Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 11 05:21:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tp9_26049/07_2023/7tp9_26049.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tp9_26049/07_2023/7tp9_26049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tp9_26049/07_2023/7tp9_26049.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tp9_26049/07_2023/7tp9_26049.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tp9_26049/07_2023/7tp9_26049.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tp9_26049/07_2023/7tp9_26049.pdb" } resolution = 3.48 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= 0.142 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 100 5.16 5 C 14770 2.51 5 N 3834 2.21 5 O 4495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 23199 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1005, 7700 Classifications: {'peptide': 1005} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 48, 'TRANS': 956} Chain breaks: 10 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 10, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 117 Chain: "B" Number of atoms: 7070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 975, 7070 Classifications: {'peptide': 975} Incomplete info: {'truncation_to_alanine': 149} Link IDs: {'PTRANS': 46, 'TRANS': 928} Chain breaks: 10 Unresolved non-hydrogen bonds: 573 Unresolved non-hydrogen angles: 738 Unresolved non-hydrogen dihedrals: 479 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 13, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 13, 'PHE:plan': 9, 'GLU:plan': 12, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 382 Chain: "C" Number of atoms: 7617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1003, 7617 Classifications: {'peptide': 1003} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 48, 'TRANS': 954} Chain breaks: 8 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 270 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 12, 'GLU:plan': 13, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 140 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 10.09, per 1000 atoms: 0.43 Number of scatterers: 23199 At special positions: 0 Unit cell: (128.52, 138.24, 180.36, 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 100 16.00 O 4495 8.00 N 3834 7.00 C 14770 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 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=2.01 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 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=2.01 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.01 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 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=2.02 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 B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 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=2.04 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 C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 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 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 61 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B1074 " " NAG B1311 " - " ASN B 165 " " NAG B1312 " - " ASN B 717 " " NAG C1301 " - " ASN C 234 " " NAG C1302 " - " ASN C 603 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 165 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C 61 " " NAG C1310 " - " ASN C1074 " " NAG C1311 " - " ASN C 122 " " NAG C1312 " - " ASN C 282 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN C1134 " " NAG M 1 " - " ASN C 717 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C 801 " Time building additional restraints: 8.20 Conformation dependent library (CDL) restraints added in 3.2 seconds 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5594 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 46 sheets defined 28.2% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.992A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.478A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.009A 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 439 through 442 Processing helix chain 'A' and resid 622 through 627 Processing helix chain 'A' and resid 634 through 639 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.129A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.599A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.480A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.745A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.269A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.891A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.825A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.757A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 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 removed outlier: 3.781A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.794A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.496A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 336 through 344 removed outlier: 3.749A pdb=" N GLU B 340 " --> pdb=" O CYS B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.741A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 404 through 409 removed outlier: 4.325A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN B 409 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 409' Processing helix chain 'B' and resid 416 through 421 removed outlier: 4.337A pdb=" N ASP B 420 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 451 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 632 through 637 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.763A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.791A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.899A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.741A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.673A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.803A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.906A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (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 removed outlier: 3.741A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.808A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.762A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.770A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.235A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.387A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.527A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 619 through 623 removed outlier: 3.563A pdb=" N VAL C 622 " --> pdb=" O GLU C 619 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA C 623 " --> pdb=" O VAL C 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 619 through 623' Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.036A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 6.119A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.618A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.583A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.617A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.829A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.599A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.663A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.623A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 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 removed outlier: 3.913A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.642A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.039A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.216A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.530A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.690A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.329A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.120A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.758A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.773A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.194A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.278A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.643A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.140A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.718A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.905A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.348A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.396A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 356 through 357 Processing sheet with id=AC7, first strand: chain 'B' and resid 376 through 379 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.047A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.508A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.652A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.080A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.488A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.670A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.522A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.581A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.722A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.970A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE6, first strand: chain 'C' and resid 718 through 722 Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 722 removed outlier: 3.575A pdb=" N PHE C1052 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.538A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1094 through 1097 970 hydrogen bonds defined for protein. 2646 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: 9.56 Time building geometry restraints manager: 8.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6394 1.33 - 1.46: 4233 1.46 - 1.58: 12931 1.58 - 1.70: 0 1.70 - 1.83: 124 Bond restraints: 23682 Sorted by residual: bond pdb=" C4 NAG D 1 " pdb=" O4 NAG D 1 " ideal model delta sigma weight residual 1.409 1.497 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C5 NAG A1306 " pdb=" O5 NAG A1306 " ideal model delta sigma weight residual 1.413 1.491 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C5 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C5 NAG C1310 " pdb=" O5 NAG C1310 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C5 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 23677 not shown) Histogram of bond angle deviations from ideal: 96.20 - 104.15: 317 104.15 - 112.10: 10562 112.10 - 120.04: 11066 120.04 - 127.99: 10245 127.99 - 135.94: 107 Bond angle restraints: 32297 Sorted by residual: angle pdb=" CA PRO B 621 " pdb=" N PRO B 621 " pdb=" CD PRO B 621 " ideal model delta sigma weight residual 112.00 100.72 11.28 1.40e+00 5.10e-01 6.49e+01 angle pdb=" CB LEU B 212 " pdb=" CG LEU B 212 " pdb=" CD1 LEU B 212 " ideal model delta sigma weight residual 110.70 132.73 -22.03 3.00e+00 1.11e-01 5.39e+01 angle pdb=" OE1 GLN A1106 " pdb=" CD GLN A1106 " pdb=" NE2 GLN A1106 " ideal model delta sigma weight residual 122.60 117.30 5.30 1.00e+00 1.00e+00 2.81e+01 angle pdb=" OE1 GLN B 965 " pdb=" CD GLN B 965 " pdb=" NE2 GLN B 965 " ideal model delta sigma weight residual 122.60 117.31 5.29 1.00e+00 1.00e+00 2.79e+01 angle pdb=" CA PHE C 565 " pdb=" CB PHE C 565 " pdb=" CG PHE C 565 " ideal model delta sigma weight residual 113.80 119.07 -5.27 1.00e+00 1.00e+00 2.78e+01 ... (remaining 32292 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 12675 17.54 - 35.08: 719 35.08 - 52.62: 110 52.62 - 70.16: 39 70.16 - 87.70: 32 Dihedral angle restraints: 13575 sinusoidal: 4915 harmonic: 8660 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -168.80 82.80 1 1.00e+01 1.00e-02 8.40e+01 dihedral pdb=" C TYR B 200 " pdb=" N TYR B 200 " pdb=" CA TYR B 200 " pdb=" CB TYR B 200 " ideal model delta harmonic sigma weight residual -122.60 -140.96 18.36 0 2.50e+00 1.60e-01 5.40e+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 -147.05 61.05 1 1.00e+01 1.00e-02 4.95e+01 ... (remaining 13572 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.260: 3910 0.260 - 0.521: 31 0.521 - 0.781: 1 0.781 - 1.042: 0 1.042 - 1.302: 1 Chirality restraints: 3943 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 6.97e+01 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.59e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.09e+01 ... (remaining 3940 not shown) Planarity restraints: 4141 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 633 " 0.203 2.00e-02 2.50e+03 1.06e-01 2.81e+02 pdb=" CG TRP B 633 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP B 633 " -0.123 2.00e-02 2.50e+03 pdb=" CD2 TRP B 633 " -0.042 2.00e-02 2.50e+03 pdb=" NE1 TRP B 633 " -0.060 2.00e-02 2.50e+03 pdb=" CE2 TRP B 633 " 0.038 2.00e-02 2.50e+03 pdb=" CE3 TRP B 633 " -0.134 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 633 " 0.135 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 633 " -0.075 2.00e-02 2.50e+03 pdb=" CH2 TRP B 633 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 709 " -0.136 2.00e-02 2.50e+03 1.46e-01 2.67e+02 pdb=" CG ASN B 709 " 0.069 2.00e-02 2.50e+03 pdb=" OD1 ASN B 709 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN B 709 " 0.227 2.00e-02 2.50e+03 pdb=" C1 NAG B1308 " -0.178 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.136 2.00e-02 2.50e+03 1.43e-01 2.56e+02 pdb=" CG ASN A 331 " -0.078 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.216 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " 0.175 2.00e-02 2.50e+03 ... (remaining 4138 not shown) Histogram of nonbonded interaction distances: 2.52 - 2.99: 11649 2.99 - 3.47: 22306 3.47 - 3.95: 37041 3.95 - 4.42: 41338 4.42 - 4.90: 69426 Nonbonded interactions: 181760 Sorted by model distance: nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.518 2.440 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.519 2.440 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.523 2.440 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.523 2.440 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.530 2.440 ... (remaining 181755 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 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 66 or resid 82 throug \ h 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or re \ sid 89 through 95 or (resid 96 through 97 and (name N or name CA or name C or na \ me O or name CB )) or resid 98 through 109 or (resid 110 through 113 and (name N \ or name CA or name C or name O or name CB )) or resid 116 through 124 or (resid \ 125 and (name N or name CA or name C or name O or name CB )) or resid 126 throu \ gh 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or \ resid 133 or (resid 134 through 138 and (name N or name CA or name C or name O \ or name CB )) or resid 139 through 140 or resid 166 through 168 or (resid 169 an \ d (name N or name CA or name C or name O or name CB )) or resid 170 through 171 \ or (resid 172 and (name N or name CA or name C or name O or name CB )) or resid \ 186 through 190 or (resid 191 and (name N or name CA or name C or name O or name \ CB )) or resid 192 through 197 or (resid 198 and (name N or name CA or name C o \ r name O or name CB )) or resid 199 through 210 or (resid 211 and (name N or nam \ e CA or name C or name O or name CB )) or resid 212 or (resid 213 and (name N or \ name CA or name C or name O or name CB )) or resid 214 or (resid 215 and (name \ N or name CA or name C or name O or name CB )) or resid 216 through 217 or (resi \ d 218 and (name N or name CA or name C or name O or name CB )) or resid 219 thro \ ugh 223 or (resid 224 and (name N or name CA or name C or name O or name CB )) o \ r resid 225 through 238 or (resid 239 and (name N or name CA or name C or name O \ or name CB )) or resid 240 through 263 or resid 265 through 308 or (resid 309 a \ nd (name N or name CA or name C or name O or name CB )) or resid 310 through 323 \ or (resid 324 and (name N or name CA or name C or name O or name CB )) or resid \ 325 through 332 or (resid 333 through 334 and (name N or name CA or name C or n \ ame O or name CB )) or resid 335 through 345 or (resid 346 through 360 and (name \ N or name CA or name C or name O or name CB )) or resid 361 or (resid 362 throu \ gh 378 and (name N or name CA or name C or name O or name CB )) or resid 379 or \ (resid 380 and (name N or name CA or name C or name O or name CB )) or resid 381 \ or (resid 382 through 383 and (name N or name CA or name C or name O or name CB \ )) or resid 384 or (resid 385 through 390 and (name N or name CA or name C or n \ ame O or name CB )) or resid 391 or (resid 392 through 403 and (name N or name C \ A or name C or name O or name CB )) or (resid 404 through 411 and (name N or nam \ e CA or name C or name O or name CB )) or resid 412 through 413 or (resid 414 th \ rough 415 and (name N or name CA or name C or name O or name CB )) or resid 416 \ or (resid 417 through 425 and (name N or name CA or name C or name O or name CB \ )) or resid 426 through 427 or (resid 428 through 430 and (name N or name CA or \ name C or name O or name CB )) or resid 431 through 432 or (resid 433 through 44 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 457 or (resi \ d 462 and (name N or name CA or name C or name O or name CB )) or resid 463 or ( \ resid 464 through 466 and (name N or name CA or name C or name O or name CB )) o \ r resid 491 or (resid 492 through 495 and (name N or name CA or name C or name O \ or name CB )) or resid 496 or (resid 497 through 498 and (name N or name CA or \ name C or name O or name CB )) or resid 499 or (resid 500 through 503 and (name \ N or name CA or name C or name O or name CB )) or (resid 504 through 506 and (na \ me N or name CA or name C or name O or name CB )) or resid 507 or (resid 508 thr \ ough 515 and (name N or name CA or name C or name O or name CB )) or (resid 522 \ through 524 and (name N or name CA or name C or name O or name CB )) or resid 52 \ 5 through 528 or (resid 529 and (name N or name CA or name C or name O or name C \ B )) or resid 530 through 553 or (resid 554 and (name N or name CA or name C or \ name O or name CB )) or resid 555 through 793 or (resid 794 and (name N or name \ CA or name C or name O or name CB )) or resid 795 or (resid 796 and (name N or n \ ame CA or name C or name O or name CB )) or resid 797 through 810 or (resid 811 \ and (name N or name CA or name C or name O or name CB )) or resid 813 through 82 \ 7 or resid 856 through 866 or (resid 867 through 868 and (name N or name CA or n \ ame C or name O or name CB )) or resid 869 through 939 or (resid 940 and (name N \ or name CA or name C or name O or name CB )) or resid 941 through 984 or (resid \ 985 and (name N or name CA or name C or name O or name CB )) or resid 986 throu \ gh 987 or (resid 988 through 989 and (name N or name CA or name C or name O or n \ ame CB )) or resid 990 through 1141 or (resid 1142 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1143 through 1144 or (resid 1145 through 11 \ 46 and (name N or name CA or name C or name O or name CB )) or resid 1147 or res \ id 1301 through 1310)) selection = (chain 'B' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or re \ sid 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 through 109 or (resid 110 through 113 and (name N or name CA or name C \ or name O or name CB )) or resid 116 through 128 or (resid 129 and (name N or n \ ame CA or name C or name O or name CB )) or resid 130 through 134 or (resid 135 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 140 or resid 166 through 168 or (resid 169 and (name N or name CA or n \ ame C or name O or name CB )) or resid 170 through 187 or (resid 188 and (name N \ or name CA or name C or name O or name CB )) or resid 189 through 190 or (resid \ 191 and (name N or name CA or name C or name O or name CB )) or resid 192 throu \ gh 195 or (resid 196 and (name N or name CA or name C or name O or name CB )) or \ resid 197 or (resid 198 and (name N or name CA or name C or name O or name CB ) \ ) or resid 199 through 210 or (resid 211 and (name N or name CA or name C or nam \ e O or name CB )) or resid 212 or (resid 213 and (name N or name CA or name C or \ name O or name CB )) or resid 214 through 241 or (resid 242 through 263 and (na \ me N or name CA or name C or name O or name CB )) or resid 265 through 280 or (r \ esid 281 and (name N or name CA or name C or name O or name CB )) or resid 282 t \ hrough 323 or (resid 324 and (name N or name CA or name C or name O or name CB ) \ ) or resid 325 through 442 or resid 452 or resid 462 through 501 or resid 503 th \ rough 567 or (resid 568 and (name N or name CA or name C or name O or name CB )) \ or resid 569 through 570 or (resid 571 and (name N or name CA or name C or name \ O or name CB )) or resid 572 through 581 or (resid 582 through 583 and (name N \ or name CA or name C or name O or name CB )) or resid 584 through 585 or (resid \ 586 and (name N or name CA or name C or name O or name CB )) or resid 587 throug \ h 618 or (resid 619 and (name N or name CA or name C or name O or name CB )) or \ resid 620 through 676 or resid 690 through 744 or (resid 745 and (name N or name \ CA or name C or name O or name CB )) or resid 746 through 810 or (resid 811 and \ (name N or name CA or name C or name O or name CB )) or resid 813 through 827 o \ r resid 856 through 866 or (resid 867 through 868 and (name N or name CA or name \ C or name O or name CB )) or resid 869 through 920 or (resid 921 and (name N or \ name CA or name C or name O or name CB )) or resid 922 through 939 or (resid 94 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 941 through \ 984 or (resid 985 and (name N or name CA or name C or name O or name CB )) or re \ sid 986 through 987 or (resid 988 through 989 and (name N or name CA or name C o \ r name O or name CB )) or resid 990 through 1072 or (resid 1073 and (name N or n \ ame CA or name C or name O or name CB )) or resid 1074 through 1117 or (resid 11 \ 18 and (name N or name CA or name C or name O or name CB )) or resid 1119 throug \ h 1143 or (resid 1144 through 1146 and (name N or name CA or name C or name O or \ name CB )) or resid 1147 or resid 1301 through 1310)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 110 or (resid 111 through 113 and (name N or name CA or name C o \ r name O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (n \ ame N or name CA or name C or name O or name CB )) or resid 139 through 140 or r \ esid 166 through 187 or (resid 188 and (name N or name CA or name C or name O or \ name CB )) or resid 189 through 195 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB )) or resid 197 through 217 or (resid 218 and (name N o \ r name CA or name C or name O or name CB )) or resid 219 through 223 or (resid 2 \ 24 and (name N or name CA or name C or name O or name CB )) or resid 225 through \ 238 or (resid 239 and (name N or name CA or name C or name O or name CB )) or r \ esid 240 through 308 or (resid 309 and (name N or name CA or name C or name O or \ name CB )) or resid 310 through 332 or (resid 333 through 334 and (name N or na \ me CA or name C or name O or name CB )) or resid 335 through 344 or (resid 345 t \ hrough 360 and (name N or name CA or name C or name O or name CB )) or resid 361 \ or (resid 362 through 378 and (name N or name CA or name C or name O or name CB \ )) or resid 379 or (resid 380 and (name N or name CA or name C or name O or nam \ e CB )) or resid 381 or (resid 382 through 383 and (name N or name CA or name C \ or name O or name CB )) or resid 384 or (resid 385 through 390 and (name N or na \ me CA or name C or name O or name CB )) or resid 391 or (resid 392 through 403 a \ nd (name N or name CA or name C or name O or name CB )) or (resid 404 through 41 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 412 through \ 413 or (resid 414 through 415 and (name N or name CA or name C or name O or name \ CB )) or (resid 416 through 425 and (name N or name CA or name C or name O or n \ ame CB )) or resid 426 or (resid 427 through 430 and (name N or name CA or name \ C or name O or name CB )) or resid 431 through 432 or (resid 433 through 442 and \ (name N or name CA or name C or name O or name CB )) or resid 452 or resid 462 \ through 463 or (resid 464 through 466 and (name N or name CA or name C or name O \ or name CB )) or resid 491 or (resid 492 through 495 and (name N or name CA or \ name C or name O or name CB )) or resid 496 or (resid 497 through 498 and (name \ N or name CA or name C or name O or name CB )) or resid 499 through 500 or (resi \ d 501 and (name N or name CA or name C or name O or name CB )) or (resid 503 and \ (name N or name CA or name C or name O or name CB )) or (resid 504 through 506 \ and (name N or name CA or name C or name O or name CB )) or resid 507 or (resid \ 508 through 515 and (name N or name CA or name C or name O or name CB )) or (res \ id 522 through 524 and (name N or name CA or name C or name O or name CB )) or r \ esid 525 through 527 or (resid 528 through 529 and (name N or name CA or name C \ or name O or name CB )) or resid 530 through 553 or (resid 554 and (name N or na \ me CA or name C or name O or name CB )) or resid 555 through 567 or (resid 568 a \ nd (name N or name CA or name C or name O or name CB )) or resid 569 through 570 \ or (resid 571 and (name N or name CA or name C or name O or name CB )) or resid \ 572 through 581 or (resid 582 through 583 and (name N or name CA or name C or n \ ame O or name CB )) or resid 584 through 585 or (resid 586 and (name N or name C \ A or name C or name O or name CB )) or resid 587 through 618 or (resid 619 and ( \ name N or name CA or name C or name O or name CB )) or resid 620 through 645 or \ (resid 646 through 647 and (name N or name CA or name C or name O or name CB )) \ or resid 648 through 793 or (resid 794 and (name N or name CA or name C or name \ O or name CB )) or resid 795 or (resid 796 and (name N or name CA or name C or n \ ame O or name CB )) or resid 797 through 920 or (resid 921 and (name N or name C \ A or name C or name O or name CB )) or resid 922 through 1072 or (resid 1073 and \ (name N or name CA or name C or name O or name CB )) or resid 1074 through 1117 \ or (resid 1118 and (name N or name CA or name C or name O or name CB )) or resi \ d 1119 through 1141 or (resid 1142 and (name N or name CA or name C or name O or \ name CB )) or resid 1143 or (resid 1144 through 1146 and (name N or name CA or \ name C or name O or name CB )) or resid 1147 or resid 1301 through 1310)) } 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 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: 3.650 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: 7.860 Check model and map are aligned: 0.300 Set scattering table: 0.170 Process input model: 54.580 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 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 : 0.014 0.088 23682 Z= 0.888 Angle : 1.767 22.028 32297 Z= 1.171 Chirality : 0.098 1.302 3943 Planarity : 0.014 0.179 4095 Dihedral : 12.861 87.695 7870 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 0.02 Ramachandran Plot: Outliers : 0.72 % Allowed : 6.88 % Favored : 92.40 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.21 % 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: -0.96 (0.15), residues: 2921 helix: -0.48 (0.18), residues: 660 sheet: 0.33 (0.22), residues: 514 loop : -1.00 (0.14), residues: 1747 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 58 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 7 residues processed: 80 average time/residue: 0.4142 time to fit residues: 52.1330 Evaluate side-chains 41 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 34 time to evaluate : 3.030 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.3856 time to fit residues: 7.4463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 151 optimal weight: 7.9990 chunk 120 optimal weight: 0.6980 chunk 232 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 173 optimal weight: 0.8980 chunk 269 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 914 ASN A 955 ASN B 690 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 23682 Z= 0.180 Angle : 0.658 12.379 32297 Z= 0.348 Chirality : 0.046 0.280 3943 Planarity : 0.004 0.164 4095 Dihedral : 6.078 33.460 3155 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.25 % Favored : 95.55 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.04 % 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: -0.15 (0.15), residues: 2921 helix: 1.25 (0.20), residues: 675 sheet: 0.09 (0.20), residues: 583 loop : -0.73 (0.15), residues: 1663 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 40 time to evaluate : 2.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 53 average time/residue: 0.3624 time to fit residues: 33.9136 Evaluate side-chains 36 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 31 time to evaluate : 3.009 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 5 average time/residue: 0.4222 time to fit residues: 6.7691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 0.0470 chunk 83 optimal weight: 6.9990 chunk 224 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 270 optimal weight: 6.9990 chunk 291 optimal weight: 10.0000 chunk 240 optimal weight: 10.0000 chunk 267 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 216 optimal weight: 9.9990 overall best weight: 4.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 GLN A 907 ASN A 913 GLN B 540 ASN B 907 ASN ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.050 23682 Z= 0.390 Angle : 0.673 12.818 32297 Z= 0.347 Chirality : 0.047 0.198 3943 Planarity : 0.005 0.167 4095 Dihedral : 5.580 32.849 3155 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.58 % Favored : 94.25 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -0.25 (0.15), residues: 2921 helix: 1.24 (0.20), residues: 681 sheet: -0.05 (0.20), residues: 608 loop : -0.81 (0.15), residues: 1632 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 34 time to evaluate : 2.733 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 9 residues processed: 57 average time/residue: 0.3818 time to fit residues: 37.1408 Evaluate side-chains 39 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 30 time to evaluate : 2.534 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 9 average time/residue: 0.2743 time to fit residues: 7.5785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 5.9990 chunk 203 optimal weight: 7.9990 chunk 140 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 128 optimal weight: 30.0000 chunk 181 optimal weight: 6.9990 chunk 271 optimal weight: 3.9990 chunk 287 optimal weight: 1.9990 chunk 141 optimal weight: 8.9990 chunk 256 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 23682 Z= 0.346 Angle : 0.614 10.916 32297 Z= 0.317 Chirality : 0.045 0.206 3943 Planarity : 0.004 0.157 4095 Dihedral : 5.293 35.249 3155 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.34 % Favored : 94.56 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -0.26 (0.15), residues: 2921 helix: 1.35 (0.20), residues: 687 sheet: -0.17 (0.21), residues: 594 loop : -0.83 (0.15), residues: 1640 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 30 time to evaluate : 2.597 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 10 residues processed: 47 average time/residue: 0.3244 time to fit residues: 28.3798 Evaluate side-chains 40 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 30 time to evaluate : 2.430 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.2834 time to fit residues: 8.1513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 10.0000 chunk 162 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 213 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 198 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 146 optimal weight: 3.9990 chunk 257 optimal weight: 0.7980 chunk 72 optimal weight: 0.0770 overall best weight: 1.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 935 GLN ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 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 : 0.003 0.061 23682 Z= 0.177 Angle : 0.529 11.172 32297 Z= 0.274 Chirality : 0.043 0.215 3943 Planarity : 0.004 0.152 4095 Dihedral : 4.807 35.622 3155 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.72 % Favored : 95.17 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: 0.02 (0.16), residues: 2921 helix: 1.82 (0.20), residues: 686 sheet: -0.07 (0.21), residues: 595 loop : -0.73 (0.15), residues: 1640 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 30 time to evaluate : 2.569 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 5 residues processed: 46 average time/residue: 0.3106 time to fit residues: 26.9851 Evaluate side-chains 35 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 30 time to evaluate : 2.451 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 5 average time/residue: 0.3292 time to fit residues: 5.8919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 7.9990 chunk 258 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 168 optimal weight: 30.0000 chunk 70 optimal weight: 6.9990 chunk 287 optimal weight: 0.6980 chunk 238 optimal weight: 9.9990 chunk 133 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 150 optimal weight: 20.0000 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1135 ASN ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 23682 Z= 0.337 Angle : 0.582 10.915 32297 Z= 0.299 Chirality : 0.045 0.222 3943 Planarity : 0.004 0.156 4095 Dihedral : 4.901 36.400 3155 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.75 % Favored : 94.15 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -0.12 (0.15), residues: 2921 helix: 1.63 (0.20), residues: 689 sheet: -0.13 (0.21), residues: 595 loop : -0.80 (0.15), residues: 1637 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 29 time to evaluate : 2.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 44 average time/residue: 0.3283 time to fit residues: 27.3252 Evaluate side-chains 40 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 29 time to evaluate : 2.695 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 11 average time/residue: 0.2714 time to fit residues: 8.5999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 277 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 163 optimal weight: 3.9990 chunk 209 optimal weight: 0.4980 chunk 162 optimal weight: 0.9980 chunk 241 optimal weight: 9.9990 chunk 160 optimal weight: 4.9990 chunk 286 optimal weight: 1.9990 chunk 179 optimal weight: 7.9990 chunk 174 optimal weight: 5.9990 chunk 132 optimal weight: 50.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 23682 Z= 0.211 Angle : 0.517 9.851 32297 Z= 0.268 Chirality : 0.043 0.258 3943 Planarity : 0.004 0.152 4095 Dihedral : 4.648 36.633 3155 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.10 % Favored : 94.80 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: 0.02 (0.16), residues: 2921 helix: 1.87 (0.20), residues: 688 sheet: -0.09 (0.21), residues: 587 loop : -0.76 (0.15), residues: 1646 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 29 time to evaluate : 2.658 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 35 average time/residue: 0.3501 time to fit residues: 24.4055 Evaluate side-chains 31 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 2.856 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.2394 time to fit residues: 5.1906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 0.9990 chunk 114 optimal weight: 0.5980 chunk 170 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 chunk 181 optimal weight: 0.0470 chunk 195 optimal weight: 9.9990 chunk 141 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 225 optimal weight: 10.0000 overall best weight: 2.9284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 23682 Z= 0.245 Angle : 0.531 9.797 32297 Z= 0.274 Chirality : 0.043 0.228 3943 Planarity : 0.004 0.151 4095 Dihedral : 4.608 37.128 3155 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.44 % Favored : 94.45 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -0.01 (0.16), residues: 2921 helix: 1.84 (0.20), residues: 687 sheet: -0.10 (0.21), residues: 597 loop : -0.77 (0.15), residues: 1637 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 2.553 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 32 average time/residue: 0.3065 time to fit residues: 19.9876 Evaluate side-chains 31 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 2.578 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.2038 time to fit residues: 4.5775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 7.9990 chunk 274 optimal weight: 2.9990 chunk 250 optimal weight: 20.0000 chunk 266 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 209 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 241 optimal weight: 10.0000 chunk 252 optimal weight: 7.9990 chunk 265 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A1048 HIS C 188 ASN ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 23682 Z= 0.336 Angle : 0.575 9.528 32297 Z= 0.296 Chirality : 0.045 0.230 3943 Planarity : 0.004 0.150 4095 Dihedral : 4.757 37.071 3155 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.13 % Favored : 93.77 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -0.19 (0.15), residues: 2921 helix: 1.63 (0.20), residues: 687 sheet: -0.19 (0.20), residues: 616 loop : -0.88 (0.15), residues: 1618 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 2.759 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 31 average time/residue: 0.3758 time to fit residues: 22.3554 Evaluate side-chains 29 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 2.670 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1779 time to fit residues: 3.5436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 1.9990 chunk 282 optimal weight: 4.9990 chunk 172 optimal weight: 0.9980 chunk 133 optimal weight: 30.0000 chunk 196 optimal weight: 6.9990 chunk 295 optimal weight: 0.0570 chunk 272 optimal weight: 0.7980 chunk 235 optimal weight: 30.0000 chunk 24 optimal weight: 2.9990 chunk 181 optimal weight: 10.0000 chunk 144 optimal weight: 7.9990 overall best weight: 1.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 23682 Z= 0.152 Angle : 0.489 9.111 32297 Z= 0.254 Chirality : 0.043 0.234 3943 Planarity : 0.004 0.148 4095 Dihedral : 4.380 36.817 3155 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.79 % Favored : 95.10 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: 0.12 (0.16), residues: 2921 helix: 2.03 (0.20), residues: 687 sheet: -0.03 (0.20), residues: 604 loop : -0.74 (0.15), residues: 1630 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 29 time to evaluate : 2.619 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 31 average time/residue: 0.3857 time to fit residues: 23.1829 Evaluate side-chains 31 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 29 time to evaluate : 2.958 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.5711 time to fit residues: 5.2132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 5.9990 chunk 250 optimal weight: 5.9990 chunk 72 optimal weight: 0.0000 chunk 217 optimal weight: 4.9990 chunk 34 optimal weight: 40.0000 chunk 65 optimal weight: 8.9990 chunk 235 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 242 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 10.0000 overall best weight: 3.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.061525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.043512 restraints weight = 121429.009| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.73 r_work: 0.2857 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 23682 Z= 0.268 Angle : 0.523 9.039 32297 Z= 0.269 Chirality : 0.043 0.221 3943 Planarity : 0.004 0.148 4095 Dihedral : 4.463 37.221 3155 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.72 % Favored : 94.18 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: 0.02 (0.16), residues: 2921 helix: 1.91 (0.20), residues: 688 sheet: -0.07 (0.20), residues: 609 loop : -0.79 (0.15), residues: 1624 =============================================================================== Job complete usr+sys time: 3186.61 seconds wall clock time: 60 minutes 12.44 seconds (3612.44 seconds total)