Starting phenix.real_space_refine on Sat Jul 4 22:44:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lww_23559/07_2026/7lww_23559.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lww_23559/07_2026/7lww_23559.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7lww_23559/07_2026/7lww_23559.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lww_23559/07_2026/7lww_23559.cif" model { file = "/net/cci-nas-00/data/ceres_data/7lww_23559/07_2026/7lww_23559.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lww_23559/07_2026/7lww_23559.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lww_23559/07_2026/7lww_23559.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lww_23559/07_2026/7lww_23559.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= -0.000 sd= 0.076 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 101 5.16 5 C 15176 2.51 5 N 3896 2.21 5 O 4613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23786 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7708 Classifications: {'peptide': 995} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 46, 'TRANS': 948} Chain breaks: 8 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 7702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7702 Classifications: {'peptide': 995} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 46, 'TRANS': 948} Chain breaks: 8 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 3, 'GLN:plan1': 4, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "C" Number of atoms: 7676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7676 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 46, 'TRANS': 945} Chain breaks: 8 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 6, 'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 53 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 5.15, per 1000 atoms: 0.22 Number of scatterers: 23786 At special positions: 0 Unit cell: (129.349, 135.763, 192.42, 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 101 16.00 O 4613 8.00 N 3896 7.00 C 15176 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 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=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.06 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 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=2.02 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=2.05 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.00 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 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.01 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 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=2.01 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 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 234 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG B1301 " - " ASN B 234 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B 282 " " NAG C1301 " - " ASN C1074 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 61 " " NAG C1306 " - " ASN C 122 " " NAG C1307 " - " ASN C 282 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 616 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN A1134 " " NAG H 1 " - " ASN B 331 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN B1134 " " NAG K 1 " - " ASN B 801 " " 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: 1.76 Conformation dependent library (CDL) restraints added in 927.4 milliseconds 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5580 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 46 sheets defined 27.6% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.832A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.749A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.814A 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 443 removed outlier: 3.610A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.789A 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: 3.802A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.562A 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: 3.701A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.626A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.298A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.173A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 142 removed outlier: 3.916A pdb=" N LEU B 141 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.925A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.546A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.285A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.947A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 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: 3.847A 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: 3.814A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.175A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.560A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.719A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.377A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.249A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.237A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.926A 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 438 through 443 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.794A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.515A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 4.386A pdb=" N GLN C 926 " --> pdb=" O LEU C 922 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N SER C 929 " --> pdb=" O ASN C 925 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.636A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.701A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1143 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.452A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.866A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.549A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.285A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.153A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.990A 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: 3.926A 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: 6.957A 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: 6.040A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.554A 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: 6.850A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.034A 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: 6.492A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.492A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.000A 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: 4.590A 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: 8.575A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.363A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.290A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 10.511A pdb=" N SER B 221 " --> pdb=" O PRO B 209 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ARG B 34 " --> pdb=" O SER B 221 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N LEU B 223 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 6.890A 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: 3.970A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.774A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.414A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.367A 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: 5.466A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.756A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.545A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.576A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.386A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.366A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.553A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 9.120A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.827A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.678A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.714A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.438A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.378A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.378A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.866A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.709A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE8, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.236A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.469A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.870A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1041 hydrogen bonds defined for protein. 2838 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: 5.15 Time building geometry restraints manager: 2.38 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: 6353 1.33 - 1.46: 4477 1.46 - 1.58: 13344 1.58 - 1.70: 0 1.70 - 1.82: 125 Bond restraints: 24299 Sorted by residual: bond pdb=" CA PRO B 792 " pdb=" C PRO B 792 " ideal model delta sigma weight residual 1.514 1.539 -0.025 5.50e-03 3.31e+04 2.10e+01 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C5 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C5 NAG A1306 " pdb=" O5 NAG A1306 " 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 C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.43e+01 ... (remaining 24294 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 27296 2.44 - 4.88: 5522 4.88 - 7.32: 238 7.32 - 9.76: 11 9.76 - 12.20: 3 Bond angle restraints: 33070 Sorted by residual: angle pdb=" CA PHE B 559 " pdb=" CB PHE B 559 " pdb=" CG PHE B 559 " ideal model delta sigma weight residual 113.80 120.41 -6.61 1.00e+00 1.00e+00 4.37e+01 angle pdb=" CA ASP C 198 " pdb=" CB ASP C 198 " pdb=" CG ASP C 198 " ideal model delta sigma weight residual 112.60 119.16 -6.56 1.00e+00 1.00e+00 4.31e+01 angle pdb=" CA PHE B 106 " pdb=" CB PHE B 106 " pdb=" CG PHE B 106 " ideal model delta sigma weight residual 113.80 119.67 -5.87 1.00e+00 1.00e+00 3.44e+01 angle pdb=" C ASP C 111 " pdb=" N SER C 112 " pdb=" CA SER C 112 " ideal model delta sigma weight residual 121.54 132.32 -10.78 1.91e+00 2.74e-01 3.18e+01 angle pdb=" OE1 GLN B 965 " pdb=" CD GLN B 965 " pdb=" NE2 GLN B 965 " ideal model delta sigma weight residual 122.60 117.03 5.57 1.00e+00 1.00e+00 3.11e+01 ... (remaining 33065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 13130 18.05 - 36.09: 703 36.09 - 54.14: 123 54.14 - 72.18: 43 72.18 - 90.23: 23 Dihedral angle restraints: 14022 sinusoidal: 5355 harmonic: 8667 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual 93.00 -178.26 -88.74 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -149.06 63.06 1 1.00e+01 1.00e-02 5.25e+01 dihedral pdb=" C ASP C 198 " pdb=" N ASP C 198 " pdb=" CA ASP C 198 " pdb=" CB ASP C 198 " ideal model delta harmonic sigma weight residual -122.60 -138.15 15.55 0 2.50e+00 1.60e-01 3.87e+01 ... (remaining 14019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.279: 3916 0.279 - 0.558: 25 0.558 - 0.838: 1 0.838 - 1.117: 0 1.117 - 1.396: 3 Chirality restraints: 3945 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.01e+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 -2.59 0.19 2.00e-02 2.50e+03 8.78e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.57e+01 ... (remaining 3942 not shown) Planarity restraints: 4233 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 886 " 0.375 2.00e-02 2.50e+03 2.01e-01 1.01e+03 pdb=" CG TRP C 886 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP C 886 " -0.093 2.00e-02 2.50e+03 pdb=" CD2 TRP C 886 " -0.181 2.00e-02 2.50e+03 pdb=" NE1 TRP C 886 " -0.144 2.00e-02 2.50e+03 pdb=" CE2 TRP C 886 " -0.019 2.00e-02 2.50e+03 pdb=" CE3 TRP C 886 " -0.291 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 886 " 0.227 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 886 " -0.085 2.00e-02 2.50e+03 pdb=" CH2 TRP C 886 " 0.239 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 904 " -0.207 2.00e-02 2.50e+03 1.27e-01 3.23e+02 pdb=" CG TYR C 904 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR C 904 " 0.085 2.00e-02 2.50e+03 pdb=" CD2 TYR C 904 " 0.105 2.00e-02 2.50e+03 pdb=" CE1 TYR C 904 " 0.092 2.00e-02 2.50e+03 pdb=" CE2 TYR C 904 " 0.103 2.00e-02 2.50e+03 pdb=" CZ TYR C 904 " 0.018 2.00e-02 2.50e+03 pdb=" OH TYR C 904 " -0.219 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.093 2.00e-02 2.50e+03 1.05e-01 1.38e+02 pdb=" CG ASN A 331 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.172 2.00e-02 2.50e+03 pdb=" C1 NAG A1303 " -0.125 2.00e-02 2.50e+03 ... (remaining 4230 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 11406 2.99 - 3.47: 22314 3.47 - 3.94: 39320 3.94 - 4.42: 43733 4.42 - 4.90: 73753 Nonbonded interactions: 190526 Sorted by model distance: nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.511 3.040 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.523 3.040 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.525 3.040 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.530 3.040 nonbonded pdb=" OE1 GLU A 516 " pdb=" OH TYR B 200 " model vdw 2.532 3.040 ... (remaining 190521 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 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 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 95 or (resid 96 through 97 and (name N or name CA or name C or name O or name \ CB )) or resid 98 through 109 or (resid 110 and (name N or name CA or name C or \ name O or name CB )) or resid 111 through 114 or (resid 115 and (name N or name \ CA or name C or name O or name CB )) or resid 116 through 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 13 \ 9 through 143 or (resid 165 through 166 and (name N or name CA or name C or name \ O or name CB )) or resid 167 through 168 or (resid 169 and (name N or name CA o \ r name C or name O or name CB )) or resid 170 through 171 or (resid 172 and (nam \ e N or name CA or name C or name O or name CB )) or resid 186 through 190 or (re \ sid 191 and (name N or name CA or name C or name O or name CB )) or resid 192 th \ rough 196 or (resid 197 and (name N or name CA or name C or name O or name CB )) \ or resid 198 through 213 or (resid 214 through 215 and (name N or name CA or na \ me C or name O or name CB )) or resid 216 through 217 or (resid 218 and (name N \ or name CA or name C or name O or name CB )) or resid 219 through 238 or (resid \ 239 and (name N or name CA or name C or name O or name CB )) or resid 240 throug \ h 308 or (resid 309 and (name N or name CA or name C or name O or name CB )) or \ resid 310 through 479 or (resid 480 and (name N or name CA or name C or name O o \ r name CB )) or resid 481 through 487 or (resid 488 and (name N or name CA or na \ me C or name O or name CB )) or resid 489 through 527 or (resid 528 and (name N \ or name CA or name C or name O or name CB )) or resid 529 through 810 or (resid \ 811 and (name N or name CA or name C or name O or name CB )) or resid 813 throug \ h 827 or resid 855 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 1141 or (resid 1142 and ( \ name N or name CA or name C or name O or name CB )) or resid 1143 through 1144 o \ r (resid 1145 through 1146 and (name N or name CA or name C or name O or name CB \ )) or resid 1147 through 1308)) selection = (chain 'B' and (resid 27 through 66 or resid 82 through 87 or (resid 88 and (nam \ e N or name CA or name C or name O or name CB )) or resid 89 through 96 or (resi \ d 97 and (name N or name CA or name C or name O or name CB )) or resid 98 or (re \ sid 99 and (name N or name CA or name C or name O or name CB )) or resid 100 thr \ ough 109 or (resid 110 and (name N or name CA or name C or name O or name CB )) \ or resid 111 through 114 or (resid 115 and (name N or name CA or name C or name \ O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (name N o \ r name CA or name C or name O or name CB )) or resid 139 through 164 or (resid 1 \ 66 and (name N or name CA or name C or name O or name CB )) or resid 167 through \ 168 or (resid 169 and (name N or name CA or name C or name O or name CB )) or r \ esid 170 through 190 or (resid 191 and (name N or name CA or name C or name O or \ name CB )) or resid 192 through 195 or (resid 196 through 197 and (name N or na \ me CA or name C or name O or name CB )) or resid 198 through 241 or (resid 242 t \ hrough 264 and (name N or name CA or name C or name O or name CB )) or resid 265 \ through 280 or (resid 281 and (name N or name CA or name C or name O or name CB \ )) or resid 282 through 567 or (resid 568 and (name N or name CA or name C or n \ ame O or name CB )) or resid 569 through 582 or (resid 583 and (name N or name C \ A 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 through 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 na \ me C or name O or name CB )) or resid 746 through 747 or (resid 748 and (name N \ or name CA or name C or name O or name CB )) or resid 749 through 810 or (resid \ 811 and (name N or name CA or name C or name O or name CB )) or resid 813 or (re \ sid 814 and (name N or name CA or name C or name O or name CB )) or resid 815 th \ rough 827 or resid 855 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 1091 or (resid 1092 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1093 through 11 \ 43 or (resid 1144 through 1146 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1147 through 1308)) 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 134 or (resid 135 through 138 and (name N or name CA or name C o \ r name O or name CB )) or resid 139 through 143 or (resid 165 through 166 and (n \ ame N or name CA or name C or name O or name CB )) or resid 167 through 195 or ( \ resid 196 through 197 and (name N or name CA or name C or name O or name CB )) o \ r resid 198 through 213 or (resid 214 through 215 and (name N or name CA or name \ C or name O or name CB )) or resid 216 through 217 or (resid 218 and (name N or \ name CA or name C or name O or name CB )) or resid 219 through 238 or (resid 23 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 240 through \ 308 or (resid 309 and (name N or name CA or name C or name O or name CB )) or re \ sid 310 through 479 or (resid 480 and (name N or name CA or name C or name O or \ name CB )) or resid 481 through 487 or (resid 488 and (name N or name CA or name \ C or name O or name CB )) or resid 489 through 527 or (resid 528 and (name N or \ name CA or name C or name O or name CB )) or resid 529 through 567 or (resid 56 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 569 through \ 582 or (resid 583 and (name N or name CA or name C or name O or name CB )) or re \ sid 584 through 585 or (resid 586 and (name N or name CA 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 813 or (resid 814 and (name N or \ name CA or name C or name O or name CB )) or resid 815 through 1091 or (resid 1 \ 092 and (name N or name CA or name C or name O or name CB )) or resid 1093 throu \ gh 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 na \ me O or name CB )) or resid 1147 through 1308)) } 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: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 21.520 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.077 24386 Z= 0.785 Angle : 1.805 12.205 33294 Z= 1.193 Chirality : 0.104 1.396 3945 Planarity : 0.014 0.206 4195 Dihedral : 12.775 90.229 8331 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 0.09 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.29 % Favored : 94.40 % Rotamer: Outliers : 0.55 % Allowed : 1.96 % Favored : 97.49 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.14), residues: 2928 helix: -1.07 (0.16), residues: 697 sheet: 0.52 (0.21), residues: 559 loop : -0.62 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 408 TYR 0.219 0.021 TYR C 904 PHE 0.077 0.012 PHE A 718 TRP 0.375 0.033 TRP C 886 HIS 0.014 0.003 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01370 / 0.79 (24299) covalent geometry : angle 1.78268 / 1.19 (33070) SS BOND : bond 0.01326 / 0.81 ( 37) SS BOND : angle 2.16341 / 1.48 ( 74) hydrogen bonds : bond 0.16241 / 10.33 ( 1029) hydrogen bonds : angle 8.35369 / 5.85 ( 2838) link_BETA1-4 : bond 0.02539 / 1.67 ( 12) link_BETA1-4 : angle 4.32746 / 2.79 ( 36) link_NAG-ASN : bond 0.01337 / 0.86 ( 38) link_NAG-ASN : angle 4.52825 / 3.14 ( 114) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 357 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.7622 (m) cc_final: 0.7164 (p) REVERT: A 205 SER cc_start: 0.8654 (p) cc_final: 0.7985 (m) REVERT: A 207 HIS cc_start: 0.7439 (m170) cc_final: 0.7092 (t-90) REVERT: A 421 TYR cc_start: 0.7471 (m-80) cc_final: 0.7130 (m-80) REVERT: A 492 LEU cc_start: 0.7183 (mt) cc_final: 0.6951 (mm) REVERT: A 541 PHE cc_start: 0.6723 (p90) cc_final: 0.6443 (p90) REVERT: A 574 ASP cc_start: 0.7172 (t70) cc_final: 0.6801 (t0) REVERT: A 902 MET cc_start: 0.8740 (mmm) cc_final: 0.8385 (mmt) REVERT: A 964 LYS cc_start: 0.8662 (mttt) cc_final: 0.8442 (mtpt) REVERT: C 105 ILE cc_start: 0.8199 (mt) cc_final: 0.7969 (pt) REVERT: C 529 LYS cc_start: 0.8609 (tptt) cc_final: 0.8201 (mptp) REVERT: C 556 ASN cc_start: 0.6816 (p0) cc_final: 0.6391 (p0) REVERT: C 882 ILE cc_start: 0.9189 (mt) cc_final: 0.8976 (mm) REVERT: C 926 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8144 (pt0) REVERT: C 990 GLU cc_start: 0.7523 (tt0) cc_final: 0.7236 (tt0) REVERT: C 1100 THR cc_start: 0.8144 (p) cc_final: 0.7938 (m) outliers start: 14 outliers final: 6 residues processed: 368 average time/residue: 0.4612 time to fit residues: 201.0893 Evaluate side-chains 189 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 182 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 926 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 913 GLN A 957 GLN A 969 ASN A1010 GLN A1088 HIS A1101 HIS B 271 GLN B 540 ASN B 675 GLN B 755 GLN B 978 ASN B1088 HIS C 81 ASN C 764 ASN C 779 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.177463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.139473 restraints weight = 30645.275| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.80 r_work: 0.3151 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24386 Z= 0.149 Angle : 0.669 8.636 33294 Z= 0.348 Chirality : 0.047 0.304 3945 Planarity : 0.004 0.066 4195 Dihedral : 6.164 88.603 3195 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.83 % Favored : 97.03 % Rotamer: Outliers : 1.65 % Allowed : 8.06 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.15), residues: 2928 helix: 1.24 (0.20), residues: 673 sheet: 0.51 (0.19), residues: 707 loop : -0.53 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 567 TYR 0.031 0.002 TYR C 369 PHE 0.026 0.002 PHE B 92 TRP 0.015 0.002 TRP A 353 HIS 0.007 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (24299) covalent geometry : angle 0.64827 / 0.34 (33070) SS BOND : bond 0.00386 / 0.24 ( 37) SS BOND : angle 1.21654 / 0.85 ( 74) hydrogen bonds : bond 0.05247 / 3.40 ( 1029) hydrogen bonds : angle 6.36502 / 4.42 ( 2838) link_BETA1-4 : bond 0.00540 / 0.34 ( 12) link_BETA1-4 : angle 1.87221 / 1.35 ( 36) link_NAG-ASN : bond 0.00415 / 0.26 ( 38) link_NAG-ASN : angle 2.60345 / 1.81 ( 114) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 218 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.7722 (p) cc_final: 0.7215 (t) REVERT: A 128 ILE cc_start: 0.8655 (mt) cc_final: 0.8452 (mp) REVERT: A 205 SER cc_start: 0.8862 (p) cc_final: 0.8496 (m) REVERT: A 304 LYS cc_start: 0.8691 (mmtm) cc_final: 0.8486 (mppt) REVERT: A 324 GLU cc_start: 0.6205 (OUTLIER) cc_final: 0.5792 (mt-10) REVERT: A 360 ASN cc_start: 0.7685 (m110) cc_final: 0.7126 (t0) REVERT: A 456 PHE cc_start: 0.7796 (OUTLIER) cc_final: 0.7536 (p90) REVERT: A 461 LEU cc_start: 0.7046 (mt) cc_final: 0.6607 (mt) REVERT: A 465 GLU cc_start: 0.7805 (tt0) cc_final: 0.7411 (tm-30) REVERT: A 559 PHE cc_start: 0.7436 (m-80) cc_final: 0.7211 (m-80) REVERT: A 902 MET cc_start: 0.8708 (mmm) cc_final: 0.8500 (mmt) REVERT: A 994 ASP cc_start: 0.8768 (t0) cc_final: 0.8511 (OUTLIER) REVERT: B 745 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7829 (p0) REVERT: C 529 LYS cc_start: 0.8771 (tptt) cc_final: 0.8383 (mptp) REVERT: C 556 ASN cc_start: 0.6924 (p0) cc_final: 0.6574 (p0) REVERT: C 990 GLU cc_start: 0.7625 (tt0) cc_final: 0.7184 (mm-30) outliers start: 42 outliers final: 18 residues processed: 247 average time/residue: 0.3828 time to fit residues: 116.6975 Evaluate side-chains 169 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 790 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 282 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 203 optimal weight: 10.0000 chunk 261 optimal weight: 0.7980 chunk 142 optimal weight: 0.4980 chunk 118 optimal weight: 4.9990 chunk 108 optimal weight: 20.0000 chunk 200 optimal weight: 4.9990 chunk 116 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN A 317 ASN A 969 ASN A1002 GLN B 675 GLN B 755 GLN B 901 GLN B1088 HIS C 81 ASN C 271 GLN C 440 ASN C 690 GLN C 926 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.174975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.136424 restraints weight = 30517.792| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.77 r_work: 0.3116 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 24386 Z= 0.185 Angle : 0.626 9.932 33294 Z= 0.322 Chirality : 0.046 0.211 3945 Planarity : 0.004 0.060 4195 Dihedral : 5.365 43.444 3189 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.35 % Favored : 96.58 % Rotamer: Outliers : 2.00 % Allowed : 9.78 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.15), residues: 2928 helix: 1.40 (0.20), residues: 681 sheet: 0.49 (0.19), residues: 702 loop : -0.59 (0.15), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1039 TYR 0.030 0.002 TYR A 508 PHE 0.019 0.002 PHE B 92 TRP 0.014 0.002 TRP C 886 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (24299) covalent geometry : angle 0.60760 / 0.32 (33070) SS BOND : bond 0.00303 / 0.20 ( 37) SS BOND : angle 1.62965 / 1.10 ( 74) hydrogen bonds : bond 0.05033 / 3.25 ( 1029) hydrogen bonds : angle 6.07528 / 4.24 ( 2838) link_BETA1-4 : bond 0.00476 / 0.30 ( 12) link_BETA1-4 : angle 1.55713 / 1.07 ( 36) link_NAG-ASN : bond 0.00246 / 0.17 ( 38) link_NAG-ASN : angle 2.17332 / 1.49 ( 114) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 176 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8707 (mt) cc_final: 0.8504 (mp) REVERT: A 205 SER cc_start: 0.9015 (p) cc_final: 0.8668 (m) REVERT: A 360 ASN cc_start: 0.7743 (m110) cc_final: 0.7027 (t0) REVERT: A 408 ARG cc_start: 0.7531 (ptt-90) cc_final: 0.7275 (ptt-90) REVERT: A 421 TYR cc_start: 0.7633 (m-80) cc_final: 0.7421 (m-10) REVERT: A 456 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.7601 (p90) REVERT: A 461 LEU cc_start: 0.6776 (mt) cc_final: 0.6317 (mt) REVERT: A 465 GLU cc_start: 0.7797 (tt0) cc_final: 0.7385 (pp20) REVERT: A 990 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7884 (mt-10) REVERT: A 994 ASP cc_start: 0.8674 (t0) cc_final: 0.8392 (t0) REVERT: B 52 GLN cc_start: 0.8336 (tm-30) cc_final: 0.7996 (tm-30) REVERT: B 237 ARG cc_start: 0.7809 (ttm-80) cc_final: 0.7330 (mtp-110) REVERT: B 745 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7873 (p0) REVERT: C 529 LYS cc_start: 0.8787 (tptt) cc_final: 0.8442 (mptp) REVERT: C 556 ASN cc_start: 0.6890 (p0) cc_final: 0.6584 (p0) REVERT: C 794 ILE cc_start: 0.7943 (pp) cc_final: 0.7601 (pt) REVERT: C 990 GLU cc_start: 0.7578 (tt0) cc_final: 0.7259 (mm-30) outliers start: 51 outliers final: 28 residues processed: 213 average time/residue: 0.3823 time to fit residues: 100.1377 Evaluate side-chains 182 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 1038 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 114 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 chunk 213 optimal weight: 4.9990 chunk 279 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 136 optimal weight: 30.0000 chunk 229 optimal weight: 9.9990 chunk 201 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 244 optimal weight: 0.9980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN A 969 ASN A1048 HIS B 556 ASN B 675 GLN B 755 GLN B1048 HIS C 81 ASN C 901 GLN C1101 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.172229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.133070 restraints weight = 30623.566| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.77 r_work: 0.3062 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 24386 Z= 0.265 Angle : 0.663 9.515 33294 Z= 0.339 Chirality : 0.048 0.204 3945 Planarity : 0.004 0.055 4195 Dihedral : 5.370 43.494 3189 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.42 % Favored : 96.55 % Rotamer: Outliers : 2.40 % Allowed : 10.41 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.15), residues: 2928 helix: 1.35 (0.20), residues: 667 sheet: 0.31 (0.19), residues: 689 loop : -0.65 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1039 TYR 0.028 0.002 TYR A 453 PHE 0.019 0.002 PHE C1121 TRP 0.019 0.002 TRP C 886 HIS 0.008 0.002 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00649 / 0.27 (24299) covalent geometry : angle 0.64887 / 0.34 (33070) SS BOND : bond 0.00280 / 0.18 ( 37) SS BOND : angle 1.44486 / 1.00 ( 74) hydrogen bonds : bond 0.05380 / 3.47 ( 1029) hydrogen bonds : angle 6.09059 / 4.29 ( 2838) link_BETA1-4 : bond 0.00339 / 0.21 ( 12) link_BETA1-4 : angle 1.47730 / 0.99 ( 36) link_NAG-ASN : bond 0.00263 / 0.18 ( 38) link_NAG-ASN : angle 2.08407 / 1.43 ( 114) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 175 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.8409 (mp10) cc_final: 0.8018 (mm-40) REVERT: A 128 ILE cc_start: 0.8697 (mt) cc_final: 0.8449 (mp) REVERT: A 360 ASN cc_start: 0.7774 (m110) cc_final: 0.7056 (t0) REVERT: A 408 ARG cc_start: 0.7513 (ptt-90) cc_final: 0.7242 (ptt-90) REVERT: A 421 TYR cc_start: 0.7807 (m-80) cc_final: 0.7576 (m-10) REVERT: A 456 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.7591 (p90) REVERT: A 461 LEU cc_start: 0.7005 (mt) cc_final: 0.6766 (mt) REVERT: A 465 GLU cc_start: 0.7925 (tt0) cc_final: 0.7480 (pp20) REVERT: A 1118 ASP cc_start: 0.8664 (p0) cc_final: 0.8296 (m-30) REVERT: B 52 GLN cc_start: 0.8382 (tm-30) cc_final: 0.8030 (tm-30) REVERT: B 745 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.8197 (p0) REVERT: C 529 LYS cc_start: 0.8863 (tptt) cc_final: 0.8513 (mptp) REVERT: C 556 ASN cc_start: 0.6928 (p0) cc_final: 0.6588 (p0) REVERT: C 794 ILE cc_start: 0.7973 (pp) cc_final: 0.7676 (pt) REVERT: C 990 GLU cc_start: 0.7599 (tt0) cc_final: 0.7215 (mm-30) outliers start: 61 outliers final: 38 residues processed: 219 average time/residue: 0.4140 time to fit residues: 110.8802 Evaluate side-chains 191 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 1038 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 31 optimal weight: 5.9990 chunk 268 optimal weight: 0.0470 chunk 200 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 265 optimal weight: 0.6980 chunk 195 optimal weight: 0.0980 chunk 121 optimal weight: 6.9990 chunk 183 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 111 optimal weight: 0.0870 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 913 GLN A1048 HIS B 675 GLN B 755 GLN C 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.177030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.138681 restraints weight = 30332.711| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.83 r_work: 0.3147 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 24386 Z= 0.101 Angle : 0.547 11.864 33294 Z= 0.280 Chirality : 0.044 0.182 3945 Planarity : 0.004 0.052 4195 Dihedral : 4.794 42.818 3189 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.69 % Allowed : 11.71 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.15), residues: 2928 helix: 1.92 (0.21), residues: 655 sheet: 0.45 (0.19), residues: 680 loop : -0.45 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 319 TYR 0.028 0.001 TYR A 453 PHE 0.026 0.001 PHE B 92 TRP 0.009 0.001 TRP A 353 HIS 0.003 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 (24299) covalent geometry : angle 0.53200 / 0.28 (33070) SS BOND : bond 0.00171 / 0.11 ( 37) SS BOND : angle 1.88060 / 1.21 ( 74) hydrogen bonds : bond 0.03958 / 2.55 ( 1029) hydrogen bonds : angle 5.62552 / 3.93 ( 2838) link_BETA1-4 : bond 0.00427 / 0.27 ( 12) link_BETA1-4 : angle 1.07094 / 0.72 ( 36) link_NAG-ASN : bond 0.00286 / 0.18 ( 38) link_NAG-ASN : angle 1.64534 / 1.15 ( 114) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 183 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: A 115 GLN cc_start: 0.8371 (mp10) cc_final: 0.8003 (mm-40) REVERT: A 128 ILE cc_start: 0.8685 (mt) cc_final: 0.8418 (mp) REVERT: A 360 ASN cc_start: 0.7720 (m110) cc_final: 0.7038 (t0) REVERT: A 408 ARG cc_start: 0.7573 (ptt-90) cc_final: 0.7257 (ptt-90) REVERT: A 456 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.7515 (p90) REVERT: A 465 GLU cc_start: 0.7921 (tt0) cc_final: 0.7508 (pp20) REVERT: A 994 ASP cc_start: 0.8622 (t0) cc_final: 0.8316 (t0) REVERT: A 1118 ASP cc_start: 0.8634 (p0) cc_final: 0.8330 (m-30) REVERT: B 52 GLN cc_start: 0.8442 (tm-30) cc_final: 0.8110 (tm-30) REVERT: C 529 LYS cc_start: 0.8857 (tptt) cc_final: 0.8529 (mptp) REVERT: C 556 ASN cc_start: 0.6946 (p0) cc_final: 0.6604 (p0) REVERT: C 878 LEU cc_start: 0.8989 (tp) cc_final: 0.8720 (mt) outliers start: 43 outliers final: 21 residues processed: 214 average time/residue: 0.4096 time to fit residues: 108.1179 Evaluate side-chains 173 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 480 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 81 optimal weight: 2.9990 chunk 263 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 271 optimal weight: 0.8980 chunk 284 optimal weight: 0.9980 chunk 247 optimal weight: 8.9990 chunk 72 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 139 optimal weight: 10.0000 chunk 97 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 969 ASN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 755 GLN B 779 GLN C 81 ASN C1048 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.176092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.138031 restraints weight = 30459.278| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.86 r_work: 0.3139 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 24386 Z= 0.114 Angle : 0.537 8.859 33294 Z= 0.273 Chirality : 0.044 0.295 3945 Planarity : 0.004 0.049 4195 Dihedral : 4.646 43.535 3189 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.93 % Allowed : 12.26 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.16), residues: 2928 helix: 1.96 (0.21), residues: 668 sheet: 0.48 (0.19), residues: 699 loop : -0.35 (0.16), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 319 TYR 0.026 0.001 TYR A 453 PHE 0.023 0.001 PHE A 168 TRP 0.007 0.001 TRP C 436 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (24299) covalent geometry : angle 0.52335 / 0.27 (33070) SS BOND : bond 0.00235 / 0.16 ( 37) SS BOND : angle 1.45158 / 0.95 ( 74) hydrogen bonds : bond 0.03934 / 2.54 ( 1029) hydrogen bonds : angle 5.48610 / 3.83 ( 2838) link_BETA1-4 : bond 0.00405 / 0.25 ( 12) link_BETA1-4 : angle 1.07009 / 0.70 ( 36) link_NAG-ASN : bond 0.00188 / 0.12 ( 38) link_NAG-ASN : angle 1.74514 / 1.24 ( 114) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 168 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.8366 (mp10) cc_final: 0.8020 (mm-40) REVERT: A 128 ILE cc_start: 0.8715 (mt) cc_final: 0.8514 (mp) REVERT: A 360 ASN cc_start: 0.7735 (m110) cc_final: 0.7062 (t0) REVERT: A 408 ARG cc_start: 0.7595 (ptt-90) cc_final: 0.7351 (ptt-90) REVERT: A 456 PHE cc_start: 0.7661 (OUTLIER) cc_final: 0.7264 (p90) REVERT: A 465 GLU cc_start: 0.7901 (tt0) cc_final: 0.7629 (pp20) REVERT: A 1118 ASP cc_start: 0.8716 (p0) cc_final: 0.8404 (m-30) REVERT: B 52 GLN cc_start: 0.8486 (tm-30) cc_final: 0.8141 (tm-30) REVERT: B 170 TYR cc_start: 0.7753 (t80) cc_final: 0.7426 (t80) REVERT: C 529 LYS cc_start: 0.8863 (tptt) cc_final: 0.8534 (mptp) REVERT: C 556 ASN cc_start: 0.6968 (p0) cc_final: 0.6636 (p0) REVERT: C 794 ILE cc_start: 0.7767 (pp) cc_final: 0.7400 (pt) outliers start: 49 outliers final: 25 residues processed: 208 average time/residue: 0.3698 time to fit residues: 95.1483 Evaluate side-chains 171 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 1038 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 242 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 272 optimal weight: 0.7980 chunk 234 optimal weight: 2.9990 chunk 105 optimal weight: 20.0000 chunk 145 optimal weight: 5.9990 chunk 65 optimal weight: 0.0470 chunk 198 optimal weight: 10.0000 chunk 135 optimal weight: 8.9990 overall best weight: 2.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN A1048 HIS ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 755 GLN C 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.172980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.134540 restraints weight = 30210.476| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.83 r_work: 0.3084 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 24386 Z= 0.205 Angle : 0.592 10.594 33294 Z= 0.301 Chirality : 0.046 0.230 3945 Planarity : 0.004 0.049 4195 Dihedral : 4.868 44.063 3189 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.96 % Allowed : 12.77 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.15), residues: 2928 helix: 1.79 (0.21), residues: 661 sheet: 0.39 (0.19), residues: 709 loop : -0.44 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 983 TYR 0.025 0.001 TYR A 453 PHE 0.028 0.002 PHE B 92 TRP 0.008 0.001 TRP C 436 HIS 0.007 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.21 (24299) covalent geometry : angle 0.57785 / 0.30 (33070) SS BOND : bond 0.00379 / 0.24 ( 37) SS BOND : angle 1.66505 / 1.08 ( 74) hydrogen bonds : bond 0.04610 / 2.97 ( 1029) hydrogen bonds : angle 5.66016 / 3.96 ( 2838) link_BETA1-4 : bond 0.00331 / 0.20 ( 12) link_BETA1-4 : angle 1.17137 / 0.76 ( 36) link_NAG-ASN : bond 0.00228 / 0.14 ( 38) link_NAG-ASN : angle 1.84601 / 1.28 ( 114) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 156 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.8368 (mp10) cc_final: 0.8058 (mm-40) REVERT: A 360 ASN cc_start: 0.7817 (m110) cc_final: 0.7085 (t0) REVERT: A 408 ARG cc_start: 0.7655 (ptt-90) cc_final: 0.7293 (pmt-80) REVERT: A 456 PHE cc_start: 0.7692 (OUTLIER) cc_final: 0.7305 (p90) REVERT: A 492 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.6823 (tt) REVERT: A 1118 ASP cc_start: 0.8723 (p0) cc_final: 0.8519 (m-30) REVERT: B 52 GLN cc_start: 0.8516 (tm-30) cc_final: 0.8153 (tm-30) REVERT: C 408 ARG cc_start: 0.7943 (ppp80) cc_final: 0.7706 (ppp80) REVERT: C 529 LYS cc_start: 0.8833 (tptt) cc_final: 0.8543 (mptp) REVERT: C 556 ASN cc_start: 0.6929 (p0) cc_final: 0.6652 (p0) REVERT: C 794 ILE cc_start: 0.7897 (pp) cc_final: 0.7544 (pt) outliers start: 50 outliers final: 30 residues processed: 196 average time/residue: 0.3715 time to fit residues: 90.6538 Evaluate side-chains 181 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 1038 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 130 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 237 optimal weight: 0.9980 chunk 216 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 131 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 165 optimal weight: 0.9990 chunk 292 optimal weight: 0.6980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 755 GLN C 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.172427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.131934 restraints weight = 30387.765| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.93 r_work: 0.3066 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 24386 Z= 0.218 Angle : 0.607 9.691 33294 Z= 0.308 Chirality : 0.046 0.184 3945 Planarity : 0.004 0.049 4195 Dihedral : 4.932 43.821 3189 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.69 % Allowed : 13.52 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.15), residues: 2928 helix: 1.59 (0.20), residues: 675 sheet: 0.28 (0.19), residues: 703 loop : -0.50 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 983 TYR 0.025 0.002 TYR A 453 PHE 0.030 0.002 PHE A 168 TRP 0.009 0.001 TRP C 436 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.22 (24299) covalent geometry : angle 0.59242 / 0.30 (33070) SS BOND : bond 0.00314 / 0.21 ( 37) SS BOND : angle 1.70536 / 1.11 ( 74) hydrogen bonds : bond 0.04728 / 3.05 ( 1029) hydrogen bonds : angle 5.73675 / 4.03 ( 2838) link_BETA1-4 : bond 0.00323 / 0.20 ( 12) link_BETA1-4 : angle 1.16997 / 0.77 ( 36) link_NAG-ASN : bond 0.00240 / 0.15 ( 38) link_NAG-ASN : angle 1.89542 / 1.31 ( 114) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 160 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.7752 (OUTLIER) cc_final: 0.7306 (p) REVERT: A 115 GLN cc_start: 0.8368 (mp10) cc_final: 0.8067 (mm-40) REVERT: A 360 ASN cc_start: 0.7763 (m110) cc_final: 0.7071 (t0) REVERT: A 408 ARG cc_start: 0.7720 (ptt-90) cc_final: 0.7336 (pmt-80) REVERT: A 456 PHE cc_start: 0.7705 (OUTLIER) cc_final: 0.7317 (p90) REVERT: A 492 LEU cc_start: 0.7311 (tp) cc_final: 0.6906 (tt) REVERT: B 52 GLN cc_start: 0.8559 (tm-30) cc_final: 0.8197 (tm-30) REVERT: B 170 TYR cc_start: 0.7608 (t80) cc_final: 0.7234 (t80) REVERT: C 408 ARG cc_start: 0.8009 (ppp80) cc_final: 0.7794 (ppp80) REVERT: C 556 ASN cc_start: 0.7047 (p0) cc_final: 0.6772 (p0) REVERT: C 697 MET cc_start: 0.9027 (ptm) cc_final: 0.8816 (ptp) REVERT: C 990 GLU cc_start: 0.7539 (tt0) cc_final: 0.7317 (mm-30) outliers start: 43 outliers final: 31 residues processed: 196 average time/residue: 0.3719 time to fit residues: 91.3158 Evaluate side-chains 184 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 1038 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 11 optimal weight: 10.0000 chunk 136 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 236 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 248 optimal weight: 0.8980 chunk 110 optimal weight: 20.0000 chunk 283 optimal weight: 0.9980 chunk 184 optimal weight: 0.6980 chunk 172 optimal weight: 0.5980 chunk 140 optimal weight: 30.0000 overall best weight: 1.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN A1101 HIS ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 755 GLN C 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.173004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.133564 restraints weight = 30419.726| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.81 r_work: 0.3091 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24386 Z= 0.181 Angle : 0.589 10.578 33294 Z= 0.297 Chirality : 0.046 0.217 3945 Planarity : 0.004 0.049 4195 Dihedral : 4.841 43.614 3189 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.85 % Allowed : 13.40 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.15), residues: 2928 helix: 1.67 (0.21), residues: 675 sheet: 0.30 (0.19), residues: 693 loop : -0.48 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 983 TYR 0.025 0.001 TYR C 453 PHE 0.032 0.001 PHE B 92 TRP 0.009 0.001 TRP A 353 HIS 0.003 0.001 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 (24299) covalent geometry : angle 0.57176 / 0.29 (33070) SS BOND : bond 0.00288 / 0.20 ( 37) SS BOND : angle 1.54943 / 1.02 ( 74) hydrogen bonds : bond 0.04446 / 2.87 ( 1029) hydrogen bonds : angle 5.64533 / 3.96 ( 2838) link_BETA1-4 : bond 0.00340 / 0.21 ( 12) link_BETA1-4 : angle 1.06488 / 0.71 ( 36) link_NAG-ASN : bond 0.00273 / 0.18 ( 38) link_NAG-ASN : angle 2.14795 / 1.47 ( 114) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 156 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.7767 (OUTLIER) cc_final: 0.7325 (p) REVERT: A 115 GLN cc_start: 0.8348 (mp10) cc_final: 0.8056 (mm-40) REVERT: A 360 ASN cc_start: 0.7759 (m110) cc_final: 0.7077 (t0) REVERT: A 408 ARG cc_start: 0.7711 (ptt-90) cc_final: 0.7324 (pmt-80) REVERT: A 456 PHE cc_start: 0.7675 (OUTLIER) cc_final: 0.7243 (p90) REVERT: A 492 LEU cc_start: 0.7304 (tp) cc_final: 0.6915 (tt) REVERT: A 565 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.7145 (p90) REVERT: B 170 TYR cc_start: 0.7768 (t80) cc_final: 0.7313 (t80) REVERT: C 408 ARG cc_start: 0.8024 (ppp80) cc_final: 0.7800 (ppp80) REVERT: C 556 ASN cc_start: 0.7090 (p0) cc_final: 0.6802 (p0) REVERT: C 794 ILE cc_start: 0.7944 (pp) cc_final: 0.7540 (pt) outliers start: 47 outliers final: 34 residues processed: 194 average time/residue: 0.3279 time to fit residues: 80.4721 Evaluate side-chains 185 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 148 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 1038 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 269 optimal weight: 0.6980 chunk 232 optimal weight: 10.0000 chunk 287 optimal weight: 1.9990 chunk 114 optimal weight: 0.0020 chunk 24 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 210 optimal weight: 5.9990 chunk 140 optimal weight: 20.0000 chunk 271 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 177 optimal weight: 0.6980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 969 ASN A1101 HIS B 271 GLN B 675 GLN B 710 ASN B 755 GLN C 81 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.175533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.142622 restraints weight = 30554.770| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.53 r_work: 0.3211 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24386 Z= 0.107 Angle : 0.544 10.297 33294 Z= 0.276 Chirality : 0.044 0.198 3945 Planarity : 0.004 0.049 4195 Dihedral : 4.581 44.019 3189 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.61 % Allowed : 13.75 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.16), residues: 2928 helix: 1.96 (0.21), residues: 676 sheet: 0.44 (0.19), residues: 696 loop : -0.37 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 983 TYR 0.026 0.001 TYR C 453 PHE 0.038 0.001 PHE A 168 TRP 0.012 0.001 TRP B 64 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (24299) covalent geometry : angle 0.53288 / 0.27 (33070) SS BOND : bond 0.00225 / 0.16 ( 37) SS BOND : angle 1.27129 / 0.83 ( 74) hydrogen bonds : bond 0.03772 / 2.43 ( 1029) hydrogen bonds : angle 5.38306 / 3.76 ( 2838) link_BETA1-4 : bond 0.00420 / 0.26 ( 12) link_BETA1-4 : angle 0.93775 / 0.62 ( 36) link_NAG-ASN : bond 0.00271 / 0.17 ( 38) link_NAG-ASN : angle 1.65054 / 1.14 ( 114) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 164 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.7689 (OUTLIER) cc_final: 0.7330 (p) REVERT: A 360 ASN cc_start: 0.7759 (m110) cc_final: 0.7105 (t0) REVERT: A 408 ARG cc_start: 0.7734 (ptt-90) cc_final: 0.7427 (pmt-80) REVERT: A 456 PHE cc_start: 0.7562 (OUTLIER) cc_final: 0.7084 (p90) REVERT: A 492 LEU cc_start: 0.7273 (tp) cc_final: 0.6910 (tt) REVERT: A 587 ILE cc_start: 0.7016 (mp) cc_final: 0.6713 (tp) REVERT: A 994 ASP cc_start: 0.8486 (t0) cc_final: 0.8145 (t0) REVERT: B 170 TYR cc_start: 0.7699 (t80) cc_final: 0.7356 (t80) REVERT: C 408 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7808 (ppp80) REVERT: C 556 ASN cc_start: 0.7160 (p0) cc_final: 0.6867 (p0) REVERT: C 794 ILE cc_start: 0.7934 (pp) cc_final: 0.7522 (pt) outliers start: 41 outliers final: 28 residues processed: 198 average time/residue: 0.3206 time to fit residues: 80.3172 Evaluate side-chains 181 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 1038 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 73 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 215 optimal weight: 4.9990 chunk 292 optimal weight: 2.9990 chunk 275 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 969 ASN B 271 GLN B 675 GLN B 710 ASN B 755 GLN C 81 ASN C 690 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.172909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.134783 restraints weight = 30448.082| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.85 r_work: 0.3090 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 24386 Z= 0.210 Angle : 0.609 10.110 33294 Z= 0.309 Chirality : 0.046 0.255 3945 Planarity : 0.004 0.048 4195 Dihedral : 4.785 44.315 3189 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.61 % Allowed : 14.07 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.15), residues: 2928 helix: 1.69 (0.20), residues: 683 sheet: 0.31 (0.19), residues: 709 loop : -0.43 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 983 TYR 0.024 0.001 TYR C 453 PHE 0.029 0.002 PHE B 92 TRP 0.020 0.001 TRP B 64 HIS 0.004 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.21 (24299) covalent geometry : angle 0.59338 / 0.30 (33070) SS BOND : bond 0.00380 / 0.27 ( 37) SS BOND : angle 2.00079 / 1.33 ( 74) hydrogen bonds : bond 0.04523 / 2.92 ( 1029) hydrogen bonds : angle 5.59048 / 3.93 ( 2838) link_BETA1-4 : bond 0.00333 / 0.20 ( 12) link_BETA1-4 : angle 1.07915 / 0.71 ( 36) link_NAG-ASN : bond 0.00225 / 0.14 ( 38) link_NAG-ASN : angle 1.82493 / 1.26 ( 114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6493.31 seconds wall clock time: 111 minutes 34.12 seconds (6694.12 seconds total)