Starting phenix.real_space_refine on Tue Jan 21 08:26:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rm0_19347/01_2025/8rm0_19347.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rm0_19347/01_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_19347/01_2025/8rm0_19347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rm0_19347/01_2025/8rm0_19347.map" model { file = "/net/cci-nas-00/data/ceres_data/8rm0_19347/01_2025/8rm0_19347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rm0_19347/01_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 9.68, per 1000 atoms: 0.59 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: 4.81 Conformation dependent library (CDL) restraints added in 2.2 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: 2.27 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: 5.71 Time building geometry restraints manager: 5.51 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: 11.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 38.670 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.060 ------------------------------------------------------------------------------- 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 16707 Z= 0.272 Angle : 0.725 7.517 22881 Z= 0.375 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 *********************** 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 : 1.655 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: 0.3344 time to fit residues: 330.7046 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 : 1.840 ------------------------------------------------------------------------------- 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 = 31)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.101819 restraints weight = 29065.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.105422 restraints weight = 13877.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.107756 restraints weight = 8078.583| |-----------------------------------------------------------------------------| 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 16707 Z= 0.201 Angle : 0.678 10.310 22881 Z= 0.334 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 *********************** 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 : 1.782 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: 0.7613 (t80) cc_final: 0.7316 (t80) REVERT: A 151 TYR cc_start: 0.7455 (p90) cc_final: 0.7159 (p90) REVERT: A 158 ILE cc_start: 0.8568 (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: 0.7394 (tp30) cc_final: 0.6735 (tp30) REVERT: A 198 GLU cc_start: 0.7052 (mt-10) cc_final: 0.6456 (mt-10) REVERT: A 211 GLU cc_start: 0.8122 (tp30) cc_final: 0.7622 (tp30) REVERT: A 227 LYS cc_start: 0.8597 (tptm) cc_final: 0.8327 (tppt) REVERT: A 249 GLU cc_start: 0.7516 (mm-30) cc_final: 0.6857 (mm-30) REVERT: A 251 LEU cc_start: 0.8325 (tp) cc_final: 0.7809 (tt) REVERT: A 252 ILE cc_start: 0.8776 (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: 0.7650 (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: 0.7191 (t70) cc_final: 0.6747 (t70) REVERT: A 495 GLU cc_start: 0.6933 (pt0) cc_final: 0.6708 (pt0) REVERT: A 500 TYR cc_start: 0.8327 (t80) cc_final: 0.7986 (t80) REVERT: A 510 TYR cc_start: 0.7615 (m-80) cc_final: 0.7172 (m-80) REVERT: A 519 LEU cc_start: 0.8239 (mm) cc_final: 0.7926 (mp) REVERT: A 533 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.7856 (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: 0.7131 (tt0) REVERT: A 599 ILE cc_start: 0.8444 (tp) cc_final: 0.8222 (mm) REVERT: A 612 ARG cc_start: 0.7429 (tpp80) cc_final: 0.6994 (mmm-85) REVERT: A 624 HIS cc_start: 0.6344 (m-70) cc_final: 0.6088 (m-70) REVERT: A 652 ARG cc_start: 0.7817 (mtp85) cc_final: 0.7461 (mtp-110) REVERT: A 675 MET cc_start: 0.7990 (mmm) cc_final: 0.7582 (mmm) REVERT: A 676 LYS cc_start: 0.8667 (mttt) cc_final: 0.8328 (mttm) REVERT: A 702 GLU cc_start: 0.7367 (mt-10) cc_final: 0.7017 (mt-10) REVERT: A 724 ASN cc_start: 0.8081 (t0) cc_final: 0.7830 (t0) REVERT: A 803 SER cc_start: 0.8149 (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: 0.6787 (tp30) REVERT: B 198 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6389 (mt-10) REVERT: B 206 VAL cc_start: 0.8233 (m) cc_final: 0.7870 (p) REVERT: B 252 ILE cc_start: 0.8705 (mt) cc_final: 0.8381 (tp) REVERT: B 258 LEU cc_start: 0.8722 (mt) cc_final: 0.8504 (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: 0.7639 (mmm) cc_final: 0.7429 (mmm) REVERT: B 338 ASN cc_start: 0.7673 (t0) cc_final: 0.7365 (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: 0.8465 (p) REVERT: B 356 ARG cc_start: 0.7871 (tpp-160) cc_final: 0.7514 (tpp-160) REVERT: B 468 ASP cc_start: 0.7115 (t70) cc_final: 0.6649 (t0) REVERT: B 495 GLU cc_start: 0.7190 (pt0) cc_final: 0.6972 (pt0) REVERT: B 535 ASN cc_start: 0.7201 (t0) cc_final: 0.6779 (t0) REVERT: B 551 TYR cc_start: 0.8052 (m-80) cc_final: 0.7717 (m-80) REVERT: B 591 GLN cc_start: 0.7312 (tt0) cc_final: 0.7093 (tt0) REVERT: B 611 LEU cc_start: 0.7225 (tp) cc_final: 0.6728 (tp) REVERT: B 635 VAL cc_start: 0.7720 (m) cc_final: 0.7492 (p) REVERT: B 658 TYR cc_start: 0.8390 (m-80) cc_final: 0.8079 (m-80) REVERT: B 665 GLN cc_start: 0.8409 (tt0) cc_final: 0.7956 (tm-30) REVERT: B 667 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7995 (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: 0.7843 (m) REVERT: B 810 TYR cc_start: 0.7922 (m-80) cc_final: 0.7658 (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: 0.6921 (mtt) cc_final: 0.6323 (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: 0.7664 (mm-30) cc_final: 0.7391 (mm-30) REVERT: C 451 HIS cc_start: 0.7842 (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: 0.7565 (m-80) cc_final: 0.7124 (m-80) REVERT: C 544 ASP cc_start: 0.8318 (t70) cc_final: 0.7963 (t70) REVERT: C 591 GLN cc_start: 0.7231 (tt0) cc_final: 0.7010 (tt0) REVERT: C 601 ASP cc_start: 0.7107 (m-30) cc_final: 0.6794 (m-30) REVERT: C 646 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7498 (tmm-80) REVERT: C 654 ILE cc_start: 0.8537 (mt) cc_final: 0.7927 (mt) REVERT: C 656 TRP cc_start: 0.8522 (m100) cc_final: 0.8137 (m-90) REVERT: C 665 GLN cc_start: 0.8355 (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: 0.7281 (ptp-170) cc_final: 0.7072 (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: 0.7273 (m-80) outliers start: 29 outliers final: 17 residues processed: 621 average time/residue: 0.3120 time to fit residues: 275.0734 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 : 1.781 ------------------------------------------------------------------------------- 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: 0.0170 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: 1.5824 ------------------------------------------------------------------------------- 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 451 HIS B 637 HIS C 600 ASN C 636 GLN C 637 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.114527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.096681 restraints weight = 28820.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.100200 restraints weight = 14074.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.102536 restraints weight = 8301.697| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 16707 Z= 0.332 Angle : 0.738 11.685 22881 Z= 0.365 Chirality : 0.051 0.317 2763 Planarity : 0.006 0.055 2880 Dihedral : 11.588 90.982 3246 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.53 % Allowed : 16.92 % Favored : 78.54 % 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: -0.91 (0.19), residues: 2052 helix: -0.14 (0.22), residues: 555 sheet: -0.11 (0.27), residues: 414 loop : -1.01 (0.19), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 326 HIS 0.013 0.002 HIS C 639 PHE 0.017 0.002 PHE B 396 TYR 0.024 0.002 TYR B 360 ARG 0.007 0.001 ARG B 407 *********************** 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 658 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 587 time to evaluate : 1.731 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: A 150 PHE cc_start: 0.7626 (t80) cc_final: 0.7290 (t80) REVERT: A 158 ILE cc_start: 0.8671 (mt) cc_final: 0.8297 (mm) REVERT: A 194 GLU cc_start: 0.7536 (tp30) cc_final: 0.6850 (tp30) REVERT: A 198 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6569 (mt-10) REVERT: A 211 GLU cc_start: 0.8252 (tp30) cc_final: 0.7869 (tp30) REVERT: A 251 LEU cc_start: 0.8242 (tp) cc_final: 0.7729 (tt) REVERT: A 252 ILE cc_start: 0.8812 (mt) cc_final: 0.8370 (tp) REVERT: A 258 LEU cc_start: 0.8691 (mt) cc_final: 0.8428 (mm) REVERT: A 334 LEU cc_start: 0.8733 (mt) cc_final: 0.8475 (mt) REVERT: A 438 ARG cc_start: 0.7505 (mmm160) cc_final: 0.7074 (tpt90) REVERT: A 468 ASP cc_start: 0.7337 (t70) cc_final: 0.6829 (t70) REVERT: A 495 GLU cc_start: 0.6953 (pt0) cc_final: 0.6726 (pt0) REVERT: A 500 TYR cc_start: 0.8414 (t80) cc_final: 0.7908 (t80) REVERT: A 510 TYR cc_start: 0.7920 (m-80) cc_final: 0.7308 (m-80) REVERT: A 540 VAL cc_start: 0.8427 (p) cc_final: 0.8004 (m) REVERT: A 591 GLN cc_start: 0.7253 (tt0) cc_final: 0.7014 (tt0) REVERT: A 624 HIS cc_start: 0.6336 (m-70) cc_final: 0.5999 (m-70) REVERT: A 635 VAL cc_start: 0.7947 (m) cc_final: 0.7603 (p) REVERT: A 636 GLN cc_start: 0.7810 (tp40) cc_final: 0.7544 (tp40) REVERT: A 653 ARG cc_start: 0.7940 (ttm170) cc_final: 0.7615 (mtt90) REVERT: A 665 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8297 (tt0) REVERT: A 675 MET cc_start: 0.7999 (mmm) cc_final: 0.7617 (mmm) REVERT: A 676 LYS cc_start: 0.8725 (mttt) cc_final: 0.8336 (mttm) REVERT: A 683 ARG cc_start: 0.7925 (mmt-90) cc_final: 0.7675 (mmt90) REVERT: A 702 GLU cc_start: 0.7250 (mt-10) cc_final: 0.6960 (mt-10) REVERT: A 803 SER cc_start: 0.8276 (t) cc_final: 0.7779 (p) REVERT: B 206 VAL cc_start: 0.8283 (m) cc_final: 0.8018 (p) REVERT: B 249 GLU cc_start: 0.7640 (mm-30) cc_final: 0.6748 (mm-30) REVERT: B 252 ILE cc_start: 0.8762 (mt) cc_final: 0.8323 (tp) REVERT: B 273 TRP cc_start: 0.8818 (m-10) cc_final: 0.8492 (m-10) REVERT: B 295 LYS cc_start: 0.8874 (mptt) cc_final: 0.8541 (mptt) REVERT: B 318 CYS cc_start: 0.5416 (OUTLIER) cc_final: 0.5073 (p) REVERT: B 338 ASN cc_start: 0.7812 (t0) cc_final: 0.7459 (t0) REVERT: B 339 GLU cc_start: 0.7728 (tp30) cc_final: 0.7450 (tp30) REVERT: B 340 LEU cc_start: 0.8699 (tp) cc_final: 0.8488 (tt) REVERT: B 341 THR cc_start: 0.8733 (m) cc_final: 0.8387 (p) REVERT: B 347 LEU cc_start: 0.8428 (mt) cc_final: 0.8208 (mp) REVERT: B 356 ARG cc_start: 0.7875 (tpp-160) cc_final: 0.7563 (tpp-160) REVERT: B 386 VAL cc_start: 0.8764 (m) cc_final: 0.8510 (t) REVERT: B 468 ASP cc_start: 0.7246 (t70) cc_final: 0.6755 (t0) REVERT: B 495 GLU cc_start: 0.7338 (pt0) cc_final: 0.7053 (pt0) REVERT: B 504 LYS cc_start: 0.8081 (mtpp) cc_final: 0.7866 (mtpp) REVERT: B 520 LYS cc_start: 0.8263 (mmmm) cc_final: 0.7892 (mtpp) REVERT: B 551 TYR cc_start: 0.8089 (m-80) cc_final: 0.7761 (m-80) REVERT: B 611 LEU cc_start: 0.7393 (tp) cc_final: 0.6935 (tp) REVERT: B 658 TYR cc_start: 0.8460 (m-80) cc_final: 0.8183 (m-80) REVERT: B 665 GLN cc_start: 0.8381 (tt0) cc_final: 0.7978 (tm-30) REVERT: B 669 GLN cc_start: 0.8014 (mt0) cc_final: 0.7802 (mm110) REVERT: B 676 LYS cc_start: 0.8685 (mttt) cc_final: 0.8405 (mttp) REVERT: B 776 VAL cc_start: 0.8044 (t) cc_final: 0.7749 (m) REVERT: B 810 TYR cc_start: 0.8058 (m-80) cc_final: 0.7816 (m-80) REVERT: C 180 ASN cc_start: 0.7730 (m110) cc_final: 0.7506 (m110) REVERT: C 193 THR cc_start: 0.8085 (t) cc_final: 0.7835 (t) REVERT: C 194 GLU cc_start: 0.7472 (tp30) cc_final: 0.6921 (tp30) REVERT: C 197 ASN cc_start: 0.7534 (m110) cc_final: 0.7160 (m-40) REVERT: C 198 GLU cc_start: 0.6921 (mt-10) cc_final: 0.6377 (mt-10) REVERT: C 252 ILE cc_start: 0.8816 (tp) cc_final: 0.8571 (tt) REVERT: C 295 LYS cc_start: 0.8687 (mptt) cc_final: 0.8408 (mptt) REVERT: C 305 LYS cc_start: 0.8263 (pttp) cc_final: 0.8035 (pttp) REVERT: C 384 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7409 (mm-30) REVERT: C 386 VAL cc_start: 0.8753 (m) cc_final: 0.8481 (t) REVERT: C 468 ASP cc_start: 0.7359 (t70) cc_final: 0.6842 (t70) REVERT: C 495 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6838 (pm20) REVERT: C 500 TYR cc_start: 0.8328 (t80) cc_final: 0.7819 (t80) REVERT: C 510 TYR cc_start: 0.7956 (m-80) cc_final: 0.7296 (m-80) REVERT: C 516 LEU cc_start: 0.7845 (tt) cc_final: 0.7559 (mt) REVERT: C 544 ASP cc_start: 0.8311 (t70) cc_final: 0.8049 (t0) REVERT: C 591 GLN cc_start: 0.7214 (tt0) cc_final: 0.7001 (tt0) REVERT: C 601 ASP cc_start: 0.7127 (m-30) cc_final: 0.6693 (m-30) REVERT: C 611 LEU cc_start: 0.7644 (tp) cc_final: 0.7151 (tp) REVERT: C 646 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7442 (tmm-80) REVERT: C 654 ILE cc_start: 0.8553 (mt) cc_final: 0.8026 (mt) REVERT: C 656 TRP cc_start: 0.8598 (m100) cc_final: 0.8217 (m-90) REVERT: C 669 GLN cc_start: 0.7762 (mp10) cc_final: 0.7445 (mp10) REVERT: C 675 MET cc_start: 0.8030 (mmm) cc_final: 0.7815 (mmm) REVERT: C 676 LYS cc_start: 0.8849 (mttt) cc_final: 0.8574 (mttm) REVERT: C 683 ARG cc_start: 0.7857 (mpt180) cc_final: 0.7393 (mmt90) REVERT: C 711 ILE cc_start: 0.8754 (pt) cc_final: 0.8544 (mp) REVERT: C 721 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7427 (tp-100) REVERT: C 773 VAL cc_start: 0.8704 (t) cc_final: 0.8454 (m) REVERT: C 842 PHE cc_start: 0.7695 (m-10) cc_final: 0.7449 (m-80) outliers start: 71 outliers final: 44 residues processed: 612 average time/residue: 0.3118 time to fit residues: 274.4455 Evaluate side-chains 623 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 574 time to evaluate : 1.796 ------------------------------------------------------------------------------- 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 358 LEU Chi-restraints excluded: chain A residue 390 ASN 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 650 MET 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 A residue 699 THR Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 279 ILE 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 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 741 SER Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 462 ASN 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 617 THR Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 646 ARG 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: 2.9990 chunk 122 optimal weight: 0.5980 chunk 185 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 132 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 88 optimal weight: 0.2980 chunk 194 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.116960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.099126 restraints weight = 28848.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.102684 restraints weight = 14056.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.104986 restraints weight = 8269.099| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 16707 Z= 0.207 Angle : 0.679 14.809 22881 Z= 0.330 Chirality : 0.048 0.289 2763 Planarity : 0.005 0.049 2880 Dihedral : 11.065 93.439 3246 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.15 % Allowed : 19.92 % Favored : 75.93 % 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: -0.77 (0.19), residues: 2052 helix: 0.06 (0.23), residues: 552 sheet: 0.13 (0.28), residues: 399 loop : -1.03 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 326 HIS 0.006 0.001 HIS C 639 PHE 0.018 0.002 PHE B 396 TYR 0.022 0.001 TYR C 706 ARG 0.006 0.001 ARG B 407 *********************** 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 646 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 581 time to evaluate : 2.023 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: A 150 PHE cc_start: 0.7621 (t80) cc_final: 0.7350 (t80) REVERT: A 158 ILE cc_start: 0.8619 (mt) cc_final: 0.8323 (mm) REVERT: A 194 GLU cc_start: 0.7492 (tp30) cc_final: 0.6863 (tp30) REVERT: A 198 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6509 (mt-10) REVERT: A 211 GLU cc_start: 0.8186 (tp30) cc_final: 0.7817 (tp30) REVERT: A 251 LEU cc_start: 0.8199 (tp) cc_final: 0.7652 (tt) REVERT: A 252 ILE cc_start: 0.8763 (mt) cc_final: 0.8367 (tp) REVERT: A 258 LEU cc_start: 0.8671 (mt) cc_final: 0.8433 (mm) REVERT: A 318 CYS cc_start: 0.5434 (OUTLIER) cc_final: 0.4788 (p) REVERT: A 334 LEU cc_start: 0.8646 (mt) cc_final: 0.8402 (mt) REVERT: A 438 ARG cc_start: 0.7499 (mmm160) cc_final: 0.6848 (tpt90) REVERT: A 468 ASP cc_start: 0.7287 (t70) cc_final: 0.6812 (t70) REVERT: A 495 GLU cc_start: 0.6871 (pt0) cc_final: 0.6663 (pt0) REVERT: A 500 TYR cc_start: 0.8363 (t80) cc_final: 0.7863 (t80) REVERT: A 510 TYR cc_start: 0.7738 (m-80) cc_final: 0.7179 (m-80) REVERT: A 520 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8082 (mtmm) REVERT: A 591 GLN cc_start: 0.7217 (tt0) cc_final: 0.7005 (tt0) REVERT: A 624 HIS cc_start: 0.6262 (m-70) cc_final: 0.6023 (m-70) REVERT: A 665 GLN cc_start: 0.8571 (tt0) cc_final: 0.8268 (tt0) REVERT: A 675 MET cc_start: 0.7944 (mmm) cc_final: 0.7519 (mmm) REVERT: A 676 LYS cc_start: 0.8682 (mttt) cc_final: 0.8305 (mttm) REVERT: A 702 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6929 (mt-10) REVERT: B 206 VAL cc_start: 0.8293 (m) cc_final: 0.8049 (p) REVERT: B 249 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7108 (mm-30) REVERT: B 252 ILE cc_start: 0.8708 (mt) cc_final: 0.8322 (tp) REVERT: B 273 TRP cc_start: 0.8834 (m-10) cc_final: 0.8503 (m-10) REVERT: B 338 ASN cc_start: 0.7803 (t0) cc_final: 0.7435 (t0) REVERT: B 339 GLU cc_start: 0.7677 (tp30) cc_final: 0.7450 (tp30) REVERT: B 341 THR cc_start: 0.8714 (m) cc_final: 0.8396 (p) REVERT: B 356 ARG cc_start: 0.7843 (tpp-160) cc_final: 0.7539 (tpp-160) REVERT: B 408 TYR cc_start: 0.7687 (p90) cc_final: 0.7467 (p90) REVERT: B 495 GLU cc_start: 0.7275 (pt0) cc_final: 0.7015 (pt0) REVERT: B 520 LYS cc_start: 0.8277 (mmmm) cc_final: 0.7945 (mtpp) REVERT: B 551 TYR cc_start: 0.8076 (m-80) cc_final: 0.7743 (m-80) REVERT: B 611 LEU cc_start: 0.7381 (tp) cc_final: 0.6927 (tp) REVERT: B 658 TYR cc_start: 0.8460 (m-80) cc_final: 0.8176 (m-80) REVERT: B 665 GLN cc_start: 0.8404 (tt0) cc_final: 0.7979 (tm-30) REVERT: B 676 LYS cc_start: 0.8694 (mttt) cc_final: 0.8424 (mttp) REVERT: B 707 TYR cc_start: 0.8273 (m-10) cc_final: 0.8054 (m-10) REVERT: B 776 VAL cc_start: 0.8062 (t) cc_final: 0.7755 (m) REVERT: B 810 TYR cc_start: 0.8053 (m-80) cc_final: 0.7824 (m-80) REVERT: B 825 VAL cc_start: 0.8222 (OUTLIER) cc_final: 0.7940 (p) REVERT: C 193 THR cc_start: 0.7994 (t) cc_final: 0.7768 (t) REVERT: C 194 GLU cc_start: 0.7343 (tp30) cc_final: 0.6794 (tp30) REVERT: C 197 ASN cc_start: 0.7430 (m110) cc_final: 0.7140 (m-40) REVERT: C 198 GLU cc_start: 0.6883 (mt-10) cc_final: 0.6371 (mt-10) REVERT: C 211 GLU cc_start: 0.7954 (tp30) cc_final: 0.7725 (tp30) REVERT: C 295 LYS cc_start: 0.8699 (mptt) cc_final: 0.8390 (mptt) REVERT: C 305 LYS cc_start: 0.8230 (pttp) cc_final: 0.8021 (pttp) REVERT: C 384 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7361 (mm-30) REVERT: C 468 ASP cc_start: 0.7315 (t70) cc_final: 0.6798 (t70) REVERT: C 500 TYR cc_start: 0.8230 (t80) cc_final: 0.7530 (t80) REVERT: C 504 LYS cc_start: 0.8090 (ttmm) cc_final: 0.7750 (ttmm) REVERT: C 510 TYR cc_start: 0.7731 (m-80) cc_final: 0.7223 (m-80) REVERT: C 516 LEU cc_start: 0.7723 (tt) cc_final: 0.7500 (mt) REVERT: C 544 ASP cc_start: 0.8316 (t70) cc_final: 0.8090 (t0) REVERT: C 599 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8297 (mm) REVERT: C 601 ASP cc_start: 0.7116 (m-30) cc_final: 0.6858 (m-30) REVERT: C 642 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7969 (mm) REVERT: C 648 MET cc_start: 0.7986 (mmt) cc_final: 0.7505 (mmp) REVERT: C 651 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7240 (tt0) REVERT: C 653 ARG cc_start: 0.8000 (ttm170) cc_final: 0.7644 (mtm-85) REVERT: C 654 ILE cc_start: 0.8536 (mt) cc_final: 0.7973 (mt) REVERT: C 656 TRP cc_start: 0.8552 (m100) cc_final: 0.8151 (m-90) REVERT: C 669 GLN cc_start: 0.7622 (mp10) cc_final: 0.7173 (mp10) REVERT: C 676 LYS cc_start: 0.8851 (mttt) cc_final: 0.8556 (mttm) REVERT: C 683 ARG cc_start: 0.7861 (mpt180) cc_final: 0.7641 (mpt180) REVERT: C 842 PHE cc_start: 0.7640 (m-10) cc_final: 0.7421 (m-80) outliers start: 65 outliers final: 42 residues processed: 606 average time/residue: 0.3138 time to fit residues: 269.7650 Evaluate side-chains 609 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 562 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 231 GLU 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 520 LYS 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 625 ASP Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 699 THR 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 375 SER Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 488 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 811 LEU Chi-restraints excluded: chain B residue 825 VAL 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 387 LEU Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 533 MET 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 759 LEU 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: 3.9990 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 0.0000 chunk 76 optimal weight: 0.9990 chunk 131 optimal weight: 8.9990 chunk 59 optimal weight: 0.0870 chunk 58 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 643 ASN B 492 GLN B 535 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.115809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.097915 restraints weight = 29426.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.101497 restraints weight = 14228.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.103853 restraints weight = 8338.650| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 16707 Z= 0.238 Angle : 0.695 18.563 22881 Z= 0.339 Chirality : 0.049 0.296 2763 Planarity : 0.005 0.047 2880 Dihedral : 10.753 94.384 3246 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.92 % Allowed : 20.56 % Favored : 74.52 % 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: -0.76 (0.19), residues: 2052 helix: 0.13 (0.23), residues: 552 sheet: 0.16 (0.29), residues: 381 loop : -1.05 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 326 HIS 0.009 0.001 HIS C 639 PHE 0.017 0.002 PHE A 396 TYR 0.033 0.002 TYR A 276 ARG 0.008 0.001 ARG B 407 *********************** 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 665 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 588 time to evaluate : 1.677 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: A 147 GLN cc_start: 0.8061 (tm-30) cc_final: 0.7706 (tm-30) REVERT: A 150 PHE cc_start: 0.7619 (t80) cc_final: 0.7368 (t80) REVERT: A 194 GLU cc_start: 0.7507 (tp30) cc_final: 0.6874 (tp30) REVERT: A 198 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6538 (mt-10) REVERT: A 211 GLU cc_start: 0.8240 (tp30) cc_final: 0.7853 (tp30) REVERT: A 251 LEU cc_start: 0.8179 (tp) cc_final: 0.7673 (tt) REVERT: A 252 ILE cc_start: 0.8755 (mt) cc_final: 0.8381 (tp) REVERT: A 334 LEU cc_start: 0.8665 (mt) cc_final: 0.8416 (mt) REVERT: A 339 GLU cc_start: 0.7704 (tp30) cc_final: 0.7504 (tp30) REVERT: A 382 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8026 (mtt-85) REVERT: A 438 ARG cc_start: 0.7544 (mmm160) cc_final: 0.7054 (tpt90) REVERT: A 468 ASP cc_start: 0.7348 (t70) cc_final: 0.6828 (t70) REVERT: A 500 TYR cc_start: 0.8409 (t80) cc_final: 0.7799 (t80) REVERT: A 510 TYR cc_start: 0.7804 (m-80) cc_final: 0.7183 (m-80) REVERT: A 516 LEU cc_start: 0.7825 (mt) cc_final: 0.7597 (mp) REVERT: A 591 GLN cc_start: 0.7162 (tt0) cc_final: 0.6947 (tt0) REVERT: A 624 HIS cc_start: 0.6303 (m-70) cc_final: 0.6088 (m-70) REVERT: A 653 ARG cc_start: 0.7803 (ttm170) cc_final: 0.7596 (mtt90) REVERT: A 672 ASP cc_start: 0.7992 (m-30) cc_final: 0.7768 (m-30) REVERT: A 675 MET cc_start: 0.7906 (mmm) cc_final: 0.7542 (mmm) REVERT: A 676 LYS cc_start: 0.8671 (mttt) cc_final: 0.8304 (mttm) REVERT: A 702 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6980 (mt-10) REVERT: B 206 VAL cc_start: 0.8290 (m) cc_final: 0.8060 (p) REVERT: B 249 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7238 (mm-30) REVERT: B 252 ILE cc_start: 0.8689 (mt) cc_final: 0.8365 (tp) REVERT: B 273 TRP cc_start: 0.8823 (m-10) cc_final: 0.8542 (m-10) REVERT: B 338 ASN cc_start: 0.7843 (t0) cc_final: 0.7481 (t0) REVERT: B 339 GLU cc_start: 0.7751 (tp30) cc_final: 0.7542 (tp30) REVERT: B 341 THR cc_start: 0.8708 (m) cc_final: 0.8354 (p) REVERT: B 386 VAL cc_start: 0.8696 (m) cc_final: 0.8438 (t) REVERT: B 495 GLU cc_start: 0.7326 (pt0) cc_final: 0.7045 (pt0) REVERT: B 520 LYS cc_start: 0.8277 (mmmm) cc_final: 0.7953 (mtpp) REVERT: B 551 TYR cc_start: 0.8096 (m-80) cc_final: 0.7767 (m-80) REVERT: B 611 LEU cc_start: 0.7490 (tp) cc_final: 0.6816 (tp) REVERT: B 635 VAL cc_start: 0.7970 (m) cc_final: 0.7712 (p) REVERT: B 658 TYR cc_start: 0.8467 (m-80) cc_final: 0.8159 (m-80) REVERT: B 665 GLN cc_start: 0.8389 (tt0) cc_final: 0.8008 (tm-30) REVERT: B 676 LYS cc_start: 0.8686 (mttt) cc_final: 0.8414 (mttp) REVERT: B 776 VAL cc_start: 0.8065 (t) cc_final: 0.7771 (m) REVERT: B 810 TYR cc_start: 0.8100 (m-80) cc_final: 0.7856 (m-80) REVERT: C 193 THR cc_start: 0.8076 (t) cc_final: 0.7771 (t) REVERT: C 194 GLU cc_start: 0.7469 (tp30) cc_final: 0.6916 (tp30) REVERT: C 197 ASN cc_start: 0.7478 (m110) cc_final: 0.7182 (m-40) REVERT: C 198 GLU cc_start: 0.6883 (mt-10) cc_final: 0.6517 (mt-10) REVERT: C 211 GLU cc_start: 0.8022 (tp30) cc_final: 0.7738 (tp30) REVERT: C 251 LEU cc_start: 0.8377 (tp) cc_final: 0.8025 (tt) REVERT: C 295 LYS cc_start: 0.8697 (mptt) cc_final: 0.8431 (mptt) REVERT: C 305 LYS cc_start: 0.8232 (pttp) cc_final: 0.8020 (pttp) REVERT: C 356 ARG cc_start: 0.7485 (tpp-160) cc_final: 0.7284 (tpp-160) REVERT: C 382 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7971 (mtt-85) REVERT: C 468 ASP cc_start: 0.7344 (t70) cc_final: 0.6819 (t70) REVERT: C 500 TYR cc_start: 0.8287 (t80) cc_final: 0.8006 (t80) REVERT: C 504 LYS cc_start: 0.8097 (ttmm) cc_final: 0.7824 (ttmm) REVERT: C 510 TYR cc_start: 0.7770 (m-80) cc_final: 0.7210 (m-80) REVERT: C 516 LEU cc_start: 0.7748 (tt) cc_final: 0.7540 (mt) REVERT: C 526 THR cc_start: 0.8671 (t) cc_final: 0.8429 (p) REVERT: C 544 ASP cc_start: 0.8328 (t70) cc_final: 0.8088 (t0) REVERT: C 599 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8307 (mm) REVERT: C 601 ASP cc_start: 0.7017 (m-30) cc_final: 0.6656 (m-30) REVERT: C 642 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7975 (mm) REVERT: C 648 MET cc_start: 0.7962 (mmt) cc_final: 0.7530 (mmp) REVERT: C 651 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7243 (tt0) REVERT: C 653 ARG cc_start: 0.7985 (ttm170) cc_final: 0.7583 (mtt90) REVERT: C 654 ILE cc_start: 0.8550 (mt) cc_final: 0.7976 (mt) REVERT: C 656 TRP cc_start: 0.8573 (m100) cc_final: 0.8172 (m-90) REVERT: C 669 GLN cc_start: 0.7636 (mp10) cc_final: 0.7142 (mp10) REVERT: C 676 LYS cc_start: 0.8841 (mttt) cc_final: 0.8532 (mttm) REVERT: C 683 ARG cc_start: 0.7869 (mpt180) cc_final: 0.7495 (mmt90) REVERT: C 721 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7457 (tp-100) outliers start: 77 outliers final: 57 residues processed: 619 average time/residue: 0.3036 time to fit residues: 268.8043 Evaluate side-chains 643 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 581 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL 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 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 533 MET 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 625 ASP Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 722 ILE Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain B residue 158 ILE 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 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 502 GLU Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 625 ASP 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 757 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 825 VAL 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 533 MET 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 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: 2.9990 chunk 42 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 191 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 168 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 643 ASN C 180 ASN C 591 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.113258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.095684 restraints weight = 28881.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.099169 restraints weight = 13779.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.101451 restraints weight = 8020.656| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 16707 Z= 0.384 Angle : 0.779 18.743 22881 Z= 0.382 Chirality : 0.052 0.344 2763 Planarity : 0.005 0.051 2880 Dihedral : 10.917 94.368 3246 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 5.49 % Allowed : 21.33 % Favored : 73.18 % 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: -1.02 (0.18), residues: 2052 helix: -0.09 (0.22), residues: 546 sheet: -0.02 (0.29), residues: 372 loop : -1.20 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 326 HIS 0.015 0.001 HIS C 639 PHE 0.023 0.002 PHE A 396 TYR 0.037 0.002 TYR A 276 ARG 0.009 0.001 ARG C 612 *********************** 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 667 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 581 time to evaluate : 1.747 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: A 147 GLN cc_start: 0.7991 (tm-30) cc_final: 0.7516 (tm-30) REVERT: A 194 GLU cc_start: 0.7582 (tp30) cc_final: 0.6988 (tp30) REVERT: A 198 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6668 (mt-10) REVERT: A 211 GLU cc_start: 0.8244 (tp30) cc_final: 0.7884 (tp30) REVERT: A 251 LEU cc_start: 0.8267 (tp) cc_final: 0.7750 (tt) REVERT: A 252 ILE cc_start: 0.8790 (mt) cc_final: 0.8376 (tt) REVERT: A 334 LEU cc_start: 0.8705 (mt) cc_final: 0.8491 (mt) REVERT: A 339 GLU cc_start: 0.7748 (tp30) cc_final: 0.7536 (tp30) REVERT: A 382 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.8046 (mtt-85) REVERT: A 468 ASP cc_start: 0.7401 (t70) cc_final: 0.6921 (t70) REVERT: A 510 TYR cc_start: 0.7924 (m-80) cc_final: 0.7304 (m-80) REVERT: A 520 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8200 (mtmm) REVERT: A 591 GLN cc_start: 0.7105 (tt0) cc_final: 0.6900 (tt0) REVERT: A 624 HIS cc_start: 0.6353 (m-70) cc_final: 0.6138 (m-70) REVERT: A 650 MET cc_start: 0.7382 (mtp) cc_final: 0.7165 (mtm) REVERT: A 653 ARG cc_start: 0.7862 (ttm170) cc_final: 0.7556 (mtt90) REVERT: A 665 GLN cc_start: 0.8561 (tt0) cc_final: 0.8319 (tt0) REVERT: A 675 MET cc_start: 0.7931 (mmm) cc_final: 0.7504 (mmm) REVERT: A 676 LYS cc_start: 0.8716 (mttt) cc_final: 0.8325 (mttm) REVERT: A 702 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7092 (mt-10) REVERT: A 764 ARG cc_start: 0.7453 (ttt90) cc_final: 0.7144 (tpt90) REVERT: B 173 ILE cc_start: 0.8363 (mt) cc_final: 0.8020 (mm) REVERT: B 206 VAL cc_start: 0.8206 (m) cc_final: 0.7921 (p) REVERT: B 249 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7306 (mm-30) REVERT: B 252 ILE cc_start: 0.8689 (mt) cc_final: 0.8409 (tp) REVERT: B 273 TRP cc_start: 0.8816 (m-10) cc_final: 0.8549 (m-10) REVERT: B 384 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7475 (mp0) REVERT: B 386 VAL cc_start: 0.8734 (m) cc_final: 0.8477 (t) REVERT: B 495 GLU cc_start: 0.7408 (pt0) cc_final: 0.7150 (pt0) REVERT: B 551 TYR cc_start: 0.8129 (m-80) cc_final: 0.7804 (m-80) REVERT: B 611 LEU cc_start: 0.7640 (tp) cc_final: 0.7067 (tp) REVERT: B 635 VAL cc_start: 0.8149 (m) cc_final: 0.7843 (t) REVERT: B 658 TYR cc_start: 0.8467 (m-80) cc_final: 0.8147 (m-80) REVERT: B 659 MET cc_start: 0.8400 (ttm) cc_final: 0.8123 (ttp) REVERT: B 665 GLN cc_start: 0.8377 (tt0) cc_final: 0.8060 (tm-30) REVERT: B 676 LYS cc_start: 0.8688 (mttt) cc_final: 0.8321 (mttm) REVERT: B 846 LEU cc_start: 0.6921 (mt) cc_final: 0.6554 (mt) REVERT: C 193 THR cc_start: 0.8091 (t) cc_final: 0.7816 (t) REVERT: C 194 GLU cc_start: 0.7513 (tp30) cc_final: 0.6973 (tp30) REVERT: C 197 ASN cc_start: 0.7549 (m110) cc_final: 0.7259 (m-40) REVERT: C 198 GLU cc_start: 0.6934 (mt-10) cc_final: 0.6687 (mt-10) REVERT: C 211 GLU cc_start: 0.8055 (tp30) cc_final: 0.7770 (tp30) REVERT: C 251 LEU cc_start: 0.8437 (tp) cc_final: 0.8085 (tt) REVERT: C 295 LYS cc_start: 0.8724 (mptt) cc_final: 0.8397 (mptt) REVERT: C 356 ARG cc_start: 0.7529 (tpp-160) cc_final: 0.7311 (tpp-160) REVERT: C 468 ASP cc_start: 0.7387 (t70) cc_final: 0.6840 (t70) REVERT: C 500 TYR cc_start: 0.8347 (t80) cc_final: 0.7883 (t80) REVERT: C 504 LYS cc_start: 0.8125 (ttmm) cc_final: 0.7722 (ttmm) REVERT: C 510 TYR cc_start: 0.7943 (m-80) cc_final: 0.7237 (m-80) REVERT: C 516 LEU cc_start: 0.7915 (tt) cc_final: 0.7711 (mt) REVERT: C 526 THR cc_start: 0.8700 (t) cc_final: 0.8476 (p) REVERT: C 544 ASP cc_start: 0.8355 (t70) cc_final: 0.8132 (t0) REVERT: C 599 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8290 (tt) REVERT: C 601 ASP cc_start: 0.7071 (m-30) cc_final: 0.6589 (m-30) REVERT: C 604 LEU cc_start: 0.8703 (mp) cc_final: 0.8353 (mp) REVERT: C 635 VAL cc_start: 0.8011 (m) cc_final: 0.7798 (t) REVERT: C 642 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7987 (mm) REVERT: C 648 MET cc_start: 0.7962 (mmt) cc_final: 0.7595 (mmt) REVERT: C 653 ARG cc_start: 0.8011 (ttm170) cc_final: 0.7643 (mtt90) REVERT: C 669 GLN cc_start: 0.7690 (mp10) cc_final: 0.7157 (mp10) REVERT: C 676 LYS cc_start: 0.8858 (mttt) cc_final: 0.8428 (mttm) REVERT: C 683 ARG cc_start: 0.7884 (mpt180) cc_final: 0.7550 (mmt90) REVERT: C 721 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7417 (tp-100) REVERT: C 842 PHE cc_start: 0.7628 (m-80) cc_final: 0.7251 (m-80) outliers start: 86 outliers final: 65 residues processed: 621 average time/residue: 0.3180 time to fit residues: 281.1941 Evaluate side-chains 644 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 574 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 235 CYS 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 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 478 PHE Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain A residue 540 VAL 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 625 ASP Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 235 CYS Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 316 LEU 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 518 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 710 ILE Chi-restraints excluded: chain B residue 741 SER 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 300 SER Chi-restraints excluded: chain C residue 316 LEU 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 509 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 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 721 GLN 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: 0.0870 chunk 161 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 167 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 643 ASN B 639 HIS ** B 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.117273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.099321 restraints weight = 28565.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.102998 restraints weight = 13751.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.105372 restraints weight = 8005.567| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 16707 Z= 0.199 Angle : 0.719 17.896 22881 Z= 0.346 Chirality : 0.049 0.304 2763 Planarity : 0.005 0.046 2880 Dihedral : 10.518 94.208 3246 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.79 % Allowed : 23.50 % Favored : 71.71 % 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: 0.02 (0.23), residues: 552 sheet: 0.16 (0.29), residues: 372 loop : -1.10 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 326 HIS 0.008 0.001 HIS B 225 PHE 0.018 0.001 PHE A 396 TYR 0.034 0.002 TYR B 276 ARG 0.014 0.001 ARG B 407 *********************** 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 660 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 585 time to evaluate : 1.810 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: 0.7995 (tm-30) cc_final: 0.7481 (tm-30) REVERT: A 150 PHE cc_start: 0.7595 (t80) cc_final: 0.7365 (t80) REVERT: A 194 GLU cc_start: 0.7542 (tp30) cc_final: 0.6928 (tp30) REVERT: A 198 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6676 (mt-10) REVERT: A 211 GLU cc_start: 0.8207 (tp30) cc_final: 0.7846 (tp30) REVERT: A 251 LEU cc_start: 0.8197 (tp) cc_final: 0.7701 (tt) REVERT: A 252 ILE cc_start: 0.8784 (mt) cc_final: 0.8425 (tt) REVERT: A 334 LEU cc_start: 0.8604 (mt) cc_final: 0.8390 (mt) REVERT: A 339 GLU cc_start: 0.7746 (tp30) cc_final: 0.7458 (tp30) REVERT: A 341 THR cc_start: 0.8576 (m) cc_final: 0.8230 (p) REVERT: A 382 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.8039 (mtt-85) REVERT: A 468 ASP cc_start: 0.7416 (t70) cc_final: 0.6903 (t70) REVERT: A 500 TYR cc_start: 0.8273 (t80) cc_final: 0.7852 (t80) REVERT: A 502 GLU cc_start: 0.7929 (tp30) cc_final: 0.7716 (tp30) REVERT: A 510 TYR cc_start: 0.7783 (m-80) cc_final: 0.7189 (m-80) REVERT: A 520 LYS cc_start: 0.8386 (mtmm) cc_final: 0.8180 (mtmm) REVERT: A 533 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7980 (tpp) REVERT: A 535 ASN cc_start: 0.7546 (t0) cc_final: 0.7091 (t0) REVERT: A 665 GLN cc_start: 0.8530 (tt0) cc_final: 0.8278 (tt0) REVERT: A 675 MET cc_start: 0.7938 (mmm) cc_final: 0.7535 (mmm) REVERT: A 676 LYS cc_start: 0.8651 (mttt) cc_final: 0.8264 (mttm) REVERT: A 702 GLU cc_start: 0.7291 (mt-10) cc_final: 0.6901 (mt-10) REVERT: A 764 ARG cc_start: 0.7444 (ttt90) cc_final: 0.7081 (tpt90) REVERT: B 206 VAL cc_start: 0.8265 (m) cc_final: 0.8014 (p) REVERT: B 249 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7264 (mm-30) REVERT: B 252 ILE cc_start: 0.8692 (mt) cc_final: 0.8386 (tp) REVERT: B 273 TRP cc_start: 0.8818 (m-10) cc_final: 0.8566 (m-10) REVERT: B 341 THR cc_start: 0.8723 (m) cc_final: 0.8385 (p) REVERT: B 386 VAL cc_start: 0.8717 (m) cc_final: 0.8436 (t) REVERT: B 474 TYR cc_start: 0.8366 (t80) cc_final: 0.8097 (t80) REVERT: B 495 GLU cc_start: 0.7323 (pt0) cc_final: 0.7054 (pt0) REVERT: B 551 TYR cc_start: 0.8123 (m-80) cc_final: 0.7788 (m-80) REVERT: B 658 TYR cc_start: 0.8417 (m-80) cc_final: 0.8141 (m-80) REVERT: B 665 GLN cc_start: 0.8349 (tt0) cc_final: 0.8056 (tm-30) REVERT: B 676 LYS cc_start: 0.8669 (mttt) cc_final: 0.8384 (mttp) REVERT: B 810 TYR cc_start: 0.7998 (m-80) cc_final: 0.7708 (m-80) REVERT: C 194 GLU cc_start: 0.7453 (tp30) cc_final: 0.6931 (tp30) REVERT: C 198 GLU cc_start: 0.6917 (mt-10) cc_final: 0.6607 (mt-10) REVERT: C 211 GLU cc_start: 0.8016 (tp30) cc_final: 0.7727 (tp30) REVERT: C 249 GLU cc_start: 0.7392 (mm-30) cc_final: 0.6628 (mm-30) REVERT: C 251 LEU cc_start: 0.8371 (tp) cc_final: 0.8025 (tt) REVERT: C 295 LYS cc_start: 0.8720 (mptt) cc_final: 0.8385 (mptt) REVERT: C 382 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7918 (mtt-85) REVERT: C 468 ASP cc_start: 0.7367 (t70) cc_final: 0.6827 (t70) REVERT: C 504 LYS cc_start: 0.8059 (ttmm) cc_final: 0.7739 (mtpp) REVERT: C 510 TYR cc_start: 0.7795 (m-80) cc_final: 0.7171 (m-80) REVERT: C 516 LEU cc_start: 0.7893 (tt) cc_final: 0.7661 (mt) REVERT: C 526 THR cc_start: 0.8609 (t) cc_final: 0.8372 (p) REVERT: C 544 ASP cc_start: 0.8346 (t70) cc_final: 0.8127 (t0) REVERT: C 599 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8305 (mm) REVERT: C 601 ASP cc_start: 0.6996 (m-30) cc_final: 0.6629 (m-30) REVERT: C 604 LEU cc_start: 0.8659 (mp) cc_final: 0.8411 (mp) REVERT: C 642 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7908 (mm) REVERT: C 653 ARG cc_start: 0.8009 (ttm170) cc_final: 0.7607 (mtt90) REVERT: C 656 TRP cc_start: 0.8568 (m100) cc_final: 0.8183 (m-90) REVERT: C 669 GLN cc_start: 0.7637 (mp10) cc_final: 0.7032 (mp10) REVERT: C 676 LYS cc_start: 0.8807 (mttt) cc_final: 0.8488 (mttm) REVERT: C 683 ARG cc_start: 0.7888 (mpt180) cc_final: 0.7405 (mmt90) REVERT: C 842 PHE cc_start: 0.7535 (m-80) cc_final: 0.7003 (m-80) outliers start: 75 outliers final: 58 residues processed: 616 average time/residue: 0.3139 time to fit residues: 272.5271 Evaluate side-chains 641 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 578 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 188 THR 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 316 LEU Chi-restraints excluded: chain A residue 318 CYS 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 531 ASN 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 619 MET Chi-restraints excluded: chain A residue 625 ASP 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 825 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 235 CYS Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 316 LEU 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 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- 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: 2.9990 chunk 147 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 84 optimal weight: 0.0040 chunk 81 optimal weight: 0.0970 chunk 153 optimal weight: 5.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN A 643 ASN B 225 HIS B 643 ASN C 197 ASN ** C 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.115796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.097874 restraints weight = 28550.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.101529 restraints weight = 13855.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.103902 restraints weight = 8070.598| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 16707 Z= 0.267 Angle : 0.736 18.558 22881 Z= 0.356 Chirality : 0.050 0.302 2763 Planarity : 0.005 0.045 2880 Dihedral : 10.484 93.759 3246 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 5.24 % Allowed : 24.33 % 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: -0.88 (0.19), residues: 2052 helix: 0.03 (0.22), residues: 552 sheet: 0.11 (0.29), residues: 372 loop : -1.13 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 326 HIS 0.009 0.001 HIS C 639 PHE 0.022 0.002 PHE A 396 TYR 0.032 0.002 TYR B 276 ARG 0.010 0.001 ARG A 407 *********************** 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 673 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 591 time to evaluate : 1.865 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: 0.7989 (tm-30) cc_final: 0.7424 (tm-30) REVERT: A 150 PHE cc_start: 0.7631 (t80) cc_final: 0.7393 (t80) REVERT: A 194 GLU cc_start: 0.7564 (tp30) cc_final: 0.6961 (tp30) REVERT: A 198 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6687 (mt-10) REVERT: A 211 GLU cc_start: 0.8230 (tp30) cc_final: 0.7849 (tp30) REVERT: A 251 LEU cc_start: 0.8235 (tp) cc_final: 0.7754 (tt) REVERT: A 252 ILE cc_start: 0.8822 (mt) cc_final: 0.8427 (tt) REVERT: A 334 LEU cc_start: 0.8643 (mt) cc_final: 0.8433 (mt) REVERT: A 339 GLU cc_start: 0.7759 (tp30) cc_final: 0.7478 (tp30) REVERT: A 341 THR cc_start: 0.8593 (m) cc_final: 0.8230 (p) REVERT: A 382 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8056 (mtt-85) REVERT: A 408 TYR cc_start: 0.7681 (p90) cc_final: 0.7423 (p90) REVERT: A 468 ASP cc_start: 0.7466 (t70) cc_final: 0.6908 (t70) REVERT: A 500 TYR cc_start: 0.8319 (t80) cc_final: 0.7830 (t80) REVERT: A 502 GLU cc_start: 0.7987 (tp30) cc_final: 0.7774 (tp30) REVERT: A 510 TYR cc_start: 0.7870 (m-80) cc_final: 0.7243 (m-80) REVERT: A 520 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8111 (mtmm) REVERT: A 533 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.7993 (tpp) REVERT: A 535 ASN cc_start: 0.7632 (t0) cc_final: 0.7205 (t0) REVERT: A 665 GLN cc_start: 0.8549 (tt0) cc_final: 0.8310 (tt0) REVERT: A 675 MET cc_start: 0.7964 (mmm) cc_final: 0.7563 (mmm) REVERT: A 676 LYS cc_start: 0.8686 (mttt) cc_final: 0.8296 (mttm) REVERT: A 764 ARG cc_start: 0.7455 (ttt90) cc_final: 0.7111 (tpt90) REVERT: B 206 VAL cc_start: 0.8198 (m) cc_final: 0.7973 (p) REVERT: B 249 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7316 (mm-30) REVERT: B 252 ILE cc_start: 0.8680 (mt) cc_final: 0.8363 (tp) REVERT: B 273 TRP cc_start: 0.8818 (m-10) cc_final: 0.8565 (m-10) REVERT: B 298 MET cc_start: 0.7268 (mmm) cc_final: 0.7008 (mmm) REVERT: B 386 VAL cc_start: 0.8696 (m) cc_final: 0.8468 (t) REVERT: B 474 TYR cc_start: 0.8340 (t80) cc_final: 0.8038 (t80) REVERT: B 495 GLU cc_start: 0.7368 (pt0) cc_final: 0.7083 (pt0) REVERT: B 551 TYR cc_start: 0.8142 (m-80) cc_final: 0.7807 (m-80) REVERT: B 635 VAL cc_start: 0.8079 (m) cc_final: 0.7720 (t) REVERT: B 658 TYR cc_start: 0.8417 (m-80) cc_final: 0.8080 (m-80) REVERT: B 665 GLN cc_start: 0.8369 (tt0) cc_final: 0.8071 (tm-30) REVERT: B 676 LYS cc_start: 0.8672 (mttt) cc_final: 0.8396 (mttp) REVERT: C 194 GLU cc_start: 0.7527 (tp30) cc_final: 0.6940 (tp30) REVERT: C 197 ASN cc_start: 0.7585 (m110) cc_final: 0.7115 (m-40) REVERT: C 198 GLU cc_start: 0.6947 (mt-10) cc_final: 0.6728 (mt-10) REVERT: C 211 GLU cc_start: 0.8050 (tp30) cc_final: 0.7753 (tp30) REVERT: C 249 GLU cc_start: 0.7433 (mm-30) cc_final: 0.6747 (mm-30) REVERT: C 251 LEU cc_start: 0.8418 (tp) cc_final: 0.8045 (tt) REVERT: C 295 LYS cc_start: 0.8720 (mptt) cc_final: 0.8387 (mptt) REVERT: C 382 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7967 (mtt-85) REVERT: C 468 ASP cc_start: 0.7414 (t70) cc_final: 0.6918 (t70) REVERT: C 500 TYR cc_start: 0.8242 (t80) cc_final: 0.7920 (t80) REVERT: C 504 LYS cc_start: 0.8007 (ttmm) cc_final: 0.7728 (ttmm) REVERT: C 510 TYR cc_start: 0.7870 (m-80) cc_final: 0.7206 (m-80) REVERT: C 516 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7705 (mt) REVERT: C 544 ASP cc_start: 0.8345 (t70) cc_final: 0.8127 (t0) REVERT: C 599 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8305 (tt) REVERT: C 601 ASP cc_start: 0.6974 (m-30) cc_final: 0.6576 (m-30) REVERT: C 604 LEU cc_start: 0.8661 (mp) cc_final: 0.8401 (mp) REVERT: C 611 LEU cc_start: 0.7595 (tp) cc_final: 0.7293 (tp) REVERT: C 642 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7910 (mm) REVERT: C 648 MET cc_start: 0.8047 (mmt) cc_final: 0.7620 (mmp) REVERT: C 653 ARG cc_start: 0.8017 (ttm170) cc_final: 0.7619 (mtt90) REVERT: C 669 GLN cc_start: 0.7598 (mp10) cc_final: 0.7074 (mp10) REVERT: C 676 LYS cc_start: 0.8798 (mttt) cc_final: 0.8368 (mttm) REVERT: C 683 ARG cc_start: 0.7919 (mpt180) cc_final: 0.7469 (mmt90) REVERT: C 842 PHE cc_start: 0.7540 (m-80) cc_final: 0.6950 (m-80) outliers start: 82 outliers final: 64 residues processed: 626 average time/residue: 0.3160 time to fit residues: 279.8994 Evaluate side-chains 655 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 584 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 188 THR 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 316 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 478 PHE Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 533 MET 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 619 MET Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 660 SER 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 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 272 ILE Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 316 LEU 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 625 ASP 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 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 222 GLN 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 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 478 PHE Chi-restraints excluded: chain C residue 516 LEU 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 825 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 155 optimal weight: 0.0570 chunk 138 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN A 591 GLN A 643 ASN A 836 GLN ** B 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 GLN B 643 ASN C 636 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.113267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.095687 restraints weight = 28987.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.099213 restraints weight = 14147.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.101525 restraints weight = 8307.811| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 16707 Z= 0.439 Angle : 0.833 20.512 22881 Z= 0.410 Chirality : 0.054 0.355 2763 Planarity : 0.005 0.047 2880 Dihedral : 10.782 93.173 3246 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 5.75 % Allowed : 24.39 % Favored : 69.86 % 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: -1.14 (0.18), residues: 2052 helix: -0.20 (0.22), residues: 546 sheet: -0.10 (0.28), residues: 393 loop : -1.29 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 720 HIS 0.016 0.001 HIS C 639 PHE 0.023 0.002 PHE A 396 TYR 0.035 0.002 TYR B 276 ARG 0.010 0.001 ARG B 407 *********************** 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 672 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 582 time to evaluate : 1.789 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: 0.7957 (tm-30) cc_final: 0.7393 (tm-30) REVERT: A 151 TYR cc_start: 0.8147 (p90) cc_final: 0.7926 (p90) REVERT: A 194 GLU cc_start: 0.7580 (tp30) cc_final: 0.7004 (tp30) REVERT: A 198 GLU cc_start: 0.7072 (mt-10) cc_final: 0.6739 (mt-10) REVERT: A 211 GLU cc_start: 0.8274 (tp30) cc_final: 0.7902 (tp30) REVERT: A 251 LEU cc_start: 0.8299 (tp) cc_final: 0.7818 (tt) REVERT: A 252 ILE cc_start: 0.8839 (mt) cc_final: 0.8415 (tt) REVERT: A 334 LEU cc_start: 0.8725 (mt) cc_final: 0.8513 (mt) REVERT: A 339 GLU cc_start: 0.7749 (tp30) cc_final: 0.7515 (tp30) REVERT: A 382 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8042 (mtt-85) REVERT: A 468 ASP cc_start: 0.7476 (t70) cc_final: 0.6920 (t70) REVERT: A 510 TYR cc_start: 0.7995 (m-80) cc_final: 0.7369 (m-80) REVERT: A 535 ASN cc_start: 0.7671 (t0) cc_final: 0.7245 (t0) REVERT: A 604 LEU cc_start: 0.8825 (mp) cc_final: 0.8576 (mm) REVERT: A 665 GLN cc_start: 0.8574 (tt0) cc_final: 0.8328 (tt0) REVERT: A 675 MET cc_start: 0.7953 (mmm) cc_final: 0.7536 (mmm) REVERT: A 676 LYS cc_start: 0.8721 (mttt) cc_final: 0.8311 (mttm) REVERT: A 721 GLN cc_start: 0.8073 (tm-30) cc_final: 0.7047 (tp40) REVERT: A 764 ARG cc_start: 0.7522 (ttt90) cc_final: 0.7178 (tpt90) REVERT: B 147 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7381 (tm-30) REVERT: B 173 ILE cc_start: 0.8363 (mt) cc_final: 0.8055 (mm) REVERT: B 194 GLU cc_start: 0.7563 (tp30) cc_final: 0.7037 (tp30) REVERT: B 249 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7333 (mm-30) REVERT: B 252 ILE cc_start: 0.8675 (mt) cc_final: 0.8428 (tp) REVERT: B 273 TRP cc_start: 0.8791 (m-10) cc_final: 0.8521 (m-10) REVERT: B 298 MET cc_start: 0.7374 (mmm) cc_final: 0.7112 (mmm) REVERT: B 386 VAL cc_start: 0.8737 (m) cc_final: 0.8484 (t) REVERT: B 474 TYR cc_start: 0.8373 (t80) cc_final: 0.8161 (t80) REVERT: B 495 GLU cc_start: 0.7471 (pt0) cc_final: 0.7201 (pt0) REVERT: B 551 TYR cc_start: 0.8165 (m-80) cc_final: 0.7821 (m-80) REVERT: B 635 VAL cc_start: 0.8219 (m) cc_final: 0.7922 (t) REVERT: B 658 TYR cc_start: 0.8447 (m-80) cc_final: 0.8141 (m-80) REVERT: B 676 LYS cc_start: 0.8687 (mttt) cc_final: 0.8315 (mttm) REVERT: B 721 GLN cc_start: 0.8120 (tm-30) cc_final: 0.7820 (tm-30) REVERT: C 194 GLU cc_start: 0.7517 (tp30) cc_final: 0.6980 (tp30) REVERT: C 211 GLU cc_start: 0.8099 (tp30) cc_final: 0.7807 (tp30) REVERT: C 251 LEU cc_start: 0.8409 (tp) cc_final: 0.8058 (tt) REVERT: C 295 LYS cc_start: 0.8734 (mptt) cc_final: 0.8407 (mptt) REVERT: C 382 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7978 (mtt-85) REVERT: C 500 TYR cc_start: 0.8301 (t80) cc_final: 0.7856 (t80) REVERT: C 504 LYS cc_start: 0.8052 (ttmm) cc_final: 0.7690 (ttmm) REVERT: C 510 TYR cc_start: 0.7986 (m-80) cc_final: 0.7360 (m-80) REVERT: C 516 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7711 (mt) REVERT: C 526 THR cc_start: 0.8608 (t) cc_final: 0.8381 (p) REVERT: C 544 ASP cc_start: 0.8339 (t70) cc_final: 0.8120 (t0) REVERT: C 599 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8454 (tp) REVERT: C 601 ASP cc_start: 0.6989 (m-30) cc_final: 0.6596 (m-30) REVERT: C 604 LEU cc_start: 0.8649 (mp) cc_final: 0.8394 (mp) REVERT: C 611 LEU cc_start: 0.7648 (tp) cc_final: 0.7367 (tp) REVERT: C 635 VAL cc_start: 0.8133 (m) cc_final: 0.7884 (t) REVERT: C 642 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7990 (mm) REVERT: C 648 MET cc_start: 0.8049 (mmt) cc_final: 0.7569 (mmp) REVERT: C 653 ARG cc_start: 0.8022 (ttm170) cc_final: 0.7689 (mtt90) REVERT: C 669 GLN cc_start: 0.7650 (mp10) cc_final: 0.7103 (mp10) REVERT: C 676 LYS cc_start: 0.8872 (mttt) cc_final: 0.8595 (mttm) REVERT: C 683 ARG cc_start: 0.7944 (mpt180) cc_final: 0.7516 (mmt90) REVERT: C 721 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7231 (tp40) REVERT: C 842 PHE cc_start: 0.7549 (m-80) cc_final: 0.6865 (m-80) outliers start: 90 outliers final: 69 residues processed: 619 average time/residue: 0.3244 time to fit residues: 282.5335 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 : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 188 THR 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 316 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 478 PHE Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 533 MET 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 619 MET Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 660 SER 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 762 CYS 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 158 ILE 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 272 ILE Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 316 LEU 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 591 GLN Chi-restraints excluded: chain B residue 619 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 710 ILE Chi-restraints excluded: chain B residue 741 SER 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 300 SER Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 318 CYS 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 478 PHE Chi-restraints excluded: chain C residue 516 LEU 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 721 GLN Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 762 CYS Chi-restraints excluded: chain C residue 825 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 35 optimal weight: 0.7980 chunk 138 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 200 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 179 optimal weight: 4.9990 chunk 201 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 643 ASN 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 = 0.3424 r_free = 0.3424 target = 0.114012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.096541 restraints weight = 28890.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.100101 restraints weight = 13928.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.102425 restraints weight = 8116.796| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 16707 Z= 0.259 Angle : 0.779 19.454 22881 Z= 0.377 Chirality : 0.050 0.307 2763 Planarity : 0.005 0.046 2880 Dihedral : 10.485 92.324 3246 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.85 % Allowed : 25.99 % Favored : 69.16 % 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: -1.01 (0.19), residues: 2052 helix: -0.09 (0.22), residues: 552 sheet: 0.03 (0.28), residues: 393 loop : -1.23 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 326 HIS 0.008 0.001 HIS C 639 PHE 0.022 0.002 PHE A 396 TYR 0.030 0.002 TYR B 276 ARG 0.010 0.001 ARG A 407 ********************** 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 651 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 575 time to evaluate : 1.761 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: 0.7946 (tm-30) cc_final: 0.7347 (tm-30) REVERT: A 194 GLU cc_start: 0.7561 (tp30) cc_final: 0.6963 (tp30) REVERT: A 198 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6701 (mt-10) REVERT: A 211 GLU cc_start: 0.8233 (tp30) cc_final: 0.7878 (tp30) REVERT: A 251 LEU cc_start: 0.8259 (tp) cc_final: 0.7765 (tt) REVERT: A 252 ILE cc_start: 0.8832 (mt) cc_final: 0.8415 (tt) REVERT: A 339 GLU cc_start: 0.7775 (tp30) cc_final: 0.7475 (tp30) REVERT: A 341 THR cc_start: 0.8571 (m) cc_final: 0.8197 (p) REVERT: A 382 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8019 (mtt-85) REVERT: A 468 ASP cc_start: 0.7476 (t70) cc_final: 0.7079 (t70) REVERT: A 510 TYR cc_start: 0.7934 (m-80) cc_final: 0.7338 (m-80) REVERT: A 535 ASN cc_start: 0.7667 (t0) cc_final: 0.7226 (t0) REVERT: A 604 LEU cc_start: 0.8770 (mp) cc_final: 0.8545 (mm) REVERT: A 675 MET cc_start: 0.7966 (mmm) cc_final: 0.7603 (mmm) REVERT: A 676 LYS cc_start: 0.8684 (mttt) cc_final: 0.8289 (mttm) REVERT: A 721 GLN cc_start: 0.8102 (tm-30) cc_final: 0.7079 (tp40) REVERT: A 764 ARG cc_start: 0.7513 (ttt90) cc_final: 0.7247 (tpt90) REVERT: B 147 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7496 (tm-30) REVERT: B 249 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7276 (mm-30) REVERT: B 252 ILE cc_start: 0.8672 (mt) cc_final: 0.8354 (tp) REVERT: B 273 TRP cc_start: 0.8789 (m-10) cc_final: 0.8542 (m-10) REVERT: B 298 MET cc_start: 0.7384 (mmm) cc_final: 0.7064 (mmm) REVERT: B 386 VAL cc_start: 0.8712 (m) cc_final: 0.8459 (t) REVERT: B 474 TYR cc_start: 0.8302 (t80) cc_final: 0.8057 (t80) REVERT: B 495 GLU cc_start: 0.7461 (pt0) cc_final: 0.7169 (pt0) REVERT: B 551 TYR cc_start: 0.8147 (m-80) cc_final: 0.7809 (m-80) REVERT: B 658 TYR cc_start: 0.8366 (m-80) cc_final: 0.8091 (m-80) REVERT: B 676 LYS cc_start: 0.8653 (mttt) cc_final: 0.8387 (mttp) REVERT: B 721 GLN cc_start: 0.8090 (tm-30) cc_final: 0.7817 (tm-30) REVERT: C 170 VAL cc_start: 0.8502 (OUTLIER) cc_final: 0.8220 (m) REVERT: C 194 GLU cc_start: 0.7497 (tp30) cc_final: 0.6991 (tp30) REVERT: C 211 GLU cc_start: 0.8066 (tp30) cc_final: 0.7781 (tp30) REVERT: C 249 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6689 (mm-30) REVERT: C 251 LEU cc_start: 0.8387 (tp) cc_final: 0.8033 (tt) REVERT: C 295 LYS cc_start: 0.8742 (mptt) cc_final: 0.8374 (mptt) REVERT: C 382 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7970 (mtt-85) REVERT: C 500 TYR cc_start: 0.8227 (t80) cc_final: 0.7826 (t80) REVERT: C 504 LYS cc_start: 0.8026 (ttmm) cc_final: 0.7727 (ttmm) REVERT: C 510 TYR cc_start: 0.7905 (m-80) cc_final: 0.7210 (m-80) REVERT: C 516 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7716 (mt) REVERT: C 544 ASP cc_start: 0.8354 (t70) cc_final: 0.8147 (t0) REVERT: C 599 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8330 (tt) REVERT: C 601 ASP cc_start: 0.6979 (m-30) cc_final: 0.6584 (m-30) REVERT: C 604 LEU cc_start: 0.8650 (mp) cc_final: 0.8435 (mp) REVERT: C 642 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7915 (mm) REVERT: C 648 MET cc_start: 0.8038 (mmt) cc_final: 0.7620 (mmp) REVERT: C 653 ARG cc_start: 0.8016 (ttm170) cc_final: 0.7609 (mtt90) REVERT: C 669 GLN cc_start: 0.7611 (mp10) cc_final: 0.7057 (mp10) REVERT: C 676 LYS cc_start: 0.8822 (mttt) cc_final: 0.8520 (mttm) REVERT: C 683 ARG cc_start: 0.7933 (mpt180) cc_final: 0.7500 (mmt90) REVERT: C 721 GLN cc_start: 0.7706 (tt0) cc_final: 0.7191 (tp40) REVERT: C 842 PHE cc_start: 0.7480 (m-80) cc_final: 0.6778 (m-80) outliers start: 76 outliers final: 59 residues processed: 609 average time/residue: 0.3274 time to fit residues: 279.3781 Evaluate side-chains 632 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 566 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 316 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 478 PHE Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 625 ASP 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 762 CYS Chi-restraints excluded: chain A residue 825 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 319 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 493 ASP Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 591 GLN Chi-restraints excluded: chain B residue 619 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 710 ILE Chi-restraints excluded: chain B residue 741 SER 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 170 VAL Chi-restraints excluded: chain C residue 222 GLN 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 516 LEU 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 759 LEU Chi-restraints excluded: chain C residue 762 CYS Chi-restraints excluded: chain C residue 825 VAL 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: 1.9990 chunk 135 optimal weight: 0.8980 chunk 146 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 60 optimal weight: 8.9990 chunk 178 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN 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 = 0.3455 r_free = 0.3455 target = 0.116618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.098900 restraints weight = 28674.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.102537 restraints weight = 13806.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.104920 restraints weight = 8013.182| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 16707 Z= 0.217 Angle : 0.746 18.812 22881 Z= 0.358 Chirality : 0.049 0.300 2763 Planarity : 0.005 0.046 2880 Dihedral : 10.048 89.359 3246 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 4.53 % Allowed : 26.05 % Favored : 69.41 % 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: -0.88 (0.19), residues: 2052 helix: 0.01 (0.22), residues: 552 sheet: 0.17 (0.27), residues: 423 loop : -1.21 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 326 HIS 0.007 0.001 HIS C 639 PHE 0.019 0.001 PHE A 396 TYR 0.028 0.002 TYR B 276 ARG 0.008 0.001 ARG A 407 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5858.66 seconds wall clock time: 105 minutes 47.96 seconds (6347.96 seconds total)