Starting phenix.real_space_refine on Fri Jun 20 05:41:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tp8_26048/06_2025/7tp8_26048.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tp8_26048/06_2025/7tp8_26048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tp8_26048/06_2025/7tp8_26048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tp8_26048/06_2025/7tp8_26048.map" model { file = "/net/cci-nas-00/data/ceres_data/7tp8_26048/06_2025/7tp8_26048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tp8_26048/06_2025/7tp8_26048.cif" } resolution = 3.4 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= 0.144 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 6 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: {'PCIS': 1, 'PTRANS': 47, '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: 13.39, per 1000 atoms: 0.58 Number of scatterers: 23199 At special positions: 0 Unit cell: (128.52, 133.92, 181.44, 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 6.01 Conformation dependent library (CDL) restraints added in 2.7 seconds 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5594 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 44 sheets defined 27.8% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.49 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.191A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.128A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 4.238A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.953A 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 438 through 442 Processing helix chain 'A' and resid 632 through 638 removed outlier: 3.594A pdb=" N VAL A 635 " --> pdb=" O THR A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.698A 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: 3.509A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.609A 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 891 removed outlier: 3.539A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.673A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.528A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.601A 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: 3.663A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (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: 3.862A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.565A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 371 Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 404 through 408 Processing helix chain 'B' and resid 416 through 421 removed outlier: 3.566A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 441 No H-bonds generated for 'chain 'B' and resid 439 through 441' Processing helix chain 'B' and resid 447 through 450 removed outlier: 3.976A pdb=" N ASN B 450 " --> pdb=" O GLY B 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 447 through 450' Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 629 through 634 Processing helix chain 'B' and resid 635 through 637 No H-bonds generated for 'chain 'B' and resid 635 through 637' Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.818A 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: 3.897A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.761A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY B 891 " --> pdb=" O THR B 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 891' Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.661A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.511A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.738A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.827A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.855A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.233A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.777A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.227A 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: 3.520A pdb=" N VAL C 622 " --> pdb=" O GLU C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.897A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 6.121A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.593A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.817A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.604A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.596A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 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 removed outlier: 3.733A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.652A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.297A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1143 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.176A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.917A 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: 7.319A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.667A 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 314 removed outlier: 4.105A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 328 removed outlier: 6.226A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.754A 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: 3.928A 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: 6.667A 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: 6.652A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.771A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.551A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.551A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.581A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.789A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.249A 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: 3.788A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.651A pdb=" N ASN B 125 " --> pdb=" O ASN B 122 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.395A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.175A 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: 4.973A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.137A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.137A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.151A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.602A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.501A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.796A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.533A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.788A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.956A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.383A 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: 5.662A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.715A 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: 6.855A 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 removed outlier: 3.668A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.387A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.583A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.883A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.604A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1017 hydrogen bonds defined for protein. 2760 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.97 Time building geometry restraints manager: 6.88 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: 6482 1.33 - 1.46: 4028 1.46 - 1.58: 13048 1.58 - 1.70: 0 1.70 - 1.82: 124 Bond restraints: 23682 Sorted by residual: bond pdb=" C5 NAG C1310 " pdb=" O5 NAG C1310 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C5 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C5 NAG A1306 " pdb=" O5 NAG A1306 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C5 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C5 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.38e+01 ... (remaining 23677 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.34: 31833 4.34 - 8.68: 461 8.68 - 13.02: 2 13.02 - 17.35: 0 17.35 - 21.69: 1 Bond angle restraints: 32297 Sorted by residual: angle pdb=" CB LEU B 212 " pdb=" CG LEU B 212 " pdb=" CD1 LEU B 212 " ideal model delta sigma weight residual 110.70 132.39 -21.69 3.00e+00 1.11e-01 5.23e+01 angle pdb=" CA PHE A 329 " pdb=" CB PHE A 329 " pdb=" CG PHE A 329 " ideal model delta sigma weight residual 113.80 119.78 -5.98 1.00e+00 1.00e+00 3.57e+01 angle pdb=" C GLU C 619 " pdb=" N VAL C 620 " pdb=" CA VAL C 620 " ideal model delta sigma weight residual 120.33 124.93 -4.60 8.00e-01 1.56e+00 3.30e+01 angle pdb=" C ARG C 634 " pdb=" N VAL C 635 " pdb=" CA VAL C 635 " ideal model delta sigma weight residual 120.86 130.42 -9.56 1.67e+00 3.59e-01 3.28e+01 angle pdb=" CA VAL C 620 " pdb=" C VAL C 620 " pdb=" N PRO C 621 " ideal model delta sigma weight residual 120.83 124.25 -3.42 6.10e-01 2.69e+00 3.15e+01 ... (remaining 32292 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 13874 17.94 - 35.87: 714 35.87 - 53.81: 129 53.81 - 71.74: 44 71.74 - 89.68: 32 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 -164.04 78.04 1 1.00e+01 1.00e-02 7.61e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -155.83 69.83 1 1.00e+01 1.00e-02 6.29e+01 dihedral pdb=" C TRP C 633 " pdb=" N TRP C 633 " pdb=" CA TRP C 633 " pdb=" CB TRP C 633 " ideal model delta harmonic sigma weight residual -122.60 -140.86 18.26 0 2.50e+00 1.60e-01 5.33e+01 ... (remaining 14790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.260: 3914 0.260 - 0.519: 27 0.519 - 0.779: 1 0.779 - 1.038: 0 1.038 - 1.298: 1 Chirality restraints: 3943 Sorted by residual: chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.41e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.31e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.94e+01 ... (remaining 3940 not shown) Planarity restraints: 4141 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 603 " 0.136 2.00e-02 2.50e+03 1.41e-01 2.50e+02 pdb=" CG ASN B 603 " -0.087 2.00e-02 2.50e+03 pdb=" OD1 ASN B 603 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN B 603 " -0.212 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " 0.169 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 657 " -0.132 2.00e-02 2.50e+03 1.39e-01 2.41e+02 pdb=" CG ASN B 657 " 0.077 2.00e-02 2.50e+03 pdb=" OD1 ASN B 657 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN B 657 " 0.213 2.00e-02 2.50e+03 pdb=" C1 NAG B1309 " -0.167 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 633 " -0.128 2.00e-02 2.50e+03 8.70e-02 1.89e+02 pdb=" CG TRP C 633 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP C 633 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 TRP C 633 " 0.038 2.00e-02 2.50e+03 pdb=" NE1 TRP C 633 " 0.102 2.00e-02 2.50e+03 pdb=" CE2 TRP C 633 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 633 " 0.137 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 633 " -0.106 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 633 " 0.056 2.00e-02 2.50e+03 pdb=" CH2 TRP C 633 " -0.103 2.00e-02 2.50e+03 ... (remaining 4138 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 11553 3.00 - 3.47: 22170 3.47 - 3.95: 36913 3.95 - 4.42: 41115 4.42 - 4.90: 69850 Nonbonded interactions: 181601 Sorted by model distance: nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.519 3.040 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.522 3.040 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.526 3.040 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.527 3.040 nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.542 3.040 ... (remaining 181596 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: 2.530 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: 0.010 Extract box with map and model: 0.880 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 53.390 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 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 : 0.013 0.076 23777 Z= 0.769 Angle : 1.790 21.692 32545 Z= 1.174 Chirality : 0.098 1.298 3943 Planarity : 0.012 0.120 4095 Dihedral : 12.517 89.681 9088 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 0.07 Ramachandran Plot: Outliers : 0.92 % Allowed : 6.26 % Favored : 92.81 % Rotamer: Outliers : 0.98 % Allowed : 2.64 % Favored : 96.38 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.98 (0.14), residues: 2921 helix: -0.76 (0.17), residues: 663 sheet: 0.52 (0.23), residues: 480 loop : -0.93 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.137 0.023 TRP C 633 HIS 0.009 0.003 HIS A 625 PHE 0.134 0.011 PHE C 318 TYR 0.130 0.018 TYR C 380 ARG 0.008 0.001 ARG B 328 Details of bonding type rmsd link_NAG-ASN : bond 0.01119 ( 46) link_NAG-ASN : angle 4.62578 ( 138) link_BETA1-4 : bond 0.02438 ( 12) link_BETA1-4 : angle 4.35498 ( 36) hydrogen bonds : bond 0.16957 ( 1005) hydrogen bonds : angle 8.43695 ( 2760) SS BOND : bond 0.00964 ( 37) SS BOND : angle 2.05733 ( 74) covalent geometry : bond 0.01344 (23682) covalent geometry : angle 1.76286 (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 80 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 57 time to evaluate : 2.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 ARG cc_start: 0.6409 (tpt90) cc_final: 0.6186 (tpt90) REVERT: C 197 ILE cc_start: 0.8306 (mt) cc_final: 0.8046 (tt) REVERT: C 615 VAL cc_start: 0.8692 (OUTLIER) cc_final: 0.8294 (p) REVERT: C 987 VAL cc_start: 0.8766 (t) cc_final: 0.8533 (m) outliers start: 23 outliers final: 7 residues processed: 80 average time/residue: 0.4082 time to fit residues: 51.8765 Evaluate side-chains 41 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 615 VAL 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: 9.9990 chunk 225 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 151 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 chunk 232 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 141 optimal weight: 7.9990 chunk 173 optimal weight: 0.9990 chunk 269 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN A 935 GLN B 343 ASN B1002 GLN B1088 HIS C 628 GLN C 955 ASN C 965 GLN C1088 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.065255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.046336 restraints weight = 104951.088| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 3.39 r_work: 0.2852 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23777 Z= 0.148 Angle : 0.680 9.916 32545 Z= 0.354 Chirality : 0.046 0.260 3943 Planarity : 0.004 0.045 4095 Dihedral : 6.524 57.758 4389 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.18 % Favored : 95.52 % Rotamer: Outliers : 0.55 % Allowed : 4.26 % Favored : 95.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.15), residues: 2921 helix: 1.18 (0.20), residues: 670 sheet: 0.50 (0.19), residues: 661 loop : -0.82 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 633 HIS 0.005 0.001 HIS C 625 PHE 0.017 0.001 PHE B 643 TYR 0.022 0.002 TYR C 473 ARG 0.006 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 46) link_NAG-ASN : angle 3.27667 ( 138) link_BETA1-4 : bond 0.00732 ( 12) link_BETA1-4 : angle 1.79403 ( 36) hydrogen bonds : bond 0.05317 ( 1005) hydrogen bonds : angle 6.29853 ( 2760) SS BOND : bond 0.00256 ( 37) SS BOND : angle 1.16010 ( 74) covalent geometry : bond 0.00319 (23682) covalent geometry : angle 0.64297 (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 50 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 2.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1126 CYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7856 (m) REVERT: C 197 ILE cc_start: 0.8569 (mt) cc_final: 0.8238 (tt) REVERT: C 615 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8182 (p) outliers start: 13 outliers final: 7 residues processed: 50 average time/residue: 0.3580 time to fit residues: 30.8126 Evaluate side-chains 41 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 634 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 182 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 284 optimal weight: 1.9990 chunk 254 optimal weight: 1.9990 chunk 69 optimal weight: 0.0070 chunk 278 optimal weight: 3.9990 chunk 264 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 128 optimal weight: 30.0000 chunk 162 optimal weight: 5.9990 chunk 271 optimal weight: 6.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.064687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.045485 restraints weight = 104124.212| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.99 r_work: 0.2857 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2143 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= 0.151 Angle : 0.580 8.342 32545 Z= 0.300 Chirality : 0.045 0.211 3943 Planarity : 0.004 0.042 4095 Dihedral : 5.700 59.530 4387 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.69 % Favored : 95.07 % Rotamer: Outliers : 0.72 % Allowed : 4.98 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.15), residues: 2921 helix: 1.82 (0.20), residues: 665 sheet: 0.61 (0.20), residues: 625 loop : -0.76 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 633 HIS 0.005 0.001 HIS A1058 PHE 0.013 0.001 PHE B 888 TYR 0.019 0.001 TYR A1067 ARG 0.006 0.000 ARG C 634 Details of bonding type rmsd link_NAG-ASN : bond 0.00360 ( 46) link_NAG-ASN : angle 2.22360 ( 138) link_BETA1-4 : bond 0.00348 ( 12) link_BETA1-4 : angle 1.26520 ( 36) hydrogen bonds : bond 0.04447 ( 1005) hydrogen bonds : angle 5.70385 ( 2760) SS BOND : bond 0.00263 ( 37) SS BOND : angle 0.81286 ( 74) covalent geometry : bond 0.00350 (23682) covalent geometry : angle 0.56119 (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 52 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 35 time to evaluate : 2.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 231 ILE cc_start: 0.8963 (pt) cc_final: 0.8718 (mm) REVERT: C 197 ILE cc_start: 0.8354 (mt) cc_final: 0.8035 (tt) outliers start: 17 outliers final: 8 residues processed: 49 average time/residue: 0.3121 time to fit residues: 28.2898 Evaluate side-chains 40 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 2.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 731 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 137 optimal weight: 50.0000 chunk 228 optimal weight: 0.7980 chunk 151 optimal weight: 0.9990 chunk 221 optimal weight: 0.0270 chunk 57 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 239 optimal weight: 7.9990 chunk 271 optimal weight: 7.9990 chunk 199 optimal weight: 9.9990 chunk 270 optimal weight: 0.8980 chunk 153 optimal weight: 0.9980 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 628 GLN B 907 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.065603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.046922 restraints weight = 105409.077| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.38 r_work: 0.2877 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23777 Z= 0.092 Angle : 0.507 8.162 32545 Z= 0.262 Chirality : 0.043 0.281 3943 Planarity : 0.003 0.042 4095 Dihedral : 5.059 58.631 4383 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.36 % Favored : 96.44 % Rotamer: Outliers : 0.81 % Allowed : 5.28 % Favored : 93.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.16), residues: 2921 helix: 2.23 (0.21), residues: 660 sheet: 0.57 (0.19), residues: 659 loop : -0.63 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 633 HIS 0.004 0.001 HIS C 625 PHE 0.009 0.001 PHE B1121 TYR 0.018 0.001 TYR A1067 ARG 0.006 0.000 ARG C 634 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 46) link_NAG-ASN : angle 1.88057 ( 138) link_BETA1-4 : bond 0.00395 ( 12) link_BETA1-4 : angle 1.15329 ( 36) hydrogen bonds : bond 0.03683 ( 1005) hydrogen bonds : angle 5.35728 ( 2760) SS BOND : bond 0.00183 ( 37) SS BOND : angle 0.63358 ( 74) covalent geometry : bond 0.00189 (23682) covalent geometry : angle 0.49155 (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 51 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 32 time to evaluate : 2.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 6 residues processed: 50 average time/residue: 0.3258 time to fit residues: 29.4701 Evaluate side-chains 36 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 2.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 634 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 131 optimal weight: 0.3980 chunk 86 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 137 optimal weight: 40.0000 chunk 20 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 chunk 248 optimal weight: 0.0470 chunk 249 optimal weight: 20.0000 chunk 163 optimal weight: 6.9990 overall best weight: 1.8884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN B 641 ASN B 907 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.064985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.045708 restraints weight = 105385.647| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.05 r_work: 0.2863 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23777 Z= 0.125 Angle : 0.506 8.214 32545 Z= 0.262 Chirality : 0.043 0.192 3943 Planarity : 0.003 0.043 4095 Dihedral : 4.848 59.288 4383 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.94 % Favored : 95.82 % Rotamer: Outliers : 0.60 % Allowed : 5.66 % Favored : 93.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.16), residues: 2921 helix: 2.34 (0.21), residues: 658 sheet: 0.56 (0.19), residues: 660 loop : -0.63 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 633 HIS 0.005 0.001 HIS A1058 PHE 0.014 0.001 PHE C 65 TYR 0.019 0.001 TYR A1067 ARG 0.006 0.000 ARG C 634 Details of bonding type rmsd link_NAG-ASN : bond 0.00231 ( 46) link_NAG-ASN : angle 1.81759 ( 138) link_BETA1-4 : bond 0.00335 ( 12) link_BETA1-4 : angle 1.14481 ( 36) hydrogen bonds : bond 0.03850 ( 1005) hydrogen bonds : angle 5.28878 ( 2760) SS BOND : bond 0.00228 ( 37) SS BOND : angle 0.59576 ( 74) covalent geometry : bond 0.00288 (23682) covalent geometry : angle 0.49184 (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 46 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 32 time to evaluate : 3.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 902 MET cc_start: 0.9168 (tpt) cc_final: 0.8757 (tpp) outliers start: 14 outliers final: 10 residues processed: 44 average time/residue: 0.4105 time to fit residues: 34.7909 Evaluate side-chains 41 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 3.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 731 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 8 optimal weight: 0.7980 chunk 147 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 206 optimal weight: 20.0000 chunk 194 optimal weight: 5.9990 chunk 295 optimal weight: 5.9990 chunk 273 optimal weight: 3.9990 chunk 216 optimal weight: 0.1980 chunk 60 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 913 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.064142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.044689 restraints weight = 104377.045| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.16 r_work: 0.2816 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23777 Z= 0.126 Angle : 0.496 8.277 32545 Z= 0.257 Chirality : 0.043 0.188 3943 Planarity : 0.003 0.043 4095 Dihedral : 4.750 58.679 4383 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.94 % Favored : 95.86 % Rotamer: Outliers : 0.68 % Allowed : 5.96 % Favored : 93.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.51 (0.16), residues: 2921 helix: 2.42 (0.21), residues: 652 sheet: 0.48 (0.20), residues: 620 loop : -0.58 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 633 HIS 0.004 0.001 HIS A1058 PHE 0.014 0.001 PHE C 65 TYR 0.019 0.001 TYR A1067 ARG 0.006 0.000 ARG C 634 Details of bonding type rmsd link_NAG-ASN : bond 0.00219 ( 46) link_NAG-ASN : angle 1.73614 ( 138) link_BETA1-4 : bond 0.00357 ( 12) link_BETA1-4 : angle 1.09297 ( 36) hydrogen bonds : bond 0.03784 ( 1005) hydrogen bonds : angle 5.21614 ( 2760) SS BOND : bond 0.00195 ( 37) SS BOND : angle 0.55973 ( 74) covalent geometry : bond 0.00289 (23682) covalent geometry : angle 0.48290 (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 48 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 32 time to evaluate : 2.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 902 MET cc_start: 0.9128 (tpt) cc_final: 0.8757 (tpp) REVERT: C 473 TYR cc_start: 0.2308 (OUTLIER) cc_final: 0.1518 (t80) outliers start: 16 outliers final: 12 residues processed: 47 average time/residue: 0.3309 time to fit residues: 29.1643 Evaluate side-chains 45 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 32 time to evaluate : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 731 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 270 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 279 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 268 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 175 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 273 optimal weight: 0.0050 chunk 82 optimal weight: 0.4980 chunk 165 optimal weight: 6.9990 overall best weight: 1.5000 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.064484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.045000 restraints weight = 105544.315| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.18 r_work: 0.2829 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23777 Z= 0.105 Angle : 0.474 8.048 32545 Z= 0.245 Chirality : 0.042 0.179 3943 Planarity : 0.003 0.044 4095 Dihedral : 4.525 57.940 4383 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.90 % Favored : 95.89 % Rotamer: Outliers : 0.60 % Allowed : 6.26 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.58 (0.16), residues: 2921 helix: 2.55 (0.21), residues: 652 sheet: 0.49 (0.20), residues: 612 loop : -0.54 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 633 HIS 0.003 0.001 HIS A1058 PHE 0.013 0.001 PHE C 65 TYR 0.019 0.001 TYR A1067 ARG 0.005 0.000 ARG C 634 Details of bonding type rmsd link_NAG-ASN : bond 0.00218 ( 46) link_NAG-ASN : angle 1.59437 ( 138) link_BETA1-4 : bond 0.00372 ( 12) link_BETA1-4 : angle 1.05000 ( 36) hydrogen bonds : bond 0.03525 ( 1005) hydrogen bonds : angle 5.06655 ( 2760) SS BOND : bond 0.00184 ( 37) SS BOND : angle 0.52753 ( 74) covalent geometry : bond 0.00234 (23682) covalent geometry : angle 0.46208 (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 46 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 32 time to evaluate : 2.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 902 MET cc_start: 0.9218 (tpt) cc_final: 0.8776 (tpp) REVERT: C 473 TYR cc_start: 0.1963 (OUTLIER) cc_final: 0.1371 (t80) outliers start: 14 outliers final: 12 residues processed: 45 average time/residue: 0.3277 time to fit residues: 27.4099 Evaluate side-chains 44 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 31 time to evaluate : 2.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 859 THR 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: 9.9990 chunk 219 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 215 optimal weight: 0.6980 chunk 263 optimal weight: 4.9990 chunk 264 optimal weight: 0.0770 chunk 224 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 162 optimal weight: 4.9990 overall best weight: 3.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 935 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.063587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.044765 restraints weight = 105630.303| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.54 r_work: 0.2773 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 23777 Z= 0.180 Angle : 0.522 8.377 32545 Z= 0.269 Chirality : 0.044 0.184 3943 Planarity : 0.003 0.043 4095 Dihedral : 4.710 58.733 4383 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.18 % Favored : 95.62 % Rotamer: Outliers : 0.81 % Allowed : 6.22 % Favored : 92.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.43 (0.15), residues: 2921 helix: 2.37 (0.21), residues: 654 sheet: 0.43 (0.20), residues: 602 loop : -0.63 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 633 HIS 0.006 0.001 HIS A1058 PHE 0.014 0.001 PHE B 201 TYR 0.019 0.001 TYR A1067 ARG 0.006 0.000 ARG C 634 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 46) link_NAG-ASN : angle 1.73976 ( 138) link_BETA1-4 : bond 0.00282 ( 12) link_BETA1-4 : angle 1.10210 ( 36) hydrogen bonds : bond 0.04108 ( 1005) hydrogen bonds : angle 5.24006 ( 2760) SS BOND : bond 0.00232 ( 37) SS BOND : angle 0.62833 ( 74) covalent geometry : bond 0.00423 (23682) covalent geometry : angle 0.50946 (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 51 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 32 time to evaluate : 2.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 902 MET cc_start: 0.9225 (tpt) cc_final: 0.8895 (tpp) REVERT: C 473 TYR cc_start: 0.2221 (OUTLIER) cc_final: 0.1392 (t80) outliers start: 19 outliers final: 14 residues processed: 50 average time/residue: 0.3112 time to fit residues: 28.8433 Evaluate side-chains 47 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 32 time to evaluate : 2.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 859 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 116 optimal weight: 7.9990 chunk 286 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 128 optimal weight: 30.0000 chunk 245 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN B1088 HIS C 957 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.062752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.043853 restraints weight = 105686.468| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 3.52 r_work: 0.2734 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 23777 Z= 0.270 Angle : 0.605 9.119 32545 Z= 0.310 Chirality : 0.046 0.217 3943 Planarity : 0.004 0.048 4095 Dihedral : 5.171 58.496 4383 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.72 % Favored : 95.07 % Rotamer: Outliers : 0.77 % Allowed : 6.43 % Favored : 92.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.09 (0.15), residues: 2921 helix: 1.89 (0.20), residues: 667 sheet: 0.23 (0.19), residues: 615 loop : -0.80 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B1102 HIS 0.008 0.001 HIS A1058 PHE 0.021 0.002 PHE B 201 TYR 0.019 0.002 TYR A 369 ARG 0.005 0.001 ARG C 634 Details of bonding type rmsd link_NAG-ASN : bond 0.00346 ( 46) link_NAG-ASN : angle 1.97388 ( 138) link_BETA1-4 : bond 0.00241 ( 12) link_BETA1-4 : angle 1.15318 ( 36) hydrogen bonds : bond 0.04754 ( 1005) hydrogen bonds : angle 5.50476 ( 2760) SS BOND : bond 0.00318 ( 37) SS BOND : angle 0.80275 ( 74) covalent geometry : bond 0.00644 (23682) covalent geometry : angle 0.59115 (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 49 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 31 time to evaluate : 2.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 473 TYR cc_start: 0.2608 (OUTLIER) cc_final: 0.1229 (t80) outliers start: 18 outliers final: 15 residues processed: 48 average time/residue: 0.3514 time to fit residues: 30.9146 Evaluate side-chains 46 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 30 time to evaluate : 3.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 907 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 20 optimal weight: 4.9990 chunk 228 optimal weight: 5.9990 chunk 109 optimal weight: 0.2980 chunk 10 optimal weight: 0.4980 chunk 244 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 170 optimal weight: 0.8980 chunk 248 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 55 optimal weight: 20.0000 chunk 223 optimal weight: 7.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 935 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.063382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.044471 restraints weight = 105374.366| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 3.44 r_work: 0.2770 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 23777 Z= 0.152 Angle : 0.519 8.844 32545 Z= 0.267 Chirality : 0.043 0.203 3943 Planarity : 0.003 0.053 4095 Dihedral : 4.913 56.657 4383 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.38 % Favored : 95.45 % Rotamer: Outliers : 0.55 % Allowed : 6.51 % Favored : 92.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.21 (0.15), residues: 2921 helix: 2.14 (0.21), residues: 663 sheet: 0.18 (0.20), residues: 600 loop : -0.71 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 633 HIS 0.005 0.001 HIS C 625 PHE 0.016 0.001 PHE B 201 TYR 0.019 0.001 TYR A1067 ARG 0.004 0.000 ARG C 634 Details of bonding type rmsd link_NAG-ASN : bond 0.00231 ( 46) link_NAG-ASN : angle 1.74484 ( 138) link_BETA1-4 : bond 0.00303 ( 12) link_BETA1-4 : angle 1.02780 ( 36) hydrogen bonds : bond 0.04105 ( 1005) hydrogen bonds : angle 5.28409 ( 2760) SS BOND : bond 0.00224 ( 37) SS BOND : angle 0.61667 ( 74) covalent geometry : bond 0.00353 (23682) covalent geometry : angle 0.50659 (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 42 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 29 time to evaluate : 2.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 902 MET cc_start: 0.9231 (tpt) cc_final: 0.8891 (tpp) REVERT: C 473 TYR cc_start: 0.2516 (OUTLIER) cc_final: 0.1207 (t80) outliers start: 13 outliers final: 12 residues processed: 41 average time/residue: 0.3274 time to fit residues: 24.8828 Evaluate side-chains 42 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 29 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 907 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 2 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 138 optimal weight: 50.0000 chunk 225 optimal weight: 7.9990 chunk 207 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 284 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 48 optimal weight: 0.0770 chunk 95 optimal weight: 0.7980 overall best weight: 1.7542 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.063857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.045121 restraints weight = 104758.538| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 3.52 r_work: 0.2787 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23777 Z= 0.117 Angle : 0.487 8.782 32545 Z= 0.252 Chirality : 0.043 0.183 3943 Planarity : 0.003 0.055 4095 Dihedral : 4.646 56.310 4383 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.55 % Favored : 95.31 % Rotamer: Outliers : 0.60 % Allowed : 6.47 % Favored : 92.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.38 (0.16), residues: 2921 helix: 2.40 (0.21), residues: 655 sheet: 0.23 (0.19), residues: 605 loop : -0.63 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 633 HIS 0.005 0.001 HIS C 625 PHE 0.013 0.001 PHE B 201 TYR 0.022 0.001 TYR A 369 ARG 0.004 0.000 ARG C 634 Details of bonding type rmsd link_NAG-ASN : bond 0.00212 ( 46) link_NAG-ASN : angle 1.61765 ( 138) link_BETA1-4 : bond 0.00332 ( 12) link_BETA1-4 : angle 1.00673 ( 36) hydrogen bonds : bond 0.03722 ( 1005) hydrogen bonds : angle 5.10811 ( 2760) SS BOND : bond 0.00200 ( 37) SS BOND : angle 0.56931 ( 74) covalent geometry : bond 0.00265 (23682) covalent geometry : angle 0.47580 (32297) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9950.74 seconds wall clock time: 173 minutes 58.57 seconds (10438.57 seconds total)