Starting phenix.real_space_refine on Sun Jun 22 11:47:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8err_28559/06_2025/8err_28559.cif Found real_map, /net/cci-nas-00/data/ceres_data/8err_28559/06_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_28559/06_2025/8err_28559.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8err_28559/06_2025/8err_28559.map" model { file = "/net/cci-nas-00/data/ceres_data/8err_28559/06_2025/8err_28559.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8err_28559/06_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 15.09, per 1000 atoms: 0.59 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: 6.10 Conformation dependent library (CDL) restraints added in 3.4 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: 4.37 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: 13.15 Time building geometry restraints manager: 7.31 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: 0.010 Normalize map: mean=0, sd=1: 58.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.900 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 64.090 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.970 ------------------------------------------------------------------------------- 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 : 2.610 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: 0.3859 time to fit residues: 213.6155 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 : 2.941 ------------------------------------------------------------------------------- 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 = 28670.152| |-----------------------------------------------------------------------------| r_work (start): 0.4282 rms_B_bonded: 0.48 r_work: 0.4210 rms_B_bonded: 0.87 restraints_weight: 0.5000 r_work: 0.4178 rms_B_bonded: 1.34 restraints_weight: 0.2500 r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 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 : 2.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.6703 (mttt) cc_final: 0.5879 (tptt) REVERT: B 821 LEU cc_start: 0.8264 (tm) cc_final: 0.7957 (tp) REVERT: B 1139 ASP cc_start: 0.7206 (t0) cc_final: 0.6828 (t0) REVERT: C 1019 ARG cc_start: 0.8191 (tpt170) cc_final: 0.7894 (ttp-110) outliers start: 31 outliers final: 17 residues processed: 213 average time/residue: 0.3683 time to fit residues: 129.5754 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 : 2.775 ------------------------------------------------------------------------------- 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: 0.9990 chunk 85 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 253 optimal weight: 0.0870 chunk 302 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 243 optimal weight: 40.0000 chunk 64 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 68 optimal weight: 0.2980 overall best weight: 0.8562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 613 GLN B 762 GLN B 804 GLN B 935 GLN C 935 GLN C1005 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.204827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.196291 restraints weight = 28490.781| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 0.52 r_work: 0.4163 rms_B_bonded: 0.95 restraints_weight: 0.5000 r_work: 0.4127 rms_B_bonded: 1.48 restraints_weight: 0.2500 r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26409 Z= 0.152 Angle : 0.578 11.184 36337 Z= 0.297 Chirality : 0.048 0.469 4396 Planarity : 0.005 0.042 4752 Dihedral : 4.870 54.599 4962 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.61 % Favored : 97.36 % Rotamer: Outliers : 1.97 % Allowed : 7.25 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.69 (0.14), residues: 3672 helix: 1.05 (0.21), residues: 643 sheet: 1.35 (0.16), residues: 1010 loop : -0.17 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 886 HIS 0.007 0.001 HIS C1058 PHE 0.018 0.002 PHE A 275 TYR 0.022 0.001 TYR B1067 ARG 0.005 0.001 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00583 ( 49) link_NAG-ASN : angle 2.51154 ( 147) link_BETA1-4 : bond 0.00459 ( 1) link_BETA1-4 : angle 0.95256 ( 3) hydrogen bonds : bond 0.05135 ( 1184) hydrogen bonds : angle 5.60886 ( 3219) SS BOND : bond 0.00411 ( 49) SS BOND : angle 1.40070 ( 98) covalent geometry : bond 0.00360 (26310) covalent geometry : angle 0.55205 (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 208 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 170 time to evaluate : 3.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 821 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8056 (tp) REVERT: C 1019 ARG cc_start: 0.8244 (tpt170) cc_final: 0.8043 (ttp-110) outliers start: 38 outliers final: 25 residues processed: 196 average time/residue: 0.3518 time to fit residues: 115.9196 Evaluate side-chains 184 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 2.791 ------------------------------------------------------------------------------- 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 620 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 794 ILE 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 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 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: 0.9990 chunk 114 optimal weight: 0.9980 chunk 332 optimal weight: 20.0000 chunk 134 optimal weight: 0.0370 chunk 29 optimal weight: 3.9990 chunk 321 optimal weight: 10.0000 chunk 218 optimal weight: 0.0070 chunk 30 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 213 optimal weight: 0.7980 chunk 279 optimal weight: 1.9990 overall best weight: 0.5076 ------------------------------------------------------------------------------- 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 C 907 ASN C 913 GLN C1005 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.205844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.197667 restraints weight = 28747.495| |-----------------------------------------------------------------------------| r_work (start): 0.4256 rms_B_bonded: 0.49 r_work: 0.4160 rms_B_bonded: 0.65 restraints_weight: 0.5000 r_work: 0.4121 rms_B_bonded: 1.20 restraints_weight: 0.2500 r_work: 0.4045 rms_B_bonded: 2.48 restraints_weight: 0.1250 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.2643 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= 0.111 Angle : 0.533 17.645 36337 Z= 0.269 Chirality : 0.046 0.407 4396 Planarity : 0.004 0.043 4752 Dihedral : 4.680 52.940 4962 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.21 % Favored : 97.77 % Rotamer: Outliers : 1.86 % Allowed : 8.18 % Favored : 89.96 % 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: 0.74 (0.14), residues: 3672 helix: 1.17 (0.21), residues: 646 sheet: 1.37 (0.16), residues: 999 loop : -0.15 (0.13), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.004 0.001 HIS C1058 PHE 0.013 0.001 PHE B 65 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 0.00492 ( 49) link_NAG-ASN : angle 2.85258 ( 147) link_BETA1-4 : bond 0.00232 ( 1) link_BETA1-4 : angle 0.96823 ( 3) hydrogen bonds : bond 0.04249 ( 1184) hydrogen bonds : angle 5.32479 ( 3219) SS BOND : bond 0.00224 ( 49) SS BOND : angle 1.23459 ( 98) covalent geometry : bond 0.00249 (26310) covalent geometry : angle 0.49878 (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 207 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 2.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7732 (mtm-85) cc_final: 0.7456 (mtm110) REVERT: B 821 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8125 (tp) REVERT: B 886 TRP cc_start: 0.7800 (p90) cc_final: 0.6650 (p-90) outliers start: 36 outliers final: 24 residues processed: 196 average time/residue: 0.3366 time to fit residues: 110.2156 Evaluate side-chains 175 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 2.559 ------------------------------------------------------------------------------- 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 540 ASN Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 859 THR 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 131 CYS 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 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: 5.9990 chunk 31 optimal weight: 1.9990 chunk 320 optimal weight: 8.9990 chunk 85 optimal weight: 0.8980 chunk 240 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 325 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 192 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN B 965 GLN C1005 GLN C1135 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.194461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.181235 restraints weight = 28865.008| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 0.70 r_work: 0.3715 rms_B_bonded: 0.92 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work: 0.3550 rms_B_bonded: 2.88 restraints_weight: 0.1250 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 26409 Z= 0.286 Angle : 0.700 12.246 36337 Z= 0.357 Chirality : 0.053 0.447 4396 Planarity : 0.005 0.064 4752 Dihedral : 5.387 55.598 4962 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.16 % Favored : 96.81 % Rotamer: Outliers : 2.64 % Allowed : 9.01 % Favored : 88.35 % 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: 0.20 (0.14), residues: 3672 helix: 0.42 (0.20), residues: 660 sheet: 1.07 (0.16), residues: 1029 loop : -0.44 (0.14), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 886 HIS 0.013 0.002 HIS B1058 PHE 0.037 0.003 PHE A 541 TYR 0.026 0.002 TYR B 453 ARG 0.007 0.001 ARG A1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00503 ( 49) link_NAG-ASN : angle 2.77149 ( 147) link_BETA1-4 : bond 0.00368 ( 1) link_BETA1-4 : angle 0.76338 ( 3) hydrogen bonds : bond 0.06439 ( 1184) hydrogen bonds : angle 5.67093 ( 3219) SS BOND : bond 0.00461 ( 49) SS BOND : angle 1.83789 ( 98) covalent geometry : bond 0.00718 (26310) covalent geometry : angle 0.67276 (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 : 2.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 703 ASN cc_start: 0.8507 (m-40) cc_final: 0.8298 (m-40) REVERT: B 821 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8406 (tp) REVERT: C 763 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8151 (mt) outliers start: 51 outliers final: 34 residues processed: 199 average time/residue: 0.3381 time to fit residues: 113.2132 Evaluate side-chains 189 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 153 time to evaluate : 2.716 ------------------------------------------------------------------------------- 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 603 ASN Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 794 ILE 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 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 723 THR 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 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: 10.0000 chunk 123 optimal weight: 0.3980 chunk 352 optimal weight: 8.9990 chunk 162 optimal weight: 0.8980 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: 2.9990 chunk 351 optimal weight: 30.0000 chunk 191 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN B1005 GLN C 613 GLN C 644 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.197651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.187409 restraints weight = 28597.966| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 0.58 r_work: 0.3926 rms_B_bonded: 0.71 restraints_weight: 0.5000 r_work: 0.3872 rms_B_bonded: 1.40 restraints_weight: 0.2500 r_work: 0.3826 rms_B_bonded: 2.13 restraints_weight: 0.1250 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26409 Z= 0.123 Angle : 0.540 11.016 36337 Z= 0.274 Chirality : 0.047 0.381 4396 Planarity : 0.004 0.050 4752 Dihedral : 4.875 52.477 4960 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.34 % Favored : 97.63 % Rotamer: Outliers : 2.07 % Allowed : 10.25 % Favored : 87.68 % 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: 0.43 (0.14), residues: 3672 helix: 0.88 (0.21), residues: 655 sheet: 1.16 (0.16), residues: 1016 loop : -0.35 (0.14), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS C1058 PHE 0.017 0.001 PHE C 140 TYR 0.023 0.001 TYR B 453 ARG 0.004 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 49) link_NAG-ASN : angle 2.37934 ( 147) link_BETA1-4 : bond 0.00238 ( 1) link_BETA1-4 : angle 0.76454 ( 3) hydrogen bonds : bond 0.04512 ( 1184) hydrogen bonds : angle 5.22595 ( 3219) SS BOND : bond 0.00304 ( 49) SS BOND : angle 1.26165 ( 98) covalent geometry : bond 0.00288 (26310) covalent geometry : angle 0.51557 (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 198 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 2.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 821 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8322 (tp) REVERT: B 886 TRP cc_start: 0.7946 (p90) cc_final: 0.6599 (p-90) outliers start: 40 outliers final: 30 residues processed: 184 average time/residue: 0.3520 time to fit residues: 110.5032 Evaluate side-chains 177 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 2.634 ------------------------------------------------------------------------------- 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 620 VAL Chi-restraints excluded: chain A residue 719 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 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 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 127 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 633 TRP 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: 0.8980 chunk 243 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 chunk 294 optimal weight: 0.9990 chunk 363 optimal weight: 50.0000 chunk 84 optimal weight: 3.9990 chunk 300 optimal weight: 0.3980 chunk 261 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 307 optimal weight: 20.0000 chunk 78 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 613 GLN C 762 GLN ** C 907 ASN ** 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 = 0.196979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.183628 restraints weight = 28783.868| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 0.72 r_work: 0.3756 rms_B_bonded: 0.91 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 2.03 restraints_weight: 0.2500 r_work: 0.3616 rms_B_bonded: 2.78 restraints_weight: 0.1250 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26409 Z= 0.142 Angle : 0.556 12.538 36337 Z= 0.279 Chirality : 0.048 0.379 4396 Planarity : 0.004 0.052 4752 Dihedral : 4.750 52.404 4958 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.02 % Allowed : 10.25 % 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: 0.51 (0.14), residues: 3672 helix: 1.03 (0.21), residues: 649 sheet: 1.20 (0.16), residues: 1007 loop : -0.32 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.006 0.001 HIS C1058 PHE 0.017 0.001 PHE B 65 TYR 0.023 0.001 TYR B 453 ARG 0.003 0.000 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 49) link_NAG-ASN : angle 2.62447 ( 147) link_BETA1-4 : bond 0.00257 ( 1) link_BETA1-4 : angle 0.79624 ( 3) hydrogen bonds : bond 0.04684 ( 1184) hydrogen bonds : angle 5.16210 ( 3219) SS BOND : bond 0.00288 ( 49) SS BOND : angle 1.18508 ( 98) covalent geometry : bond 0.00341 (26310) covalent geometry : angle 0.52867 (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 198 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 159 time to evaluate : 2.870 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 981 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.7704 (t80) REVERT: B 331 ASN cc_start: 0.7041 (OUTLIER) cc_final: 0.4806 (m-40) REVERT: B 821 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8391 (tp) outliers start: 39 outliers final: 30 residues processed: 182 average time/residue: 0.4130 time to fit residues: 128.8655 Evaluate side-chains 184 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 2.986 ------------------------------------------------------------------------------- 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 620 VAL Chi-restraints excluded: chain A residue 719 THR 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 39 optimal weight: 3.9990 chunk 199 optimal weight: 0.9980 chunk 252 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 299 optimal weight: 0.4980 chunk 137 optimal weight: 50.0000 chunk 142 optimal weight: 10.0000 chunk 363 optimal weight: 50.0000 chunk 26 optimal weight: 0.6980 chunk 206 optimal weight: 0.0670 overall best weight: 1.0520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN B 965 GLN C 613 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.195942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.182516 restraints weight = 28649.979| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 0.71 r_work: 0.3733 rms_B_bonded: 0.93 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work: 0.3507 rms_B_bonded: 3.64 restraints_weight: 0.1250 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26409 Z= 0.165 Angle : 0.565 9.520 36337 Z= 0.286 Chirality : 0.048 0.369 4396 Planarity : 0.004 0.055 4752 Dihedral : 4.826 52.179 4958 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.17 % Allowed : 10.56 % Favored : 87.27 % 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: 0.46 (0.14), residues: 3672 helix: 0.96 (0.21), residues: 653 sheet: 1.22 (0.16), residues: 1001 loop : -0.36 (0.14), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.006 0.001 HIS B1058 PHE 0.019 0.002 PHE C 140 TYR 0.022 0.001 TYR A 265 ARG 0.004 0.000 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00469 ( 49) link_NAG-ASN : angle 2.34059 ( 147) link_BETA1-4 : bond 0.00419 ( 1) link_BETA1-4 : angle 0.75030 ( 3) hydrogen bonds : bond 0.04986 ( 1184) hydrogen bonds : angle 5.20186 ( 3219) SS BOND : bond 0.00278 ( 49) SS BOND : angle 1.23698 ( 98) covalent geometry : bond 0.00405 (26310) covalent geometry : angle 0.54337 (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 198 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 156 time to evaluate : 8.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 981 PHE cc_start: 0.7958 (OUTLIER) cc_final: 0.7606 (t80) REVERT: B 821 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8400 (tp) REVERT: C 763 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8144 (mt) outliers start: 42 outliers final: 31 residues processed: 184 average time/residue: 0.4802 time to fit residues: 153.0460 Evaluate side-chains 184 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 2.649 ------------------------------------------------------------------------------- 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 981 PHE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 63 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 199 optimal weight: 0.9980 chunk 186 optimal weight: 0.8980 chunk 268 optimal weight: 0.9990 chunk 308 optimal weight: 20.0000 chunk 277 optimal weight: 0.6980 chunk 262 optimal weight: 3.9990 chunk 107 optimal weight: 20.0000 chunk 337 optimal weight: 20.0000 chunk 36 optimal weight: 0.6980 chunk 247 optimal weight: 5.9990 chunk 216 optimal weight: 2.9990 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.196513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.186133 restraints weight = 28838.094| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 0.60 r_work: 0.3913 rms_B_bonded: 0.74 restraints_weight: 0.5000 r_work: 0.3859 rms_B_bonded: 1.46 restraints_weight: 0.2500 r_work: 0.3811 rms_B_bonded: 2.22 restraints_weight: 0.1250 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26409 Z= 0.142 Angle : 0.547 9.650 36337 Z= 0.276 Chirality : 0.048 0.365 4396 Planarity : 0.004 0.056 4752 Dihedral : 4.718 52.516 4958 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.92 % Allowed : 10.82 % Favored : 87.27 % 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: 0.55 (0.14), residues: 3672 helix: 1.07 (0.21), residues: 655 sheet: 1.27 (0.16), residues: 989 loop : -0.31 (0.14), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.005 0.001 HIS B1058 PHE 0.014 0.001 PHE C 898 TYR 0.021 0.001 TYR B 453 ARG 0.002 0.000 ARG A1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 49) link_NAG-ASN : angle 2.21029 ( 147) link_BETA1-4 : bond 0.00308 ( 1) link_BETA1-4 : angle 0.74983 ( 3) hydrogen bonds : bond 0.04644 ( 1184) hydrogen bonds : angle 5.12009 ( 3219) SS BOND : bond 0.00242 ( 49) SS BOND : angle 1.27163 ( 98) covalent geometry : bond 0.00343 (26310) covalent geometry : angle 0.52580 (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: 37 poor density : 155 time to evaluate : 2.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 981 PHE cc_start: 0.7694 (OUTLIER) cc_final: 0.7426 (t80) REVERT: B 821 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8357 (tp) REVERT: C 763 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8062 (mt) outliers start: 37 outliers final: 31 residues processed: 179 average time/residue: 0.3671 time to fit residues: 110.2103 Evaluate side-chains 182 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 2.349 ------------------------------------------------------------------------------- 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 981 PHE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 63 THR 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 133 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 366 optimal weight: 7.9990 chunk 62 optimal weight: 0.3980 chunk 157 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 357 optimal weight: 6.9990 chunk 230 optimal weight: 3.9990 chunk 353 optimal weight: 10.0000 chunk 271 optimal weight: 0.0980 overall best weight: 0.6384 ------------------------------------------------------------------------------- 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 907 ASN ** 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 = 0.4242 r_free = 0.4242 target = 0.197275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.186899 restraints weight = 28753.307| |-----------------------------------------------------------------------------| r_work (start): 0.4140 rms_B_bonded: 0.60 r_work: 0.3920 rms_B_bonded: 0.74 restraints_weight: 0.5000 r_work: 0.3866 rms_B_bonded: 1.44 restraints_weight: 0.2500 r_work: 0.3816 rms_B_bonded: 2.23 restraints_weight: 0.1250 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26409 Z= 0.121 Angle : 0.527 10.875 36337 Z= 0.265 Chirality : 0.047 0.354 4396 Planarity : 0.004 0.054 4752 Dihedral : 4.565 52.392 4958 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.92 % Allowed : 11.02 % 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: 0.63 (0.14), residues: 3672 helix: 1.20 (0.21), residues: 655 sheet: 1.30 (0.16), residues: 990 loop : -0.27 (0.14), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.003 0.001 HIS C1058 PHE 0.018 0.001 PHE C 140 TYR 0.021 0.001 TYR B 453 ARG 0.004 0.000 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00413 ( 49) link_NAG-ASN : angle 2.11516 ( 147) link_BETA1-4 : bond 0.00257 ( 1) link_BETA1-4 : angle 0.75254 ( 3) hydrogen bonds : bond 0.04314 ( 1184) hydrogen bonds : angle 5.03101 ( 3219) SS BOND : bond 0.00269 ( 49) SS BOND : angle 1.08556 ( 98) covalent geometry : bond 0.00282 (26310) covalent geometry : angle 0.50777 (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 187 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 150 time to evaluate : 3.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 981 PHE cc_start: 0.7690 (OUTLIER) cc_final: 0.7433 (t80) REVERT: B 821 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8352 (tp) REVERT: B 886 TRP cc_start: 0.7865 (p90) cc_final: 0.6486 (p-90) REVERT: C 763 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8025 (mt) outliers start: 37 outliers final: 31 residues processed: 174 average time/residue: 0.3575 time to fit residues: 103.8867 Evaluate side-chains 182 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 2.773 ------------------------------------------------------------------------------- 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 981 PHE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 63 THR 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: 1.9990 chunk 355 optimal weight: 50.0000 chunk 349 optimal weight: 9.9990 chunk 108 optimal weight: 0.8980 chunk 266 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 271 optimal weight: 0.4980 chunk 90 optimal weight: 0.8980 chunk 313 optimal weight: 6.9990 chunk 254 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 965 GLN C 613 GLN ** C 907 ASN ** 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 = 0.4227 r_free = 0.4227 target = 0.195739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.185361 restraints weight = 28728.300| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 0.60 r_work: 0.3910 rms_B_bonded: 0.75 restraints_weight: 0.5000 r_work: 0.3859 rms_B_bonded: 1.40 restraints_weight: 0.2500 r_work: 0.3809 rms_B_bonded: 2.18 restraints_weight: 0.1250 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26409 Z= 0.165 Angle : 0.565 10.702 36337 Z= 0.285 Chirality : 0.048 0.367 4396 Planarity : 0.004 0.056 4752 Dihedral : 4.694 52.652 4958 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.24 % Favored : 96.73 % 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: 0.53 (0.14), residues: 3672 helix: 1.11 (0.21), residues: 650 sheet: 1.24 (0.16), residues: 991 loop : -0.32 (0.14), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.006 0.001 HIS B1058 PHE 0.016 0.002 PHE B1121 TYR 0.022 0.001 TYR A 265 ARG 0.004 0.000 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00432 ( 49) link_NAG-ASN : angle 2.18644 ( 147) link_BETA1-4 : bond 0.00309 ( 1) link_BETA1-4 : angle 0.68384 ( 3) hydrogen bonds : bond 0.04923 ( 1184) hydrogen bonds : angle 5.14776 ( 3219) SS BOND : bond 0.00275 ( 49) SS BOND : angle 1.28879 ( 98) covalent geometry : bond 0.00406 (26310) covalent geometry : angle 0.54514 (36089) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15293.31 seconds wall clock time: 266 minutes 5.24 seconds (15965.24 seconds total)