 84244 Nonbonded interactions: 198207 Sorted by model distance: nonbonded pdb=" OD1 ASN C 125 " pdb=" O6 NAG C1304 " model vdw 2.270 2.440 nonbonded pdb=" OD1 ASN A 125 " pdb=" O6 NAG A1304 " model vdw 2.270 2.440 nonbonded pdb=" OD1 ASN B 125 " pdb=" O6 NAG B1304 " model vdw 2.270 2.440 nonbonded pdb=" OH TYR B 37 " pdb=" O TYR B 54 " model vdw 2.316 2.440 nonbonded pdb=" OH TYR C 37 " pdb=" O TYR C 54 " model vdw 2.316 2.440 ... (remaining 198202 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 16431 2.51 5 N 4173 2.21 5 O 5103 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 2.490 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: 15.420 Check model and map are aligned: 0.370 Convert atoms to be neutral: 0.220 Process input model: 66.780 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:13.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 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 : 0.005 0.037 26373 Z= 0.333 Angle : 0.714 9.315 35898 Z= 0.414 Chirality : 0.050 0.284 4314 Planarity : 0.006 0.098 4533 Dihedral : 12.203 88.423 9441 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.14), residues: 3129 helix: 0.46 (0.19), residues: 750 sheet: -0.01 (0.19), residues: 726 loop : -1.49 (0.13), residues: 1653 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 371 time to evaluate : 2.923 Fit side-chains outliers start: 24 outliers final: 3 residues processed: 393 average time/residue: 1.2618 time to fit residues: 578.1197 Evaluate side-chains 246 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 243 time to evaluate : 2.635 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 2 average time/residue: 0.2594 time to fit residues: 4.6533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 5.9990 chunk 241 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 249 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 151 optimal weight: 0.7980 chunk 185 optimal weight: 2.9990 chunk 288 optimal weight: 0.2980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN A 213 ASN A 360 ASN A 388 ASN A 501 ASN A 544 ASN A 804 GLN A 955 ASN A1010 GLN A1083 HIS A1119 ASN B 132 ASN B 360 ASN B 388 ASN B 501 ASN B 544 ASN B 755 GLN B 955 ASN B1083 HIS B1119 ASN C 125 ASN C 132 ASN C 360 ASN C 388 ASN C 493 GLN C 501 ASN C 544 ASN C 675 GLN C 755 GLN C 804 GLN C1010 GLN C1083 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 26373 Z= 0.219 Angle : 0.598 9.713 35898 Z= 0.331 Chirality : 0.046 0.192 4314 Planarity : 0.005 0.054 4533 Dihedral : 5.221 35.485 3837 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 1.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.14), residues: 3129 helix: 0.94 (0.19), residues: 771 sheet: 0.49 (0.19), residues: 726 loop : -1.33 (0.14), residues: 1632 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 257 time to evaluate : 2.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 24 residues processed: 287 average time/residue: 1.2990 time to fit residues: 438.0102 Evaluate side-chains 241 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 217 time to evaluate : 2.732 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 12 residues processed: 12 average time/residue: 0.8237 time to fit residues: 17.1695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 0.0470 chunk 89 optimal weight: 0.0980 chunk 240 optimal weight: 0.2980 chunk 196 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 289 optimal weight: 1.9990 chunk 312 optimal weight: 0.9990 chunk 257 optimal weight: 1.9990 chunk 286 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 232 optimal weight: 0.3980 overall best weight: 0.3478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 493 GLN A 762 GLN A 804 GLN A 955 ASN A1010 GLN B 493 GLN B 755 GLN B 804 GLN B 955 ASN C 755 GLN C 901 GLN C1010 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.064 26373 Z= 0.149 Angle : 0.509 7.626 35898 Z= 0.280 Chirality : 0.043 0.159 4314 Planarity : 0.004 0.099 4533 Dihedral : 5.024 39.767 3837 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer Outliers : 2.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.15), residues: 3129 helix: 1.49 (0.20), residues: 750 sheet: 0.74 (0.19), residues: 726 loop : -1.28 (0.14), residues: 1653 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 238 time to evaluate : 2.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 30 residues processed: 282 average time/residue: 1.2075 time to fit residues: 403.8048 Evaluate side-chains 244 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 214 time to evaluate : 2.857 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 22 residues processed: 9 average time/residue: 0.5955 time to fit residues: 11.0862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 0.0970 chunk 217 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 194 optimal weight: 0.0050 chunk 290 optimal weight: 0.3980 chunk 307 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 275 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 762 GLN A 955 ASN A1010 GLN B 213 ASN B 690 GLN B 755 GLN B 901 GLN B 955 ASN C 132 ASN C 675 GLN C 755 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 26373 Z= 0.164 Angle : 0.512 9.437 35898 Z= 0.278 Chirality : 0.043 0.155 4314 Planarity : 0.004 0.053 4533 Dihedral : 4.952 39.448 3837 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer Outliers : 2.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.15), residues: 3129 helix: 1.66 (0.20), residues: 750 sheet: 0.81 (0.19), residues: 717 loop : -1.25 (0.14), residues: 1662 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 224 time to evaluate : 2.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 38 residues processed: 274 average time/residue: 1.2080 time to fit residues: 391.1344 Evaluate side-chains 250 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 212 time to evaluate : 2.865 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 28 residues processed: 10 average time/residue: 0.7475 time to fit residues: 13.4203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 0.5980 chunk 174 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 228 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 262 optimal weight: 5.9990 chunk 212 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 chunk 275 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 ASN A 317 ASN A 955 ASN B 388 ASN B 544 ASN B 675 GLN B 690 GLN B 755 GLN B 901 GLN B 955 ASN C 544 ASN C 690 GLN C 755 GLN C 901 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.066 26373 Z= 0.394 Angle : 0.646 9.288 35898 Z= 0.350 Chirality : 0.049 0.165 4314 Planarity : 0.005 0.067 4533 Dihedral : 5.392 47.560 3837 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer Outliers : 2.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.14), residues: 3129 helix: 0.97 (0.19), residues: 774 sheet: 0.58 (0.20), residues: 702 loop : -1.45 (0.13), residues: 1653 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 228 time to evaluate : 2.821 Fit side-chains revert: symmetry clash outliers start: 74 outliers final: 46 residues processed: 287 average time/residue: 1.2092 time to fit residues: 413.2380 Evaluate side-chains 252 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 206 time to evaluate : 2.754 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 36 residues processed: 10 average time/residue: 0.7247 time to fit residues: 12.8775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 1.9990 chunk 276 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 75 optimal weight: 0.0020 chunk 307 optimal weight: 2.9990 chunk 255 optimal weight: 1.9990 chunk 142 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 overall best weight: 1.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 215 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 690 GLN B 755 GLN B 955 ASN C 755 GLN C1135 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.119 26373 Z= 0.277 Angle : 0.606 13.823 35898 Z= 0.329 Chirality : 0.046 0.184 4314 Planarity : 0.005 0.107 4533 Dihedral : 5.329 45.792 3837 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer Outliers : 2.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.14), residues: 3129 helix: 1.01 (0.19), residues: 774 sheet: 0.66 (0.20), residues: 720 loop : -1.51 (0.14), residues: 1635 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 216 time to evaluate : 3.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 53 residues processed: 275 average time/residue: 1.1317 time to fit residues: 372.6914 Evaluate side-chains 262 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 209 time to evaluate : 2.662 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 46 residues processed: 7 average time/residue: 0.4480 time to fit residues: 8.0639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 224 optimal weight: 0.7980 chunk 174 optimal weight: 1.9990 chunk 259 optimal weight: 0.9980 chunk 171 optimal weight: 0.5980 chunk 306 optimal weight: 0.7980 chunk 191 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 141 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 675 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 675 GLN B 755 GLN B 955 ASN C 675 GLN C 755 GLN C 901 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.093 26373 Z= 0.191 Angle : 0.529 9.285 35898 Z= 0.287 Chirality : 0.043 0.179 4314 Planarity : 0.004 0.097 4533 Dihedral : 5.144 43.880 3837 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.15), residues: 3129 helix: 1.38 (0.20), residues: 750 sheet: 0.78 (0.20), residues: 714 loop : -1.42 (0.14), residues: 1665 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 223 time to evaluate : 3.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 48 residues processed: 281 average time/residue: 1.1415 time to fit residues: 387.7882 Evaluate side-chains 263 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 215 time to evaluate : 2.867 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 43 residues processed: 6 average time/residue: 1.1534 time to fit residues: 12.2542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 59 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 208 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 240 optimal weight: 2.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN A 675 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 755 GLN B 955 ASN C 755 GLN C 901 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.117 26373 Z= 0.389 Angle : 0.645 10.814 35898 Z= 0.350 Chirality : 0.048 0.205 4314 Planarity : 0.005 0.119 4533 Dihedral : 5.435 45.759 3837 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer Outliers : 2.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 3129 helix: 0.88 (0.19), residues: 774 sheet: 0.64 (0.20), residues: 693 loop : -1.52 (0.14), residues: 1662 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 208 time to evaluate : 2.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 53 residues processed: 274 average time/residue: 1.0853 time to fit residues: 357.5687 Evaluate side-chains 259 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 206 time to evaluate : 3.029 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 49 residues processed: 5 average time/residue: 0.2670 time to fit residues: 6.3469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 1.9990 chunk 293 optimal weight: 0.9980 chunk 267 optimal weight: 2.9990 chunk 285 optimal weight: 0.5980 chunk 171 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 224 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 258 optimal weight: 0.9980 chunk 270 optimal weight: 4.9990 chunk 284 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 213 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 755 GLN B 787 GLN B 955 ASN C 544 ASN C 755 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.114 26373 Z= 0.229 Angle : 0.560 12.994 35898 Z= 0.304 Chirality : 0.044 0.188 4314 Planarity : 0.005 0.130 4533 Dihedral : 5.240 44.176 3837 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer Outliers : 2.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.15), residues: 3129 helix: 1.22 (0.20), residues: 750 sheet: 0.65 (0.20), residues: 708 loop : -1.47 (0.14), residues: 1671 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 212 time to evaluate : 3.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 51 residues processed: 269 average time/residue: 1.1195 time to fit residues: 362.9238 Evaluate side-chains 258 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 207 time to evaluate : 2.946 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 47 residues processed: 4 average time/residue: 1.4056 time to fit residues: 10.4070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 0.9990 chunk 302 optimal weight: 0.9990 chunk 184 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 209 optimal weight: 0.0040 chunk 316 optimal weight: 0.0570 chunk 291 optimal weight: 0.9990 chunk 252 optimal weight: 0.4980 chunk 26 optimal weight: 2.9990 chunk 194 optimal weight: 0.0040 chunk 154 optimal weight: 2.9990 overall best weight: 0.2722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 755 GLN B 787 GLN B 901 GLN B 955 ASN C 544 ASN C 675 GLN C 755 GLN C 901 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.056 26373 Z= 0.136 Angle : 0.493 10.307 35898 Z= 0.267 Chirality : 0.042 0.220 4314 Planarity : 0.004 0.065 4533 Dihedral : 4.906 42.370 3837 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.15), residues: 3129 helix: 1.60 (0.20), residues: 747 sheet: 0.81 (0.20), residues: 714 loop : -1.34 (0.14), residues: 1668 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 224 time to evaluate : 2.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 39 residues processed: 273 average time/residue: 1.1390 time to fit residues: 372.9852 Evaluate side-chains 249 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 210 time to evaluate : 3.119 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 39 residues processed: 1 average time/residue: 0.3184 time to fit residues: 5.0024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 0.5980 chunk 268 optimal weight: 4.9990 chunk 77 optimal weight: 0.0070 chunk 232 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 252 optimal weight: 0.2980 chunk 105 optimal weight: 2.9990 chunk 259 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN B 755 GLN B 787 GLN B 955 ASN C 46 ASN C 544 ASN C 751 ASN C 755 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.155657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.130499 restraints weight = 30436.112| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.74 r_work: 0.3479 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 1.52 restraints_weight: 0.2500 r_work: 0.3450 rms_B_bonded: 1.59 restraints_weight: 0.1250 r_work: 0.3433 rms_B_bonded: 1.74 restraints_weight: 0.0625 r_work: 0.3412 rms_B_bonded: 1.97 restraints_weight: 0.0312 r_work: 0.3387 rms_B_bonded: 2.31 restraints_weight: 0.0156 r_work: 0.3357 rms_B_bonded: 2.76 restraints_weight: 0.0078 r_work: 0.3318 rms_B_bonded: 3.39 restraints_weight: 0.0039 r_work: 0.3269 rms_B_bonded: 4.26 restraints_weight: 0.0020 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.180 26373 Z= 0.179 Angle : 0.531 16.798 35898 Z= 0.288 Chirality : 0.043 0.210 4314 Planarity : 0.005 0.150 4533 Dihedral : 4.889 42.656 3837 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.15), residues: 3129 helix: 1.74 (0.20), residues: 735 sheet: 0.77 (0.20), residues: 720 loop : -1.32 (0.14), residues: 1674 =============================================================================== Job complete usr+sys time: 6663.43 seconds wall clock time: 120 minutes 42.78 seconds (7242.78 seconds total)