Starting phenix.real_space_refine on Sat May 24 20:04:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8err_28559/05_2025/8err_28559.cif Found real_map, /net/cci-nas-00/data/ceres_data/8err_28559/05_2025/8err_28559.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8err_28559/05_2025/8err_28559.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8err_28559/05_2025/8err_28559.map" model { file = "/net/cci-nas-00/data/ceres_data/8err_28559/05_2025/8err_28559.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8err_28559/05_2025/8err_28559.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.079 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 122 5.16 5 C 16395 2.51 5 N 4465 2.21 5 O 4798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 119 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25780 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 7537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1018, 7537 Classifications: {'peptide': 1018} Incomplete info: {'truncation_to_alanine': 174} Link IDs: {'PTRANS': 55, 'TRANS': 962} Chain breaks: 8 Unresolved non-hydrogen bonds: 460 Unresolved non-hydrogen angles: 580 Unresolved non-hydrogen dihedrals: 354 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'ASN:plan1': 15, 'ASP:plan': 21, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 246 Chain: "B" Number of atoms: 6965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1009, 6965 Classifications: {'peptide': 1009} Incomplete info: {'truncation_to_alanine': 328} Link IDs: {'PTRANS': 55, 'TRANS': 953} Chain breaks: 9 Unresolved non-hydrogen bonds: 977 Unresolved non-hydrogen angles: 1253 Unresolved non-hydrogen dihedrals: 750 Unresolved non-hydrogen chiralities: 120 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 27, 'TYR:plan': 5, 'ASN:plan1': 33, 'HIS:plan': 4, 'PHE:plan': 13, 'GLU:plan': 23, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 512 Chain: "C" Number of atoms: 7164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 7164 Classifications: {'peptide': 1037} Incomplete info: {'truncation_to_alanine': 308} Link IDs: {'PTRANS': 57, 'TRANS': 979} Chain breaks: 9 Unresolved non-hydrogen bonds: 1020 Unresolved non-hydrogen angles: 1308 Unresolved non-hydrogen dihedrals: 828 Unresolved non-hydrogen chiralities: 97 Planarities with less than four sites: {'GLN:plan1': 13, 'ARG:plan': 11, 'TYR:plan': 14, 'ASN:plan1': 25, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 17, 'GLU:plan': 20, 'ASP:plan': 30} Unresolved non-hydrogen planarities: 585 Chain: "H" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 591 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 6, 'TRANS': 110} Unresolved non-hydrogen bonds: 337 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 278 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 3, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 163 Chain: "L" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 547 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 344 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 142 Chain: "E" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 591 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 6, 'TRANS': 110} Unresolved non-hydrogen bonds: 337 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 278 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 3, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 163 Chain: "F" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 547 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 344 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 142 Chain: "I" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 591 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 6, 'TRANS': 110} Unresolved non-hydrogen bonds: 337 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 278 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 3, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 163 Chain: "J" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 547 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 344 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 142 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Time building chain proxies: 15.44, per 1000 atoms: 0.60 Number of scatterers: 25780 At special positions: 0 Unit cell: (171, 131, 209, 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 122 16.00 O 4798 8.00 N 4465 7.00 C 16395 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=49, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.06 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 707 " - pdb=" SG CYS C 883 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.06 Simple disulfide: pdb=" SG CYS A 883 " - pdb=" SG CYS B 707 " distance=2.08 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.23 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.15 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.22 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=2.20 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.06 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.06 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B 883 " - pdb=" SG CYS C 707 " distance=2.06 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.20 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.14 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.07 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=2.01 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.10 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.13 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 91 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 97 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 91 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 97 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 91 " distance=2.03 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 603 " " NAG A1309 " - " ASN A 616 " " NAG A1310 " - " ASN A 657 " " NAG A1311 " - " ASN A 709 " " NAG A1312 " - " ASN A 717 " " NAG A1313 " - " ASN A 801 " " NAG A1314 " - " ASN A1074 " " NAG A1315 " - " ASN A1098 " " NAG A1316 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 603 " " NAG B1309 " - " ASN B 616 " " NAG B1310 " - " ASN B 657 " " NAG B1311 " - " ASN B 709 " " NAG B1312 " - " ASN B 717 " " NAG B1313 " - " ASN B1074 " " NAG B1314 " - " ASN B1098 " " NAG B1315 " - " ASN B1134 " " NAG C1301 " - " ASN C 17 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 122 " " NAG C1304 " - " ASN C 165 " " NAG C1305 " - " ASN C 234 " " NAG C1306 " - " ASN C 282 " " NAG C1307 " - " ASN C 331 " " NAG C1308 " - " ASN C 343 " " NAG C1309 " - " ASN C 603 " " NAG C1310 " - " ASN C 616 " " NAG C1311 " - " ASN C 657 " " NAG C1312 " - " ASN C 709 " " NAG C1313 " - " ASN C 717 " " NAG C1314 " - " ASN C 801 " " NAG C1315 " - " ASN C1074 " " NAG C1316 " - " ASN C1098 " " NAG C1317 " - " ASN C1134 " " NAG D 1 " - " ASN B 801 " Time building additional restraints: 6.50 Conformation dependent library (CDL) restraints added in 3.7 seconds 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7000 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 65 sheets defined 21.1% alpha, 36.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.69 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.819A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 removed outlier: 3.864A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU A 371 " --> pdb=" O LEU A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 371' Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.622A 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: 3.694A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.632A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 751 Processing helix chain 'A' and resid 752 through 756 Processing helix chain 'A' and resid 757 through 783 removed outlier: 4.295A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 823 Processing helix chain 'A' and resid 851 through 855 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.665A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.224A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.582A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 933 Processing helix chain 'A' and resid 934 through 938 Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.995A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 968 Processing helix chain 'A' and resid 978 through 983 removed outlier: 3.648A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 978 through 983' Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.634A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 993 " --> pdb=" O ALA A 989 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1145 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.764A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.991A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.382A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 751 Processing helix chain 'B' and resid 757 through 783 removed outlier: 3.850A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 823 Processing helix chain 'B' and resid 851 through 855 removed outlier: 3.559A pdb=" N PHE B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 851 through 855' Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.515A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.737A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 944 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.043A 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 977 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.808A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1145 removed outlier: 3.510A pdb=" N GLU B1144 " --> pdb=" O LEU B1141 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.776A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 370 removed outlier: 3.969A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.714A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.727A pdb=" N VAL C 635 " --> pdb=" O PRO C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 756 removed outlier: 4.000A pdb=" N LEU C 753 " --> pdb=" O SER C 750 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU C 754 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.649A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 821 Processing helix chain 'C' and resid 822 through 824 No H-bonds generated for 'chain 'C' and resid 822 through 824' Processing helix chain 'C' and resid 850 through 855 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.977A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.563A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.810A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 946 removed outlier: 4.203A pdb=" N LEU C 945 " --> pdb=" O PRO C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 948 through 965 Processing helix chain 'C' and resid 977 through 982 removed outlier: 3.547A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.525A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1145 Processing helix chain 'L' and resid 27 through 31 removed outlier: 4.118A pdb=" N VAL L 30 " --> pdb=" O SER L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 86 removed outlier: 4.114A pdb=" N GLU L 86 " --> pdb=" O ALA L 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 31 removed outlier: 4.072A pdb=" N VAL F 30 " --> pdb=" O SER F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 86 removed outlier: 3.794A pdb=" N GLU F 86 " --> pdb=" O ALA F 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 86 removed outlier: 3.776A pdb=" N GLU J 86 " --> pdb=" O ALA J 83 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 8.312A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.701A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.832A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.322A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.245A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.171A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.237A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.376A pdb=" N PHE A 238 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 13.284A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 12.999A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 11.056A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 11.143A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.245A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.171A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.237A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.535A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.242A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.598A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.665A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.157A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N LYS C 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ASN A 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.947A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.947A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.552A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB9, first strand: chain 'A' and resid 796 through 797 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.837A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.369A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.872A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.704A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.767A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLU B 132 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N CYS B 136 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASP B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ARG B 158 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 7.806A pdb=" N ASN B 394 " --> pdb=" O ALA B 522 " (cutoff:3.500A) removed outlier: 9.707A pdb=" N ALA B 522 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.571A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.648A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.507A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.507A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.474A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 787 through 789 Processing sheet with id=AD7, first strand: chain 'B' and resid 796 through 797 Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.973A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 28 removed outlier: 6.082A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.523A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.646A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL C 126 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TYR C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N GLU C 132 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N CYS C 136 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TYR C 160 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ASP C 138 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ARG C 158 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 13.227A pdb=" N PHE C 238 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 13.082A pdb=" N PHE C 135 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 12.889A pdb=" N THR C 240 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 10.839A pdb=" N ASN C 137 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 11.381A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL C 126 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TYR C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N GLU C 132 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N CYS C 136 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TYR C 160 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ASP C 138 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ARG C 158 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.790A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.288A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.601A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.601A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 796 through 797 Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.900A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF6, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.744A pdb=" N VAL H 36 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LEU H 52 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TRP H 38 " --> pdb=" O LEU H 50 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AF8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.528A pdb=" N VAL L 11 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TRP L 38 " --> pdb=" O MET L 50 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.528A pdb=" N VAL L 11 " --> pdb=" O THR L 108 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AG2, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AG3, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.733A pdb=" N VAL E 36 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LEU E 52 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TRP E 38 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.558A pdb=" N VAL F 11 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLN F 40 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU F 49 " --> pdb=" O GLN F 40 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.558A pdb=" N VAL F 11 " --> pdb=" O THR F 108 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 19 through 24 Processing sheet with id=AG7, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AG8, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.659A pdb=" N VAL I 36 " --> pdb=" O LEU I 52 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LEU I 52 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TRP I 38 " --> pdb=" O LEU I 50 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.671A pdb=" N GLY J 13 " --> pdb=" O THR J 108 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLN J 40 " --> pdb=" O LEU J 49 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N LEU J 49 " --> pdb=" O GLN J 40 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.671A pdb=" N GLY J 13 " --> pdb=" O THR J 108 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 19 through 24 1245 hydrogen bonds defined for protein. 3219 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: 14.81 Time building geometry restraints manager: 7.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 4302 1.31 - 1.44: 6825 1.44 - 1.58: 15036 1.58 - 1.72: 2 1.72 - 1.86: 145 Bond restraints: 26310 Sorted by residual: bond pdb=" C ASN A 616 " pdb=" O ASN A 616 " ideal model delta sigma weight residual 1.236 1.169 0.067 1.21e-02 6.83e+03 3.06e+01 bond pdb=" CB LEU A1141 " pdb=" CG LEU A1141 " ideal model delta sigma weight residual 1.530 1.629 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" N PRO C 728 " pdb=" CD PRO C 728 " ideal model delta sigma weight residual 1.473 1.539 -0.066 1.40e-02 5.10e+03 2.21e+01 bond pdb=" C ASN A 657 " pdb=" O ASN A 657 " ideal model delta sigma weight residual 1.232 1.172 0.060 1.32e-02 5.74e+03 2.06e+01 bond pdb=" C ASN B 616 " pdb=" O ASN B 616 " ideal model delta sigma weight residual 1.234 1.189 0.045 1.00e-02 1.00e+04 2.05e+01 ... (remaining 26305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 34392 2.68 - 5.37: 1328 5.37 - 8.05: 360 8.05 - 10.74: 6 10.74 - 13.42: 3 Bond angle restraints: 36089 Sorted by residual: angle pdb=" C LEU B 861 " pdb=" N PRO B 862 " pdb=" CA PRO B 862 " ideal model delta sigma weight residual 119.66 126.31 -6.65 7.20e-01 1.93e+00 8.53e+01 angle pdb=" C LEU A 861 " pdb=" N PRO A 862 " pdb=" CA PRO A 862 " ideal model delta sigma weight residual 119.66 126.03 -6.37 7.20e-01 1.93e+00 7.82e+01 angle pdb=" C GLN I 41 " pdb=" N PRO I 42 " pdb=" CA PRO I 42 " ideal model delta sigma weight residual 119.66 125.58 -5.92 7.20e-01 1.93e+00 6.77e+01 angle pdb=" C GLN H 41 " pdb=" N PRO H 42 " pdb=" CA PRO H 42 " ideal model delta sigma weight residual 119.66 125.49 -5.83 7.20e-01 1.93e+00 6.55e+01 angle pdb=" N ASN A 801 " pdb=" CA ASN A 801 " pdb=" C ASN A 801 " ideal model delta sigma weight residual 108.76 95.34 13.42 1.69e+00 3.50e-01 6.31e+01 ... (remaining 36084 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 15636 17.83 - 35.67: 435 35.67 - 53.50: 101 53.50 - 71.33: 40 71.33 - 89.16: 18 Dihedral angle restraints: 16230 sinusoidal: 5406 harmonic: 10824 Sorted by residual: dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual 93.00 -177.84 -89.16 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" N ASN A 801 " pdb=" C ASN A 801 " pdb=" CA ASN A 801 " pdb=" CB ASN A 801 " ideal model delta harmonic sigma weight residual 122.80 100.86 21.94 0 2.50e+00 1.60e-01 7.70e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual -86.00 -43.57 -42.43 1 1.00e+01 1.00e-02 2.51e+01 ... (remaining 16227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 3999 0.129 - 0.257: 339 0.257 - 0.386: 57 0.386 - 0.514: 0 0.514 - 0.643: 1 Chirality restraints: 4396 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.47e+01 chirality pdb=" CA ASN A 801 " pdb=" N ASN A 801 " pdb=" C ASN A 801 " pdb=" CB ASN A 801 " both_signs ideal model delta sigma weight residual False 2.51 3.15 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" C1 NAG C1315 " pdb=" ND2 ASN C1074 " pdb=" C2 NAG C1315 " pdb=" O5 NAG C1315 " both_signs ideal model delta sigma weight residual False -2.40 -2.78 0.38 2.00e-01 2.50e+01 3.57e+00 ... (remaining 4393 not shown) Planarity restraints: 4801 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 122 " -0.232 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" CG ASN C 122 " 0.106 2.00e-02 2.50e+03 pdb=" OD1 ASN C 122 " -0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN C 122 " 0.514 2.00e-02 2.50e+03 pdb=" C1 NAG C1303 " -0.366 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1312 " 0.104 2.00e-02 2.50e+03 8.58e-02 9.21e+01 pdb=" C7 NAG C1312 " -0.029 2.00e-02 2.50e+03 pdb=" C8 NAG C1312 " 0.079 2.00e-02 2.50e+03 pdb=" N2 NAG C1312 " -0.136 2.00e-02 2.50e+03 pdb=" O7 NAG C1312 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1098 " -0.052 2.00e-02 2.50e+03 5.16e-02 3.33e+01 pdb=" CG ASN C1098 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN C1098 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN C1098 " 0.076 2.00e-02 2.50e+03 pdb=" C1 NAG C1316 " -0.063 2.00e-02 2.50e+03 ... (remaining 4798 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 8756 2.86 - 3.37: 21070 3.37 - 3.88: 39543 3.88 - 4.39: 44240 4.39 - 4.90: 76265 Nonbonded interactions: 189874 Sorted by model distance: nonbonded pdb=" OD1 ASP A 389 " pdb=" NZ LYS A 528 " model vdw 2.346 3.120 nonbonded pdb=" N SER A 112 " pdb=" O PHE A 133 " model vdw 2.428 3.120 nonbonded pdb=" O GLU A 619 " pdb=" CG GLU A 619 " model vdw 2.447 3.440 nonbonded pdb=" OD1 ASN B 165 " pdb=" O5 NAG B1303 " model vdw 2.453 3.040 nonbonded pdb=" O THR C 739 " pdb=" O ILE C 742 " model vdw 2.470 3.040 ... (remaining 189869 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 26 through 28 or (resid 29 through 31 and (name N or name \ CA or name C or name O or name CB )) or resid 32 or (resid 33 and (name N or nam \ e CA or name C or name O or name CB )) or resid 34 through 35 or (resid 36 and ( \ name N or name CA or name C or name O or name CB )) or resid 37 through 39 or (r \ esid 40 through 41 and (name N or name CA or name C or name O or name CB )) or r \ esid 42 through 44 or (resid 45 through 46 and (name N or name CA or name C or n \ ame O or name CB )) or resid 47 through 50 or (resid 51 and (name N or name CA o \ r name C or name O or name CB )) or resid 52 through 59 or (resid 60 and (name N \ or name CA or name C or name O or name CB )) or resid 61 or (resid 62 and (name \ N or name CA or name C or name O or name CB )) or resid 63 through 65 or (resid \ 66 through 68 and (name N or name CA or name C or name O or name CB )) or (resi \ d 78 through 81 and (name N or name CA or name C or name O or name CB )) or resi \ d 82 or (resid 83 and (name N or name CA or name C or name O or name CB )) or re \ sid 84 through 86 or (resid 87 through 88 and (name N or name CA or name C or na \ me O or name CB )) or resid 89 through 94 or (resid 95 through 100 and (name N o \ r name CA or name C or name O or name CB )) or resid 101 or (resid 102 and (name \ N or name CA or name C or name O or name CB )) or resid 103 through 116 or (res \ id 117 through 120 and (name N or name CA or name C or name O or name CB )) or r \ esid 121 through 127 or (resid 128 through 130 and (name N or name CA or name C \ or name O or name CB )) or resid 131 through 132 or (resid 133 through 138 and ( \ name N or name CA or name C or name O or name CB )) or resid 139 or (resid 140 t \ hrough 164 and (name N or name CA or name C or name O or name CB )) or resid 165 \ through 187 or (resid 188 through 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 198 and (name N o \ r name CA or name C or name O or name CB )) or resid 199 through 202 or (resid 2 \ 03 and (name N or name CA or name C or name O or name CB )) or resid 204 through \ 206 or (resid 207 through 208 and (name N or name CA or name C or name O or nam \ e CB )) or resid 209 through 210 or resid 216 through 217 or (resid 218 and (nam \ e N or name CA or name C or name O or name CB )) or resid 219 through 228 or (re \ sid 229 and (name N or name CA or name C or name O or name CB )) or resid 230 or \ (resid 231 and (name N or name CA or name C or name O or name CB )) or resid 23 \ 2 or (resid 233 and (name N or name CA or name C or name O or name CB )) or resi \ d 234 or (resid 235 through 243 and (name N or name CA or name C or name O or na \ me CB )) or resid 263 through 266 or (resid 267 and (name N or name CA or name C \ or name O or name CB )) or resid 268 through 270 or (resid 271 and (name N or n \ ame CA or name C or name O or name CB )) or resid 272 through 279 or (resid 280 \ through 281 and (name N or name CA or name C or name O or name CB )) or resid 28 \ 2 through 288 or (resid 289 and (name N or name CA or name C or name O or name C \ B )) or resid 290 through 293 or (resid 294 and (name N or name CA or name C or \ name O or name CB )) or resid 295 through 307 or (resid 308 through 309 and (nam \ e N or name CA or name C or name O or name CB )) or resid 310 through 313 or (re \ sid 314 and (name N or name CA or name C or name O or name CB )) or resid 315 th \ rough 316 or (resid 317 and (name N or name CA or name C or name O or name CB )) \ or resid 318 through 319 or (resid 320 through 321 and (name N or name CA or na \ me C or name O or name CB )) or resid 322 or (resid 323 through 327 and (name N \ or name CA or name C or name O or name CB )) or resid 328 through 331 or (resid \ 332 through 335 and (name N or name CA or name C or name O or name CB )) or resi \ d 336 through 339 or (resid 340 through 342 and (name N or name CA or name C or \ name O or name CB )) or resid 343 through 344 or (resid 345 through 360 and (nam \ e N or name CA or name C or name O or name CB )) or resid 361 or (resid 362 thro \ ugh 364 and (name N or name CA or name C or name O or name CB )) or resid 365 th \ rough 366 or (resid 367 through 372 and (name N or name CA or name C or name O o \ r name CB )) or resid 373 or (resid 374 through 378 and (name N or name CA or na \ me C or name O or name CB )) or resid 379 or (resid 380 and (name N or name CA o \ r name C or name O or name CB )) or resid 381 or (resid 382 through 383 and (nam \ e N or name CA or name C or name O or name CB )) or resid 384 or (resid 385 thro \ ugh 390 and (name N or name CA or name C or name O or name CB )) or resid 391 or \ (resid 392 through 403 and (name N or name CA or name C or name O or name CB )) \ or resid 404 or (resid 405 through 411 and (name N or name CA or name C or name \ O or name CB )) or resid 412 through 413 or (resid 414 through 415 and (name N \ or name CA or name C or name O or name CB )) or resid 416 or (resid 417 through \ 425 and (name N or name CA or name C or name O or name CB )) or resid 426 throug \ h 428 or (resid 429 through 430 and (name N or name CA or name C or name O or na \ me CB )) or resid 431 through 432 or (resid 433 through 446 and (name N or name \ CA or name C or name O or name CB )) or resid 447 or (resid 448 through 462 and \ (name N or name CA or name C or name O or name CB )) or resid 463 or (resid 464 \ through 475 and (name N or name CA or name C or name O or name CB )) or resid 47 \ 6 through 488 or (resid 489 through 490 and (name N or name CA or name C or name \ O or name CB )) or resid 491 or (resid 492 through 498 and (name N or name CA o \ r name C or name O or name CB )) or resid 499 or (resid 500 through 501 and (nam \ e N or name CA or name C or name O or name CB )) or resid 502 or (resid 503 and \ (name N or name CA or name C or name O or name CB )) or resid 504 or (resid 505 \ through 506 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 7 or (resid 508 through 516 and (name N or name CA or name C or name O or name C \ B )) or (resid 524 and (name N or name CA or name C or name O or name CB )) or r \ esid 525 through 527 or (resid 528 through 537 and (name N or name CA or name C \ or name O or name CB )) or resid 538 or (resid 539 through 542 and (name N or na \ me CA or name C or name O or name CB )) or resid 543 or (resid 544 and (name N o \ r name CA or name C or name O or name CB )) or resid 545 through 546 or (resid 5 \ 47 and (name N or name CA or name C or name O or name CB )) or resid 548 or (res \ id 549 and (name N or name CA or name C or name O or name CB )) or resid 550 or \ (resid 551 through 556 and (name N or name CA or name C or name O or name CB )) \ or resid 557 through 559 or (resid 560 and (name N or name CA or name C or name \ O or name CB )) or resid 561 or (resid 562 and (name N or name CA or name C or n \ ame O or name CB )) or resid 563 through 572 or (resid 573 through 576 and (name \ N or name CA or name C or name O or name CB )) or resid 577 or (resid 578 and ( \ name N or name CA or name C or name O or name CB )) or resid 579 or (resid 580 t \ hrough 584 and (name N or name CA or name C or name O or name CB )) or resid 585 \ through 586 or (resid 587 through 588 and (name N or name CA or name C or name \ O or name CB )) or resid 589 through 591 or (resid 592 and (name N or name CA or \ name C or name O or name CB )) or resid 593 through 601 or (resid 602 and (name \ N or name CA or name C or name O or name CB )) or resid 603 or (resid 604 throu \ gh 606 and (name N or name CA or name C or name O or name CB )) or resid 607 thr \ ough 614 or (resid 615 and (name N or name CA or name C or name O or name CB )) \ or resid 616 through 617 or (resid 618 through 620 and (name N or name CA or nam \ e C or name O or name CB )) or resid 621 through 644 or (resid 645 through 647 a \ nd (name N or name CA or name C or name O or name CB )) or resid 648 through 660 \ or (resid 661 and (name N or name CA or name C or name O or name CB )) or resid \ 662 through 676 or resid 690 through 701 or (resid 702 and (name N or name CA o \ r name C or name O or name CB )) or resid 703 through 707 or (resid 708 and (nam \ e N or name CA or name C or name O or name CB )) or resid 709 through 734 or (re \ sid 735 through 737 and (name N or name CA or name C or name O or name CB )) or \ resid 738 or (resid 739 through 740 and (name N or name CA or name C or name O o \ r name CB )) or resid 741 through 754 or (resid 755 and (name N or name CA or na \ me C or name O or name CB )) or resid 756 through 779 or (resid 780 and (name N \ or name CA or name C or name O or name CB )) or resid 781 through 784 or (resid \ 785 through 786 and (name N or name CA or name C or name O or name CB )) or resi \ d 787 through 789 or (resid 790 and (name N or name CA or name C or name O or na \ me CB )) or resid 791 through 813 or (resid 814 and (name N or name CA or name C \ or name O or name CB )) or resid 815 through 858 or (resid 859 and (name N or n \ ame CA or name C or name O or name CB )) or resid 860 through 865 or (resid 866 \ through 868 and (name N or name CA or name C or name O or name CB )) or resid 86 \ 9 through 920 or (resid 921 and (name N or name CA or name C or name O or name C \ B )) or resid 922 through 935 or (resid 936 through 937 and (name N or name CA o \ r name C or name O or name CB )) or resid 938 through 966 or (resid 967 through \ 968 and (name N or name CA or name C or name O or name CB )) or resid 969 throug \ h 990 or (resid 991 and (name N or name CA or name C or name O or name CB )) or \ resid 992 through 994 or (resid 995 and (name N or name CA or name C or name O o \ r name CB )) or resid 996 through 1009 or (resid 1010 and (name N or name CA or \ name C or name O or name CB )) or resid 1011 through 1036 or (resid 1037 through \ 1038 and (name N or name CA or name C or name O or name CB )) or resid 1039 thr \ ough 1040 or (resid 1041 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1042 through 1071 or (resid 1072 through 1073 and (name N or name CA \ or name C or name O or name CB )) or resid 1074 through 1127 or (resid 1128 and \ (name N or name CA or name C or name O or name CB )) or resid 1129 through 1145 \ or resid 1301 through 1315)) selection = (chain 'B' and (resid 26 through 50 or (resid 51 and (name N or name CA or name \ C or name O or name CB )) or resid 52 through 104 or (resid 105 and (name N or n \ ame CA or name C or name O or name CB )) or resid 106 through 172 or (resid 173 \ and (name N or name CA or name C or name O or name CB )) or resid 174 through 28 \ 5 or (resid 286 through 289 and (name N or name CA or name C or name O or name C \ B )) or resid 290 through 297 or (resid 298 and (name N or name CA or name C or \ name O or name CB )) or resid 299 through 307 or (resid 308 through 309 and (nam \ e N or name CA or name C or name O or name CB )) or resid 310 through 333 or (re \ sid 334 through 335 and (name N or name CA or name C or name O or name CB )) or \ resid 336 through 341 or (resid 342 and (name N or name CA or name C or name O o \ r name CB )) or resid 343 through 346 or (resid 347 through 360 and (name N or n \ ame CA or name C or name O or name CB )) or resid 361 through 379 or (resid 380 \ and (name N or name CA or name C or name O or name CB )) or resid 381 through 39 \ 1 or (resid 392 through 403 and (name N or name CA or name C or name O or name C \ B )) or (resid 404 through 411 and (name N or name CA or name C or name O or nam \ e CB )) or resid 412 through 413 or (resid 414 through 415 and (name N or name C \ A or name C or name O or name CB )) or (resid 416 through 425 and (name N or nam \ e CA or name C or name O or name CB )) or resid 426 through 428 or (resid 429 th \ rough 430 and (name N or name CA or name C or name O or name CB )) or resid 431 \ through 435 or (resid 436 through 446 and (name N or name CA or name C or name O \ or name CB )) or (resid 447 through 462 and (name N or name CA or name C or nam \ e O or name CB )) or resid 463 or (resid 464 through 475 and (name N or name CA \ or name C or name O or name CB )) or resid 476 through 488 or (resid 489 through \ 490 and (name N or name CA or name C or name O or name CB )) or resid 491 or (r \ esid 492 through 498 and (name N or name CA or name C or name O or name CB )) or \ resid 499 through 500 or (resid 501 and (name N or name CA or name C or name O \ or name CB )) or resid 502 through 507 or (resid 508 through 516 and (name N or \ name CA or name C or name O or name CB )) or resid 524 through 535 or (resid 536 \ through 537 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 38 through 559 or (resid 560 and (name N or name CA or name C or name O or name \ CB )) or resid 561 or (resid 562 and (name N or name CA or name C or name O or n \ ame CB )) or resid 563 through 591 or (resid 592 and (name N or name CA or name \ C or name O or name CB )) or resid 593 through 598 or (resid 599 and (name N or \ name CA or name C or name O or name CB )) or resid 600 through 601 or (resid 602 \ and (name N or name CA or name C or name O or name CB )) or resid 603 or (resid \ 604 through 606 and (name N or name CA or name C or name O or name CB )) or res \ id 607 through 618 or (resid 619 through 620 and (name N or name CA or name C or \ name O or name CB )) or resid 621 through 645 or (resid 646 through 647 and (na \ me N or name CA or name C or name O or name CB )) or resid 648 through 674 or (r \ esid 675 through 676 and (name N or name CA or name C or name O or name CB )) or \ resid 690 through 701 or (resid 702 and (name N or name CA or name C or name O \ or name CB )) or resid 703 or (resid 704 and (name N or name CA or name C or nam \ e O or name CB )) or resid 705 through 709 or (resid 710 through 711 and (name N \ or name CA or name C or name O or name CB )) or resid 712 through 736 or (resid \ 737 and (name N or name CA or name C or name O or name CB )) or resid 738 throu \ gh 739 or (resid 740 and (name N or name CA or name C or name O or name CB )) or \ resid 741 through 744 or (resid 745 through 748 and (name N or name CA or name \ C or name O or name CB )) or resid 749 through 750 or (resid 751 and (name N or \ name CA or name C or name O or name CB )) or resid 752 through 754 or (resid 755 \ and (name N or name CA or name C or name O or name CB )) or resid 756 through 7 \ 57 or (resid 758 and (name N or name CA or name C or name O or name CB )) or res \ id 759 through 785 or (resid 786 and (name N or name CA or name C or name O or n \ ame CB )) or resid 787 through 789 or (resid 790 and (name N or name CA or name \ C or name O or name CB )) or resid 791 through 813 or (resid 814 and (name N or \ name CA or name C or name O or name CB )) or resid 815 through 858 or (resid 859 \ and (name N or name CA or name C or name O or name CB )) or resid 860 through 8 \ 65 or (resid 866 through 868 and (name N or name CA or name C or name O or name \ CB )) or resid 869 through 935 or (resid 936 through 937 and (name N or name CA \ or name C or name O or name CB )) or resid 938 through 973 or (resid 974 and (na \ me N or name CA or name C or name O or name CB )) or resid 975 through 979 or (r \ esid 980 and (name N or name CA or name C or name O or name CB )) or resid 981 t \ hrough 982 or (resid 983 through 986 and (name N or name CA or name C or name O \ or name CB )) or resid 987 through 993 or (resid 994 through 995 and (name N or \ name CA or name C or name O or name CB )) or resid 996 through 1004 or (resid 10 \ 05 and (name N or name CA or name C or name O or name CB )) or resid 1006 throug \ h 1037 or (resid 1038 and (name N or name CA or name C or name O or name CB )) o \ r resid 1039 through 1072 or (resid 1073 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1074 through 1083 or (resid 1084 and (name N or name \ CA or name C or name O or name CB )) or resid 1085 through 1110 or (resid 1111 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1112 through 11 \ 44 or (resid 1145 and (name N or name CA or name C or name O or name CB )) or re \ sid 1301 through 1315)) selection = (chain 'C' and (resid 26 through 29 or (resid 30 through 31 and (name N or name \ CA or name C or name O or name CB )) or resid 32 or (resid 33 and (name N or nam \ e CA or name C or name O or name CB )) or resid 34 through 35 or (resid 36 and ( \ name N or name CA or name C or name O or name CB )) or resid 37 through 39 or (r \ esid 40 through 41 and (name N or name CA or name C or name O or name CB )) or r \ esid 42 through 45 or (resid 46 and (name N or name CA or name C or name O or na \ me CB )) or resid 47 through 61 or (resid 62 and (name N or name CA or name C or \ name O or name CB )) or resid 63 through 65 or (resid 66 through 68 and (name N \ or name CA or name C or name O or name CB )) or (resid 78 through 81 and (name \ N or name CA or name C or name O or name CB )) or resid 82 or (resid 83 and (nam \ e N or name CA or name C or name O or name CB )) or resid 84 through 86 or (resi \ d 87 through 88 and (name N or name CA or name C or name O or name CB )) or resi \ d 89 through 93 or (resid 94 through 100 and (name N or name CA or name C or nam \ e O or name CB )) or resid 101 or (resid 102 and (name N or name CA or name C or \ name O or name CB )) or resid 103 through 104 or (resid 105 and (name N or name \ CA or name C or name O or name CB )) or resid 106 through 109 or (resid 110 thr \ ough 120 and (name N or name CA or name C or name O or name CB )) or resid 121 t \ hrough 124 or (resid 125 through 130 and (name N or name CA or name C or name O \ or name CB )) or resid 131 or (resid 132 through 138 and (name N or name CA or n \ ame C or name O or name CB )) or resid 139 or (resid 140 through 164 and (name N \ or name CA or name C or name O or name CB )) or resid 165 through 166 or (resid \ 167 and (name N or name CA or name C or name O or name CB )) or resid 168 or (r \ esid 169 and (name N or name CA or name C or name O or name CB )) or resid 170 t \ hrough 186 or (resid 187 through 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 198 and (name N or \ name CA or name C or name O or name CB )) or resid 199 through 202 or (resid 203 \ and (name N or name CA or name C or name O or name CB )) or resid 204 through 2 \ 06 or (resid 207 through 208 and (name N or name CA or name C or name O or name \ CB )) or resid 209 through 210 or resid 216 through 227 or (resid 228 through 22 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 230 or (resi \ d 231 and (name N or name CA or name C or name O or name CB )) or resid 232 or ( \ resid 233 and (name N or name CA or name C or name O or name CB )) or resid 234 \ or (resid 235 through 243 and (name N or name CA or name C or name O or name CB \ )) or resid 263 through 266 or (resid 267 and (name N or name CA or name C or na \ me O or name CB )) or resid 268 through 270 or (resid 271 and (name N or name CA \ or name C or name O or name CB )) or resid 272 through 279 or (resid 280 throug \ h 281 and (name N or name CA or name C or name O or name CB )) or resid 282 thro \ ugh 285 or (resid 286 through 289 and (name N or name CA or name C or name O or \ name CB )) or resid 290 through 297 or (resid 298 and (name N or name CA or name \ C or name O or name CB )) or resid 299 through 308 or (resid 309 and (name N or \ name CA or name C or name O or name CB )) or resid 310 through 313 or (resid 31 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 315 through \ 325 or (resid 326 through 327 and (name N or name CA or name C or name O or name \ CB )) or resid 328 through 534 or (resid 535 through 537 and (name N or name CA \ or name C or name O or name CB )) or resid 538 through 540 or (resid 541 throug \ h 542 and (name N or name CA or name C or name O or name CB )) or resid 543 thro \ ugh 550 or (resid 551 through 556 and (name N or name CA or name C or name O or \ name CB )) or resid 557 through 581 or (resid 582 through 584 and (name N or nam \ e CA or name C or name O or name CB )) or resid 585 through 586 or (resid 587 th \ rough 588 and (name N or name CA or name C or name O or name CB )) or resid 589 \ through 598 or (resid 599 and (name N or name CA or name C or name O or name CB \ )) or resid 600 through 614 or (resid 615 and (name N or name CA or name C or na \ me O or name CB )) or resid 616 through 617 or (resid 618 through 620 and (name \ N or name CA or name C or name O or name CB )) or resid 621 or resid 641 through \ 644 or (resid 645 through 647 and (name N or name CA or name C or name O or nam \ e CB )) or resid 648 through 658 or (resid 659 and (name N or name CA or name C \ or name O or name CB )) or resid 660 through 676 or (resid 690 through 691 and ( \ name N or name CA or name C or name O or name CB )) or resid 692 through 709 or \ (resid 710 through 711 and (name N or name CA or name C or name O or name CB )) \ or resid 712 through 734 or (resid 735 through 737 and (name N or name CA or nam \ e C or name O or name CB )) or resid 738 or (resid 739 through 740 and (name N o \ r name CA or name C or name O or name CB )) or resid 741 through 744 or (resid 7 \ 45 through 748 and (name N or name CA or name C or name O or name CB )) or resid \ 749 or (resid 750 through 751 and (name N or name CA or name C or name O or nam \ e CB )) or resid 752 through 779 or (resid 780 and (name N or name CA or name C \ or name O or name CB )) or resid 781 through 784 or (resid 785 through 786 and ( \ name N or name CA or name C or name O or name CB )) or resid 787 through 826 or \ resid 850 through 966 or (resid 967 through 968 and (name N or name CA or name C \ or name O or name CB )) or resid 969 through 972 or (resid 973 through 974 and \ (name N or name CA or name C or name O or name CB )) or resid 975 through 979 or \ (resid 980 and (name N or name CA or name C or name O or name CB )) or resid 98 \ 1 through 982 or (resid 983 through 986 and (name N or name CA or name C or name \ O or name CB )) or resid 987 through 989 or (resid 990 through 991 and (name N \ or name CA or name C or name O or name CB )) or resid 992 through 993 or (resid \ 994 through 995 and (name N or name CA or name C or name O or name CB )) or resi \ d 996 through 1004 or (resid 1005 and (name N or name CA or name C or name O or \ name CB )) or resid 1006 through 1009 or (resid 1010 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1011 through 1036 or (resid 1037 through \ 1038 and (name N or name CA or name C or name O or name CB )) or resid 1039 thro \ ugh 1071 or (resid 1072 through 1073 and (name N or name CA or name C or name O \ or name CB )) or resid 1074 through 1083 or (resid 1084 and (name N or name CA o \ r name C or name O or name CB )) or resid 1085 through 1124 or (resid 1125 and ( \ name N or name CA or name C or name O or name CB )) or resid 1126 through 1135 o \ r (resid 1136 and (name N or name CA or name C or name O or name CB )) or resid \ 1137 through 1145 or resid 1301 through 1315)) } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'L' } 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: 10.670 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: 1.040 Check model and map are aligned: 0.180 Set scattering table: 0.250 Process input model: 66.800 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 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 : 0.011 0.203 26409 Z= 0.603 Angle : 1.378 24.661 36337 Z= 0.922 Chirality : 0.080 0.643 4396 Planarity : 0.005 0.086 4752 Dihedral : 9.906 88.141 9083 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.00 % Favored : 96.68 % Rotamer: Outliers : 0.88 % Allowed : 1.45 % Favored : 97.67 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.13), residues: 3672 helix: -0.69 (0.19), residues: 653 sheet: 1.23 (0.16), residues: 970 loop : 0.04 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP B 886 HIS 0.005 0.001 HIS A1083 PHE 0.016 0.003 PHE C 140 TYR 0.035 0.004 TYR C 796 ARG 0.003 0.000 ARG C 34 Details of bonding type rmsd link_NAG-ASN : bond 0.05506 ( 49) link_NAG-ASN : angle 3.57790 ( 147) link_BETA1-4 : bond 0.07881 ( 1) link_BETA1-4 : angle 2.64731 ( 3) hydrogen bonds : bond 0.19019 ( 1184) hydrogen bonds : angle 8.60471 ( 3219) SS BOND : bond 0.06154 ( 49) SS BOND : angle 4.76482 ( 98) covalent geometry : bond 0.01004 (26310) covalent geometry : angle 1.34068 (36089) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 340 time to evaluate : 2.723 Fit side-chains revert: symmetry clash REVERT: A 367 VAL cc_start: 0.8649 (t) cc_final: 0.8395 (m) REVERT: A 444 LYS cc_start: 0.6759 (mttt) cc_final: 0.5956 (mmtt) REVERT: B 403 ARG cc_start: 0.6115 (mtm180) cc_final: 0.5090 (mtt180) REVERT: C 697 MET cc_start: 0.8219 (ptm) cc_final: 0.7973 (ptm) REVERT: C 763 LEU cc_start: 0.8482 (tt) cc_final: 0.8033 (mp) REVERT: C 1019 ARG cc_start: 0.8143 (tpt170) cc_final: 0.7862 (ttp-110) outliers start: 17 outliers final: 4 residues processed: 352 average time/residue: 0.3823 time to fit residues: 208.6686 Evaluate side-chains 191 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 187 time to evaluate : 2.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 309 optimal weight: 8.9990 chunk 278 optimal weight: 0.6980 chunk 154 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 187 optimal weight: 0.5980 chunk 148 optimal weight: 2.9990 chunk 287 optimal weight: 0.8980 chunk 111 optimal weight: 8.9990 chunk 174 optimal weight: 0.5980 chunk 214 optimal weight: 0.4980 chunk 333 optimal weight: 50.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN A 536 ASN A 540 ASN A 613 GLN A 804 GLN A1002 GLN B 613 GLN B 992 GLN B1023 ASN C1101 HIS C1125 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.208315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.200070 restraints weight = 28669.697| |-----------------------------------------------------------------------------| r_work (start): 0.4282 rms_B_bonded: 0.48 r_work: 0.4211 rms_B_bonded: 0.87 restraints_weight: 0.5000 r_work: 0.4173 rms_B_bonded: 1.46 restraints_weight: 0.2500 r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 26409 Z= 0.142 Angle : 0.624 14.347 36337 Z= 0.320 Chirality : 0.049 0.495 4396 Planarity : 0.005 0.041 4752 Dihedral : 5.227 56.317 4962 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.02 % Favored : 97.96 % Rotamer: Outliers : 1.60 % Allowed : 5.43 % Favored : 92.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.14), residues: 3672 helix: 0.79 (0.21), residues: 643 sheet: 1.49 (0.16), residues: 970 loop : -0.06 (0.13), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 436 HIS 0.007 0.001 HIS C1058 PHE 0.023 0.002 PHE B 58 TYR 0.024 0.001 TYR B 265 ARG 0.003 0.001 ARG A1014 Details of bonding type rmsd link_NAG-ASN : bond 0.01187 ( 49) link_NAG-ASN : angle 2.80390 ( 147) link_BETA1-4 : bond 0.00521 ( 1) link_BETA1-4 : angle 1.46573 ( 3) hydrogen bonds : bond 0.05097 ( 1184) hydrogen bonds : angle 6.08391 ( 3219) SS BOND : bond 0.00212 ( 49) SS BOND : angle 1.37837 ( 98) covalent geometry : bond 0.00311 (26310) covalent geometry : angle 0.59533 (36089) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 2.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.6711 (mttt) cc_final: 0.5885 (tptt) REVERT: B 821 LEU cc_start: 0.8267 (tm) cc_final: 0.7960 (tp) REVERT: B 1139 ASP cc_start: 0.7214 (t0) cc_final: 0.6837 (t0) REVERT: C 1019 ARG cc_start: 0.8196 (tpt170) cc_final: 0.7896 (ttp-110) outliers start: 31 outliers final: 17 residues processed: 213 average time/residue: 0.3446 time to fit residues: 119.9916 Evaluate side-chains 177 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 8 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 253 optimal weight: 0.0070 chunk 302 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 243 optimal weight: 40.0000 chunk 64 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 68 optimal weight: 0.0570 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN B 613 GLN B 762 GLN B 804 GLN B 935 GLN C 935 GLN C1005 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.205347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.196874 restraints weight = 28522.167| |-----------------------------------------------------------------------------| r_work (start): 0.4247 rms_B_bonded: 0.51 r_work: 0.4171 rms_B_bonded: 0.93 restraints_weight: 0.5000 r_work: 0.4137 rms_B_bonded: 1.44 restraints_weight: 0.2500 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26409 Z= 0.139 Angle : 0.563 11.083 36337 Z= 0.290 Chirality : 0.048 0.464 4396 Planarity : 0.004 0.041 4752 Dihedral : 4.819 53.733 4962 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.56 % Favored : 97.41 % Rotamer: Outliers : 1.86 % Allowed : 7.30 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.14), residues: 3672 helix: 1.11 (0.21), residues: 643 sheet: 1.41 (0.16), residues: 1000 loop : -0.14 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 886 HIS 0.007 0.001 HIS C1058 PHE 0.018 0.002 PHE B 58 TYR 0.022 0.001 TYR B1067 ARG 0.005 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 49) link_NAG-ASN : angle 2.47509 ( 147) link_BETA1-4 : bond 0.00720 ( 1) link_BETA1-4 : angle 1.00091 ( 3) hydrogen bonds : bond 0.04953 ( 1184) hydrogen bonds : angle 5.57901 ( 3219) SS BOND : bond 0.00261 ( 49) SS BOND : angle 1.32134 ( 98) covalent geometry : bond 0.00323 (26310) covalent geometry : angle 0.53844 (36089) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 170 time to evaluate : 3.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 821 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8039 (tp) REVERT: C 1019 ARG cc_start: 0.8262 (tpt170) cc_final: 0.8036 (ttp-110) outliers start: 36 outliers final: 24 residues processed: 195 average time/residue: 0.3532 time to fit residues: 115.5760 Evaluate side-chains 183 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 2.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 175 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 332 optimal weight: 30.0000 chunk 134 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 321 optimal weight: 7.9990 chunk 218 optimal weight: 0.1980 chunk 30 optimal weight: 0.0970 chunk 38 optimal weight: 2.9990 chunk 213 optimal weight: 0.6980 chunk 279 optimal weight: 1.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN B 965 GLN C1005 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.206012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.196064 restraints weight = 28784.968| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 0.56 r_work: 0.4085 rms_B_bonded: 0.70 restraints_weight: 0.5000 r_work: 0.4042 rms_B_bonded: 1.30 restraints_weight: 0.2500 r_work: 0.3987 rms_B_bonded: 2.21 restraints_weight: 0.1250 r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 26409 Z= 0.110 Angle : 0.533 15.521 36337 Z= 0.270 Chirality : 0.047 0.409 4396 Planarity : 0.004 0.043 4752 Dihedral : 4.641 53.126 4962 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.21 % Favored : 97.77 % Rotamer: Outliers : 1.92 % Allowed : 7.97 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.14), residues: 3672 helix: 1.20 (0.21), residues: 646 sheet: 1.39 (0.16), residues: 992 loop : -0.13 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.004 0.001 HIS C1058 PHE 0.017 0.001 PHE A 541 TYR 0.024 0.001 TYR B 453 ARG 0.004 0.000 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00508 ( 49) link_NAG-ASN : angle 2.81046 ( 147) link_BETA1-4 : bond 0.00369 ( 1) link_BETA1-4 : angle 0.96437 ( 3) hydrogen bonds : bond 0.04254 ( 1184) hydrogen bonds : angle 5.32656 ( 3219) SS BOND : bond 0.00307 ( 49) SS BOND : angle 1.31805 ( 98) covalent geometry : bond 0.00247 (26310) covalent geometry : angle 0.49935 (36089) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 2.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7816 (mtm-85) cc_final: 0.7543 (mtm110) REVERT: B 821 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8143 (tp) REVERT: B 886 TRP cc_start: 0.7776 (p90) cc_final: 0.6635 (p-90) outliers start: 37 outliers final: 23 residues processed: 197 average time/residue: 0.3366 time to fit residues: 109.4008 Evaluate side-chains 174 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 346 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 320 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 240 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 325 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 192 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN A1002 GLN B 901 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN C1135 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.196760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.183501 restraints weight = 28837.756| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 0.73 r_work: 0.3862 rms_B_bonded: 0.88 restraints_weight: 0.5000 r_work: 0.3812 rms_B_bonded: 1.51 restraints_weight: 0.2500 r_work: 0.3749 rms_B_bonded: 2.49 restraints_weight: 0.1250 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 26409 Z= 0.331 Angle : 0.752 16.845 36337 Z= 0.380 Chirality : 0.055 0.469 4396 Planarity : 0.006 0.075 4752 Dihedral : 5.700 56.003 4962 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.24 % Favored : 96.73 % Rotamer: Outliers : 2.64 % Allowed : 8.85 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.13), residues: 3672 helix: 0.26 (0.20), residues: 660 sheet: 1.05 (0.16), residues: 1011 loop : -0.51 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP B 886 HIS 0.014 0.003 HIS B1058 PHE 0.024 0.003 PHE B1121 TYR 0.026 0.002 TYR A 265 ARG 0.007 0.001 ARG A1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00570 ( 49) link_NAG-ASN : angle 3.27100 ( 147) link_BETA1-4 : bond 0.01605 ( 1) link_BETA1-4 : angle 1.11912 ( 3) hydrogen bonds : bond 0.06870 ( 1184) hydrogen bonds : angle 5.79647 ( 3219) SS BOND : bond 0.00509 ( 49) SS BOND : angle 1.99756 ( 98) covalent geometry : bond 0.00827 (26310) covalent geometry : angle 0.71725 (36089) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 164 time to evaluate : 2.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 821 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8345 (tp) REVERT: C 763 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8158 (mt) outliers start: 51 outliers final: 33 residues processed: 200 average time/residue: 0.3305 time to fit residues: 110.8384 Evaluate side-chains 187 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 4.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 128 optimal weight: 5.9990 chunk 123 optimal weight: 0.6980 chunk 352 optimal weight: 8.9990 chunk 162 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 178 optimal weight: 0.6980 chunk 185 optimal weight: 0.9990 chunk 351 optimal weight: 30.0000 chunk 191 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1005 GLN C 613 GLN C 644 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.197377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.187291 restraints weight = 28617.040| |-----------------------------------------------------------------------------| r_work (start): 0.4144 rms_B_bonded: 0.57 r_work: 0.3924 rms_B_bonded: 0.71 restraints_weight: 0.5000 r_work: 0.3880 rms_B_bonded: 1.24 restraints_weight: 0.2500 r_work: 0.3835 rms_B_bonded: 1.96 restraints_weight: 0.1250 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26409 Z= 0.136 Angle : 0.557 14.883 36337 Z= 0.280 Chirality : 0.048 0.385 4396 Planarity : 0.004 0.053 4752 Dihedral : 5.073 58.842 4960 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.31 % Favored : 97.66 % Rotamer: Outliers : 2.28 % Allowed : 9.99 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.14), residues: 3672 helix: 0.78 (0.21), residues: 654 sheet: 1.13 (0.16), residues: 1007 loop : -0.38 (0.14), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.004 0.001 HIS C1058 PHE 0.017 0.001 PHE C 140 TYR 0.022 0.001 TYR B 453 ARG 0.004 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00450 ( 49) link_NAG-ASN : angle 2.80165 ( 147) link_BETA1-4 : bond 0.00464 ( 1) link_BETA1-4 : angle 0.81052 ( 3) hydrogen bonds : bond 0.04598 ( 1184) hydrogen bonds : angle 5.26780 ( 3219) SS BOND : bond 0.00331 ( 49) SS BOND : angle 1.31121 ( 98) covalent geometry : bond 0.00321 (26310) covalent geometry : angle 0.52533 (36089) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 160 time to evaluate : 2.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7582 (tt0) REVERT: A 981 PHE cc_start: 0.7719 (OUTLIER) cc_final: 0.7467 (t80) REVERT: B 821 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8265 (tp) REVERT: B 886 TRP cc_start: 0.7903 (p90) cc_final: 0.6558 (p-90) outliers start: 44 outliers final: 30 residues processed: 188 average time/residue: 0.3360 time to fit residues: 105.4686 Evaluate side-chains 180 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 2.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 192 optimal weight: 0.9990 chunk 243 optimal weight: 30.0000 chunk 42 optimal weight: 3.9990 chunk 294 optimal weight: 0.9980 chunk 363 optimal weight: 50.0000 chunk 84 optimal weight: 3.9990 chunk 300 optimal weight: 0.4980 chunk 261 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 307 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 613 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.195012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.184274 restraints weight = 28821.040| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 0.62 r_work: 0.3900 rms_B_bonded: 0.77 restraints_weight: 0.5000 r_work: 0.3838 rms_B_bonded: 1.58 restraints_weight: 0.2500 r_work: 0.3768 rms_B_bonded: 2.73 restraints_weight: 0.1250 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 26409 Z= 0.197 Angle : 0.613 14.123 36337 Z= 0.307 Chirality : 0.050 0.406 4396 Planarity : 0.005 0.055 4752 Dihedral : 5.148 58.651 4958 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.38 % Allowed : 10.46 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.14), residues: 3672 helix: 0.77 (0.21), residues: 653 sheet: 1.09 (0.16), residues: 999 loop : -0.44 (0.14), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 436 HIS 0.008 0.002 HIS C1058 PHE 0.017 0.002 PHE A1121 TYR 0.024 0.002 TYR A 265 ARG 0.004 0.001 ARG A1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00481 ( 49) link_NAG-ASN : angle 2.84307 ( 147) link_BETA1-4 : bond 0.00431 ( 1) link_BETA1-4 : angle 0.73207 ( 3) hydrogen bonds : bond 0.05420 ( 1184) hydrogen bonds : angle 5.36578 ( 3219) SS BOND : bond 0.00347 ( 49) SS BOND : angle 1.40834 ( 98) covalent geometry : bond 0.00491 (26310) covalent geometry : angle 0.58325 (36089) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 159 time to evaluate : 2.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 331 ASN cc_start: 0.6868 (OUTLIER) cc_final: 0.4746 (m-40) REVERT: B 821 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8380 (tp) REVERT: C 613 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7715 (mt0) outliers start: 46 outliers final: 31 residues processed: 187 average time/residue: 0.3458 time to fit residues: 107.6003 Evaluate side-chains 188 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 2.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 39 optimal weight: 2.9990 chunk 199 optimal weight: 0.8980 chunk 252 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 131 optimal weight: 9.9990 chunk 299 optimal weight: 0.2980 chunk 137 optimal weight: 50.0000 chunk 142 optimal weight: 7.9990 chunk 363 optimal weight: 9.9990 chunk 26 optimal weight: 0.6980 chunk 206 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN A 644 GLN B1005 GLN C 613 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.196954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.186755 restraints weight = 28652.941| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 0.57 r_work: 0.3921 rms_B_bonded: 0.71 restraints_weight: 0.5000 r_work: 0.3873 rms_B_bonded: 1.32 restraints_weight: 0.2500 r_work: 0.3823 rms_B_bonded: 2.12 restraints_weight: 0.1250 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26409 Z= 0.126 Angle : 0.544 13.522 36337 Z= 0.273 Chirality : 0.047 0.372 4396 Planarity : 0.004 0.054 4752 Dihedral : 4.852 58.820 4956 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.97 % Allowed : 11.18 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.14), residues: 3672 helix: 1.06 (0.21), residues: 643 sheet: 1.16 (0.16), residues: 998 loop : -0.34 (0.14), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS C1058 PHE 0.018 0.001 PHE A 168 TYR 0.020 0.001 TYR B 453 ARG 0.007 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00672 ( 49) link_NAG-ASN : angle 2.52666 ( 147) link_BETA1-4 : bond 0.00139 ( 1) link_BETA1-4 : angle 0.71471 ( 3) hydrogen bonds : bond 0.04516 ( 1184) hydrogen bonds : angle 5.16266 ( 3219) SS BOND : bond 0.00251 ( 49) SS BOND : angle 1.13260 ( 98) covalent geometry : bond 0.00294 (26310) covalent geometry : angle 0.51792 (36089) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 151 time to evaluate : 3.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 821 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8296 (tp) REVERT: B 886 TRP cc_start: 0.7933 (p90) cc_final: 0.6718 (p90) REVERT: C 763 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8025 (mt) outliers start: 38 outliers final: 30 residues processed: 175 average time/residue: 0.3517 time to fit residues: 102.9325 Evaluate side-chains 179 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 2.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 199 optimal weight: 0.8980 chunk 186 optimal weight: 0.9990 chunk 268 optimal weight: 0.7980 chunk 308 optimal weight: 20.0000 chunk 277 optimal weight: 0.9980 chunk 262 optimal weight: 2.9990 chunk 107 optimal weight: 20.0000 chunk 337 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 247 optimal weight: 6.9990 chunk 216 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 613 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.196426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.183131 restraints weight = 28852.984| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 0.71 r_work: 0.3743 rms_B_bonded: 0.92 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work: 0.3496 rms_B_bonded: 3.83 restraints_weight: 0.1250 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26409 Z= 0.143 Angle : 0.553 13.366 36337 Z= 0.278 Chirality : 0.048 0.373 4396 Planarity : 0.004 0.054 4752 Dihedral : 4.761 52.429 4956 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.86 % Allowed : 11.13 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.14), residues: 3672 helix: 1.08 (0.21), residues: 645 sheet: 1.22 (0.16), residues: 988 loop : -0.35 (0.14), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.005 0.001 HIS B1058 PHE 0.033 0.002 PHE A 541 TYR 0.020 0.001 TYR A 265 ARG 0.006 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00576 ( 49) link_NAG-ASN : angle 2.54578 ( 147) link_BETA1-4 : bond 0.00151 ( 1) link_BETA1-4 : angle 0.71722 ( 3) hydrogen bonds : bond 0.04674 ( 1184) hydrogen bonds : angle 5.13489 ( 3219) SS BOND : bond 0.00254 ( 49) SS BOND : angle 1.16223 ( 98) covalent geometry : bond 0.00343 (26310) covalent geometry : angle 0.52688 (36089) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 2.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: 0.7767 (mp) cc_final: 0.7472 (mt) REVERT: A 981 PHE cc_start: 0.8018 (t80) cc_final: 0.7738 (t80) REVERT: B 821 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8372 (tp) REVERT: C 613 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7731 (mt0) REVERT: C 763 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8114 (mt) outliers start: 36 outliers final: 30 residues processed: 179 average time/residue: 0.3417 time to fit residues: 101.3879 Evaluate side-chains 186 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 133 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 16 optimal weight: 0.4980 chunk 366 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 chunk 157 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 357 optimal weight: 20.0000 chunk 230 optimal weight: 1.9990 chunk 353 optimal weight: 10.0000 chunk 271 optimal weight: 0.2980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.196295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.186019 restraints weight = 28760.336| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 0.59 r_work: 0.3916 rms_B_bonded: 0.73 restraints_weight: 0.5000 r_work: 0.3855 rms_B_bonded: 1.50 restraints_weight: 0.2500 r_work: 0.3811 rms_B_bonded: 2.19 restraints_weight: 0.1250 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 26409 Z= 0.149 Angle : 0.558 13.210 36337 Z= 0.280 Chirality : 0.048 0.370 4396 Planarity : 0.004 0.055 4752 Dihedral : 4.690 52.401 4956 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.71 % Allowed : 11.28 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.14), residues: 3672 helix: 1.07 (0.21), residues: 646 sheet: 1.23 (0.16), residues: 991 loop : -0.35 (0.14), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.005 0.001 HIS C1058 PHE 0.015 0.001 PHE B 106 TYR 0.021 0.001 TYR A 265 ARG 0.006 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00586 ( 49) link_NAG-ASN : angle 2.53282 ( 147) link_BETA1-4 : bond 0.00310 ( 1) link_BETA1-4 : angle 0.71884 ( 3) hydrogen bonds : bond 0.04706 ( 1184) hydrogen bonds : angle 5.13317 ( 3219) SS BOND : bond 0.00248 ( 49) SS BOND : angle 1.25261 ( 98) covalent geometry : bond 0.00362 (26310) covalent geometry : angle 0.53158 (36089) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 3.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 981 PHE cc_start: 0.7653 (t80) cc_final: 0.7395 (t80) REVERT: B 821 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8342 (tp) REVERT: C 763 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8041 (mt) outliers start: 33 outliers final: 30 residues processed: 174 average time/residue: 0.3657 time to fit residues: 106.0052 Evaluate side-chains 181 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 2.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 32 optimal weight: 0.6980 chunk 355 optimal weight: 50.0000 chunk 349 optimal weight: 9.9990 chunk 108 optimal weight: 0.0020 chunk 266 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 271 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 313 optimal weight: 7.9990 chunk 254 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN C 613 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.197064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.183725 restraints weight = 28734.257| |-----------------------------------------------------------------------------| r_work (start): 0.4109 rms_B_bonded: 0.71 r_work: 0.3771 rms_B_bonded: 0.91 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work: 0.3600 rms_B_bonded: 3.30 restraints_weight: 0.1250 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26409 Z= 0.123 Angle : 0.533 12.995 36337 Z= 0.267 Chirality : 0.047 0.359 4396 Planarity : 0.004 0.054 4752 Dihedral : 4.501 52.317 4956 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.89 % Favored : 97.09 % Rotamer: Outliers : 1.76 % Allowed : 11.18 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.14), residues: 3672 helix: 1.23 (0.21), residues: 647 sheet: 1.31 (0.16), residues: 983 loop : -0.30 (0.14), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS B1058 PHE 0.019 0.001 PHE C 140 TYR 0.020 0.001 TYR C 265 ARG 0.006 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00566 ( 49) link_NAG-ASN : angle 2.44804 ( 147) link_BETA1-4 : bond 0.00283 ( 1) link_BETA1-4 : angle 0.75964 ( 3) hydrogen bonds : bond 0.04331 ( 1184) hydrogen bonds : angle 5.04247 ( 3219) SS BOND : bond 0.00219 ( 49) SS BOND : angle 1.09337 ( 98) covalent geometry : bond 0.00289 (26310) covalent geometry : angle 0.50816 (36089) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14023.31 seconds wall clock time: 242 minutes 21.24 seconds (14541.24 seconds total)