Starting phenix.real_space_refine on Fri Jun 20 05:15:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tov_26039/06_2025/7tov_26039.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tov_26039/06_2025/7tov_26039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tov_26039/06_2025/7tov_26039.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tov_26039/06_2025/7tov_26039.map" model { file = "/net/cci-nas-00/data/ceres_data/7tov_26039/06_2025/7tov_26039.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tov_26039/06_2025/7tov_26039.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 sd= 0.158 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. Time to flip 4 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 30 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 dihedrals: 36 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 dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 13.81, per 1000 atoms: 0.60 Number of scatterers: 23199 At special positions: 0 Unit cell: (129.6, 137.16, 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=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.01 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 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=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 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=2.03 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=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 6.21 Conformation dependent library (CDL) restraints added in 2.9 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: 74 helices and 43 sheets defined 27.3% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.28 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: 3.944A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.038A 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 616 through 620 Processing helix chain 'A' and resid 634 through 639 removed outlier: 3.761A pdb=" N THR A 638 " --> pdb=" O ARG A 634 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLY A 639 " --> pdb=" O VAL A 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 634 through 639' Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.623A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.572A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.584A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.543A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.716A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.525A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (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 removed outlier: 3.683A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.639A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.518A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1129 removed outlier: 4.256A pdb=" N VAL A1128 " --> pdb=" O ASN A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.359A 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 338 through 343 Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.531A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.844A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) 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 754 removed outlier: 3.519A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.913A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.816A 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: 3.861A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.539A 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 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: 3.712A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.268A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 5.051A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.443A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 619 through 623 removed outlier: 3.645A pdb=" N ALA C 623 " --> pdb=" O VAL C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 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: 6.084A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.559A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.725A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.576A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.643A 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: 3.624A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.149A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (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 1140 through 1147 removed outlier: 4.380A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.351A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.736A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.517A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.370A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.182A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.576A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.745A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.191A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.391A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.394A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.192A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.880A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.835A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.551A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.352A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.518A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 355 through 357 removed outlier: 3.615A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 5.758A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 374 through 379 removed outlier: 6.812A pdb=" N ALA B 435 " --> pdb=" O SER B 375 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N PHE B 377 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL B 433 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.380A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (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: 4.660A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.272A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.567A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.583A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.570A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.656A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.716A 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: 6.751A 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 654 through 655 removed outlier: 5.983A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE5, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.327A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.571A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.924A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 986 hydrogen bonds defined for protein. 2694 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: 11.22 Time building geometry restraints manager: 7.11 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: 6283 1.33 - 1.46: 4134 1.46 - 1.58: 13141 1.58 - 1.70: 0 1.70 - 1.82: 124 Bond restraints: 23682 Sorted by residual: bond pdb=" CA PRO A 862 " pdb=" C PRO A 862 " ideal model delta sigma weight residual 1.517 1.546 -0.029 6.70e-03 2.23e+04 1.84e+01 bond pdb=" CA PRO C 862 " pdb=" C PRO C 862 " ideal model delta sigma weight residual 1.517 1.543 -0.026 6.70e-03 2.23e+04 1.55e+01 bond pdb=" C5 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C5 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C4 NAG D 1 " pdb=" O4 NAG D 1 " ideal model delta sigma weight residual 1.409 1.484 -0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 23677 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.22: 31662 4.22 - 8.45: 631 8.45 - 12.67: 3 12.67 - 16.90: 0 16.90 - 21.12: 1 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 112.00 100.47 11.53 1.40e+00 5.10e-01 6.78e+01 angle pdb=" CB LEU B 212 " pdb=" CG LEU B 212 " pdb=" CD1 LEU B 212 " ideal model delta sigma weight residual 110.70 131.82 -21.12 3.00e+00 1.11e-01 4.96e+01 angle pdb=" CA PHE C 565 " pdb=" CB PHE C 565 " pdb=" CG PHE C 565 " ideal model delta sigma weight residual 113.80 119.43 -5.63 1.00e+00 1.00e+00 3.17e+01 angle pdb=" CA PHE B 559 " pdb=" CB PHE B 559 " pdb=" CG PHE B 559 " ideal model delta sigma weight residual 113.80 119.31 -5.51 1.00e+00 1.00e+00 3.04e+01 angle pdb=" CA PHE C 106 " pdb=" CB PHE C 106 " pdb=" CG PHE C 106 " ideal model delta sigma weight residual 113.80 119.24 -5.44 1.00e+00 1.00e+00 2.96e+01 ... (remaining 32292 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 13901 17.87 - 35.74: 695 35.74 - 53.60: 124 53.60 - 71.47: 45 71.47 - 89.34: 28 Dihedral angle restraints: 14793 sinusoidal: 6133 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 -160.04 74.04 1 1.00e+01 1.00e-02 6.96e+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 -139.19 16.59 0 2.50e+00 1.60e-01 4.40e+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 -143.19 57.19 1 1.00e+01 1.00e-02 4.40e+01 ... (remaining 14790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.257: 3912 0.257 - 0.514: 29 0.514 - 0.772: 1 0.772 - 1.029: 0 1.029 - 1.286: 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 -2.60 0.20 2.00e-02 2.50e+03 1.00e+02 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 -2.57 0.17 2.00e-02 2.50e+03 7.27e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.65e+01 ... (remaining 3940 not shown) Planarity restraints: 4141 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 633 " -0.211 2.00e-02 2.50e+03 1.23e-01 3.76e+02 pdb=" CG TRP C 633 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TRP C 633 " 0.130 2.00e-02 2.50e+03 pdb=" CD2 TRP C 633 " 0.053 2.00e-02 2.50e+03 pdb=" NE1 TRP C 633 " 0.107 2.00e-02 2.50e+03 pdb=" CE2 TRP C 633 " -0.043 2.00e-02 2.50e+03 pdb=" CE3 TRP C 633 " 0.156 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 633 " -0.168 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 633 " 0.094 2.00e-02 2.50e+03 pdb=" CH2 TRP C 633 " -0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 633 " 0.213 2.00e-02 2.50e+03 1.14e-01 3.23e+02 pdb=" CG TRP B 633 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP B 633 " -0.117 2.00e-02 2.50e+03 pdb=" CD2 TRP B 633 " -0.058 2.00e-02 2.50e+03 pdb=" NE1 TRP B 633 " -0.070 2.00e-02 2.50e+03 pdb=" CE2 TRP B 633 " 0.028 2.00e-02 2.50e+03 pdb=" CE3 TRP B 633 " -0.161 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 633 " 0.138 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 633 " -0.069 2.00e-02 2.50e+03 pdb=" CH2 TRP B 633 " 0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1074 " 0.131 2.00e-02 2.50e+03 1.39e-01 2.41e+02 pdb=" CG ASN C1074 " -0.076 2.00e-02 2.50e+03 pdb=" OD1 ASN C1074 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN C1074 " -0.214 2.00e-02 2.50e+03 pdb=" C1 NAG C1310 " 0.166 2.00e-02 2.50e+03 ... (remaining 4138 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 11144 2.99 - 3.47: 21886 3.47 - 3.95: 37603 3.95 - 4.42: 41809 4.42 - 4.90: 70894 Nonbonded interactions: 183336 Sorted by model distance: nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.515 3.040 nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.529 3.040 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.530 3.040 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.531 3.040 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.532 3.040 ... (remaining 183331 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.930 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 56.010 Find NCS groups from input model: 1.650 Set up NCS constraints: 0.120 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 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 0.077 23777 Z= 0.792 Angle : 1.831 21.124 32545 Z= 1.205 Chirality : 0.098 1.286 3943 Planarity : 0.013 0.198 4095 Dihedral : 12.151 89.341 9088 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 0.07 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.82 % Favored : 93.74 % Rotamer: Outliers : 0.89 % Allowed : 2.34 % Favored : 96.76 % Cbeta Deviations : 0.18 % 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: -0.81 (0.14), residues: 2921 helix: -0.76 (0.17), residues: 668 sheet: 0.86 (0.22), residues: 467 loop : -0.83 (0.14), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.213 0.030 TRP B 633 HIS 0.010 0.003 HIS C1048 PHE 0.086 0.011 PHE A 718 TYR 0.147 0.019 TYR B 279 ARG 0.011 0.001 ARG B 273 Details of bonding type rmsd link_NAG-ASN : bond 0.01224 ( 46) link_NAG-ASN : angle 4.59399 ( 138) link_BETA1-4 : bond 0.02630 ( 12) link_BETA1-4 : angle 4.68999 ( 36) hydrogen bonds : bond 0.16778 ( 974) hydrogen bonds : angle 8.11450 ( 2694) SS BOND : bond 0.01114 ( 37) SS BOND : angle 2.18785 ( 74) covalent geometry : bond 0.01376 (23682) covalent geometry : angle 1.80384 (32297) *********************** 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 129 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 2.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 LEU cc_start: 0.8633 (mt) cc_final: 0.8354 (tp) REVERT: B 200 TYR cc_start: 0.7000 (m-80) cc_final: 0.6721 (m-10) REVERT: C 902 MET cc_start: 0.8766 (mmm) cc_final: 0.8527 (tpt) outliers start: 21 outliers final: 7 residues processed: 129 average time/residue: 0.3727 time to fit residues: 75.1077 Evaluate side-chains 69 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 2.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 634 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 0.9980 chunk 225 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 232 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 173 optimal weight: 0.9980 chunk 269 optimal weight: 3.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1088 HIS B1010 GLN C 955 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.109913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.076179 restraints weight = 55726.769| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.42 r_work: 0.3046 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23777 Z= 0.145 Angle : 0.709 16.959 32545 Z= 0.362 Chirality : 0.047 0.338 3943 Planarity : 0.005 0.181 4095 Dihedral : 6.094 58.515 4385 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.04 % Favored : 95.86 % Rotamer: Outliers : 0.77 % Allowed : 3.83 % Favored : 95.40 % 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: 0.09 (0.15), residues: 2921 helix: 1.37 (0.20), residues: 661 sheet: 0.67 (0.19), residues: 642 loop : -0.75 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 64 HIS 0.005 0.001 HIS C1048 PHE 0.019 0.002 PHE B 338 TYR 0.016 0.002 TYR A 265 ARG 0.004 0.000 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00496 ( 46) link_NAG-ASN : angle 3.42568 ( 138) link_BETA1-4 : bond 0.00475 ( 12) link_BETA1-4 : angle 1.90070 ( 36) hydrogen bonds : bond 0.05088 ( 974) hydrogen bonds : angle 6.17871 ( 2694) SS BOND : bond 0.00511 ( 37) SS BOND : angle 2.14089 ( 74) covalent geometry : bond 0.00311 (23682) covalent geometry : angle 0.66422 (32297) *********************** 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 95 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 2.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 LEU cc_start: 0.8755 (mt) cc_final: 0.8363 (tp) REVERT: A 1126 CYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7565 (m) REVERT: C 197 ILE cc_start: 0.9038 (mp) cc_final: 0.8785 (mm) REVERT: C 902 MET cc_start: 0.8884 (mmm) cc_final: 0.8678 (tpt) REVERT: C 1126 CYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7573 (m) outliers start: 18 outliers final: 8 residues processed: 93 average time/residue: 0.3701 time to fit residues: 55.6886 Evaluate side-chains 66 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 182 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 284 optimal weight: 0.9980 chunk 254 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 278 optimal weight: 3.9990 chunk 264 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 128 optimal weight: 50.0000 chunk 162 optimal weight: 5.9990 chunk 271 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN A 913 GLN A 914 ASN B 343 ASN C 901 GLN C 914 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.107465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.076937 restraints weight = 55753.629| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.45 r_work: 0.3006 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 23777 Z= 0.234 Angle : 0.681 10.492 32545 Z= 0.348 Chirality : 0.048 0.297 3943 Planarity : 0.005 0.159 4095 Dihedral : 5.669 44.992 4380 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.69 % Favored : 95.24 % Rotamer: Outliers : 1.02 % Allowed : 5.87 % Favored : 93.10 % 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: -0.03 (0.15), residues: 2921 helix: 1.39 (0.21), residues: 668 sheet: 0.45 (0.19), residues: 663 loop : -0.84 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 633 HIS 0.009 0.002 HIS C1048 PHE 0.015 0.002 PHE B 541 TYR 0.019 0.002 TYR B1067 ARG 0.022 0.001 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00366 ( 46) link_NAG-ASN : angle 2.83804 ( 138) link_BETA1-4 : bond 0.00382 ( 12) link_BETA1-4 : angle 1.52295 ( 36) hydrogen bonds : bond 0.05417 ( 974) hydrogen bonds : angle 6.00703 ( 2694) SS BOND : bond 0.00337 ( 37) SS BOND : angle 1.51640 ( 74) covalent geometry : bond 0.00579 (23682) covalent geometry : angle 0.65178 (32297) *********************** 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 87 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 2.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 LEU cc_start: 0.8714 (mt) cc_final: 0.8408 (tp) REVERT: C 197 ILE cc_start: 0.8846 (mp) cc_final: 0.8580 (mm) outliers start: 24 outliers final: 12 residues processed: 85 average time/residue: 0.3638 time to fit residues: 50.7490 Evaluate side-chains 70 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 2.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 137 optimal weight: 0.0770 chunk 228 optimal weight: 9.9990 chunk 151 optimal weight: 0.9990 chunk 221 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 239 optimal weight: 20.0000 chunk 271 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 270 optimal weight: 0.9980 chunk 153 optimal weight: 6.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.108749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.073293 restraints weight = 56328.966| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.33 r_work: 0.3012 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 23777 Z= 0.127 Angle : 0.577 10.479 32545 Z= 0.295 Chirality : 0.044 0.297 3943 Planarity : 0.004 0.151 4095 Dihedral : 5.218 46.765 4380 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.66 % Favored : 96.23 % Rotamer: Outliers : 1.02 % Allowed : 6.05 % Favored : 92.93 % 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: 0.19 (0.15), residues: 2921 helix: 1.77 (0.21), residues: 669 sheet: 0.42 (0.19), residues: 645 loop : -0.71 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 633 HIS 0.004 0.001 HIS C 66 PHE 0.017 0.001 PHE B 338 TYR 0.018 0.001 TYR A1067 ARG 0.009 0.000 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00368 ( 46) link_NAG-ASN : angle 2.46900 ( 138) link_BETA1-4 : bond 0.00433 ( 12) link_BETA1-4 : angle 1.29445 ( 36) hydrogen bonds : bond 0.04165 ( 974) hydrogen bonds : angle 5.60813 ( 2694) SS BOND : bond 0.00243 ( 37) SS BOND : angle 1.87571 ( 74) covalent geometry : bond 0.00297 (23682) covalent geometry : angle 0.54774 (32297) *********************** 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 86 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 2.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 LEU cc_start: 0.8757 (mt) cc_final: 0.8356 (tp) REVERT: A 1126 CYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7623 (m) REVERT: C 197 ILE cc_start: 0.8871 (mp) cc_final: 0.8602 (mm) REVERT: C 214 ARG cc_start: 0.5777 (tpm170) cc_final: 0.5519 (mmm160) outliers start: 24 outliers final: 18 residues processed: 83 average time/residue: 0.3672 time to fit residues: 50.6311 Evaluate side-chains 75 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 2.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 131 optimal weight: 50.0000 chunk 86 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 137 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 190 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 249 optimal weight: 10.0000 chunk 163 optimal weight: 1.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.108027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.073653 restraints weight = 56351.531| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.32 r_work: 0.2987 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23777 Z= 0.165 Angle : 0.587 17.782 32545 Z= 0.295 Chirality : 0.045 0.275 3943 Planarity : 0.005 0.177 4095 Dihedral : 5.097 48.460 4380 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.04 % Favored : 95.86 % Rotamer: Outliers : 1.15 % Allowed : 6.39 % Favored : 92.46 % 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: 0.16 (0.15), residues: 2921 helix: 1.74 (0.21), residues: 675 sheet: 0.45 (0.19), residues: 641 loop : -0.76 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 886 HIS 0.006 0.001 HIS C1048 PHE 0.015 0.001 PHE B 342 TYR 0.017 0.001 TYR B1067 ARG 0.006 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00323 ( 46) link_NAG-ASN : angle 2.44053 ( 138) link_BETA1-4 : bond 0.00382 ( 12) link_BETA1-4 : angle 1.21496 ( 36) hydrogen bonds : bond 0.04423 ( 974) hydrogen bonds : angle 5.58224 ( 2694) SS BOND : bond 0.00229 ( 37) SS BOND : angle 1.62117 ( 74) covalent geometry : bond 0.00399 (23682) covalent geometry : angle 0.56003 (32297) *********************** 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 89 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 62 time to evaluate : 2.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.8444 (t80) REVERT: A 368 LEU cc_start: 0.8734 (mt) cc_final: 0.8332 (tp) REVERT: C 197 ILE cc_start: 0.8776 (mp) cc_final: 0.8499 (mm) REVERT: C 214 ARG cc_start: 0.6075 (tpm170) cc_final: 0.5563 (tpm170) REVERT: C 473 TYR cc_start: 0.0398 (OUTLIER) cc_final: -0.1635 (m-10) outliers start: 27 outliers final: 18 residues processed: 86 average time/residue: 0.4226 time to fit residues: 59.9530 Evaluate side-chains 80 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 4.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 8 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 206 optimal weight: 20.0000 chunk 194 optimal weight: 0.4980 chunk 295 optimal weight: 2.9990 chunk 273 optimal weight: 0.9990 chunk 216 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 625 HIS ** 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 = 0.3943 r_free = 0.3943 target = 0.107891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.072365 restraints weight = 56064.982| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 3.34 r_work: 0.2987 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23777 Z= 0.156 Angle : 0.569 11.849 32545 Z= 0.287 Chirality : 0.044 0.274 3943 Planarity : 0.005 0.158 4095 Dihedral : 4.997 49.801 4378 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.73 % Favored : 96.17 % Rotamer: Outliers : 1.32 % Allowed : 6.85 % Favored : 91.83 % 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: 0.17 (0.15), residues: 2921 helix: 1.78 (0.21), residues: 676 sheet: 0.47 (0.19), residues: 643 loop : -0.78 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 886 HIS 0.005 0.001 HIS C1048 PHE 0.017 0.001 PHE B 342 TYR 0.017 0.001 TYR A1067 ARG 0.006 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00340 ( 46) link_NAG-ASN : angle 2.44407 ( 138) link_BETA1-4 : bond 0.00365 ( 12) link_BETA1-4 : angle 1.17610 ( 36) hydrogen bonds : bond 0.04258 ( 974) hydrogen bonds : angle 5.51205 ( 2694) SS BOND : bond 0.00233 ( 37) SS BOND : angle 1.65693 ( 74) covalent geometry : bond 0.00375 (23682) covalent geometry : angle 0.54071 (32297) *********************** 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 90 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 59 time to evaluate : 2.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.8442 (t80) REVERT: A 368 LEU cc_start: 0.8695 (mt) cc_final: 0.8277 (tp) REVERT: A 633 TRP cc_start: 0.7089 (m100) cc_final: 0.6805 (m100) REVERT: A 1126 CYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7559 (m) REVERT: C 197 ILE cc_start: 0.8782 (mp) cc_final: 0.8499 (mm) REVERT: C 473 TYR cc_start: 0.0372 (OUTLIER) cc_final: -0.1658 (m-10) outliers start: 31 outliers final: 22 residues processed: 86 average time/residue: 0.3596 time to fit residues: 50.8101 Evaluate side-chains 83 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 58 time to evaluate : 2.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 270 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 279 optimal weight: 3.9990 chunk 31 optimal weight: 0.0000 chunk 268 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 175 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 chunk 273 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.108615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.073745 restraints weight = 56102.071| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 3.18 r_work: 0.2998 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23777 Z= 0.115 Angle : 0.525 10.440 32545 Z= 0.265 Chirality : 0.043 0.268 3943 Planarity : 0.004 0.150 4095 Dihedral : 4.729 52.050 4378 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.70 % Favored : 96.23 % Rotamer: Outliers : 1.06 % Allowed : 7.41 % Favored : 91.53 % 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: 0.33 (0.15), residues: 2921 helix: 2.04 (0.21), residues: 674 sheet: 0.44 (0.19), residues: 644 loop : -0.67 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 633 HIS 0.003 0.001 HIS C1058 PHE 0.018 0.001 PHE B 342 TYR 0.017 0.001 TYR A1067 ARG 0.003 0.000 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00351 ( 46) link_NAG-ASN : angle 2.26300 ( 138) link_BETA1-4 : bond 0.00388 ( 12) link_BETA1-4 : angle 1.09648 ( 36) hydrogen bonds : bond 0.03762 ( 974) hydrogen bonds : angle 5.30232 ( 2694) SS BOND : bond 0.00200 ( 37) SS BOND : angle 1.35705 ( 74) covalent geometry : bond 0.00269 (23682) covalent geometry : angle 0.50036 (32297) *********************** 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 88 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 63 time to evaluate : 2.429 Fit side-chains revert: symmetry clash REVERT: A 318 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.8461 (t80) REVERT: A 368 LEU cc_start: 0.8726 (mt) cc_final: 0.8322 (tp) REVERT: A 633 TRP cc_start: 0.7301 (m100) cc_final: 0.6985 (m100) REVERT: C 197 ILE cc_start: 0.8781 (mp) cc_final: 0.8505 (mm) REVERT: C 473 TYR cc_start: 0.0311 (OUTLIER) cc_final: -0.1742 (m-10) outliers start: 25 outliers final: 16 residues processed: 85 average time/residue: 0.3248 time to fit residues: 46.7661 Evaluate side-chains 74 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 2.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 76 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 219 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 215 optimal weight: 8.9990 chunk 263 optimal weight: 3.9990 chunk 264 optimal weight: 4.9990 chunk 224 optimal weight: 6.9990 chunk 155 optimal weight: 0.0980 chunk 162 optimal weight: 3.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 625 HIS ** 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 = 0.3933 r_free = 0.3933 target = 0.107268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.074779 restraints weight = 56225.897| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.74 r_work: 0.2971 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 23777 Z= 0.218 Angle : 0.594 10.346 32545 Z= 0.300 Chirality : 0.046 0.270 3943 Planarity : 0.005 0.147 4095 Dihedral : 5.003 53.569 4378 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.14 % Favored : 95.79 % Rotamer: Outliers : 1.11 % Allowed : 7.75 % Favored : 91.15 % 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: 0.11 (0.15), residues: 2921 helix: 1.73 (0.21), residues: 676 sheet: 0.41 (0.19), residues: 649 loop : -0.82 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 633 HIS 0.006 0.001 HIS C1048 PHE 0.017 0.002 PHE B 342 TYR 0.016 0.001 TYR B1067 ARG 0.003 0.000 ARG C1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 46) link_NAG-ASN : angle 2.46021 ( 138) link_BETA1-4 : bond 0.00331 ( 12) link_BETA1-4 : angle 1.15460 ( 36) hydrogen bonds : bond 0.04692 ( 974) hydrogen bonds : angle 5.57369 ( 2694) SS BOND : bond 0.00376 ( 37) SS BOND : angle 1.50634 ( 74) covalent geometry : bond 0.00540 (23682) covalent geometry : angle 0.56836 (32297) *********************** 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 81 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 55 time to evaluate : 2.656 Fit side-chains revert: symmetry clash REVERT: A 318 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8504 (t80) REVERT: A 368 LEU cc_start: 0.8733 (mt) cc_final: 0.8340 (tp) REVERT: C 197 ILE cc_start: 0.8778 (mp) cc_final: 0.8505 (mm) REVERT: C 473 TYR cc_start: 0.0665 (OUTLIER) cc_final: -0.1607 (m-10) outliers start: 26 outliers final: 18 residues processed: 78 average time/residue: 0.3555 time to fit residues: 46.7768 Evaluate side-chains 73 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 53 time to evaluate : 2.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 116 optimal weight: 20.0000 chunk 286 optimal weight: 0.0870 chunk 121 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 chunk 245 optimal weight: 6.9990 chunk 52 optimal weight: 0.0020 chunk 15 optimal weight: 9.9990 chunk 165 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 43 optimal weight: 0.0040 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 487 ASN B 271 GLN ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.108229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.073041 restraints weight = 55946.060| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 3.28 r_work: 0.3005 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 23777 Z= 0.122 Angle : 0.536 11.967 32545 Z= 0.270 Chirality : 0.043 0.282 3943 Planarity : 0.004 0.145 4095 Dihedral : 4.788 54.719 4378 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.87 % Favored : 96.06 % Rotamer: Outliers : 1.15 % Allowed : 7.79 % Favored : 91.06 % 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: 0.28 (0.15), residues: 2921 helix: 2.00 (0.21), residues: 674 sheet: 0.45 (0.20), residues: 625 loop : -0.72 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 633 HIS 0.003 0.001 HIS C1048 PHE 0.019 0.001 PHE B 342 TYR 0.017 0.001 TYR A1067 ARG 0.003 0.000 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00352 ( 46) link_NAG-ASN : angle 2.28044 ( 138) link_BETA1-4 : bond 0.00374 ( 12) link_BETA1-4 : angle 1.08010 ( 36) hydrogen bonds : bond 0.03866 ( 974) hydrogen bonds : angle 5.35526 ( 2694) SS BOND : bond 0.00257 ( 37) SS BOND : angle 1.87484 ( 74) covalent geometry : bond 0.00287 (23682) covalent geometry : angle 0.50737 (32297) *********************** 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 81 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 54 time to evaluate : 2.590 Fit side-chains revert: symmetry clash REVERT: A 318 PHE cc_start: 0.8701 (OUTLIER) cc_final: 0.8484 (t80) REVERT: A 368 LEU cc_start: 0.8731 (mt) cc_final: 0.8316 (tp) REVERT: C 197 ILE cc_start: 0.8606 (mp) cc_final: 0.8299 (mm) REVERT: C 214 ARG cc_start: 0.6115 (tpm170) cc_final: 0.5900 (mmm160) REVERT: C 473 TYR cc_start: 0.0364 (OUTLIER) cc_final: -0.1730 (m-10) outliers start: 27 outliers final: 20 residues processed: 77 average time/residue: 0.3410 time to fit residues: 44.3622 Evaluate side-chains 75 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 53 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 20 optimal weight: 0.0050 chunk 228 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 244 optimal weight: 7.9990 chunk 8 optimal weight: 20.0000 chunk 170 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 223 optimal weight: 8.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 GLN C 493 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.107493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.071550 restraints weight = 56311.520| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 3.34 r_work: 0.2977 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 23777 Z= 0.186 Angle : 0.575 12.326 32545 Z= 0.289 Chirality : 0.045 0.276 3943 Planarity : 0.004 0.144 4095 Dihedral : 4.912 55.517 4378 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.21 % Favored : 95.72 % Rotamer: Outliers : 0.89 % Allowed : 8.09 % Favored : 91.02 % 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: 0.15 (0.15), residues: 2921 helix: 1.86 (0.21), residues: 675 sheet: 0.39 (0.20), residues: 623 loop : -0.79 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 633 HIS 0.006 0.001 HIS C1048 PHE 0.019 0.001 PHE B 342 TYR 0.015 0.001 TYR B1067 ARG 0.003 0.000 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 46) link_NAG-ASN : angle 2.38686 ( 138) link_BETA1-4 : bond 0.00344 ( 12) link_BETA1-4 : angle 1.11130 ( 36) hydrogen bonds : bond 0.04429 ( 974) hydrogen bonds : angle 5.48093 ( 2694) SS BOND : bond 0.00284 ( 37) SS BOND : angle 1.98410 ( 74) covalent geometry : bond 0.00454 (23682) covalent geometry : angle 0.54616 (32297) ********************** 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 74 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 2.682 Fit side-chains revert: symmetry clash REVERT: A 318 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.8527 (t80) REVERT: A 368 LEU cc_start: 0.8716 (mt) cc_final: 0.8312 (tp) REVERT: C 197 ILE cc_start: 0.8613 (mp) cc_final: 0.8308 (mm) REVERT: C 473 TYR cc_start: 0.0532 (OUTLIER) cc_final: -0.1653 (m-10) outliers start: 21 outliers final: 19 residues processed: 71 average time/residue: 0.3542 time to fit residues: 42.5867 Evaluate side-chains 71 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 50 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 2 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 138 optimal weight: 50.0000 chunk 225 optimal weight: 0.9980 chunk 207 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 284 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 95 optimal weight: 0.5980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 321 GLN ** 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 = 0.3944 r_free = 0.3944 target = 0.107939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.072719 restraints weight = 55936.289| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.20 r_work: 0.2997 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23777 Z= 0.142 Angle : 0.541 10.610 32545 Z= 0.272 Chirality : 0.044 0.283 3943 Planarity : 0.004 0.143 4095 Dihedral : 4.810 56.763 4378 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.04 % Favored : 95.93 % Rotamer: Outliers : 1.02 % Allowed : 8.00 % Favored : 90.97 % 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: 0.22 (0.15), residues: 2921 helix: 1.97 (0.21), residues: 675 sheet: 0.42 (0.20), residues: 628 loop : -0.77 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 633 HIS 0.004 0.001 HIS C1048 PHE 0.019 0.001 PHE B 342 TYR 0.017 0.001 TYR A1067 ARG 0.003 0.000 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00327 ( 46) link_NAG-ASN : angle 2.29749 ( 138) link_BETA1-4 : bond 0.00364 ( 12) link_BETA1-4 : angle 1.07463 ( 36) hydrogen bonds : bond 0.04020 ( 974) hydrogen bonds : angle 5.36774 ( 2694) SS BOND : bond 0.00264 ( 37) SS BOND : angle 1.76075 ( 74) covalent geometry : bond 0.00343 (23682) covalent geometry : angle 0.51366 (32297) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14537.09 seconds wall clock time: 250 minutes 35.22 seconds (15035.22 seconds total)