Starting phenix.real_space_refine on Sat Jun 14 21:06:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rm0_19347/06_2025/8rm0_19347.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rm0_19347/06_2025/8rm0_19347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rm0_19347/06_2025/8rm0_19347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rm0_19347/06_2025/8rm0_19347.map" model { file = "/net/cci-nas-00/data/ceres_data/8rm0_19347/06_2025/8rm0_19347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rm0_19347/06_2025/8rm0_19347.cif" } resolution = 3.8 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= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 237 atoms to isotropic. 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 102 5.16 5 C 10386 2.51 5 N 2721 2.21 5 O 3102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16311 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 5222 Classifications: {'peptide': 696} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 651} Chain breaks: 5 Unresolved non-hydrogen bonds: 458 Unresolved non-hydrogen angles: 572 Unresolved non-hydrogen dihedrals: 373 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 3, 'ASP:plan': 10, 'PHE:plan': 4, 'GLU:plan': 22, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 273 Chain: "B" Number of atoms: 5222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 5222 Classifications: {'peptide': 696} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 651} Chain breaks: 5 Unresolved non-hydrogen bonds: 458 Unresolved non-hydrogen angles: 572 Unresolved non-hydrogen dihedrals: 373 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 3, 'ASP:plan': 10, 'PHE:plan': 4, 'GLU:plan': 22, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 273 Chain: "C" Number of atoms: 5222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 5222 Classifications: {'peptide': 696} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 651} Chain breaks: 5 Unresolved non-hydrogen bonds: 458 Unresolved non-hydrogen angles: 572 Unresolved non-hydrogen dihedrals: 373 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 3, 'ASP:plan': 10, 'PHE:plan': 4, 'GLU:plan': 22, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 273 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 11.36, per 1000 atoms: 0.70 Number of scatterers: 16311 At special positions: 0 Unit cell: (111.15, 111.15, 151.05, 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 102 16.00 O 3102 8.00 N 2721 7.00 C 10386 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 503 " distance=2.04 Simple disulfide: pdb=" SG CYS A 235 " - pdb=" SG CYS A 318 " distance=2.03 Simple disulfide: pdb=" SG CYS A 256 " - pdb=" SG CYS A 380 " distance=2.03 Simple disulfide: pdb=" SG CYS A 403 " - pdb=" SG CYS A 483 " distance=2.03 Simple disulfide: pdb=" SG CYS A 417 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 446 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 762 " - pdb=" SG CYS A 770 " distance=2.02 Simple disulfide: pdb=" SG CYS A 779 " - pdb=" SG CYS A 788 " distance=2.03 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 837 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 503 " distance=2.04 Simple disulfide: pdb=" SG CYS B 235 " - pdb=" SG CYS B 318 " distance=2.03 Simple disulfide: pdb=" SG CYS B 256 " - pdb=" SG CYS B 380 " distance=2.03 Simple disulfide: pdb=" SG CYS B 403 " - pdb=" SG CYS B 483 " distance=2.03 Simple disulfide: pdb=" SG CYS B 417 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 446 " - pdb=" SG CYS B 454 " distance=2.03 Simple disulfide: pdb=" SG CYS B 762 " - pdb=" SG CYS B 770 " distance=2.02 Simple disulfide: pdb=" SG CYS B 779 " - pdb=" SG CYS B 788 " distance=2.03 Simple disulfide: pdb=" SG CYS B 819 " - pdb=" SG CYS B 837 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 503 " distance=2.04 Simple disulfide: pdb=" SG CYS C 235 " - pdb=" SG CYS C 318 " distance=2.03 Simple disulfide: pdb=" SG CYS C 256 " - pdb=" SG CYS C 380 " distance=2.03 Simple disulfide: pdb=" SG CYS C 403 " - pdb=" SG CYS C 483 " distance=2.03 Simple disulfide: pdb=" SG CYS C 417 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 446 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 762 " - pdb=" SG CYS C 770 " distance=2.02 Simple disulfide: pdb=" SG CYS C 779 " - pdb=" SG CYS C 788 " distance=2.03 Simple disulfide: pdb=" SG CYS C 819 " - pdb=" SG CYS C 837 " 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 ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA J 3 " - " MAN J 4 " " BMA N 3 " - " MAN N 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA J 3 " - " MAN J 5 " " BMA N 3 " - " MAN N 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1001 " - " ASN A 311 " " NAG A1002 " - " ASN A 346 " " NAG A1003 " - " ASN A 404 " " NAG A1004 " - " ASN A 524 " " NAG A1005 " - " ASN A 141 " " NAG B1001 " - " ASN B 311 " " NAG B1002 " - " ASN B 346 " " NAG B1003 " - " ASN B 404 " " NAG B1004 " - " ASN B 524 " " NAG B1005 " - " ASN B 141 " " NAG C1001 " - " ASN C 311 " " NAG C1002 " - " ASN C 346 " " NAG C1003 " - " ASN C 404 " " NAG C1004 " - " ASN C 524 " " NAG C1005 " - " ASN C 141 " " NAG D 1 " - " ASN A 183 " " NAG E 1 " - " ASN A 373 " " NAG F 1 " - " ASN A 390 " " NAG G 1 " - " ASN A 807 " " NAG H 1 " - " ASN B 183 " " NAG I 1 " - " ASN B 373 " " NAG J 1 " - " ASN B 390 " " NAG K 1 " - " ASN B 807 " " NAG L 1 " - " ASN C 183 " " NAG M 1 " - " ASN C 373 " " NAG N 1 " - " ASN C 390 " " NAG O 1 " - " ASN C 807 " Time building additional restraints: 4.95 Conformation dependent library (CDL) restraints added in 2.1 seconds 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4014 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 30 sheets defined 29.5% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.56 Creating SS restraints... Processing helix chain 'A' and resid 145 through 147 No H-bonds generated for 'chain 'A' and resid 145 through 147' Processing helix chain 'A' and resid 175 through 183 removed outlier: 3.644A pdb=" N SER A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 206 removed outlier: 3.719A pdb=" N GLU A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A 199 " --> pdb=" O MET A 195 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 219 removed outlier: 3.780A pdb=" N ASP A 219 " --> pdb=" O ASP A 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 216 through 219' Processing helix chain 'A' and resid 220 through 233 removed outlier: 3.876A pdb=" N GLU A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA A 233 " --> pdb=" O TYR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 276 Processing helix chain 'A' and resid 288 through 293 removed outlier: 3.935A pdb=" N LEU A 292 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 347 removed outlier: 3.765A pdb=" N SER A 345 " --> pdb=" O THR A 341 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN A 346 " --> pdb=" O LYS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 390 removed outlier: 3.624A pdb=" N VAL A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN A 390 " --> pdb=" O VAL A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 414 Processing helix chain 'A' and resid 415 through 419 removed outlier: 4.012A pdb=" N ASP A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 475 removed outlier: 3.682A pdb=" N MET A 475 " --> pdb=" O PHE A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 511 removed outlier: 4.037A pdb=" N LYS A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR A 509 " --> pdb=" O LEU A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 524 Processing helix chain 'A' and resid 534 through 538 removed outlier: 3.628A pdb=" N ALA A 538 " --> pdb=" O ASN A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 599 Processing helix chain 'A' and resid 619 through 623 Processing helix chain 'A' and resid 632 through 650 removed outlier: 3.671A pdb=" N GLN A 636 " --> pdb=" O MET A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 659 removed outlier: 4.017A pdb=" N TYR A 658 " --> pdb=" O ASP A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 669 removed outlier: 3.667A pdb=" N LEU A 664 " --> pdb=" O SER A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 681 removed outlier: 3.572A pdb=" N THR A 681 " --> pdb=" O VAL A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 876 removed outlier: 4.060A pdb=" N ILE A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA A 873 " --> pdb=" O VAL A 869 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A 876 " --> pdb=" O ILE A 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 175 through 183 removed outlier: 3.644A pdb=" N SER B 181 " --> pdb=" O ASN B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 206 removed outlier: 3.717A pdb=" N GLU B 194 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU B 199 " --> pdb=" O MET B 195 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL B 206 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 219 removed outlier: 3.779A pdb=" N ASP B 219 " --> pdb=" O ASP B 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 216 through 219' Processing helix chain 'B' and resid 220 through 233 removed outlier: 3.876A pdb=" N GLU B 231 " --> pdb=" O LYS B 227 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA B 233 " --> pdb=" O TYR B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 276 Processing helix chain 'B' and resid 288 through 293 removed outlier: 3.935A pdb=" N LEU B 292 " --> pdb=" O THR B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 347 removed outlier: 3.764A pdb=" N SER B 345 " --> pdb=" O THR B 341 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN B 346 " --> pdb=" O LYS B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 390 removed outlier: 3.625A pdb=" N VAL B 386 " --> pdb=" O ARG B 382 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 414 Processing helix chain 'B' and resid 415 through 419 removed outlier: 4.012A pdb=" N ASP B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 475 removed outlier: 3.683A pdb=" N MET B 475 " --> pdb=" O PHE B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 511 removed outlier: 4.037A pdb=" N LYS B 508 " --> pdb=" O LYS B 504 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR B 509 " --> pdb=" O LEU B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 524 Processing helix chain 'B' and resid 534 through 538 removed outlier: 3.627A pdb=" N ALA B 538 " --> pdb=" O ASN B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 599 Processing helix chain 'B' and resid 619 through 623 Processing helix chain 'B' and resid 632 through 650 removed outlier: 3.671A pdb=" N GLN B 636 " --> pdb=" O MET B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 659 removed outlier: 4.017A pdb=" N TYR B 658 " --> pdb=" O ASP B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 669 removed outlier: 3.667A pdb=" N LEU B 664 " --> pdb=" O SER B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 681 removed outlier: 3.573A pdb=" N THR B 681 " --> pdb=" O VAL B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 876 removed outlier: 4.061A pdb=" N ILE B 872 " --> pdb=" O LEU B 868 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA B 873 " --> pdb=" O VAL B 869 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS B 876 " --> pdb=" O ILE B 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 147 No H-bonds generated for 'chain 'C' and resid 145 through 147' Processing helix chain 'C' and resid 175 through 183 removed outlier: 3.644A pdb=" N SER C 181 " --> pdb=" O ASN C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 206 removed outlier: 3.718A pdb=" N GLU C 194 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU C 199 " --> pdb=" O MET C 195 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL C 206 " --> pdb=" O GLY C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 219 removed outlier: 3.778A pdb=" N ASP C 219 " --> pdb=" O ASP C 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 216 through 219' Processing helix chain 'C' and resid 220 through 233 removed outlier: 3.877A pdb=" N GLU C 231 " --> pdb=" O LYS C 227 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA C 233 " --> pdb=" O TYR C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 276 Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.936A pdb=" N LEU C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 347 removed outlier: 3.765A pdb=" N SER C 345 " --> pdb=" O THR C 341 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN C 346 " --> pdb=" O LYS C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 390 removed outlier: 3.624A pdb=" N VAL C 386 " --> pdb=" O ARG C 382 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN C 390 " --> pdb=" O VAL C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 414 Processing helix chain 'C' and resid 415 through 419 removed outlier: 4.012A pdb=" N ASP C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 475 removed outlier: 3.683A pdb=" N MET C 475 " --> pdb=" O PHE C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 511 removed outlier: 4.037A pdb=" N LYS C 508 " --> pdb=" O LYS C 504 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR C 509 " --> pdb=" O LEU C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 524 Processing helix chain 'C' and resid 534 through 538 removed outlier: 3.628A pdb=" N ALA C 538 " --> pdb=" O ASN C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'C' and resid 619 through 623 Processing helix chain 'C' and resid 632 through 650 removed outlier: 3.670A pdb=" N GLN C 636 " --> pdb=" O MET C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 659 removed outlier: 4.017A pdb=" N TYR C 658 " --> pdb=" O ASP C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 669 removed outlier: 3.668A pdb=" N LEU C 664 " --> pdb=" O SER C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 681 removed outlier: 3.572A pdb=" N THR C 681 " --> pdb=" O VAL C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 876 removed outlier: 4.060A pdb=" N ILE C 872 " --> pdb=" O LEU C 868 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA C 873 " --> pdb=" O VAL C 869 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS C 876 " --> pdb=" O ILE C 872 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 141 through 143 removed outlier: 3.929A pdb=" N GLN A 801 " --> pdb=" O LEU A 813 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 153 removed outlier: 7.372A pdb=" N LEU A 757 " --> pdb=" O ILE A 775 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE A 775 " --> pdb=" O LEU A 757 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU A 759 " --> pdb=" O VAL A 773 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL A 773 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N GLU A 761 " --> pdb=" O ASP A 771 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASP A 771 " --> pdb=" O GLU A 761 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 769 " --> pdb=" O ARG A 763 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ILE A 159 " --> pdb=" O CYS A 770 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N VAL A 772 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N THR A 161 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 10.823A pdb=" N LYS A 774 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 18.308A pdb=" N ARG A 163 " --> pdb=" O LYS A 774 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE A 159 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE A 715 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N THR A 161 " --> pdb=" O ARG A 713 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ARG A 713 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ARG A 163 " --> pdb=" O ILE A 711 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE A 711 " --> pdb=" O ARG A 163 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N SER A 168 " --> pdb=" O ILE A 615 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N THR A 617 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL A 170 " --> pdb=" O THR A 617 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 608 through 610 removed outlier: 8.228A pdb=" N TYR A 609 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL A 164 " --> pdb=" O TYR A 609 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE A 159 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE A 715 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N THR A 161 " --> pdb=" O ARG A 713 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ARG A 713 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ARG A 163 " --> pdb=" O ILE A 711 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE A 711 " --> pdb=" O ARG A 163 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ALA A 700 " --> pdb=" O THR A 692 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TYR A 688 " --> pdb=" O GLY A 704 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N TYR A 706 " --> pdb=" O VAL A 686 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N VAL A 686 " --> pdb=" O TYR A 706 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLU A 708 " --> pdb=" O SER A 684 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N SER A 684 " --> pdb=" O GLU A 708 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 495 through 498 removed outlier: 3.528A pdb=" N TYR A 236 " --> pdb=" O PHE A 317 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A 317 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N HIS A 314 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 250 through 251 Processing sheet with id=AA6, first strand: chain 'A' and resid 282 through 283 Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 Processing sheet with id=AA8, first strand: chain 'A' and resid 392 through 396 removed outlier: 3.749A pdb=" N GLU A 485 " --> pdb=" O THR A 395 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 790 through 792 removed outlier: 3.609A pdb=" N VAL A 790 " --> pdb=" O VAL A 882 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA A 792 " --> pdb=" O ILE A 880 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE A 880 " --> pdb=" O ALA A 792 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 836 through 837 Processing sheet with id=AB2, first strand: chain 'B' and resid 141 through 143 removed outlier: 3.929A pdb=" N GLN B 801 " --> pdb=" O LEU B 813 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 149 through 153 removed outlier: 7.372A pdb=" N LEU B 757 " --> pdb=" O ILE B 775 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ILE B 775 " --> pdb=" O LEU B 757 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N LEU B 759 " --> pdb=" O VAL B 773 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL B 773 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N GLU B 761 " --> pdb=" O ASP B 771 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP B 771 " --> pdb=" O GLU B 761 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 769 " --> pdb=" O ARG B 763 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ILE B 159 " --> pdb=" O CYS B 770 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N VAL B 772 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N THR B 161 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N LYS B 774 " --> pdb=" O THR B 161 " (cutoff:3.500A) removed outlier: 18.307A pdb=" N ARG B 163 " --> pdb=" O LYS B 774 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE B 159 " --> pdb=" O ILE B 715 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE B 715 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N THR B 161 " --> pdb=" O ARG B 713 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ARG B 713 " --> pdb=" O THR B 161 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ARG B 163 " --> pdb=" O ILE B 711 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE B 711 " --> pdb=" O ARG B 163 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N SER B 168 " --> pdb=" O ILE B 615 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N THR B 617 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL B 170 " --> pdb=" O THR B 617 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 608 through 610 removed outlier: 8.228A pdb=" N TYR B 609 " --> pdb=" O GLU B 162 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL B 164 " --> pdb=" O TYR B 609 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE B 159 " --> pdb=" O ILE B 715 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE B 715 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N THR B 161 " --> pdb=" O ARG B 713 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ARG B 713 " --> pdb=" O THR B 161 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ARG B 163 " --> pdb=" O ILE B 711 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE B 711 " --> pdb=" O ARG B 163 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ALA B 700 " --> pdb=" O THR B 692 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N TYR B 688 " --> pdb=" O GLY B 704 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N TYR B 706 " --> pdb=" O VAL B 686 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N VAL B 686 " --> pdb=" O TYR B 706 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLU B 708 " --> pdb=" O SER B 684 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N SER B 684 " --> pdb=" O GLU B 708 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 495 through 498 removed outlier: 3.500A pdb=" N GLU B 495 " --> pdb=" O LYS B 239 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR B 236 " --> pdb=" O PHE B 317 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE B 317 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N HIS B 314 " --> pdb=" O LEU B 542 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 250 through 251 Processing sheet with id=AB7, first strand: chain 'B' and resid 282 through 283 Processing sheet with id=AB8, first strand: chain 'B' and resid 348 through 349 Processing sheet with id=AB9, first strand: chain 'B' and resid 392 through 396 removed outlier: 3.748A pdb=" N GLU B 485 " --> pdb=" O THR B 395 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 790 through 792 removed outlier: 3.609A pdb=" N VAL B 790 " --> pdb=" O VAL B 882 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA B 792 " --> pdb=" O ILE B 880 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE B 880 " --> pdb=" O ALA B 792 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 836 through 837 Processing sheet with id=AC3, first strand: chain 'C' and resid 141 through 143 removed outlier: 3.928A pdb=" N GLN C 801 " --> pdb=" O LEU C 813 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 149 through 153 removed outlier: 7.373A pdb=" N LEU C 757 " --> pdb=" O ILE C 775 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE C 775 " --> pdb=" O LEU C 757 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU C 759 " --> pdb=" O VAL C 773 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL C 773 " --> pdb=" O LEU C 759 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N GLU C 761 " --> pdb=" O ASP C 771 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP C 771 " --> pdb=" O GLU C 761 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 769 " --> pdb=" O ARG C 763 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ILE C 159 " --> pdb=" O CYS C 770 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N VAL C 772 " --> pdb=" O ILE C 159 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N THR C 161 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N LYS C 774 " --> pdb=" O THR C 161 " (cutoff:3.500A) removed outlier: 18.307A pdb=" N ARG C 163 " --> pdb=" O LYS C 774 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE C 159 " --> pdb=" O ILE C 715 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE C 715 " --> pdb=" O ILE C 159 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N THR C 161 " --> pdb=" O ARG C 713 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ARG C 713 " --> pdb=" O THR C 161 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ARG C 163 " --> pdb=" O ILE C 711 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE C 711 " --> pdb=" O ARG C 163 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N SER C 168 " --> pdb=" O ILE C 615 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N THR C 617 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL C 170 " --> pdb=" O THR C 617 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 608 through 610 removed outlier: 8.228A pdb=" N TYR C 609 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL C 164 " --> pdb=" O TYR C 609 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE C 159 " --> pdb=" O ILE C 715 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE C 715 " --> pdb=" O ILE C 159 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N THR C 161 " --> pdb=" O ARG C 713 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ARG C 713 " --> pdb=" O THR C 161 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ARG C 163 " --> pdb=" O ILE C 711 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE C 711 " --> pdb=" O ARG C 163 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA C 700 " --> pdb=" O THR C 692 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N TYR C 688 " --> pdb=" O GLY C 704 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N TYR C 706 " --> pdb=" O VAL C 686 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N VAL C 686 " --> pdb=" O TYR C 706 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLU C 708 " --> pdb=" O SER C 684 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N SER C 684 " --> pdb=" O GLU C 708 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 495 through 498 removed outlier: 3.528A pdb=" N TYR C 236 " --> pdb=" O PHE C 317 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE C 317 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N HIS C 314 " --> pdb=" O LEU C 542 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 250 through 251 Processing sheet with id=AC8, first strand: chain 'C' and resid 282 through 283 Processing sheet with id=AC9, first strand: chain 'C' and resid 348 through 349 Processing sheet with id=AD1, first strand: chain 'C' and resid 392 through 396 removed outlier: 3.748A pdb=" N GLU C 485 " --> pdb=" O THR C 395 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 790 through 792 removed outlier: 3.609A pdb=" N VAL C 790 " --> pdb=" O VAL C 882 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA C 792 " --> pdb=" O ILE C 880 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE C 880 " --> pdb=" O ALA C 792 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 836 through 837 488 hydrogen bonds defined for protein. 1278 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: 6.01 Time building geometry restraints manager: 5.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5190 1.35 - 1.47: 4178 1.47 - 1.59: 7192 1.59 - 1.71: 0 1.71 - 1.83: 147 Bond restraints: 16707 Sorted by residual: bond pdb=" C3 BMA F 3 " pdb=" O3 BMA F 3 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.37e+00 bond pdb=" C3 BMA N 3 " pdb=" O3 BMA N 3 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.09e+00 bond pdb=" C3 BMA J 3 " pdb=" O3 BMA J 3 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.05e+00 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.30e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.23e+00 ... (remaining 16702 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 21786 1.50 - 3.01: 892 3.01 - 4.51: 145 4.51 - 6.01: 40 6.01 - 7.52: 18 Bond angle restraints: 22881 Sorted by residual: angle pdb=" N LEU C 865 " pdb=" CA LEU C 865 " pdb=" C LEU C 865 " ideal model delta sigma weight residual 109.81 117.33 -7.52 2.21e+00 2.05e-01 1.16e+01 angle pdb=" N LEU A 865 " pdb=" CA LEU A 865 " pdb=" C LEU A 865 " ideal model delta sigma weight residual 109.81 117.29 -7.48 2.21e+00 2.05e-01 1.15e+01 angle pdb=" N LEU B 865 " pdb=" CA LEU B 865 " pdb=" C LEU B 865 " ideal model delta sigma weight residual 109.81 117.29 -7.48 2.21e+00 2.05e-01 1.15e+01 angle pdb=" N GLU B 439 " pdb=" CA GLU B 439 " pdb=" C GLU B 439 " ideal model delta sigma weight residual 107.23 112.61 -5.38 1.67e+00 3.59e-01 1.04e+01 angle pdb=" N GLU A 439 " pdb=" CA GLU A 439 " pdb=" C GLU A 439 " ideal model delta sigma weight residual 107.23 112.59 -5.36 1.67e+00 3.59e-01 1.03e+01 ... (remaining 22876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.30: 10143 21.30 - 42.60: 345 42.60 - 63.90: 87 63.90 - 85.20: 51 85.20 - 106.50: 21 Dihedral angle restraints: 10647 sinusoidal: 4446 harmonic: 6201 Sorted by residual: dihedral pdb=" CB CYS B 819 " pdb=" SG CYS B 819 " pdb=" SG CYS B 837 " pdb=" CB CYS B 837 " ideal model delta sinusoidal sigma weight residual -86.00 -156.13 70.13 1 1.00e+01 1.00e-02 6.34e+01 dihedral pdb=" CB CYS A 819 " pdb=" SG CYS A 819 " pdb=" SG CYS A 837 " pdb=" CB CYS A 837 " ideal model delta sinusoidal sigma weight residual -86.00 -156.13 70.13 1 1.00e+01 1.00e-02 6.34e+01 dihedral pdb=" CB CYS C 819 " pdb=" SG CYS C 819 " pdb=" SG CYS C 837 " pdb=" CB CYS C 837 " ideal model delta sinusoidal sigma weight residual -86.00 -156.11 70.11 1 1.00e+01 1.00e-02 6.33e+01 ... (remaining 10644 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2413 0.069 - 0.138: 326 0.138 - 0.207: 18 0.207 - 0.276: 3 0.276 - 0.345: 3 Chirality restraints: 2763 Sorted by residual: chirality pdb=" C1 NAG A1001 " pdb=" ND2 ASN A 311 " pdb=" C2 NAG A1001 " pdb=" O5 NAG A1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" C1 NAG B1001 " pdb=" ND2 ASN B 311 " pdb=" C2 NAG B1001 " pdb=" O5 NAG B1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" C1 NAG C1001 " pdb=" ND2 ASN C 311 " pdb=" C2 NAG C1001 " pdb=" O5 NAG C1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 2760 not shown) Planarity restraints: 2907 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 480 " 0.047 5.00e-02 4.00e+02 7.22e-02 8.35e+00 pdb=" N PRO C 481 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO C 481 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 481 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 480 " 0.047 5.00e-02 4.00e+02 7.18e-02 8.25e+00 pdb=" N PRO B 481 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 481 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 481 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 480 " 0.047 5.00e-02 4.00e+02 7.18e-02 8.25e+00 pdb=" N PRO A 481 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 481 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 481 " 0.039 5.00e-02 4.00e+02 ... (remaining 2904 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3184 2.78 - 3.31: 14691 3.31 - 3.84: 23999 3.84 - 4.37: 25386 4.37 - 4.90: 45685 Nonbonded interactions: 112945 Sorted by model distance: nonbonded pdb=" NH1 ARG A 438 " pdb=" O GLY A 440 " model vdw 2.251 3.120 nonbonded pdb=" NH1 ARG C 438 " pdb=" O GLY C 440 " model vdw 2.251 3.120 nonbonded pdb=" NH1 ARG B 438 " pdb=" O GLY B 440 " model vdw 2.252 3.120 nonbonded pdb=" O THR B 143 " pdb=" OG SER B 827 " model vdw 2.360 3.040 nonbonded pdb=" O THR A 143 " pdb=" OG SER A 827 " model vdw 2.360 3.040 ... (remaining 112940 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'N' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 42.370 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 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 : 0.004 0.054 16782 Z= 0.199 Angle : 0.764 9.163 23079 Z= 0.383 Chirality : 0.048 0.345 2763 Planarity : 0.006 0.072 2880 Dihedral : 13.696 106.497 6552 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.19 % Allowed : 0.00 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.19), residues: 2052 helix: -0.53 (0.22), residues: 546 sheet: 0.62 (0.30), residues: 360 loop : -0.90 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 791 HIS 0.009 0.001 HIS A 742 PHE 0.014 0.001 PHE A 232 TYR 0.023 0.001 TYR C 327 ARG 0.010 0.000 ARG C 763 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 27) link_NAG-ASN : angle 3.29127 ( 81) link_ALPHA1-6 : bond 0.00511 ( 3) link_ALPHA1-6 : angle 1.72970 ( 9) link_BETA1-4 : bond 0.01135 ( 15) link_BETA1-4 : angle 2.67711 ( 45) link_ALPHA1-3 : bond 0.00890 ( 3) link_ALPHA1-3 : angle 3.34429 ( 9) hydrogen bonds : bond 0.19916 ( 482) hydrogen bonds : angle 7.25165 ( 1278) SS BOND : bond 0.00352 ( 27) SS BOND : angle 1.64097 ( 54) covalent geometry : bond 0.00399 (16707) covalent geometry : angle 0.72451 (22881) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 699 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 PHE cc_start: 0.7694 (t80) cc_final: 0.7314 (t80) REVERT: A 158 ILE cc_start: 0.8398 (mt) cc_final: 0.8189 (mm) REVERT: A 173 ILE cc_start: 0.8357 (mt) cc_final: 0.8145 (tt) REVERT: A 194 GLU cc_start: 0.7461 (tp30) cc_final: 0.6817 (tp30) REVERT: A 198 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6518 (mt-10) REVERT: A 211 GLU cc_start: 0.8202 (tp30) cc_final: 0.7913 (tp30) REVERT: A 221 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7321 (mt-10) REVERT: A 249 GLU cc_start: 0.7376 (mm-30) cc_final: 0.6839 (mm-30) REVERT: A 251 LEU cc_start: 0.8593 (tp) cc_final: 0.8234 (tt) REVERT: A 252 ILE cc_start: 0.8785 (mt) cc_final: 0.8210 (tp) REVERT: A 258 LEU cc_start: 0.8647 (mt) cc_final: 0.8442 (mm) REVERT: A 295 LYS cc_start: 0.8638 (mptt) cc_final: 0.8323 (mptt) REVERT: A 334 LEU cc_start: 0.8661 (mt) cc_final: 0.8369 (mt) REVERT: A 339 GLU cc_start: 0.7643 (tp30) cc_final: 0.7181 (tp30) REVERT: A 341 THR cc_start: 0.8675 (m) cc_final: 0.8302 (p) REVERT: A 349 ILE cc_start: 0.8576 (mt) cc_final: 0.8305 (mm) REVERT: A 384 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7719 (mp0) REVERT: A 468 ASP cc_start: 0.7204 (t70) cc_final: 0.6814 (t70) REVERT: A 495 GLU cc_start: 0.7222 (pt0) cc_final: 0.6948 (pt0) REVERT: A 500 TYR cc_start: 0.8349 (t80) cc_final: 0.7930 (t80) REVERT: A 510 TYR cc_start: 0.7943 (m-80) cc_final: 0.7375 (m-80) REVERT: A 537 ARG cc_start: 0.7428 (mtt-85) cc_final: 0.7146 (mtt-85) REVERT: A 540 VAL cc_start: 0.8284 (p) cc_final: 0.8067 (t) REVERT: A 591 GLN cc_start: 0.7405 (tt0) cc_final: 0.7096 (tt0) REVERT: A 652 ARG cc_start: 0.7796 (mtp85) cc_final: 0.7554 (mtp85) REVERT: A 653 ARG cc_start: 0.7901 (ttm170) cc_final: 0.7610 (mtm-85) REVERT: A 665 GLN cc_start: 0.8387 (tt0) cc_final: 0.8146 (tt0) REVERT: A 675 MET cc_start: 0.7928 (mmm) cc_final: 0.7710 (mmm) REVERT: A 676 LYS cc_start: 0.8632 (mttt) cc_final: 0.8293 (mttm) REVERT: A 680 ARG cc_start: 0.8402 (tpt-90) cc_final: 0.7944 (tpt-90) REVERT: A 702 GLU cc_start: 0.7403 (mt-10) cc_final: 0.7082 (mt-10) REVERT: A 803 SER cc_start: 0.8058 (t) cc_final: 0.7590 (p) REVERT: B 151 TYR cc_start: 0.7296 (p90) cc_final: 0.6872 (p90) REVERT: B 158 ILE cc_start: 0.8421 (mt) cc_final: 0.8131 (mm) REVERT: B 173 ILE cc_start: 0.8291 (mt) cc_final: 0.8011 (tt) REVERT: B 194 GLU cc_start: 0.7396 (tp30) cc_final: 0.6815 (tp30) REVERT: B 198 GLU cc_start: 0.6961 (mt-10) cc_final: 0.6435 (mt-10) REVERT: B 206 VAL cc_start: 0.8163 (m) cc_final: 0.7774 (p) REVERT: B 226 ARG cc_start: 0.8018 (mmt90) cc_final: 0.7555 (mmt90) REVERT: B 249 GLU cc_start: 0.7295 (mm-30) cc_final: 0.6659 (mm-30) REVERT: B 251 LEU cc_start: 0.8387 (tp) cc_final: 0.8020 (tt) REVERT: B 252 ILE cc_start: 0.8706 (mt) cc_final: 0.8251 (tp) REVERT: B 258 LEU cc_start: 0.8697 (mt) cc_final: 0.8491 (mm) REVERT: B 273 TRP cc_start: 0.8918 (m-10) cc_final: 0.8530 (m-10) REVERT: B 295 LYS cc_start: 0.8794 (mptt) cc_final: 0.8441 (mptt) REVERT: B 308 ARG cc_start: 0.7883 (ptt-90) cc_final: 0.7618 (ptt-90) REVERT: B 338 ASN cc_start: 0.7648 (t0) cc_final: 0.7309 (t0) REVERT: B 339 GLU cc_start: 0.7623 (tp30) cc_final: 0.7245 (tp30) REVERT: B 341 THR cc_start: 0.8658 (m) cc_final: 0.8427 (p) REVERT: B 347 LEU cc_start: 0.8348 (mt) cc_final: 0.8146 (mp) REVERT: B 349 ILE cc_start: 0.8515 (mt) cc_final: 0.8278 (mm) REVERT: B 360 TYR cc_start: 0.8055 (t80) cc_final: 0.7752 (t80) REVERT: B 372 ARG cc_start: 0.7225 (ptt90) cc_final: 0.6964 (ptt90) REVERT: B 396 PHE cc_start: 0.7847 (t80) cc_final: 0.7576 (t80) REVERT: B 468 ASP cc_start: 0.7069 (t70) cc_final: 0.6706 (t0) REVERT: B 483 CYS cc_start: 0.4869 (t) cc_final: 0.4413 (t) REVERT: B 495 GLU cc_start: 0.7202 (pt0) cc_final: 0.6899 (pt0) REVERT: B 504 LYS cc_start: 0.8015 (mtpt) cc_final: 0.7809 (mtpp) REVERT: B 535 ASN cc_start: 0.7294 (t0) cc_final: 0.7039 (t0) REVERT: B 537 ARG cc_start: 0.7492 (mtt-85) cc_final: 0.7184 (mtt-85) REVERT: B 540 VAL cc_start: 0.8226 (p) cc_final: 0.8005 (t) REVERT: B 551 TYR cc_start: 0.7994 (m-80) cc_final: 0.7771 (m-80) REVERT: B 590 VAL cc_start: 0.7744 (p) cc_final: 0.7542 (m) REVERT: B 591 GLN cc_start: 0.7359 (tt0) cc_final: 0.7022 (tt0) REVERT: B 658 TYR cc_start: 0.8442 (m-80) cc_final: 0.8105 (m-80) REVERT: B 665 GLN cc_start: 0.8423 (tt0) cc_final: 0.7971 (tm-30) REVERT: B 667 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7908 (mm-40) REVERT: B 676 LYS cc_start: 0.8622 (mttt) cc_final: 0.8372 (mttp) REVERT: B 772 VAL cc_start: 0.7915 (t) cc_final: 0.7707 (t) REVERT: B 776 VAL cc_start: 0.8086 (t) cc_final: 0.7852 (m) REVERT: B 810 TYR cc_start: 0.7960 (m-80) cc_final: 0.7728 (m-80) REVERT: C 158 ILE cc_start: 0.8453 (mt) cc_final: 0.8241 (mm) REVERT: C 173 ILE cc_start: 0.8534 (mt) cc_final: 0.8300 (tt) REVERT: C 191 LEU cc_start: 0.8393 (tp) cc_final: 0.8176 (tt) REVERT: C 193 THR cc_start: 0.7919 (t) cc_final: 0.7701 (t) REVERT: C 194 GLU cc_start: 0.7435 (tp30) cc_final: 0.6743 (tp30) REVERT: C 197 ASN cc_start: 0.7438 (m110) cc_final: 0.7212 (m-40) REVERT: C 198 GLU cc_start: 0.6914 (mt-10) cc_final: 0.6298 (mt-10) REVERT: C 275 TYR cc_start: 0.8084 (m-10) cc_final: 0.7882 (m-10) REVERT: C 295 LYS cc_start: 0.8643 (mptt) cc_final: 0.8367 (mptt) REVERT: C 305 LYS cc_start: 0.8255 (pttp) cc_final: 0.8020 (pttp) REVERT: C 339 GLU cc_start: 0.7663 (tp30) cc_final: 0.7459 (tp30) REVERT: C 349 ILE cc_start: 0.8605 (mt) cc_final: 0.8372 (mm) REVERT: C 384 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7391 (mm-30) REVERT: C 451 HIS cc_start: 0.7876 (m-70) cc_final: 0.7642 (m-70) REVERT: C 468 ASP cc_start: 0.7315 (t70) cc_final: 0.6932 (t70) REVERT: C 500 TYR cc_start: 0.8326 (t80) cc_final: 0.8020 (t80) REVERT: C 510 TYR cc_start: 0.7972 (m-80) cc_final: 0.7245 (m-80) REVERT: C 537 ARG cc_start: 0.7413 (mtt-85) cc_final: 0.7179 (mtt-85) REVERT: C 540 VAL cc_start: 0.8334 (p) cc_final: 0.8032 (t) REVERT: C 544 ASP cc_start: 0.8347 (t70) cc_final: 0.8114 (t0) REVERT: C 591 GLN cc_start: 0.7312 (tt0) cc_final: 0.6804 (tt0) REVERT: C 624 HIS cc_start: 0.6220 (m-70) cc_final: 0.6003 (m-70) REVERT: C 635 VAL cc_start: 0.7556 (m) cc_final: 0.7115 (t) REVERT: C 648 MET cc_start: 0.7955 (mmt) cc_final: 0.7550 (mmt) REVERT: C 652 ARG cc_start: 0.7827 (mtp85) cc_final: 0.7585 (mtp85) REVERT: C 653 ARG cc_start: 0.7947 (ttm170) cc_final: 0.7612 (mtm-85) REVERT: C 654 ILE cc_start: 0.8523 (mt) cc_final: 0.7931 (mt) REVERT: C 656 TRP cc_start: 0.8602 (m100) cc_final: 0.8230 (m-90) REVERT: C 676 LYS cc_start: 0.8745 (mttt) cc_final: 0.8460 (mttm) REVERT: C 683 ARG cc_start: 0.7783 (mpt180) cc_final: 0.7494 (mpt180) REVERT: C 715 ILE cc_start: 0.8583 (tt) cc_final: 0.8368 (mt) REVERT: C 763 ARG cc_start: 0.7390 (ptp-170) cc_final: 0.7176 (ptp-170) REVERT: C 773 VAL cc_start: 0.8777 (t) cc_final: 0.8576 (m) REVERT: C 842 PHE cc_start: 0.7569 (m-10) cc_final: 0.7224 (m-80) outliers start: 3 outliers final: 0 residues processed: 701 average time/residue: 0.3250 time to fit residues: 322.1761 Evaluate side-chains 594 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 594 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 2.9990 chunk 156 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 162 optimal weight: 0.6980 chunk 62 optimal weight: 0.0470 chunk 98 optimal weight: 0.1980 chunk 120 optimal weight: 2.9990 chunk 187 optimal weight: 0.8980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 600 ASN A 637 HIS A 643 ASN A 737 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN B 753 ASN C 180 ASN C 643 ASN C 836 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.119324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.101811 restraints weight = 29065.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.105403 restraints weight = 13890.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.107746 restraints weight = 8080.418| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 16782 Z= 0.136 Angle : 0.714 10.310 23079 Z= 0.343 Chirality : 0.047 0.272 2763 Planarity : 0.006 0.063 2880 Dihedral : 11.978 94.612 3246 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.85 % Allowed : 15.26 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.64 (0.19), residues: 2052 helix: -0.06 (0.22), residues: 546 sheet: 0.59 (0.30), residues: 369 loop : -0.95 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 326 HIS 0.007 0.001 HIS C 234 PHE 0.019 0.001 PHE C 150 TYR 0.025 0.001 TYR A 474 ARG 0.006 0.001 ARG C 407 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 27) link_NAG-ASN : angle 2.65226 ( 81) link_ALPHA1-6 : bond 0.01380 ( 3) link_ALPHA1-6 : angle 2.94058 ( 9) link_BETA1-4 : bond 0.00966 ( 15) link_BETA1-4 : angle 2.34111 ( 45) link_ALPHA1-3 : bond 0.00295 ( 3) link_ALPHA1-3 : angle 3.63832 ( 9) hydrogen bonds : bond 0.04792 ( 482) hydrogen bonds : angle 5.65051 ( 1278) SS BOND : bond 0.00519 ( 27) SS BOND : angle 2.06172 ( 54) covalent geometry : bond 0.00312 (16707) covalent geometry : angle 0.67828 (22881) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 612 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 PHE cc_start: 0.7614 (t80) cc_final: 0.7317 (t80) REVERT: A 151 TYR cc_start: 0.7455 (p90) cc_final: 0.7160 (p90) REVERT: A 158 ILE cc_start: 0.8569 (mt) cc_final: 0.8305 (mm) REVERT: A 186 GLN cc_start: 0.7134 (mm110) cc_final: 0.6862 (mm110) REVERT: A 194 GLU cc_start: 0.7395 (tp30) cc_final: 0.6735 (tp30) REVERT: A 198 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6456 (mt-10) REVERT: A 211 GLU cc_start: 0.8123 (tp30) cc_final: 0.7623 (tp30) REVERT: A 227 LYS cc_start: 0.8597 (tptm) cc_final: 0.8327 (tppt) REVERT: A 249 GLU cc_start: 0.7515 (mm-30) cc_final: 0.6859 (mm-30) REVERT: A 251 LEU cc_start: 0.8327 (tp) cc_final: 0.7811 (tt) REVERT: A 252 ILE cc_start: 0.8775 (mt) cc_final: 0.8376 (tp) REVERT: A 258 LEU cc_start: 0.8671 (mt) cc_final: 0.8469 (mm) REVERT: A 295 LYS cc_start: 0.8667 (mptt) cc_final: 0.8383 (mptt) REVERT: A 334 LEU cc_start: 0.8634 (mt) cc_final: 0.8398 (mt) REVERT: A 339 GLU cc_start: 0.7651 (tp30) cc_final: 0.7381 (tp30) REVERT: A 438 ARG cc_start: 0.7522 (mmm160) cc_final: 0.6992 (tpt90) REVERT: A 468 ASP cc_start: 0.7192 (t70) cc_final: 0.6747 (t70) REVERT: A 495 GLU cc_start: 0.6934 (pt0) cc_final: 0.6709 (pt0) REVERT: A 500 TYR cc_start: 0.8327 (t80) cc_final: 0.7986 (t80) REVERT: A 510 TYR cc_start: 0.7614 (m-80) cc_final: 0.7171 (m-80) REVERT: A 519 LEU cc_start: 0.8238 (mm) cc_final: 0.7926 (mp) REVERT: A 533 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.7857 (tpp) REVERT: A 540 VAL cc_start: 0.8099 (p) cc_final: 0.7491 (m) REVERT: A 591 GLN cc_start: 0.7350 (tt0) cc_final: 0.7130 (tt0) REVERT: A 599 ILE cc_start: 0.8444 (tp) cc_final: 0.8222 (mm) REVERT: A 612 ARG cc_start: 0.7428 (tpp80) cc_final: 0.6993 (mmm-85) REVERT: A 624 HIS cc_start: 0.6344 (m-70) cc_final: 0.6088 (m-70) REVERT: A 652 ARG cc_start: 0.7818 (mtp85) cc_final: 0.7461 (mtp-110) REVERT: A 675 MET cc_start: 0.7990 (mmm) cc_final: 0.7583 (mmm) REVERT: A 676 LYS cc_start: 0.8667 (mttt) cc_final: 0.8328 (mttm) REVERT: A 702 GLU cc_start: 0.7368 (mt-10) cc_final: 0.7018 (mt-10) REVERT: A 724 ASN cc_start: 0.8081 (t0) cc_final: 0.7831 (t0) REVERT: A 803 SER cc_start: 0.8150 (t) cc_final: 0.7646 (p) REVERT: B 158 ILE cc_start: 0.8453 (mt) cc_final: 0.8237 (mm) REVERT: B 194 GLU cc_start: 0.7474 (tp30) cc_final: 0.6786 (tp30) REVERT: B 198 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6388 (mt-10) REVERT: B 206 VAL cc_start: 0.8233 (m) cc_final: 0.7870 (p) REVERT: B 252 ILE cc_start: 0.8706 (mt) cc_final: 0.8381 (tp) REVERT: B 258 LEU cc_start: 0.8722 (mt) cc_final: 0.8503 (mm) REVERT: B 273 TRP cc_start: 0.8836 (m-10) cc_final: 0.8474 (m-10) REVERT: B 297 ARG cc_start: 0.8274 (mtm-85) cc_final: 0.7774 (mtm180) REVERT: B 298 MET cc_start: 0.7640 (mmm) cc_final: 0.7429 (mmm) REVERT: B 338 ASN cc_start: 0.7672 (t0) cc_final: 0.7364 (t0) REVERT: B 339 GLU cc_start: 0.7650 (tp30) cc_final: 0.7315 (tp30) REVERT: B 341 THR cc_start: 0.8737 (m) cc_final: 0.8464 (p) REVERT: B 356 ARG cc_start: 0.7871 (tpp-160) cc_final: 0.7514 (tpp-160) REVERT: B 468 ASP cc_start: 0.7116 (t70) cc_final: 0.6650 (t0) REVERT: B 495 GLU cc_start: 0.7189 (pt0) cc_final: 0.6972 (pt0) REVERT: B 535 ASN cc_start: 0.7201 (t0) cc_final: 0.6780 (t0) REVERT: B 551 TYR cc_start: 0.8052 (m-80) cc_final: 0.7717 (m-80) REVERT: B 591 GLN cc_start: 0.7311 (tt0) cc_final: 0.7094 (tt0) REVERT: B 611 LEU cc_start: 0.7225 (tp) cc_final: 0.6728 (tp) REVERT: B 635 VAL cc_start: 0.7721 (m) cc_final: 0.7492 (p) REVERT: B 658 TYR cc_start: 0.8391 (m-80) cc_final: 0.8080 (m-80) REVERT: B 665 GLN cc_start: 0.8410 (tt0) cc_final: 0.7956 (tm-30) REVERT: B 667 GLN cc_start: 0.8200 (mm-40) cc_final: 0.7996 (mm-40) REVERT: B 669 GLN cc_start: 0.7923 (mt0) cc_final: 0.7715 (mm110) REVERT: B 676 LYS cc_start: 0.8677 (mttt) cc_final: 0.8405 (mttp) REVERT: B 711 ILE cc_start: 0.8650 (pt) cc_final: 0.8441 (mt) REVERT: B 776 VAL cc_start: 0.8095 (t) cc_final: 0.7842 (m) REVERT: B 810 TYR cc_start: 0.7923 (m-80) cc_final: 0.7659 (m-80) REVERT: C 193 THR cc_start: 0.7917 (t) cc_final: 0.7703 (t) REVERT: C 194 GLU cc_start: 0.7396 (tp30) cc_final: 0.6729 (tp30) REVERT: C 197 ASN cc_start: 0.7453 (m110) cc_final: 0.7192 (m-40) REVERT: C 198 GLU cc_start: 0.6941 (mt-10) cc_final: 0.6393 (mt-10) REVERT: C 207 MET cc_start: 0.6919 (mtt) cc_final: 0.6322 (mtm) REVERT: C 295 LYS cc_start: 0.8671 (mptt) cc_final: 0.8365 (mptt) REVERT: C 305 LYS cc_start: 0.8266 (pttp) cc_final: 0.8047 (pttp) REVERT: C 384 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7390 (mm-30) REVERT: C 451 HIS cc_start: 0.7845 (m-70) cc_final: 0.7502 (m90) REVERT: C 500 TYR cc_start: 0.8157 (t80) cc_final: 0.7897 (t80) REVERT: C 510 TYR cc_start: 0.7566 (m-80) cc_final: 0.7125 (m-80) REVERT: C 544 ASP cc_start: 0.8318 (t70) cc_final: 0.7963 (t70) REVERT: C 591 GLN cc_start: 0.7230 (tt0) cc_final: 0.7009 (tt0) REVERT: C 601 ASP cc_start: 0.7107 (m-30) cc_final: 0.6794 (m-30) REVERT: C 646 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7499 (tmm-80) REVERT: C 654 ILE cc_start: 0.8536 (mt) cc_final: 0.7926 (mt) REVERT: C 656 TRP cc_start: 0.8522 (m100) cc_final: 0.8136 (m-90) REVERT: C 665 GLN cc_start: 0.8354 (tt0) cc_final: 0.8096 (tp40) REVERT: C 672 ASP cc_start: 0.8117 (m-30) cc_final: 0.7835 (m-30) REVERT: C 676 LYS cc_start: 0.8781 (mttt) cc_final: 0.8389 (mttm) REVERT: C 683 ARG cc_start: 0.7823 (mpt180) cc_final: 0.7390 (mmt90) REVERT: C 763 ARG cc_start: 0.7280 (ptp-170) cc_final: 0.7073 (ptp-170) REVERT: C 773 VAL cc_start: 0.8679 (t) cc_final: 0.8458 (m) REVERT: C 842 PHE cc_start: 0.7522 (m-10) cc_final: 0.7272 (m-80) outliers start: 29 outliers final: 17 residues processed: 621 average time/residue: 0.3167 time to fit residues: 280.5887 Evaluate side-chains 590 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 571 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 650 MET Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 837 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 85 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 203 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 199 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 643 ASN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 HIS B 637 HIS C 314 HIS C 600 ASN C 637 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.112178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.094383 restraints weight = 28911.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.097896 restraints weight = 14032.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.100186 restraints weight = 8212.754| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 16782 Z= 0.330 Angle : 0.856 12.530 23079 Z= 0.421 Chirality : 0.054 0.367 2763 Planarity : 0.006 0.058 2880 Dihedral : 11.945 90.487 3246 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 5.11 % Allowed : 16.16 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.21 (0.18), residues: 2052 helix: -0.34 (0.22), residues: 552 sheet: -0.33 (0.27), residues: 396 loop : -1.20 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 720 HIS 0.019 0.002 HIS C 639 PHE 0.024 0.003 PHE B 396 TYR 0.023 0.003 TYR A 240 ARG 0.008 0.001 ARG B 407 Details of bonding type rmsd link_NAG-ASN : bond 0.00611 ( 27) link_NAG-ASN : angle 2.83523 ( 81) link_ALPHA1-6 : bond 0.00828 ( 3) link_ALPHA1-6 : angle 3.19753 ( 9) link_BETA1-4 : bond 0.00918 ( 15) link_BETA1-4 : angle 2.48709 ( 45) link_ALPHA1-3 : bond 0.00538 ( 3) link_ALPHA1-3 : angle 3.87301 ( 9) hydrogen bonds : bond 0.07054 ( 482) hydrogen bonds : angle 5.90901 ( 1278) SS BOND : bond 0.00855 ( 27) SS BOND : angle 2.23675 ( 54) covalent geometry : bond 0.00716 (16707) covalent geometry : angle 0.82244 (22881) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 587 time to evaluate : 1.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLU cc_start: 0.7603 (tp30) cc_final: 0.6919 (tp30) REVERT: A 198 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6597 (mt-10) REVERT: A 211 GLU cc_start: 0.8288 (tp30) cc_final: 0.7931 (tp30) REVERT: A 235 CYS cc_start: 0.5718 (m) cc_final: 0.5299 (m) REVERT: A 251 LEU cc_start: 0.8238 (tp) cc_final: 0.7718 (tt) REVERT: A 252 ILE cc_start: 0.8811 (mt) cc_final: 0.8363 (tp) REVERT: A 258 LEU cc_start: 0.8678 (mt) cc_final: 0.8395 (mm) REVERT: A 334 LEU cc_start: 0.8763 (mt) cc_final: 0.8501 (mt) REVERT: A 438 ARG cc_start: 0.7500 (mmm160) cc_final: 0.7081 (tpt90) REVERT: A 468 ASP cc_start: 0.7431 (t70) cc_final: 0.6892 (t70) REVERT: A 495 GLU cc_start: 0.7033 (pt0) cc_final: 0.6797 (pt0) REVERT: A 500 TYR cc_start: 0.8422 (t80) cc_final: 0.7883 (t80) REVERT: A 510 TYR cc_start: 0.8039 (m-80) cc_final: 0.7486 (m-80) REVERT: A 540 VAL cc_start: 0.8435 (p) cc_final: 0.8015 (m) REVERT: A 591 GLN cc_start: 0.7259 (tt0) cc_final: 0.7013 (tt0) REVERT: A 624 HIS cc_start: 0.6415 (m-70) cc_final: 0.6143 (m-70) REVERT: A 635 VAL cc_start: 0.8149 (m) cc_final: 0.7817 (p) REVERT: A 636 GLN cc_start: 0.7895 (tp40) cc_final: 0.7612 (tp40) REVERT: A 648 MET cc_start: 0.8172 (mmt) cc_final: 0.7921 (mmp) REVERT: A 651 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7265 (tt0) REVERT: A 653 ARG cc_start: 0.7971 (ttm170) cc_final: 0.7663 (mtt90) REVERT: A 665 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8316 (tt0) REVERT: A 675 MET cc_start: 0.7992 (mmm) cc_final: 0.7613 (mmm) REVERT: A 676 LYS cc_start: 0.8761 (mttt) cc_final: 0.8362 (mttm) REVERT: A 702 GLU cc_start: 0.7263 (mt-10) cc_final: 0.7003 (mt-10) REVERT: A 803 SER cc_start: 0.8327 (t) cc_final: 0.7803 (p) REVERT: B 151 TYR cc_start: 0.7551 (p90) cc_final: 0.7235 (p90) REVERT: B 206 VAL cc_start: 0.8239 (m) cc_final: 0.7939 (p) REVERT: B 235 CYS cc_start: 0.5930 (m) cc_final: 0.5675 (m) REVERT: B 249 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7214 (mm-30) REVERT: B 252 ILE cc_start: 0.8748 (mt) cc_final: 0.8295 (tp) REVERT: B 273 TRP cc_start: 0.8829 (m-10) cc_final: 0.8555 (m-10) REVERT: B 339 GLU cc_start: 0.7776 (tp30) cc_final: 0.7576 (tp30) REVERT: B 347 LEU cc_start: 0.8398 (mt) cc_final: 0.8117 (mp) REVERT: B 356 ARG cc_start: 0.7946 (tpp-160) cc_final: 0.7601 (tpp-160) REVERT: B 384 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7500 (mp0) REVERT: B 386 VAL cc_start: 0.8767 (m) cc_final: 0.8526 (t) REVERT: B 468 ASP cc_start: 0.7370 (t70) cc_final: 0.6908 (t0) REVERT: B 495 GLU cc_start: 0.7411 (pt0) cc_final: 0.7116 (pt0) REVERT: B 504 LYS cc_start: 0.8066 (mtpp) cc_final: 0.7807 (mtpp) REVERT: B 551 TYR cc_start: 0.8119 (m-80) cc_final: 0.7788 (m-80) REVERT: B 611 LEU cc_start: 0.7475 (tp) cc_final: 0.6849 (tp) REVERT: B 635 VAL cc_start: 0.8247 (m) cc_final: 0.7993 (t) REVERT: B 658 TYR cc_start: 0.8466 (m-80) cc_final: 0.8177 (m-80) REVERT: B 665 GLN cc_start: 0.8413 (tt0) cc_final: 0.7979 (tm-30) REVERT: B 669 GLN cc_start: 0.8039 (mt0) cc_final: 0.7798 (mm110) REVERT: B 672 ASP cc_start: 0.8151 (m-30) cc_final: 0.7939 (m-30) REVERT: B 676 LYS cc_start: 0.8702 (mttt) cc_final: 0.8323 (mttm) REVERT: B 707 TYR cc_start: 0.8391 (m-10) cc_final: 0.8068 (m-10) REVERT: B 746 ILE cc_start: 0.8529 (mm) cc_final: 0.8321 (mm) REVERT: C 193 THR cc_start: 0.8160 (t) cc_final: 0.7901 (t) REVERT: C 197 ASN cc_start: 0.7601 (m110) cc_final: 0.7310 (m-40) REVERT: C 206 VAL cc_start: 0.8171 (p) cc_final: 0.7956 (m) REVERT: C 252 ILE cc_start: 0.8827 (tp) cc_final: 0.8584 (tt) REVERT: C 386 VAL cc_start: 0.8760 (m) cc_final: 0.8521 (t) REVERT: C 468 ASP cc_start: 0.7384 (t70) cc_final: 0.6909 (t70) REVERT: C 495 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6896 (pm20) REVERT: C 510 TYR cc_start: 0.8040 (m-80) cc_final: 0.7497 (m-80) REVERT: C 516 LEU cc_start: 0.8033 (tt) cc_final: 0.7756 (mt) REVERT: C 540 VAL cc_start: 0.8508 (p) cc_final: 0.8208 (t) REVERT: C 544 ASP cc_start: 0.8340 (t70) cc_final: 0.8073 (t0) REVERT: C 551 TYR cc_start: 0.8312 (m-80) cc_final: 0.8083 (m-80) REVERT: C 591 GLN cc_start: 0.7208 (tt0) cc_final: 0.6984 (tt0) REVERT: C 601 ASP cc_start: 0.7126 (m-30) cc_final: 0.6698 (m-30) REVERT: C 611 LEU cc_start: 0.7731 (tp) cc_final: 0.7305 (tp) REVERT: C 635 VAL cc_start: 0.8179 (m) cc_final: 0.7862 (t) REVERT: C 646 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7320 (tmm-80) REVERT: C 669 GLN cc_start: 0.7732 (mp10) cc_final: 0.7450 (mp10) REVERT: C 676 LYS cc_start: 0.8857 (mttt) cc_final: 0.8421 (mttm) REVERT: C 683 ARG cc_start: 0.7881 (mpt180) cc_final: 0.7448 (mmt90) REVERT: C 721 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7416 (tp-100) REVERT: C 724 ASN cc_start: 0.7948 (t0) cc_final: 0.7746 (t0) REVERT: C 773 VAL cc_start: 0.8703 (t) cc_final: 0.8467 (m) REVERT: C 842 PHE cc_start: 0.7722 (m-10) cc_final: 0.7380 (m-80) outliers start: 80 outliers final: 57 residues processed: 618 average time/residue: 0.3233 time to fit residues: 289.4043 Evaluate side-chains 618 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 557 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 462 ASN Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 665 GLN Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 462 ASN Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 326 TRP Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 462 ASN Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain C residue 495 GLU Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 721 GLN Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 837 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 99 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 185 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 132 optimal weight: 0.0870 chunk 9 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 643 ASN B 535 ASN C 180 ASN C 225 HIS C 314 HIS C 742 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.115756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.097783 restraints weight = 28685.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.101382 restraints weight = 13884.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.103744 restraints weight = 8137.115| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 16782 Z= 0.142 Angle : 0.726 12.313 23079 Z= 0.346 Chirality : 0.048 0.300 2763 Planarity : 0.005 0.050 2880 Dihedral : 11.228 93.150 3246 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.60 % Allowed : 21.14 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.92 (0.19), residues: 2052 helix: -0.07 (0.23), residues: 552 sheet: 0.05 (0.29), residues: 387 loop : -1.12 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 326 HIS 0.006 0.001 HIS B 639 PHE 0.020 0.002 PHE B 396 TYR 0.023 0.002 TYR A 474 ARG 0.009 0.001 ARG B 407 Details of bonding type rmsd link_NAG-ASN : bond 0.00328 ( 27) link_NAG-ASN : angle 2.53533 ( 81) link_ALPHA1-6 : bond 0.01326 ( 3) link_ALPHA1-6 : angle 3.12635 ( 9) link_BETA1-4 : bond 0.01042 ( 15) link_BETA1-4 : angle 2.36300 ( 45) link_ALPHA1-3 : bond 0.00036 ( 3) link_ALPHA1-3 : angle 4.24058 ( 9) hydrogen bonds : bond 0.04473 ( 482) hydrogen bonds : angle 5.29000 ( 1278) SS BOND : bond 0.00902 ( 27) SS BOND : angle 2.24932 ( 54) covalent geometry : bond 0.00322 (16707) covalent geometry : angle 0.68935 (22881) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 588 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 PHE cc_start: 0.7649 (t80) cc_final: 0.7329 (t80) REVERT: A 194 GLU cc_start: 0.7525 (tp30) cc_final: 0.6874 (tp30) REVERT: A 198 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6589 (mt-10) REVERT: A 211 GLU cc_start: 0.8181 (tp30) cc_final: 0.7745 (tp30) REVERT: A 251 LEU cc_start: 0.8197 (tp) cc_final: 0.7654 (tt) REVERT: A 252 ILE cc_start: 0.8779 (mt) cc_final: 0.8387 (tp) REVERT: A 258 LEU cc_start: 0.8717 (mt) cc_final: 0.8464 (mm) REVERT: A 334 LEU cc_start: 0.8620 (mt) cc_final: 0.8378 (mt) REVERT: A 341 THR cc_start: 0.8624 (m) cc_final: 0.8247 (p) REVERT: A 389 LEU cc_start: 0.8646 (mm) cc_final: 0.8441 (mt) REVERT: A 438 ARG cc_start: 0.7471 (mmm160) cc_final: 0.7003 (tpt90) REVERT: A 468 ASP cc_start: 0.7350 (t70) cc_final: 0.6816 (t70) REVERT: A 495 GLU cc_start: 0.6866 (pt0) cc_final: 0.6652 (pt0) REVERT: A 500 TYR cc_start: 0.8333 (t80) cc_final: 0.7783 (t80) REVERT: A 510 TYR cc_start: 0.7772 (m-80) cc_final: 0.7201 (m-80) REVERT: A 591 GLN cc_start: 0.7216 (tt0) cc_final: 0.7008 (tt0) REVERT: A 624 HIS cc_start: 0.6392 (m-70) cc_final: 0.6151 (m-70) REVERT: A 651 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7274 (tt0) REVERT: A 653 ARG cc_start: 0.7897 (ttm170) cc_final: 0.7569 (mtt90) REVERT: A 665 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8280 (tt0) REVERT: A 672 ASP cc_start: 0.7984 (m-30) cc_final: 0.7768 (m-30) REVERT: A 675 MET cc_start: 0.7919 (mmm) cc_final: 0.7503 (mmm) REVERT: A 676 LYS cc_start: 0.8683 (mttt) cc_final: 0.8298 (mttm) REVERT: A 702 GLU cc_start: 0.7295 (mt-10) cc_final: 0.6894 (mt-10) REVERT: A 772 VAL cc_start: 0.8199 (p) cc_final: 0.7988 (m) REVERT: B 206 VAL cc_start: 0.8275 (m) cc_final: 0.7974 (p) REVERT: B 249 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7102 (mm-30) REVERT: B 252 ILE cc_start: 0.8665 (mt) cc_final: 0.8363 (tp) REVERT: B 273 TRP cc_start: 0.8834 (m-10) cc_final: 0.8567 (m-10) REVERT: B 298 MET cc_start: 0.7520 (mmm) cc_final: 0.7314 (mmm) REVERT: B 356 ARG cc_start: 0.7862 (tpp-160) cc_final: 0.7534 (tpp-160) REVERT: B 384 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7406 (mp0) REVERT: B 408 TYR cc_start: 0.7727 (p90) cc_final: 0.7453 (p90) REVERT: B 468 ASP cc_start: 0.7295 (t70) cc_final: 0.6786 (t0) REVERT: B 495 GLU cc_start: 0.7295 (pt0) cc_final: 0.7028 (pt0) REVERT: B 504 LYS cc_start: 0.8041 (mtpp) cc_final: 0.7821 (mtpp) REVERT: B 551 TYR cc_start: 0.8112 (m-80) cc_final: 0.7762 (m-80) REVERT: B 635 VAL cc_start: 0.7912 (m) cc_final: 0.7609 (p) REVERT: B 658 TYR cc_start: 0.8433 (m-80) cc_final: 0.8125 (m-80) REVERT: B 665 GLN cc_start: 0.8429 (tt0) cc_final: 0.7978 (tm-30) REVERT: B 676 LYS cc_start: 0.8685 (mttt) cc_final: 0.8404 (mttp) REVERT: B 707 TYR cc_start: 0.8273 (m-10) cc_final: 0.8063 (m-10) REVERT: B 746 ILE cc_start: 0.8494 (mm) cc_final: 0.8273 (mm) REVERT: B 825 VAL cc_start: 0.8230 (OUTLIER) cc_final: 0.7923 (p) REVERT: C 193 THR cc_start: 0.8020 (t) cc_final: 0.7815 (t) REVERT: C 194 GLU cc_start: 0.7436 (tp30) cc_final: 0.6896 (tp30) REVERT: C 197 ASN cc_start: 0.7497 (m110) cc_final: 0.7212 (m-40) REVERT: C 252 ILE cc_start: 0.8800 (tp) cc_final: 0.8563 (tt) REVERT: C 295 LYS cc_start: 0.8715 (mptt) cc_final: 0.8383 (mptt) REVERT: C 384 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7478 (mp0) REVERT: C 468 ASP cc_start: 0.7367 (t70) cc_final: 0.6849 (t70) REVERT: C 510 TYR cc_start: 0.7802 (m-80) cc_final: 0.7234 (m-80) REVERT: C 516 LEU cc_start: 0.7880 (tt) cc_final: 0.7619 (mt) REVERT: C 544 ASP cc_start: 0.8326 (t70) cc_final: 0.8065 (t0) REVERT: C 551 TYR cc_start: 0.8291 (m-80) cc_final: 0.8045 (m-80) REVERT: C 599 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8238 (mm) REVERT: C 601 ASP cc_start: 0.7021 (m-30) cc_final: 0.6582 (m-30) REVERT: C 604 LEU cc_start: 0.8648 (mp) cc_final: 0.8382 (mp) REVERT: C 642 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7927 (mm) REVERT: C 648 MET cc_start: 0.8028 (mmt) cc_final: 0.7581 (mmp) REVERT: C 653 ARG cc_start: 0.8019 (ttm170) cc_final: 0.7640 (mtm-85) REVERT: C 656 TRP cc_start: 0.8555 (m100) cc_final: 0.8183 (m-90) REVERT: C 669 GLN cc_start: 0.7609 (mp10) cc_final: 0.7151 (mp10) REVERT: C 676 LYS cc_start: 0.8870 (mttt) cc_final: 0.8559 (mttm) REVERT: C 683 ARG cc_start: 0.7873 (mpt180) cc_final: 0.7582 (mpt180) REVERT: C 721 GLN cc_start: 0.7716 (tt0) cc_final: 0.7401 (tp-100) outliers start: 72 outliers final: 45 residues processed: 614 average time/residue: 0.3177 time to fit residues: 276.3688 Evaluate side-chains 615 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 566 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 665 GLN Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 462 ASN Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 650 MET Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 462 ASN Chi-restraints excluded: chain C residue 532 GLU Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 719 ASN Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 762 CYS Chi-restraints excluded: chain C residue 763 ARG Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 837 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 182 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 76 optimal weight: 0.0870 chunk 131 optimal weight: 4.9990 chunk 59 optimal weight: 0.0020 chunk 58 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 91 optimal weight: 0.0470 overall best weight: 1.2268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 492 GLN B 535 ASN B 600 ASN C 225 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.114273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.096345 restraints weight = 29294.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.099929 restraints weight = 14185.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.102263 restraints weight = 8316.749| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 16782 Z= 0.186 Angle : 0.758 21.350 23079 Z= 0.361 Chirality : 0.049 0.328 2763 Planarity : 0.005 0.049 2880 Dihedral : 11.073 93.958 3246 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 5.24 % Allowed : 21.39 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.95 (0.19), residues: 2052 helix: -0.03 (0.23), residues: 552 sheet: 0.07 (0.29), residues: 369 loop : -1.17 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 326 HIS 0.010 0.001 HIS B 639 PHE 0.018 0.002 PHE A 396 TYR 0.019 0.002 TYR A 474 ARG 0.009 0.001 ARG C 407 Details of bonding type rmsd link_NAG-ASN : bond 0.00358 ( 27) link_NAG-ASN : angle 2.51213 ( 81) link_ALPHA1-6 : bond 0.01179 ( 3) link_ALPHA1-6 : angle 3.16115 ( 9) link_BETA1-4 : bond 0.00982 ( 15) link_BETA1-4 : angle 2.43870 ( 45) link_ALPHA1-3 : bond 0.00331 ( 3) link_ALPHA1-3 : angle 4.06504 ( 9) hydrogen bonds : bond 0.05010 ( 482) hydrogen bonds : angle 5.24205 ( 1278) SS BOND : bond 0.00698 ( 27) SS BOND : angle 2.53959 ( 54) covalent geometry : bond 0.00412 (16707) covalent geometry : angle 0.72068 (22881) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 588 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLN cc_start: 0.8069 (tm-30) cc_final: 0.7612 (tm-30) REVERT: A 150 PHE cc_start: 0.7642 (t80) cc_final: 0.7362 (t80) REVERT: A 158 ILE cc_start: 0.8658 (mt) cc_final: 0.8281 (mm) REVERT: A 194 GLU cc_start: 0.7542 (tp30) cc_final: 0.6901 (tp30) REVERT: A 198 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6649 (mt-10) REVERT: A 211 GLU cc_start: 0.8216 (tp30) cc_final: 0.7870 (tp30) REVERT: A 251 LEU cc_start: 0.8201 (tp) cc_final: 0.7670 (tt) REVERT: A 252 ILE cc_start: 0.8768 (mt) cc_final: 0.8405 (tt) REVERT: A 258 LEU cc_start: 0.8713 (mt) cc_final: 0.8454 (mm) REVERT: A 334 LEU cc_start: 0.8677 (mt) cc_final: 0.8437 (mt) REVERT: A 339 GLU cc_start: 0.7734 (tp30) cc_final: 0.7474 (tp30) REVERT: A 341 THR cc_start: 0.8615 (m) cc_final: 0.8266 (p) REVERT: A 382 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8037 (mtt-85) REVERT: A 389 LEU cc_start: 0.8682 (mm) cc_final: 0.8477 (mt) REVERT: A 468 ASP cc_start: 0.7432 (t70) cc_final: 0.6910 (t70) REVERT: A 495 GLU cc_start: 0.6889 (pt0) cc_final: 0.6686 (pt0) REVERT: A 500 TYR cc_start: 0.8360 (t80) cc_final: 0.7748 (t80) REVERT: A 510 TYR cc_start: 0.7839 (m-80) cc_final: 0.7257 (m-80) REVERT: A 624 HIS cc_start: 0.6377 (m-70) cc_final: 0.6161 (m-70) REVERT: A 651 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7264 (tt0) REVERT: A 653 ARG cc_start: 0.7902 (ttm170) cc_final: 0.7538 (mtm-85) REVERT: A 665 GLN cc_start: 0.8566 (tt0) cc_final: 0.8294 (tt0) REVERT: A 675 MET cc_start: 0.7934 (mmm) cc_final: 0.7540 (mmm) REVERT: A 676 LYS cc_start: 0.8709 (mttt) cc_final: 0.8307 (mttm) REVERT: A 702 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6890 (mt-10) REVERT: B 206 VAL cc_start: 0.8204 (m) cc_final: 0.7926 (p) REVERT: B 249 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7302 (mm-30) REVERT: B 252 ILE cc_start: 0.8696 (mt) cc_final: 0.8359 (tp) REVERT: B 273 TRP cc_start: 0.8843 (m-10) cc_final: 0.8581 (m-10) REVERT: B 384 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7400 (mp0) REVERT: B 386 VAL cc_start: 0.8716 (m) cc_final: 0.8460 (t) REVERT: B 495 GLU cc_start: 0.7359 (pt0) cc_final: 0.7073 (pt0) REVERT: B 520 LYS cc_start: 0.8355 (mmmm) cc_final: 0.8009 (mtpp) REVERT: B 551 TYR cc_start: 0.8122 (m-80) cc_final: 0.7785 (m-80) REVERT: B 635 VAL cc_start: 0.7994 (m) cc_final: 0.7697 (t) REVERT: B 658 TYR cc_start: 0.8407 (m-80) cc_final: 0.8103 (m-80) REVERT: B 665 GLN cc_start: 0.8368 (tt0) cc_final: 0.7983 (tm-30) REVERT: B 676 LYS cc_start: 0.8695 (mttt) cc_final: 0.8414 (mttp) REVERT: B 707 TYR cc_start: 0.8199 (m-10) cc_final: 0.7994 (m-10) REVERT: C 193 THR cc_start: 0.8076 (t) cc_final: 0.7817 (t) REVERT: C 194 GLU cc_start: 0.7446 (tp30) cc_final: 0.6898 (tp30) REVERT: C 197 ASN cc_start: 0.7552 (m110) cc_final: 0.7252 (m-40) REVERT: C 251 LEU cc_start: 0.8407 (tp) cc_final: 0.8039 (tt) REVERT: C 252 ILE cc_start: 0.8816 (tp) cc_final: 0.8584 (tt) REVERT: C 382 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7921 (mtt-85) REVERT: C 468 ASP cc_start: 0.7368 (t70) cc_final: 0.6854 (t70) REVERT: C 500 TYR cc_start: 0.8254 (t80) cc_final: 0.7933 (t80) REVERT: C 504 LYS cc_start: 0.8112 (ttmm) cc_final: 0.7790 (ttmm) REVERT: C 510 TYR cc_start: 0.7884 (m-80) cc_final: 0.7253 (m-80) REVERT: C 516 LEU cc_start: 0.7925 (tt) cc_final: 0.7671 (mt) REVERT: C 544 ASP cc_start: 0.8320 (t70) cc_final: 0.8105 (t0) REVERT: C 551 TYR cc_start: 0.8319 (m-80) cc_final: 0.8090 (m-80) REVERT: C 599 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8187 (tt) REVERT: C 601 ASP cc_start: 0.7080 (m-30) cc_final: 0.6607 (m-30) REVERT: C 604 LEU cc_start: 0.8662 (mp) cc_final: 0.8428 (mp) REVERT: C 612 ARG cc_start: 0.7887 (tpp80) cc_final: 0.7679 (mmm-85) REVERT: C 635 VAL cc_start: 0.7868 (m) cc_final: 0.7639 (t) REVERT: C 642 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7922 (mm) REVERT: C 648 MET cc_start: 0.7996 (mmt) cc_final: 0.7554 (mmp) REVERT: C 651 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7177 (tt0) REVERT: C 669 GLN cc_start: 0.7668 (mp10) cc_final: 0.7178 (mp10) REVERT: C 676 LYS cc_start: 0.8861 (mttt) cc_final: 0.8548 (mttm) REVERT: C 683 ARG cc_start: 0.7876 (mpt180) cc_final: 0.7468 (mmt90) REVERT: C 721 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7425 (tp-100) REVERT: C 764 ARG cc_start: 0.7391 (ttt90) cc_final: 0.6984 (tpt90) REVERT: C 842 PHE cc_start: 0.7572 (m-80) cc_final: 0.7218 (m-80) outliers start: 82 outliers final: 63 residues processed: 621 average time/residue: 0.3085 time to fit residues: 272.9360 Evaluate side-chains 646 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 578 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 462 ASN Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 719 ASN Chi-restraints excluded: chain A residue 722 ILE Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 462 ASN Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 382 ARG Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 462 ASN Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 619 MET Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 719 ASN Chi-restraints excluded: chain C residue 721 GLN Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 762 CYS Chi-restraints excluded: chain C residue 763 ARG Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 837 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 93 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 184 optimal weight: 0.3980 chunk 42 optimal weight: 0.9980 chunk 125 optimal weight: 0.0020 chunk 104 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 168 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 535 ASN ** B 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 591 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.115880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.098282 restraints weight = 28922.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.101777 restraints weight = 13844.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.104105 restraints weight = 8087.223| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 16782 Z= 0.128 Angle : 0.723 18.011 23079 Z= 0.341 Chirality : 0.048 0.302 2763 Planarity : 0.005 0.047 2880 Dihedral : 10.698 94.072 3246 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.79 % Allowed : 22.48 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.82 (0.19), residues: 2052 helix: 0.08 (0.23), residues: 552 sheet: 0.20 (0.29), residues: 372 loop : -1.12 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 326 HIS 0.005 0.001 HIS C 639 PHE 0.020 0.001 PHE A 396 TYR 0.032 0.001 TYR B 276 ARG 0.011 0.001 ARG A 407 Details of bonding type rmsd link_NAG-ASN : bond 0.00315 ( 27) link_NAG-ASN : angle 2.38538 ( 81) link_ALPHA1-6 : bond 0.01359 ( 3) link_ALPHA1-6 : angle 3.14060 ( 9) link_BETA1-4 : bond 0.01016 ( 15) link_BETA1-4 : angle 2.41513 ( 45) link_ALPHA1-3 : bond 0.00202 ( 3) link_ALPHA1-3 : angle 4.15738 ( 9) hydrogen bonds : bond 0.03928 ( 482) hydrogen bonds : angle 4.99632 ( 1278) SS BOND : bond 0.00726 ( 27) SS BOND : angle 1.98836 ( 54) covalent geometry : bond 0.00292 (16707) covalent geometry : angle 0.68960 (22881) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 585 time to evaluate : 1.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLN cc_start: 0.8059 (tm-30) cc_final: 0.7638 (tm-30) REVERT: A 150 PHE cc_start: 0.7588 (t80) cc_final: 0.7362 (t80) REVERT: A 158 ILE cc_start: 0.8644 (mt) cc_final: 0.8278 (mm) REVERT: A 194 GLU cc_start: 0.7522 (tp30) cc_final: 0.6894 (tp30) REVERT: A 198 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6689 (mt-10) REVERT: A 211 GLU cc_start: 0.8165 (tp30) cc_final: 0.7727 (tp30) REVERT: A 251 LEU cc_start: 0.8208 (tp) cc_final: 0.7687 (tt) REVERT: A 252 ILE cc_start: 0.8772 (mt) cc_final: 0.8386 (tp) REVERT: A 258 LEU cc_start: 0.8727 (mt) cc_final: 0.8481 (mm) REVERT: A 334 LEU cc_start: 0.8590 (mt) cc_final: 0.8369 (mt) REVERT: A 339 GLU cc_start: 0.7735 (tp30) cc_final: 0.7453 (tp30) REVERT: A 341 THR cc_start: 0.8616 (m) cc_final: 0.8263 (p) REVERT: A 382 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.8035 (mtt-85) REVERT: A 438 ARG cc_start: 0.7508 (mmm160) cc_final: 0.6990 (tpt90) REVERT: A 468 ASP cc_start: 0.7376 (t70) cc_final: 0.6870 (t70) REVERT: A 500 TYR cc_start: 0.8323 (t80) cc_final: 0.7730 (t80) REVERT: A 510 TYR cc_start: 0.7755 (m-80) cc_final: 0.7174 (m-80) REVERT: A 520 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8158 (mtmm) REVERT: A 629 MET cc_start: 0.7596 (mmt) cc_final: 0.7334 (mmt) REVERT: A 651 GLU cc_start: 0.7458 (mt-10) cc_final: 0.7199 (tt0) REVERT: A 653 ARG cc_start: 0.7896 (ttm170) cc_final: 0.7555 (mtt90) REVERT: A 665 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8242 (tt0) REVERT: A 675 MET cc_start: 0.7921 (mmm) cc_final: 0.7501 (mmm) REVERT: A 676 LYS cc_start: 0.8660 (mttt) cc_final: 0.8284 (mttm) REVERT: A 702 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6876 (mt-10) REVERT: A 764 ARG cc_start: 0.7445 (ttt90) cc_final: 0.7142 (tpt90) REVERT: B 206 VAL cc_start: 0.8214 (m) cc_final: 0.7897 (p) REVERT: B 249 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7259 (mm-30) REVERT: B 252 ILE cc_start: 0.8667 (mt) cc_final: 0.8344 (tp) REVERT: B 273 TRP cc_start: 0.8811 (m-10) cc_final: 0.8547 (m-10) REVERT: B 386 VAL cc_start: 0.8706 (m) cc_final: 0.8443 (t) REVERT: B 495 GLU cc_start: 0.7311 (pt0) cc_final: 0.7044 (pt0) REVERT: B 500 TYR cc_start: 0.8396 (t80) cc_final: 0.8000 (t80) REVERT: B 520 LYS cc_start: 0.8339 (mmmm) cc_final: 0.8026 (mtpp) REVERT: B 551 TYR cc_start: 0.8114 (m-80) cc_final: 0.7778 (m-80) REVERT: B 658 TYR cc_start: 0.8375 (m-80) cc_final: 0.8080 (m-80) REVERT: B 665 GLN cc_start: 0.8352 (tt0) cc_final: 0.8004 (tm-30) REVERT: B 676 LYS cc_start: 0.8684 (mttt) cc_final: 0.8407 (mttp) REVERT: B 776 VAL cc_start: 0.8054 (t) cc_final: 0.7733 (m) REVERT: C 194 GLU cc_start: 0.7463 (tp30) cc_final: 0.6920 (tp30) REVERT: C 251 LEU cc_start: 0.8409 (tp) cc_final: 0.8049 (tt) REVERT: C 252 ILE cc_start: 0.8804 (tp) cc_final: 0.8557 (tt) REVERT: C 295 LYS cc_start: 0.8725 (mptt) cc_final: 0.8439 (mptt) REVERT: C 382 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8059 (ptp-170) REVERT: C 468 ASP cc_start: 0.7336 (t70) cc_final: 0.6794 (t70) REVERT: C 500 TYR cc_start: 0.8208 (t80) cc_final: 0.7924 (t80) REVERT: C 504 LYS cc_start: 0.8107 (ttmm) cc_final: 0.7842 (ttmm) REVERT: C 510 TYR cc_start: 0.7743 (m-80) cc_final: 0.7159 (m-80) REVERT: C 516 LEU cc_start: 0.7852 (tt) cc_final: 0.7621 (mt) REVERT: C 544 ASP cc_start: 0.8326 (t70) cc_final: 0.8121 (t0) REVERT: C 599 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8150 (tt) REVERT: C 601 ASP cc_start: 0.7080 (m-30) cc_final: 0.6627 (m-30) REVERT: C 604 LEU cc_start: 0.8647 (mp) cc_final: 0.8434 (mp) REVERT: C 642 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7903 (mm) REVERT: C 651 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7141 (tt0) REVERT: C 656 TRP cc_start: 0.8553 (m100) cc_final: 0.8163 (m-90) REVERT: C 669 GLN cc_start: 0.7667 (mp10) cc_final: 0.7150 (mp10) REVERT: C 676 LYS cc_start: 0.8803 (mttt) cc_final: 0.8523 (mttm) REVERT: C 683 ARG cc_start: 0.7840 (mpt180) cc_final: 0.7395 (mmt90) REVERT: C 721 GLN cc_start: 0.7732 (tt0) cc_final: 0.7290 (tp40) REVERT: C 764 ARG cc_start: 0.7372 (ttt90) cc_final: 0.6971 (tpt90) REVERT: C 842 PHE cc_start: 0.7538 (m-80) cc_final: 0.7075 (m-80) outliers start: 75 outliers final: 58 residues processed: 617 average time/residue: 0.3103 time to fit residues: 274.2515 Evaluate side-chains 641 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 577 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 665 GLN Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 719 ASN Chi-restraints excluded: chain A residue 722 ILE Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 462 ASN Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 382 ARG Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 462 ASN Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 619 MET Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 719 ASN Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 762 CYS Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 837 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 0.9990 chunk 161 optimal weight: 3.9990 chunk 127 optimal weight: 0.0000 chunk 3 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 167 optimal weight: 0.4980 chunk 11 optimal weight: 3.9990 chunk 30 optimal weight: 0.1980 chunk 181 optimal weight: 0.3980 chunk 86 optimal weight: 0.5980 chunk 77 optimal weight: 0.4980 overall best weight: 0.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN A 591 GLN B 600 ASN B 643 ASN C 197 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.117994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.100010 restraints weight = 28593.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.103604 restraints weight = 13795.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.105970 restraints weight = 8092.002| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 16782 Z= 0.113 Angle : 0.709 16.547 23079 Z= 0.332 Chirality : 0.047 0.291 2763 Planarity : 0.005 0.044 2880 Dihedral : 10.332 93.291 3246 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 5.04 % Allowed : 24.14 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.68 (0.19), residues: 2052 helix: 0.21 (0.23), residues: 552 sheet: 0.32 (0.29), residues: 372 loop : -1.06 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 326 HIS 0.007 0.001 HIS B 225 PHE 0.017 0.001 PHE A 396 TYR 0.031 0.001 TYR A 276 ARG 0.010 0.001 ARG C 407 Details of bonding type rmsd link_NAG-ASN : bond 0.00319 ( 27) link_NAG-ASN : angle 2.26647 ( 81) link_ALPHA1-6 : bond 0.01389 ( 3) link_ALPHA1-6 : angle 3.10755 ( 9) link_BETA1-4 : bond 0.01030 ( 15) link_BETA1-4 : angle 2.38670 ( 45) link_ALPHA1-3 : bond 0.00015 ( 3) link_ALPHA1-3 : angle 4.00299 ( 9) hydrogen bonds : bond 0.03398 ( 482) hydrogen bonds : angle 4.78841 ( 1278) SS BOND : bond 0.00718 ( 27) SS BOND : angle 1.84773 ( 54) covalent geometry : bond 0.00256 (16707) covalent geometry : angle 0.67793 (22881) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 600 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLN cc_start: 0.8056 (tm-30) cc_final: 0.7567 (tm-30) REVERT: A 158 ILE cc_start: 0.8619 (mt) cc_final: 0.8252 (mm) REVERT: A 194 GLU cc_start: 0.7506 (tp30) cc_final: 0.6890 (tp30) REVERT: A 198 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6705 (mt-10) REVERT: A 211 GLU cc_start: 0.8211 (tp30) cc_final: 0.7878 (tp30) REVERT: A 251 LEU cc_start: 0.8177 (tp) cc_final: 0.7677 (tt) REVERT: A 252 ILE cc_start: 0.8751 (mt) cc_final: 0.8404 (tt) REVERT: A 334 LEU cc_start: 0.8560 (mt) cc_final: 0.8331 (mt) REVERT: A 339 GLU cc_start: 0.7746 (tp30) cc_final: 0.7448 (tp30) REVERT: A 382 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7991 (mtt-85) REVERT: A 468 ASP cc_start: 0.7359 (t70) cc_final: 0.6834 (t70) REVERT: A 500 TYR cc_start: 0.8273 (t80) cc_final: 0.7706 (t80) REVERT: A 510 TYR cc_start: 0.7674 (m-80) cc_final: 0.7083 (m-80) REVERT: A 520 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8125 (mtmm) REVERT: A 629 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.7321 (mmt) REVERT: A 651 GLU cc_start: 0.7458 (mt-10) cc_final: 0.7155 (tt0) REVERT: A 653 ARG cc_start: 0.7852 (ttm170) cc_final: 0.7463 (mtm-85) REVERT: A 665 GLN cc_start: 0.8526 (tt0) cc_final: 0.8254 (tt0) REVERT: A 675 MET cc_start: 0.7935 (mmm) cc_final: 0.7526 (mmm) REVERT: A 676 LYS cc_start: 0.8631 (mttt) cc_final: 0.8376 (mttp) REVERT: A 721 GLN cc_start: 0.7913 (tm-30) cc_final: 0.7317 (tm-30) REVERT: A 764 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.7063 (tpt90) REVERT: B 206 VAL cc_start: 0.8230 (m) cc_final: 0.7965 (p) REVERT: B 249 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7275 (mm-30) REVERT: B 252 ILE cc_start: 0.8607 (mt) cc_final: 0.8323 (tp) REVERT: B 273 TRP cc_start: 0.8796 (m-10) cc_final: 0.8545 (m-10) REVERT: B 495 GLU cc_start: 0.7285 (pt0) cc_final: 0.7007 (pt0) REVERT: B 500 TYR cc_start: 0.8340 (t80) cc_final: 0.7982 (t80) REVERT: B 520 LYS cc_start: 0.8333 (mmmm) cc_final: 0.8014 (mtpp) REVERT: B 551 TYR cc_start: 0.8106 (m-80) cc_final: 0.7776 (m-80) REVERT: B 658 TYR cc_start: 0.8374 (m-80) cc_final: 0.8066 (m-80) REVERT: B 665 GLN cc_start: 0.8339 (tt0) cc_final: 0.8011 (tm-30) REVERT: B 676 LYS cc_start: 0.8661 (mttt) cc_final: 0.8390 (mttp) REVERT: B 742 HIS cc_start: 0.7953 (m90) cc_final: 0.7679 (m90) REVERT: B 776 VAL cc_start: 0.8053 (t) cc_final: 0.7740 (m) REVERT: C 194 GLU cc_start: 0.7426 (tp30) cc_final: 0.6829 (tp30) REVERT: C 197 ASN cc_start: 0.7537 (m110) cc_final: 0.7026 (m-40) REVERT: C 249 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6738 (mm-30) REVERT: C 251 LEU cc_start: 0.8390 (tp) cc_final: 0.8021 (tt) REVERT: C 252 ILE cc_start: 0.8754 (tp) cc_final: 0.8500 (tt) REVERT: C 295 LYS cc_start: 0.8708 (mptt) cc_final: 0.8434 (mptt) REVERT: C 347 LEU cc_start: 0.8416 (mt) cc_final: 0.8062 (tp) REVERT: C 382 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.8079 (ptp-170) REVERT: C 468 ASP cc_start: 0.7382 (t70) cc_final: 0.6845 (t70) REVERT: C 500 TYR cc_start: 0.8175 (t80) cc_final: 0.7859 (t80) REVERT: C 504 LYS cc_start: 0.8060 (ttmm) cc_final: 0.7738 (ttmm) REVERT: C 510 TYR cc_start: 0.7648 (m-80) cc_final: 0.7129 (m-80) REVERT: C 544 ASP cc_start: 0.8337 (t70) cc_final: 0.8129 (t0) REVERT: C 599 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8243 (mm) REVERT: C 601 ASP cc_start: 0.7092 (m-30) cc_final: 0.6651 (m-30) REVERT: C 642 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7967 (mm) REVERT: C 651 GLU cc_start: 0.7480 (mt-10) cc_final: 0.7050 (tt0) REVERT: C 653 ARG cc_start: 0.8010 (ttm170) cc_final: 0.7603 (mtm-85) REVERT: C 656 TRP cc_start: 0.8565 (m100) cc_final: 0.8182 (m-90) REVERT: C 669 GLN cc_start: 0.7629 (mp10) cc_final: 0.7095 (mp10) REVERT: C 676 LYS cc_start: 0.8779 (mttt) cc_final: 0.8501 (mttm) REVERT: C 683 ARG cc_start: 0.7850 (mpt180) cc_final: 0.7541 (mpt180) REVERT: C 764 ARG cc_start: 0.7425 (ttt90) cc_final: 0.6966 (tpt90) REVERT: C 842 PHE cc_start: 0.7518 (m-80) cc_final: 0.7014 (m-80) outliers start: 79 outliers final: 52 residues processed: 628 average time/residue: 0.3155 time to fit residues: 282.0532 Evaluate side-chains 633 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 574 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 591 GLN Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 719 ASN Chi-restraints excluded: chain A residue 722 ILE Chi-restraints excluded: chain A residue 764 ARG Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 650 MET Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain C residue 382 ARG Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 619 MET Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 719 ASN Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 762 CYS Chi-restraints excluded: chain C residue 763 ARG Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 837 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 72 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 147 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 167 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 81 optimal weight: 0.0040 chunk 153 optimal weight: 5.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 600 ASN B 643 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.117583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.099572 restraints weight = 28350.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.103232 restraints weight = 13699.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.105614 restraints weight = 7969.463| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 16782 Z= 0.149 Angle : 0.739 17.193 23079 Z= 0.348 Chirality : 0.049 0.294 2763 Planarity : 0.005 0.044 2880 Dihedral : 10.260 91.939 3246 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.53 % Allowed : 25.03 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.19), residues: 2052 helix: 0.18 (0.23), residues: 555 sheet: 0.31 (0.29), residues: 372 loop : -1.04 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 326 HIS 0.007 0.001 HIS C 639 PHE 0.018 0.001 PHE B 396 TYR 0.032 0.002 TYR A 276 ARG 0.009 0.001 ARG B 764 Details of bonding type rmsd link_NAG-ASN : bond 0.00281 ( 27) link_NAG-ASN : angle 2.25863 ( 81) link_ALPHA1-6 : bond 0.01293 ( 3) link_ALPHA1-6 : angle 3.28062 ( 9) link_BETA1-4 : bond 0.00949 ( 15) link_BETA1-4 : angle 2.41442 ( 45) link_ALPHA1-3 : bond 0.00091 ( 3) link_ALPHA1-3 : angle 3.94337 ( 9) hydrogen bonds : bond 0.04025 ( 482) hydrogen bonds : angle 4.81625 ( 1278) SS BOND : bond 0.00705 ( 27) SS BOND : angle 2.16069 ( 54) covalent geometry : bond 0.00340 (16707) covalent geometry : angle 0.70705 (22881) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 580 time to evaluate : 1.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLN cc_start: 0.8014 (tm-30) cc_final: 0.7523 (tm-30) REVERT: A 158 ILE cc_start: 0.8616 (mt) cc_final: 0.8274 (mm) REVERT: A 194 GLU cc_start: 0.7535 (tp30) cc_final: 0.6909 (tp30) REVERT: A 198 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6756 (mt-10) REVERT: A 211 GLU cc_start: 0.8206 (tp30) cc_final: 0.7825 (tp30) REVERT: A 251 LEU cc_start: 0.8187 (tp) cc_final: 0.7711 (tt) REVERT: A 252 ILE cc_start: 0.8771 (mt) cc_final: 0.8421 (tt) REVERT: A 334 LEU cc_start: 0.8602 (mt) cc_final: 0.8389 (mt) REVERT: A 339 GLU cc_start: 0.7760 (tp30) cc_final: 0.7500 (tp30) REVERT: A 382 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.8044 (mtt-85) REVERT: A 468 ASP cc_start: 0.7401 (t70) cc_final: 0.6906 (t70) REVERT: A 500 TYR cc_start: 0.8300 (t80) cc_final: 0.7669 (t80) REVERT: A 510 TYR cc_start: 0.7785 (m-80) cc_final: 0.7181 (m-80) REVERT: A 520 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8116 (mtmm) REVERT: A 629 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.7279 (mmt) REVERT: A 651 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7235 (tt0) REVERT: A 653 ARG cc_start: 0.7892 (ttm170) cc_final: 0.7534 (mtt90) REVERT: A 665 GLN cc_start: 0.8565 (tt0) cc_final: 0.8269 (tt0) REVERT: A 675 MET cc_start: 0.7936 (mmm) cc_final: 0.7517 (mmm) REVERT: A 676 LYS cc_start: 0.8659 (mttt) cc_final: 0.8273 (mttm) REVERT: A 683 ARG cc_start: 0.7954 (mmt-90) cc_final: 0.7729 (mmt90) REVERT: A 764 ARG cc_start: 0.7460 (ttt90) cc_final: 0.7093 (tpt90) REVERT: B 235 CYS cc_start: 0.5803 (m) cc_final: 0.5485 (m) REVERT: B 249 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7305 (mm-30) REVERT: B 252 ILE cc_start: 0.8603 (mt) cc_final: 0.8343 (tp) REVERT: B 273 TRP cc_start: 0.8816 (m-10) cc_final: 0.8560 (m-10) REVERT: B 318 CYS cc_start: 0.5452 (p) cc_final: 0.4637 (p) REVERT: B 495 GLU cc_start: 0.7313 (pt0) cc_final: 0.7029 (pt0) REVERT: B 520 LYS cc_start: 0.8354 (mmmm) cc_final: 0.8031 (mtpp) REVERT: B 551 TYR cc_start: 0.8115 (m-80) cc_final: 0.7791 (m-80) REVERT: B 599 ILE cc_start: 0.8475 (tp) cc_final: 0.8258 (mm) REVERT: B 658 TYR cc_start: 0.8408 (m-80) cc_final: 0.8107 (m-80) REVERT: B 665 GLN cc_start: 0.8343 (tt0) cc_final: 0.8002 (tm-30) REVERT: B 676 LYS cc_start: 0.8656 (mttt) cc_final: 0.8388 (mttp) REVERT: B 776 VAL cc_start: 0.8074 (t) cc_final: 0.7741 (m) REVERT: C 194 GLU cc_start: 0.7475 (tp30) cc_final: 0.6930 (tp30) REVERT: C 249 GLU cc_start: 0.7357 (mm-30) cc_final: 0.6732 (mm-30) REVERT: C 251 LEU cc_start: 0.8413 (tp) cc_final: 0.8026 (tt) REVERT: C 252 ILE cc_start: 0.8766 (tp) cc_final: 0.8509 (tt) REVERT: C 295 LYS cc_start: 0.8716 (mptt) cc_final: 0.8427 (mptt) REVERT: C 347 LEU cc_start: 0.8380 (mt) cc_final: 0.8056 (tp) REVERT: C 382 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8078 (ptp-170) REVERT: C 468 ASP cc_start: 0.7388 (t70) cc_final: 0.6887 (t70) REVERT: C 500 TYR cc_start: 0.8230 (t80) cc_final: 0.7886 (t80) REVERT: C 504 LYS cc_start: 0.8055 (ttmm) cc_final: 0.7741 (ttmm) REVERT: C 510 TYR cc_start: 0.7779 (m-80) cc_final: 0.7199 (m-80) REVERT: C 599 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8210 (tt) REVERT: C 601 ASP cc_start: 0.7032 (m-30) cc_final: 0.6607 (m-30) REVERT: C 642 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7877 (mm) REVERT: C 648 MET cc_start: 0.8047 (mmp) cc_final: 0.7534 (mmt) REVERT: C 651 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7026 (tt0) REVERT: C 669 GLN cc_start: 0.7648 (mp10) cc_final: 0.7115 (mp10) REVERT: C 676 LYS cc_start: 0.8818 (mttt) cc_final: 0.8552 (mttm) REVERT: C 683 ARG cc_start: 0.7874 (mpt180) cc_final: 0.7435 (mmt90) REVERT: C 764 ARG cc_start: 0.7428 (ttt90) cc_final: 0.6956 (tpt90) REVERT: C 842 PHE cc_start: 0.7537 (m-80) cc_final: 0.6992 (m-80) outliers start: 71 outliers final: 58 residues processed: 610 average time/residue: 0.3053 time to fit residues: 267.8918 Evaluate side-chains 637 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 573 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 462 ASN Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 591 GLN Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 719 ASN Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 462 ASN Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain C residue 382 ARG Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 462 ASN Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 619 MET Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 719 ASN Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 762 CYS Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 837 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 155 optimal weight: 0.0020 chunk 138 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 165 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN B 492 GLN B 643 ASN C 197 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.117060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.099034 restraints weight = 28605.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.102689 restraints weight = 13827.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.105067 restraints weight = 8071.207| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 16782 Z= 0.151 Angle : 0.757 17.928 23079 Z= 0.357 Chirality : 0.049 0.298 2763 Planarity : 0.005 0.044 2880 Dihedral : 10.086 89.242 3246 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.85 % Allowed : 24.90 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.19), residues: 2052 helix: 0.11 (0.23), residues: 555 sheet: 0.36 (0.29), residues: 372 loop : -1.09 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 326 HIS 0.010 0.001 HIS B 225 PHE 0.021 0.001 PHE C 539 TYR 0.032 0.002 TYR A 276 ARG 0.009 0.001 ARG B 764 Details of bonding type rmsd link_NAG-ASN : bond 0.00278 ( 27) link_NAG-ASN : angle 2.23930 ( 81) link_ALPHA1-6 : bond 0.01303 ( 3) link_ALPHA1-6 : angle 3.36282 ( 9) link_BETA1-4 : bond 0.00993 ( 15) link_BETA1-4 : angle 2.46636 ( 45) link_ALPHA1-3 : bond 0.00116 ( 3) link_ALPHA1-3 : angle 3.94935 ( 9) hydrogen bonds : bond 0.04172 ( 482) hydrogen bonds : angle 4.80223 ( 1278) SS BOND : bond 0.00737 ( 27) SS BOND : angle 2.50508 ( 54) covalent geometry : bond 0.00340 (16707) covalent geometry : angle 0.72281 (22881) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 577 time to evaluate : 2.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLN cc_start: 0.7969 (tm-30) cc_final: 0.7452 (tm-30) REVERT: A 158 ILE cc_start: 0.8629 (mt) cc_final: 0.8288 (mm) REVERT: A 194 GLU cc_start: 0.7538 (tp30) cc_final: 0.6914 (tp30) REVERT: A 198 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6660 (mt-10) REVERT: A 211 GLU cc_start: 0.8212 (tp30) cc_final: 0.7832 (tp30) REVERT: A 235 CYS cc_start: 0.5657 (m) cc_final: 0.5395 (m) REVERT: A 251 LEU cc_start: 0.8222 (tp) cc_final: 0.7757 (tt) REVERT: A 252 ILE cc_start: 0.8782 (mt) cc_final: 0.8422 (tt) REVERT: A 318 CYS cc_start: 0.5051 (p) cc_final: 0.4297 (p) REVERT: A 334 LEU cc_start: 0.8632 (mt) cc_final: 0.8406 (mt) REVERT: A 339 GLU cc_start: 0.7771 (tp30) cc_final: 0.7489 (tp30) REVERT: A 382 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8032 (mtt-85) REVERT: A 468 ASP cc_start: 0.7428 (t70) cc_final: 0.6899 (t70) REVERT: A 500 TYR cc_start: 0.8285 (t80) cc_final: 0.7678 (t80) REVERT: A 510 TYR cc_start: 0.7808 (m-80) cc_final: 0.7172 (m-80) REVERT: A 520 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8112 (mtmm) REVERT: A 535 ASN cc_start: 0.7574 (t0) cc_final: 0.7072 (t0) REVERT: A 629 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.7321 (mmt) REVERT: A 651 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7254 (tt0) REVERT: A 653 ARG cc_start: 0.7881 (ttm170) cc_final: 0.7541 (mtt90) REVERT: A 675 MET cc_start: 0.7938 (mmm) cc_final: 0.7554 (mmm) REVERT: A 676 LYS cc_start: 0.8671 (mttt) cc_final: 0.8424 (mttp) REVERT: A 721 GLN cc_start: 0.8021 (tm-30) cc_final: 0.7500 (tm-30) REVERT: A 764 ARG cc_start: 0.7458 (ttt90) cc_final: 0.7084 (tpt90) REVERT: B 147 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7376 (tm-30) REVERT: B 235 CYS cc_start: 0.5847 (m) cc_final: 0.5616 (m) REVERT: B 249 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7315 (mm-30) REVERT: B 252 ILE cc_start: 0.8612 (mt) cc_final: 0.8383 (tp) REVERT: B 273 TRP cc_start: 0.8808 (m-10) cc_final: 0.8536 (m-10) REVERT: B 318 CYS cc_start: 0.5510 (p) cc_final: 0.4764 (p) REVERT: B 495 GLU cc_start: 0.7319 (pt0) cc_final: 0.7026 (pt0) REVERT: B 551 TYR cc_start: 0.8116 (m-80) cc_final: 0.7789 (m-80) REVERT: B 599 ILE cc_start: 0.8474 (tp) cc_final: 0.8240 (mm) REVERT: B 658 TYR cc_start: 0.8405 (m-80) cc_final: 0.8092 (m-80) REVERT: B 676 LYS cc_start: 0.8646 (mttt) cc_final: 0.8383 (mttp) REVERT: B 721 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7810 (tm-30) REVERT: B 722 ILE cc_start: 0.8512 (tt) cc_final: 0.8296 (tt) REVERT: B 742 HIS cc_start: 0.7958 (m90) cc_final: 0.7360 (m90) REVERT: B 776 VAL cc_start: 0.8053 (t) cc_final: 0.7711 (m) REVERT: C 147 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7490 (tm-30) REVERT: C 194 GLU cc_start: 0.7486 (tp30) cc_final: 0.6918 (tp30) REVERT: C 197 ASN cc_start: 0.7522 (m110) cc_final: 0.7035 (m-40) REVERT: C 249 GLU cc_start: 0.7339 (mm-30) cc_final: 0.6718 (mm-30) REVERT: C 251 LEU cc_start: 0.8428 (tp) cc_final: 0.8021 (tt) REVERT: C 252 ILE cc_start: 0.8767 (tp) cc_final: 0.8503 (tt) REVERT: C 295 LYS cc_start: 0.8709 (mptt) cc_final: 0.8427 (mptt) REVERT: C 382 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8086 (ptp-170) REVERT: C 500 TYR cc_start: 0.8227 (t80) cc_final: 0.7873 (t80) REVERT: C 504 LYS cc_start: 0.8058 (ttmm) cc_final: 0.7722 (ttmm) REVERT: C 510 TYR cc_start: 0.7806 (m-80) cc_final: 0.7201 (m-80) REVERT: C 599 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8267 (tt) REVERT: C 601 ASP cc_start: 0.7045 (m-30) cc_final: 0.6617 (m-30) REVERT: C 642 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7898 (mm) REVERT: C 651 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7047 (tt0) REVERT: C 669 GLN cc_start: 0.7655 (mp10) cc_final: 0.7117 (mp10) REVERT: C 676 LYS cc_start: 0.8835 (mttt) cc_final: 0.8573 (mttm) REVERT: C 683 ARG cc_start: 0.7879 (mpt180) cc_final: 0.7431 (mmt90) REVERT: C 764 ARG cc_start: 0.7425 (ttt90) cc_final: 0.6925 (tpt90) REVERT: C 842 PHE cc_start: 0.7528 (m-80) cc_final: 0.6923 (m-80) outliers start: 76 outliers final: 60 residues processed: 611 average time/residue: 0.3544 time to fit residues: 313.2240 Evaluate side-chains 641 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 574 time to evaluate : 1.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 462 ASN Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 591 GLN Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 719 ASN Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 462 ASN Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain C residue 382 ARG Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 462 ASN Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 619 MET Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 719 ASN Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 837 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 35 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 96 optimal weight: 0.0770 chunk 44 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 179 optimal weight: 3.9990 chunk 201 optimal weight: 0.0670 overall best weight: 1.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN A 836 GLN B 600 ASN B 643 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.114703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.096837 restraints weight = 28706.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.100446 restraints weight = 13883.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.102788 restraints weight = 8098.988| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 16782 Z= 0.228 Angle : 0.814 20.767 23079 Z= 0.389 Chirality : 0.051 0.324 2763 Planarity : 0.005 0.044 2880 Dihedral : 10.099 85.300 3246 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.04 % Favored : 93.91 % Rotamer: Outliers : 4.79 % Allowed : 25.54 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.84 (0.19), residues: 2052 helix: 0.03 (0.22), residues: 549 sheet: 0.27 (0.28), residues: 390 loop : -1.15 (0.19), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 720 HIS 0.012 0.001 HIS B 639 PHE 0.021 0.002 PHE C 539 TYR 0.036 0.002 TYR A 276 ARG 0.008 0.001 ARG B 764 Details of bonding type rmsd link_NAG-ASN : bond 0.00413 ( 27) link_NAG-ASN : angle 2.35737 ( 81) link_ALPHA1-6 : bond 0.01222 ( 3) link_ALPHA1-6 : angle 3.55931 ( 9) link_BETA1-4 : bond 0.00977 ( 15) link_BETA1-4 : angle 2.63447 ( 45) link_ALPHA1-3 : bond 0.00269 ( 3) link_ALPHA1-3 : angle 3.94343 ( 9) hydrogen bonds : bond 0.05270 ( 482) hydrogen bonds : angle 5.01867 ( 1278) SS BOND : bond 0.00760 ( 27) SS BOND : angle 2.71102 ( 54) covalent geometry : bond 0.00501 (16707) covalent geometry : angle 0.77911 (22881) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 582 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7404 (tm-30) REVERT: A 158 ILE cc_start: 0.8659 (mt) cc_final: 0.8296 (mm) REVERT: A 194 GLU cc_start: 0.7562 (tp30) cc_final: 0.6959 (tp30) REVERT: A 198 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6713 (mt-10) REVERT: A 211 GLU cc_start: 0.8254 (tp30) cc_final: 0.7845 (tp30) REVERT: A 212 ILE cc_start: 0.8730 (mm) cc_final: 0.8386 (mm) REVERT: A 235 CYS cc_start: 0.5667 (m) cc_final: 0.5419 (m) REVERT: A 251 LEU cc_start: 0.8246 (tp) cc_final: 0.7773 (tt) REVERT: A 252 ILE cc_start: 0.8802 (mt) cc_final: 0.8412 (tt) REVERT: A 318 CYS cc_start: 0.5136 (p) cc_final: 0.4430 (p) REVERT: A 334 LEU cc_start: 0.8688 (mt) cc_final: 0.8473 (mt) REVERT: A 339 GLU cc_start: 0.7798 (tp30) cc_final: 0.7487 (tp30) REVERT: A 382 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.8069 (mtt-85) REVERT: A 468 ASP cc_start: 0.7460 (t70) cc_final: 0.6933 (t70) REVERT: A 510 TYR cc_start: 0.7931 (m-80) cc_final: 0.7308 (m-80) REVERT: A 520 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8110 (mtmm) REVERT: A 535 ASN cc_start: 0.7638 (t0) cc_final: 0.7133 (t0) REVERT: A 604 LEU cc_start: 0.8787 (mp) cc_final: 0.8526 (mm) REVERT: A 629 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.7431 (mmt) REVERT: A 651 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7217 (tt0) REVERT: A 653 ARG cc_start: 0.7942 (ttm170) cc_final: 0.7592 (mtt90) REVERT: A 665 GLN cc_start: 0.8544 (tt0) cc_final: 0.8320 (tt0) REVERT: A 675 MET cc_start: 0.7942 (mmm) cc_final: 0.7554 (mmm) REVERT: A 676 LYS cc_start: 0.8694 (mttt) cc_final: 0.8281 (mttm) REVERT: A 721 GLN cc_start: 0.8032 (tm-30) cc_final: 0.7449 (tm-30) REVERT: A 764 ARG cc_start: 0.7459 (ttt90) cc_final: 0.7108 (tpt90) REVERT: A 803 SER cc_start: 0.8543 (t) cc_final: 0.7892 (p) REVERT: B 147 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7300 (tm-30) REVERT: B 249 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7318 (mm-30) REVERT: B 252 ILE cc_start: 0.8696 (mt) cc_final: 0.8345 (tp) REVERT: B 273 TRP cc_start: 0.8810 (m-10) cc_final: 0.8559 (m-10) REVERT: B 318 CYS cc_start: 0.5297 (p) cc_final: 0.4627 (p) REVERT: B 495 GLU cc_start: 0.7391 (pt0) cc_final: 0.7107 (pt0) REVERT: B 551 TYR cc_start: 0.8142 (m-80) cc_final: 0.7803 (m-80) REVERT: B 599 ILE cc_start: 0.8477 (tp) cc_final: 0.8234 (mm) REVERT: B 635 VAL cc_start: 0.8099 (m) cc_final: 0.7805 (t) REVERT: B 658 TYR cc_start: 0.8416 (m-80) cc_final: 0.8133 (m-80) REVERT: B 676 LYS cc_start: 0.8656 (mttt) cc_final: 0.8394 (mttp) REVERT: B 721 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7913 (tm-30) REVERT: B 742 HIS cc_start: 0.7941 (m90) cc_final: 0.7373 (m90) REVERT: B 776 VAL cc_start: 0.8068 (t) cc_final: 0.7733 (m) REVERT: C 147 GLN cc_start: 0.8080 (tm-30) cc_final: 0.7543 (tm-30) REVERT: C 194 GLU cc_start: 0.7507 (tp30) cc_final: 0.6969 (tp30) REVERT: C 251 LEU cc_start: 0.8376 (tp) cc_final: 0.8004 (tt) REVERT: C 252 ILE cc_start: 0.8816 (tp) cc_final: 0.8563 (tt) REVERT: C 295 LYS cc_start: 0.8726 (mptt) cc_final: 0.8389 (mptt) REVERT: C 382 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8025 (mtt-85) REVERT: C 510 TYR cc_start: 0.7929 (m-80) cc_final: 0.7243 (m-80) REVERT: C 599 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8328 (tp) REVERT: C 601 ASP cc_start: 0.7061 (m-30) cc_final: 0.6637 (m-30) REVERT: C 604 LEU cc_start: 0.8649 (mp) cc_final: 0.8392 (mm) REVERT: C 635 VAL cc_start: 0.8011 (m) cc_final: 0.7761 (t) REVERT: C 642 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7934 (mm) REVERT: C 653 ARG cc_start: 0.8072 (ttm170) cc_final: 0.7771 (mtt90) REVERT: C 669 GLN cc_start: 0.7667 (mp10) cc_final: 0.7129 (mp10) REVERT: C 672 ASP cc_start: 0.7998 (m-30) cc_final: 0.7729 (m-30) REVERT: C 676 LYS cc_start: 0.8867 (mttt) cc_final: 0.8432 (mttm) REVERT: C 683 ARG cc_start: 0.7904 (mpt180) cc_final: 0.7480 (mmt90) REVERT: C 721 GLN cc_start: 0.7728 (tt0) cc_final: 0.7220 (tp40) REVERT: C 764 ARG cc_start: 0.7400 (ttt90) cc_final: 0.6935 (tpt90) REVERT: C 842 PHE cc_start: 0.7574 (m-80) cc_final: 0.6933 (m-80) outliers start: 75 outliers final: 62 residues processed: 615 average time/residue: 0.3029 time to fit residues: 267.3813 Evaluate side-chains 640 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 570 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 462 ASN Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 591 GLN Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 719 ASN Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 462 ASN Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 325 LYS Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain C residue 382 ARG Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 462 ASN Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 619 MET Chi-restraints excluded: chain C residue 629 MET Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 719 ASN Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 763 ARG Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 837 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 206 optimal weight: 10.0000 chunk 203 optimal weight: 0.5980 chunk 135 optimal weight: 0.0370 chunk 146 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 178 optimal weight: 0.3980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 639 HIS B 643 ASN C 197 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.116944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.099086 restraints weight = 28538.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.102713 restraints weight = 13828.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.105070 restraints weight = 8092.618| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 16782 Z= 0.131 Angle : 0.770 18.350 23079 Z= 0.361 Chirality : 0.049 0.305 2763 Planarity : 0.005 0.044 2880 Dihedral : 9.559 79.441 3246 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.92 % Favored : 95.03 % Rotamer: Outliers : 3.77 % Allowed : 26.76 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.19), residues: 2052 helix: 0.10 (0.23), residues: 552 sheet: 0.40 (0.28), residues: 390 loop : -1.12 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 326 HIS 0.007 0.001 HIS B 225 PHE 0.020 0.001 PHE A 396 TYR 0.027 0.002 TYR A 276 ARG 0.009 0.001 ARG A 764 Details of bonding type rmsd link_NAG-ASN : bond 0.00300 ( 27) link_NAG-ASN : angle 2.18268 ( 81) link_ALPHA1-6 : bond 0.01564 ( 3) link_ALPHA1-6 : angle 3.20236 ( 9) link_BETA1-4 : bond 0.01014 ( 15) link_BETA1-4 : angle 2.55770 ( 45) link_ALPHA1-3 : bond 0.00086 ( 3) link_ALPHA1-3 : angle 4.04768 ( 9) hydrogen bonds : bond 0.03784 ( 482) hydrogen bonds : angle 4.75427 ( 1278) SS BOND : bond 0.00859 ( 27) SS BOND : angle 2.86136 ( 54) covalent geometry : bond 0.00303 (16707) covalent geometry : angle 0.73372 (22881) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6672.50 seconds wall clock time: 117 minutes 30.40 seconds (7050.40 seconds total)