Starting phenix.real_space_refine on Sun May 18 04:43:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rm0_19347/05_2025/8rm0_19347.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rm0_19347/05_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_19347/05_2025/8rm0_19347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rm0_19347/05_2025/8rm0_19347.map" model { file = "/net/cci-nas-00/data/ceres_data/8rm0_19347/05_2025/8rm0_19347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rm0_19347/05_2025/8rm0_19347.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 237 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 10386 2.51 5 N 2721 2.21 5 O 3102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 10.22, per 1000 atoms: 0.63 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: 4.68 Conformation dependent library (CDL) restraints added in 2.1 seconds 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4014 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 30 sheets defined 29.5% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 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: 5.27 Time building geometry restraints manager: 5.33 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 38.490 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.080 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16782 Z= 0.199 Angle : 0.764 9.163 23079 Z= 0.383 Chirality : 0.048 0.345 2763 Planarity : 0.006 0.072 2880 Dihedral : 13.696 106.497 6552 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.19 % Allowed : 0.00 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.19), residues: 2052 helix: -0.53 (0.22), residues: 546 sheet: 0.62 (0.30), residues: 360 loop : -0.90 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 791 HIS 0.009 0.001 HIS A 742 PHE 0.014 0.001 PHE A 232 TYR 0.023 0.001 TYR C 327 ARG 0.010 0.000 ARG C 763 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 27) link_NAG-ASN : angle 3.29127 ( 81) link_ALPHA1-6 : bond 0.00511 ( 3) link_ALPHA1-6 : angle 1.72970 ( 9) link_BETA1-4 : bond 0.01135 ( 15) link_BETA1-4 : angle 2.67711 ( 45) link_ALPHA1-3 : bond 0.00890 ( 3) link_ALPHA1-3 : angle 3.34429 ( 9) hydrogen bonds : bond 0.19916 ( 482) hydrogen bonds : angle 7.25165 ( 1278) SS BOND : bond 0.00352 ( 27) SS BOND : angle 1.64097 ( 54) covalent geometry : bond 0.00399 (16707) covalent geometry : angle 0.72451 (22881) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 699 time to evaluate : 1.845 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: 0.3070 time to fit residues: 303.9932 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 : 1.602 ------------------------------------------------------------------------------- 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 16782 Z= 0.136 Angle : 0.714 10.310 23079 Z= 0.343 Chirality : 0.047 0.272 2763 Planarity : 0.006 0.063 2880 Dihedral : 11.978 94.612 3246 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.85 % Allowed : 15.26 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.19), residues: 2052 helix: -0.06 (0.22), residues: 546 sheet: 0.59 (0.30), residues: 369 loop : -0.95 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 326 HIS 0.007 0.001 HIS C 234 PHE 0.019 0.001 PHE C 150 TYR 0.025 0.001 TYR A 474 ARG 0.006 0.001 ARG C 407 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 27) link_NAG-ASN : angle 2.65226 ( 81) link_ALPHA1-6 : bond 0.01380 ( 3) link_ALPHA1-6 : angle 2.94058 ( 9) link_BETA1-4 : bond 0.00966 ( 15) link_BETA1-4 : angle 2.34111 ( 45) link_ALPHA1-3 : bond 0.00295 ( 3) link_ALPHA1-3 : angle 3.63832 ( 9) hydrogen bonds : bond 0.04792 ( 482) hydrogen bonds : angle 5.65051 ( 1278) SS BOND : bond 0.00519 ( 27) SS BOND : angle 2.06172 ( 54) covalent geometry : bond 0.00312 (16707) covalent geometry : angle 0.67828 (22881) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 612 time to evaluate : 1.686 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: 0.3163 time to fit residues: 279.6054 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 : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 650 MET Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 837 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 85 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 203 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 199 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 643 ASN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 HIS B 637 HIS C 314 HIS C 600 ASN C 637 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.112391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.094627 restraints weight = 28931.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.098126 restraints weight = 14029.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.100434 restraints weight = 8230.250| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 16782 Z= 0.337 Angle : 0.850 12.319 23079 Z= 0.418 Chirality : 0.054 0.368 2763 Planarity : 0.006 0.058 2880 Dihedral : 11.934 90.217 3246 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 5.04 % Allowed : 16.48 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.18), residues: 2052 helix: -0.33 (0.22), residues: 552 sheet: -0.30 (0.27), residues: 396 loop : -1.20 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP C 326 HIS 0.018 0.002 HIS C 639 PHE 0.026 0.003 PHE B 396 TYR 0.023 0.003 TYR A 240 ARG 0.008 0.001 ARG B 407 Details of bonding type rmsd link_NAG-ASN : bond 0.00596 ( 27) link_NAG-ASN : angle 2.81730 ( 81) link_ALPHA1-6 : bond 0.00831 ( 3) link_ALPHA1-6 : angle 3.18717 ( 9) link_BETA1-4 : bond 0.01034 ( 15) link_BETA1-4 : angle 2.51264 ( 45) link_ALPHA1-3 : bond 0.00541 ( 3) link_ALPHA1-3 : angle 3.86507 ( 9) hydrogen bonds : bond 0.06926 ( 482) hydrogen bonds : angle 5.89535 ( 1278) SS BOND : bond 0.01012 ( 27) SS BOND : angle 2.22901 ( 54) covalent geometry : bond 0.00720 (16707) covalent geometry : angle 0.81631 (22881) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 590 time to evaluate : 1.912 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 194 GLU cc_start: 0.7609 (tp30) cc_final: 0.6912 (tp30) REVERT: A 197 ASN cc_start: 0.7780 (m-40) cc_final: 0.7553 (m-40) REVERT: A 198 GLU cc_start: 0.7114 (mt-10) cc_final: 0.6560 (mt-10) REVERT: A 211 GLU cc_start: 0.8286 (tp30) cc_final: 0.7928 (tp30) REVERT: A 235 CYS cc_start: 0.5723 (m) cc_final: 0.5302 (m) REVERT: A 251 LEU cc_start: 0.8241 (tp) cc_final: 0.7724 (tt) REVERT: A 252 ILE cc_start: 0.8815 (mt) cc_final: 0.8371 (tp) REVERT: A 258 LEU cc_start: 0.8681 (mt) cc_final: 0.8404 (mm) REVERT: A 334 LEU cc_start: 0.8758 (mt) cc_final: 0.8494 (mt) REVERT: A 438 ARG cc_start: 0.7506 (mmm160) cc_final: 0.7089 (tpt90) REVERT: A 468 ASP cc_start: 0.7429 (t70) cc_final: 0.6887 (t70) REVERT: A 495 GLU cc_start: 0.7027 (pt0) cc_final: 0.6785 (pt0) REVERT: A 500 TYR cc_start: 0.8427 (t80) cc_final: 0.7889 (t80) REVERT: A 510 TYR cc_start: 0.8022 (m-80) cc_final: 0.7456 (m-80) REVERT: A 540 VAL cc_start: 0.8429 (p) cc_final: 0.8009 (m) REVERT: A 591 GLN cc_start: 0.7246 (tt0) cc_final: 0.6996 (tt0) REVERT: A 624 HIS cc_start: 0.6420 (m-70) cc_final: 0.6144 (m-70) REVERT: A 635 VAL cc_start: 0.8128 (m) cc_final: 0.7799 (p) REVERT: A 636 GLN cc_start: 0.7890 (tp40) cc_final: 0.7609 (tp40) REVERT: A 648 MET cc_start: 0.8198 (mmt) cc_final: 0.7926 (mmp) REVERT: A 651 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7272 (tt0) REVERT: A 653 ARG cc_start: 0.7977 (ttm170) cc_final: 0.7673 (mtt90) REVERT: A 665 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8313 (tt0) REVERT: A 675 MET cc_start: 0.7966 (mmm) cc_final: 0.7588 (mmm) REVERT: A 676 LYS cc_start: 0.8749 (mttt) cc_final: 0.8371 (mttm) REVERT: A 702 GLU cc_start: 0.7272 (mt-10) cc_final: 0.7012 (mt-10) REVERT: A 803 SER cc_start: 0.8323 (t) cc_final: 0.7797 (p) REVERT: B 151 TYR cc_start: 0.7552 (p90) cc_final: 0.7239 (p90) REVERT: B 206 VAL cc_start: 0.8219 (m) cc_final: 0.7911 (p) REVERT: B 235 CYS cc_start: 0.5945 (m) cc_final: 0.5693 (m) REVERT: B 249 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7189 (mm-30) REVERT: B 252 ILE cc_start: 0.8752 (mt) cc_final: 0.8297 (tp) REVERT: B 273 TRP cc_start: 0.8826 (m-10) cc_final: 0.8548 (m-10) REVERT: B 339 GLU cc_start: 0.7774 (tp30) cc_final: 0.7555 (tp30) REVERT: B 347 LEU cc_start: 0.8405 (mt) cc_final: 0.8119 (mp) REVERT: B 356 ARG cc_start: 0.7950 (tpp-160) cc_final: 0.7595 (tpp-160) REVERT: B 384 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7500 (mp0) REVERT: B 386 VAL cc_start: 0.8780 (m) cc_final: 0.8533 (t) REVERT: B 468 ASP cc_start: 0.7376 (t70) cc_final: 0.6916 (t0) REVERT: B 495 GLU cc_start: 0.7406 (pt0) cc_final: 0.7119 (pt0) REVERT: B 504 LYS cc_start: 0.8064 (mtpp) cc_final: 0.7816 (mtpp) REVERT: B 551 TYR cc_start: 0.8117 (m-80) cc_final: 0.7784 (m-80) REVERT: B 611 LEU cc_start: 0.7457 (tp) cc_final: 0.6884 (tp) REVERT: B 635 VAL cc_start: 0.8159 (m) cc_final: 0.7899 (t) REVERT: B 658 TYR cc_start: 0.8502 (m-80) cc_final: 0.8214 (m-80) REVERT: B 665 GLN cc_start: 0.8412 (tt0) cc_final: 0.7977 (tm-30) REVERT: B 669 GLN cc_start: 0.8042 (mt0) cc_final: 0.7810 (mm110) REVERT: B 672 ASP cc_start: 0.8148 (m-30) cc_final: 0.7936 (m-30) REVERT: B 676 LYS cc_start: 0.8701 (mttt) cc_final: 0.8328 (mttm) REVERT: B 746 ILE cc_start: 0.8527 (mm) cc_final: 0.8321 (mm) REVERT: C 193 THR cc_start: 0.8156 (t) cc_final: 0.7895 (t) REVERT: C 197 ASN cc_start: 0.7597 (m110) cc_final: 0.7310 (m-40) REVERT: C 252 ILE cc_start: 0.8821 (tp) cc_final: 0.8587 (tt) REVERT: C 305 LYS cc_start: 0.8264 (pttp) cc_final: 0.8064 (pttp) REVERT: C 386 VAL cc_start: 0.8753 (m) cc_final: 0.8503 (t) REVERT: C 468 ASP cc_start: 0.7381 (t70) cc_final: 0.6909 (t70) REVERT: C 495 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6893 (pm20) REVERT: C 510 TYR cc_start: 0.8031 (m-80) cc_final: 0.7505 (m-80) REVERT: C 516 LEU cc_start: 0.8026 (tt) cc_final: 0.7749 (mt) REVERT: C 540 VAL cc_start: 0.8501 (p) cc_final: 0.8208 (t) REVERT: C 544 ASP cc_start: 0.8338 (t70) cc_final: 0.8068 (t0) REVERT: C 551 TYR cc_start: 0.8309 (m-80) cc_final: 0.8076 (m-80) REVERT: C 591 GLN cc_start: 0.7202 (tt0) cc_final: 0.6969 (tt0) REVERT: C 601 ASP cc_start: 0.7135 (m-30) cc_final: 0.6708 (m-30) REVERT: C 611 LEU cc_start: 0.7722 (tp) cc_final: 0.7283 (tp) REVERT: C 635 VAL cc_start: 0.8134 (m) cc_final: 0.7812 (t) REVERT: C 646 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7326 (tmm-80) REVERT: C 669 GLN cc_start: 0.7712 (mp10) cc_final: 0.7425 (mp10) REVERT: C 676 LYS cc_start: 0.8858 (mttt) cc_final: 0.8423 (mttm) REVERT: C 683 ARG cc_start: 0.7881 (mpt180) cc_final: 0.7444 (mmt90) REVERT: C 721 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7437 (tp-100) REVERT: C 724 ASN cc_start: 0.7943 (t0) cc_final: 0.7731 (t0) REVERT: C 773 VAL cc_start: 0.8706 (t) cc_final: 0.8469 (m) REVERT: C 842 PHE cc_start: 0.7727 (m-10) cc_final: 0.7381 (m-80) outliers start: 79 outliers final: 56 residues processed: 620 average time/residue: 0.3121 time to fit residues: 280.2372 Evaluate side-chains 616 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 556 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 462 ASN Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 665 GLN Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 462 ASN Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 326 TRP Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 462 ASN Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain C residue 495 GLU Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 721 GLN Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 837 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 99 optimal weight: 0.2980 chunk 122 optimal weight: 0.9990 chunk 185 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 194 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 643 ASN B 535 ASN C 180 ASN C 225 HIS C 314 HIS C 742 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.115642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.097676 restraints weight = 28701.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.101272 restraints weight = 13873.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.103616 restraints weight = 8142.181| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 16782 Z= 0.148 Angle : 0.731 12.086 23079 Z= 0.349 Chirality : 0.048 0.302 2763 Planarity : 0.005 0.051 2880 Dihedral : 11.278 92.760 3246 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.47 % Allowed : 21.14 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.19), residues: 2052 helix: -0.07 (0.23), residues: 552 sheet: 0.05 (0.29), residues: 387 loop : -1.12 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 326 HIS 0.007 0.001 HIS B 639 PHE 0.021 0.002 PHE B 396 TYR 0.024 0.002 TYR C 706 ARG 0.007 0.001 ARG B 407 Details of bonding type rmsd link_NAG-ASN : bond 0.00333 ( 27) link_NAG-ASN : angle 2.55428 ( 81) link_ALPHA1-6 : bond 0.01243 ( 3) link_ALPHA1-6 : angle 3.12170 ( 9) link_BETA1-4 : bond 0.01006 ( 15) link_BETA1-4 : angle 2.35348 ( 45) link_ALPHA1-3 : bond 0.00247 ( 3) link_ALPHA1-3 : angle 4.23413 ( 9) hydrogen bonds : bond 0.04626 ( 482) hydrogen bonds : angle 5.33226 ( 1278) SS BOND : bond 0.00589 ( 27) SS BOND : angle 2.34053 ( 54) covalent geometry : bond 0.00335 (16707) covalent geometry : angle 0.69412 (22881) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 583 time to evaluate : 1.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 PHE cc_start: 0.7623 (t80) cc_final: 0.7306 (t80) REVERT: A 194 GLU cc_start: 0.7539 (tp30) cc_final: 0.6886 (tp30) REVERT: A 198 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6606 (mt-10) REVERT: A 211 GLU cc_start: 0.8191 (tp30) cc_final: 0.7742 (tp30) REVERT: A 251 LEU cc_start: 0.8197 (tp) cc_final: 0.7647 (tt) REVERT: A 252 ILE cc_start: 0.8773 (mt) cc_final: 0.8366 (tp) REVERT: A 258 LEU cc_start: 0.8717 (mt) cc_final: 0.8465 (mm) REVERT: A 334 LEU cc_start: 0.8641 (mt) cc_final: 0.8397 (mt) REVERT: A 341 THR cc_start: 0.8627 (m) cc_final: 0.8246 (p) REVERT: A 389 LEU cc_start: 0.8627 (mm) cc_final: 0.8422 (mt) REVERT: A 438 ARG cc_start: 0.7481 (mmm160) cc_final: 0.7010 (tpt90) REVERT: A 468 ASP cc_start: 0.7371 (t70) cc_final: 0.6824 (t70) REVERT: A 495 GLU cc_start: 0.6879 (pt0) cc_final: 0.6672 (pt0) REVERT: A 500 TYR cc_start: 0.8339 (t80) cc_final: 0.7788 (t80) REVERT: A 510 TYR cc_start: 0.7772 (m-80) cc_final: 0.7195 (m-80) REVERT: A 520 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8159 (mtmm) REVERT: A 624 HIS cc_start: 0.6400 (m-70) cc_final: 0.6141 (m-70) REVERT: A 651 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7268 (tt0) REVERT: A 653 ARG cc_start: 0.7902 (ttm170) cc_final: 0.7576 (mtt90) REVERT: A 665 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8279 (tt0) REVERT: A 672 ASP cc_start: 0.7989 (m-30) cc_final: 0.7761 (m-30) REVERT: A 675 MET cc_start: 0.7920 (mmm) cc_final: 0.7496 (mmm) REVERT: A 676 LYS cc_start: 0.8691 (mttt) cc_final: 0.8306 (mttm) REVERT: A 702 GLU cc_start: 0.7297 (mt-10) cc_final: 0.6895 (mt-10) REVERT: A 772 VAL cc_start: 0.8194 (p) cc_final: 0.7991 (m) REVERT: B 206 VAL cc_start: 0.8305 (m) cc_final: 0.8010 (p) REVERT: B 249 GLU cc_start: 0.7616 (mm-30) cc_final: 0.6602 (mm-30) REVERT: B 252 ILE cc_start: 0.8671 (mt) cc_final: 0.8366 (tp) REVERT: B 273 TRP cc_start: 0.8832 (m-10) cc_final: 0.8567 (m-10) REVERT: B 295 LYS cc_start: 0.8876 (mptt) cc_final: 0.8594 (mptt) REVERT: B 298 MET cc_start: 0.7525 (mmm) cc_final: 0.7308 (mmm) REVERT: B 356 ARG cc_start: 0.7870 (tpp-160) cc_final: 0.7539 (tpp-160) REVERT: B 384 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7432 (mp0) REVERT: B 408 TYR cc_start: 0.7739 (p90) cc_final: 0.7478 (p90) REVERT: B 468 ASP cc_start: 0.7304 (t70) cc_final: 0.6797 (t0) REVERT: B 495 GLU cc_start: 0.7306 (pt0) cc_final: 0.7034 (pt0) REVERT: B 504 LYS cc_start: 0.8040 (mtpp) cc_final: 0.7840 (mtpp) REVERT: B 551 TYR cc_start: 0.8100 (m-80) cc_final: 0.7748 (m-80) REVERT: B 635 VAL cc_start: 0.7937 (m) cc_final: 0.7635 (p) REVERT: B 658 TYR cc_start: 0.8439 (m-80) cc_final: 0.8179 (m-80) REVERT: B 665 GLN cc_start: 0.8423 (tt0) cc_final: 0.7984 (tm-30) REVERT: B 676 LYS cc_start: 0.8682 (mttt) cc_final: 0.8399 (mttp) REVERT: B 707 TYR cc_start: 0.8275 (m-10) cc_final: 0.8048 (m-10) REVERT: B 825 VAL cc_start: 0.8236 (OUTLIER) cc_final: 0.7936 (p) REVERT: C 193 THR cc_start: 0.8026 (t) cc_final: 0.7815 (t) REVERT: C 194 GLU cc_start: 0.7438 (tp30) cc_final: 0.6895 (tp30) REVERT: C 197 ASN cc_start: 0.7505 (m110) cc_final: 0.7233 (m-40) REVERT: C 252 ILE cc_start: 0.8802 (tp) cc_final: 0.8564 (tt) REVERT: C 295 LYS cc_start: 0.8712 (mptt) cc_final: 0.8385 (mptt) REVERT: C 384 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7444 (mp0) REVERT: C 468 ASP cc_start: 0.7372 (t70) cc_final: 0.6845 (t70) REVERT: C 510 TYR cc_start: 0.7833 (m-80) cc_final: 0.7278 (m-80) REVERT: C 516 LEU cc_start: 0.7885 (tt) cc_final: 0.7631 (mt) REVERT: C 526 THR cc_start: 0.8752 (t) cc_final: 0.8548 (p) REVERT: C 544 ASP cc_start: 0.8324 (t70) cc_final: 0.8061 (t0) REVERT: C 551 TYR cc_start: 0.8294 (m-80) cc_final: 0.8046 (m-80) REVERT: C 599 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8235 (mm) REVERT: C 601 ASP cc_start: 0.7023 (m-30) cc_final: 0.6596 (m-30) REVERT: C 604 LEU cc_start: 0.8643 (mp) cc_final: 0.8384 (mp) REVERT: C 642 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7953 (mm) REVERT: C 648 MET cc_start: 0.8033 (mmt) cc_final: 0.7577 (mmp) REVERT: C 653 ARG cc_start: 0.8015 (ttm170) cc_final: 0.7635 (mtm-85) REVERT: C 656 TRP cc_start: 0.8562 (m100) cc_final: 0.8201 (m-90) REVERT: C 669 GLN cc_start: 0.7617 (mp10) cc_final: 0.7122 (mp10) REVERT: C 676 LYS cc_start: 0.8860 (mttt) cc_final: 0.8554 (mttm) REVERT: C 683 ARG cc_start: 0.7875 (mpt180) cc_final: 0.7584 (mpt180) outliers start: 70 outliers final: 47 residues processed: 611 average time/residue: 0.3060 time to fit residues: 264.7494 Evaluate side-chains 620 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 568 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 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 532 GLU 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 686 VAL Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 462 ASN Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 650 MET Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 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 462 ASN Chi-restraints excluded: chain C residue 532 GLU Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 719 ASN Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 762 CYS Chi-restraints excluded: chain C residue 763 ARG Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 837 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 182 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 76 optimal weight: 0.0040 chunk 131 optimal weight: 10.0000 chunk 59 optimal weight: 0.0670 chunk 58 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 overall best weight: 2.8136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN B 234 HIS B 314 HIS B 492 GLN B 535 ASN B 600 ASN C 225 HIS C 314 HIS C 535 ASN ** C 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.109626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.091899 restraints weight = 29493.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.095372 restraints weight = 14353.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.097637 restraints weight = 8448.938| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.100 16782 Z= 0.381 Angle : 0.914 17.777 23079 Z= 0.448 Chirality : 0.057 0.389 2763 Planarity : 0.006 0.053 2880 Dihedral : 11.593 94.119 3246 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.41 % Favored : 92.54 % Rotamer: Outliers : 6.58 % Allowed : 20.31 % Favored : 73.12 % 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: -1.55 (0.18), residues: 2052 helix: -0.61 (0.21), residues: 552 sheet: -0.48 (0.28), residues: 390 loop : -1.44 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 720 HIS 0.021 0.002 HIS A 639 PHE 0.027 0.003 PHE B 396 TYR 0.025 0.003 TYR A 240 ARG 0.015 0.001 ARG B 612 Details of bonding type rmsd link_NAG-ASN : bond 0.00749 ( 27) link_NAG-ASN : angle 2.93015 ( 81) link_ALPHA1-6 : bond 0.00758 ( 3) link_ALPHA1-6 : angle 3.29110 ( 9) link_BETA1-4 : bond 0.00958 ( 15) link_BETA1-4 : angle 2.71689 ( 45) link_ALPHA1-3 : bond 0.00692 ( 3) link_ALPHA1-3 : angle 4.16441 ( 9) hydrogen bonds : bond 0.07405 ( 482) hydrogen bonds : angle 5.90899 ( 1278) SS BOND : bond 0.00754 ( 27) SS BOND : angle 2.94953 ( 54) covalent geometry : bond 0.00824 (16707) covalent geometry : angle 0.87539 (22881) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 558 time to evaluate : 1.734 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 194 GLU cc_start: 0.7617 (tp30) cc_final: 0.6985 (tp30) REVERT: A 198 GLU cc_start: 0.7069 (mt-10) cc_final: 0.6685 (mt-10) REVERT: A 211 GLU cc_start: 0.8284 (tp30) cc_final: 0.7973 (tp30) REVERT: A 251 LEU cc_start: 0.8276 (tp) cc_final: 0.7788 (tt) REVERT: A 252 ILE cc_start: 0.8808 (mt) cc_final: 0.8404 (tt) REVERT: A 334 LEU cc_start: 0.8752 (mt) cc_final: 0.8522 (mt) REVERT: A 339 GLU cc_start: 0.7743 (tp30) cc_final: 0.7540 (tp30) REVERT: A 382 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7979 (mtt-85) REVERT: A 468 ASP cc_start: 0.7505 (t70) cc_final: 0.6962 (t70) REVERT: A 510 TYR cc_start: 0.8036 (m-80) cc_final: 0.7454 (m-80) REVERT: A 520 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8143 (mtmm) REVERT: A 586 LEU cc_start: 0.5620 (OUTLIER) cc_final: 0.5403 (mp) REVERT: A 599 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8553 (tt) REVERT: A 624 HIS cc_start: 0.6464 (m-70) cc_final: 0.6250 (m-70) REVERT: A 675 MET cc_start: 0.7986 (mmm) cc_final: 0.7587 (mmm) REVERT: A 676 LYS cc_start: 0.8761 (mttt) cc_final: 0.8347 (mttm) REVERT: A 702 GLU cc_start: 0.7257 (mt-10) cc_final: 0.7029 (mt-10) REVERT: A 764 ARG cc_start: 0.7452 (ttt90) cc_final: 0.7219 (tpt90) REVERT: B 249 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7365 (mm-30) REVERT: B 252 ILE cc_start: 0.8709 (mt) cc_final: 0.8388 (tp) REVERT: B 356 ARG cc_start: 0.7884 (tpp-160) cc_final: 0.7541 (tpp-160) REVERT: B 384 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7495 (mp0) REVERT: B 468 ASP cc_start: 0.7471 (t70) cc_final: 0.7028 (t0) REVERT: B 495 GLU cc_start: 0.7514 (pt0) cc_final: 0.7261 (pt0) REVERT: B 551 TYR cc_start: 0.8163 (m-80) cc_final: 0.7833 (m-80) REVERT: B 586 LEU cc_start: 0.6054 (OUTLIER) cc_final: 0.5424 (mt) REVERT: B 625 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7921 (p0) REVERT: B 629 MET cc_start: 0.7840 (mmt) cc_final: 0.7623 (mmt) REVERT: B 635 VAL cc_start: 0.8309 (m) cc_final: 0.8054 (t) REVERT: B 658 TYR cc_start: 0.8409 (m-80) cc_final: 0.8095 (m-80) REVERT: B 665 GLN cc_start: 0.8404 (tt0) cc_final: 0.8030 (tm-30) REVERT: B 672 ASP cc_start: 0.8193 (m-30) cc_final: 0.7888 (m-30) REVERT: B 676 LYS cc_start: 0.8726 (mttt) cc_final: 0.8309 (mttm) REVERT: C 193 THR cc_start: 0.8155 (t) cc_final: 0.7878 (t) REVERT: C 194 GLU cc_start: 0.7492 (tp30) cc_final: 0.6983 (tp30) REVERT: C 197 ASN cc_start: 0.7599 (m110) cc_final: 0.7286 (m-40) REVERT: C 251 LEU cc_start: 0.8493 (tp) cc_final: 0.8123 (tt) REVERT: C 252 ILE cc_start: 0.8872 (tp) cc_final: 0.8582 (tt) REVERT: C 468 ASP cc_start: 0.7557 (t70) cc_final: 0.7030 (t70) REVERT: C 510 TYR cc_start: 0.8090 (m-80) cc_final: 0.7566 (m-80) REVERT: C 516 LEU cc_start: 0.8032 (tt) cc_final: 0.7795 (mt) REVERT: C 544 ASP cc_start: 0.8339 (t70) cc_final: 0.8112 (t0) REVERT: C 551 TYR cc_start: 0.8341 (m-80) cc_final: 0.8136 (m-80) REVERT: C 586 LEU cc_start: 0.5784 (OUTLIER) cc_final: 0.5582 (mp) REVERT: C 599 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8342 (tp) REVERT: C 601 ASP cc_start: 0.7105 (m-30) cc_final: 0.6644 (m-30) REVERT: C 604 LEU cc_start: 0.8731 (mp) cc_final: 0.8526 (mp) REVERT: C 612 ARG cc_start: 0.7983 (tpp80) cc_final: 0.7743 (mmm-85) REVERT: C 635 VAL cc_start: 0.8211 (m) cc_final: 0.7973 (t) REVERT: C 669 GLN cc_start: 0.7627 (mp10) cc_final: 0.7187 (mp10) REVERT: C 676 LYS cc_start: 0.8910 (mttt) cc_final: 0.8636 (mttm) REVERT: C 683 ARG cc_start: 0.7926 (mpt180) cc_final: 0.7511 (mmt90) REVERT: C 842 PHE cc_start: 0.7671 (m-80) cc_final: 0.7215 (m-80) outliers start: 103 outliers final: 80 residues processed: 611 average time/residue: 0.2926 time to fit residues: 256.3509 Evaluate side-chains 646 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 558 time to evaluate : 1.709 ------------------------------------------------------------------------------- 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 214 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 462 ASN Chi-restraints excluded: chain A residue 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 532 GLU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 599 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 660 SER 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 809 SER 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 279 ILE Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 341 THR 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 540 VAL Chi-restraints excluded: chain B residue 586 LEU 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 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 318 CYS Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 326 TRP Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 462 ASN Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain C residue 488 SER 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 586 LEU Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 603 ASN 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 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 722 ILE 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: 2.9990 chunk 3 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 184 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 191 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 168 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 639 HIS A 643 ASN A 860 HIS A 862 GLN B 314 HIS B 492 GLN B 639 HIS C 314 HIS ** C 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.114007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.096251 restraints weight = 28806.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.099798 restraints weight = 14085.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.102109 restraints weight = 8303.564| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 16782 Z= 0.154 Angle : 0.764 17.110 23079 Z= 0.363 Chirality : 0.049 0.316 2763 Planarity : 0.005 0.049 2880 Dihedral : 10.918 94.217 3246 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 5.43 % Allowed : 22.86 % 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: -1.19 (0.19), residues: 2052 helix: -0.23 (0.22), residues: 552 sheet: -0.13 (0.29), residues: 375 loop : -1.30 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 326 HIS 0.007 0.001 HIS C 639 PHE 0.020 0.002 PHE B 396 TYR 0.025 0.002 TYR A 474 ARG 0.009 0.001 ARG A 407 Details of bonding type rmsd link_NAG-ASN : bond 0.00326 ( 27) link_NAG-ASN : angle 2.54143 ( 81) link_ALPHA1-6 : bond 0.01308 ( 3) link_ALPHA1-6 : angle 3.16630 ( 9) link_BETA1-4 : bond 0.00978 ( 15) link_BETA1-4 : angle 2.50380 ( 45) link_ALPHA1-3 : bond 0.00311 ( 3) link_ALPHA1-3 : angle 4.38657 ( 9) hydrogen bonds : bond 0.04491 ( 482) hydrogen bonds : angle 5.27663 ( 1278) SS BOND : bond 0.00743 ( 27) SS BOND : angle 2.22604 ( 54) covalent geometry : bond 0.00350 (16707) covalent geometry : angle 0.72774 (22881) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 584 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLN cc_start: 0.7968 (tm-30) cc_final: 0.7431 (tm-30) REVERT: A 150 PHE cc_start: 0.7625 (t80) cc_final: 0.7374 (t80) REVERT: A 151 TYR cc_start: 0.8073 (p90) cc_final: 0.7845 (p90) REVERT: A 194 GLU cc_start: 0.7466 (tp30) cc_final: 0.6886 (tp30) REVERT: A 198 GLU cc_start: 0.7025 (mt-10) cc_final: 0.6601 (mt-10) REVERT: A 211 GLU cc_start: 0.8202 (tp30) cc_final: 0.7894 (tp30) REVERT: A 251 LEU cc_start: 0.8206 (tp) cc_final: 0.7720 (tt) REVERT: A 252 ILE cc_start: 0.8793 (mt) cc_final: 0.8394 (tt) REVERT: A 258 LEU cc_start: 0.8730 (mt) cc_final: 0.8465 (mm) REVERT: A 339 GLU cc_start: 0.7693 (tp30) cc_final: 0.7451 (tp30) REVERT: A 382 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7989 (mtt-85) REVERT: A 468 ASP cc_start: 0.7436 (t70) cc_final: 0.6903 (t70) REVERT: A 500 TYR cc_start: 0.8216 (t80) cc_final: 0.7814 (t80) REVERT: A 510 TYR cc_start: 0.7851 (m-80) cc_final: 0.7279 (m-80) REVERT: A 520 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8142 (mtmm) REVERT: A 665 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8272 (tp40) REVERT: A 675 MET cc_start: 0.7958 (mmm) cc_final: 0.7492 (mmm) REVERT: A 676 LYS cc_start: 0.8721 (mttt) cc_final: 0.8472 (mttm) REVERT: A 702 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6913 (mt-10) REVERT: A 764 ARG cc_start: 0.7445 (ttt90) cc_final: 0.7171 (tpt90) REVERT: B 249 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7274 (mm-30) REVERT: B 252 ILE cc_start: 0.8682 (mt) cc_final: 0.8354 (tp) REVERT: B 273 TRP cc_start: 0.8812 (m-10) cc_final: 0.8610 (m-10) REVERT: B 356 ARG cc_start: 0.7803 (tpp-160) cc_final: 0.7530 (tpp-160) REVERT: B 495 GLU cc_start: 0.7432 (pt0) cc_final: 0.7177 (pt0) REVERT: B 535 ASN cc_start: 0.7709 (t0) cc_final: 0.7474 (t0) REVERT: B 551 TYR cc_start: 0.8122 (m-80) cc_final: 0.7779 (m-80) REVERT: B 612 ARG cc_start: 0.7874 (tpp80) cc_final: 0.7578 (tpp80) REVERT: B 658 TYR cc_start: 0.8370 (m-80) cc_final: 0.8076 (m-80) REVERT: B 665 GLN cc_start: 0.8359 (tt0) cc_final: 0.8037 (tm-30) REVERT: B 676 LYS cc_start: 0.8669 (mttt) cc_final: 0.8383 (mttp) REVERT: B 810 TYR cc_start: 0.8032 (m-80) cc_final: 0.7768 (m-10) REVERT: B 825 VAL cc_start: 0.8268 (OUTLIER) cc_final: 0.7851 (p) REVERT: C 194 GLU cc_start: 0.7435 (tp30) cc_final: 0.6974 (tp30) REVERT: C 251 LEU cc_start: 0.8437 (tp) cc_final: 0.8061 (tt) REVERT: C 252 ILE cc_start: 0.8854 (tp) cc_final: 0.8592 (tt) REVERT: C 295 LYS cc_start: 0.8746 (mptt) cc_final: 0.8392 (mptt) REVERT: C 382 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7925 (mtt-85) REVERT: C 468 ASP cc_start: 0.7364 (t70) cc_final: 0.6830 (t70) REVERT: C 500 TYR cc_start: 0.8213 (t80) cc_final: 0.7898 (t80) REVERT: C 504 LYS cc_start: 0.8113 (ttmm) cc_final: 0.7756 (ttmm) REVERT: C 510 TYR cc_start: 0.7894 (m-80) cc_final: 0.7281 (m-80) REVERT: C 516 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7729 (mt) REVERT: C 544 ASP cc_start: 0.8341 (t70) cc_final: 0.8120 (t0) REVERT: C 599 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8214 (tt) REVERT: C 601 ASP cc_start: 0.7096 (m-30) cc_final: 0.6635 (m-30) REVERT: C 629 MET cc_start: 0.7667 (mmm) cc_final: 0.7457 (mmt) REVERT: C 642 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7907 (mm) REVERT: C 648 MET cc_start: 0.8072 (mmt) cc_final: 0.7647 (mmp) REVERT: C 653 ARG cc_start: 0.8007 (ttm170) cc_final: 0.7679 (mtm-85) REVERT: C 669 GLN cc_start: 0.7607 (mp10) cc_final: 0.7090 (mp10) REVERT: C 676 LYS cc_start: 0.8821 (mttt) cc_final: 0.8506 (mttm) REVERT: C 683 ARG cc_start: 0.7882 (mpt180) cc_final: 0.7586 (mpt180) REVERT: C 721 GLN cc_start: 0.7740 (tt0) cc_final: 0.7271 (tp40) REVERT: C 764 ARG cc_start: 0.7336 (ttt90) cc_final: 0.6766 (tpt90) REVERT: C 842 PHE cc_start: 0.7502 (m-80) cc_final: 0.6847 (m-80) outliers start: 85 outliers final: 61 residues processed: 616 average time/residue: 0.3364 time to fit residues: 297.0224 Evaluate side-chains 640 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 571 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 462 ASN Chi-restraints excluded: chain A residue 478 PHE Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 665 GLN Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 719 ASN Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 221 GLU 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 318 CYS Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 462 ASN Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain C residue 140 VAL 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 318 CYS 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 0.8980 chunk 161 optimal weight: 0.2980 chunk 127 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 167 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 181 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN B 643 ASN C 197 ASN ** C 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.114691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.096914 restraints weight = 28781.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.100496 restraints weight = 13947.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.102812 restraints weight = 8147.178| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 16782 Z= 0.143 Angle : 0.736 16.608 23079 Z= 0.349 Chirality : 0.048 0.307 2763 Planarity : 0.005 0.048 2880 Dihedral : 10.645 94.238 3246 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 5.43 % Allowed : 24.27 % Favored : 70.31 % 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: -0.98 (0.19), residues: 2052 helix: -0.08 (0.22), residues: 552 sheet: 0.07 (0.29), residues: 390 loop : -1.21 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 326 HIS 0.006 0.001 HIS C 639 PHE 0.020 0.001 PHE A 396 TYR 0.037 0.002 TYR B 276 ARG 0.011 0.001 ARG B 407 Details of bonding type rmsd link_NAG-ASN : bond 0.00308 ( 27) link_NAG-ASN : angle 2.42098 ( 81) link_ALPHA1-6 : bond 0.01330 ( 3) link_ALPHA1-6 : angle 3.21853 ( 9) link_BETA1-4 : bond 0.01005 ( 15) link_BETA1-4 : angle 2.47193 ( 45) link_ALPHA1-3 : bond 0.00217 ( 3) link_ALPHA1-3 : angle 4.16369 ( 9) hydrogen bonds : bond 0.04309 ( 482) hydrogen bonds : angle 5.10916 ( 1278) SS BOND : bond 0.00734 ( 27) SS BOND : angle 2.08498 ( 54) covalent geometry : bond 0.00328 (16707) covalent geometry : angle 0.70217 (22881) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 587 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLN cc_start: 0.7967 (tm-30) cc_final: 0.7404 (tm-30) REVERT: A 150 PHE cc_start: 0.7628 (t80) cc_final: 0.7412 (t80) REVERT: A 194 GLU cc_start: 0.7456 (tp30) cc_final: 0.6874 (tp30) REVERT: A 198 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6626 (mt-10) REVERT: A 211 GLU cc_start: 0.8207 (tp30) cc_final: 0.7865 (tp30) REVERT: A 212 ILE cc_start: 0.8712 (mm) cc_final: 0.8395 (mm) REVERT: A 251 LEU cc_start: 0.8223 (tp) cc_final: 0.7732 (tt) REVERT: A 252 ILE cc_start: 0.8795 (mt) cc_final: 0.8414 (tt) REVERT: A 258 LEU cc_start: 0.8722 (mt) cc_final: 0.8457 (mm) REVERT: A 339 GLU cc_start: 0.7769 (tp30) cc_final: 0.7458 (tp30) REVERT: A 340 LEU cc_start: 0.8513 (tp) cc_final: 0.8303 (tt) REVERT: A 382 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7967 (mtt-85) REVERT: A 468 ASP cc_start: 0.7426 (t70) cc_final: 0.6888 (t70) REVERT: A 500 TYR cc_start: 0.8211 (t80) cc_final: 0.7803 (t80) REVERT: A 510 TYR cc_start: 0.7831 (m-80) cc_final: 0.7254 (m-80) REVERT: A 520 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8116 (mtmm) REVERT: A 653 ARG cc_start: 0.7889 (ttm170) cc_final: 0.7688 (ttm170) REVERT: A 665 GLN cc_start: 0.8489 (tt0) cc_final: 0.8260 (tp40) REVERT: A 675 MET cc_start: 0.7951 (mmm) cc_final: 0.7544 (mmm) REVERT: A 676 LYS cc_start: 0.8692 (mttt) cc_final: 0.8267 (mttm) REVERT: A 702 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6925 (mt-10) REVERT: A 764 ARG cc_start: 0.7438 (ttt90) cc_final: 0.7112 (tpt90) REVERT: B 249 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7294 (mm-30) REVERT: B 252 ILE cc_start: 0.8656 (mt) cc_final: 0.8313 (tp) REVERT: B 273 TRP cc_start: 0.8825 (m-10) cc_final: 0.8579 (m-10) REVERT: B 356 ARG cc_start: 0.7822 (tpp-160) cc_final: 0.7471 (tpp-160) REVERT: B 408 TYR cc_start: 0.7731 (p90) cc_final: 0.7485 (p90) REVERT: B 474 TYR cc_start: 0.8284 (t80) cc_final: 0.7995 (t80) REVERT: B 495 GLU cc_start: 0.7375 (pt0) cc_final: 0.7119 (pt0) REVERT: B 551 TYR cc_start: 0.8124 (m-80) cc_final: 0.7784 (m-80) REVERT: B 658 TYR cc_start: 0.8389 (m-80) cc_final: 0.8109 (m-80) REVERT: B 665 GLN cc_start: 0.8328 (tt0) cc_final: 0.8032 (tm-30) REVERT: B 670 LYS cc_start: 0.8965 (mmtp) cc_final: 0.8757 (mmtp) REVERT: B 676 LYS cc_start: 0.8664 (mttt) cc_final: 0.8390 (mttp) REVERT: C 194 GLU cc_start: 0.7432 (tp30) cc_final: 0.6944 (tp30) REVERT: C 251 LEU cc_start: 0.8427 (tp) cc_final: 0.8042 (tt) REVERT: C 252 ILE cc_start: 0.8788 (tp) cc_final: 0.8532 (tt) REVERT: C 295 LYS cc_start: 0.8746 (mptt) cc_final: 0.8385 (mptt) REVERT: C 347 LEU cc_start: 0.8383 (mt) cc_final: 0.8062 (tp) REVERT: C 382 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7894 (mtt-85) REVERT: C 468 ASP cc_start: 0.7425 (t70) cc_final: 0.6909 (t70) REVERT: C 500 TYR cc_start: 0.8232 (t80) cc_final: 0.7865 (t80) REVERT: C 504 LYS cc_start: 0.8119 (ttmm) cc_final: 0.7778 (ttmm) REVERT: C 510 TYR cc_start: 0.7844 (m-80) cc_final: 0.7242 (m-80) REVERT: C 516 LEU cc_start: 0.7942 (tt) cc_final: 0.7692 (mt) REVERT: C 544 ASP cc_start: 0.8328 (t70) cc_final: 0.8118 (t0) REVERT: C 599 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8242 (tt) REVERT: C 601 ASP cc_start: 0.7065 (m-30) cc_final: 0.6642 (m-30) REVERT: C 642 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7906 (mm) REVERT: C 653 ARG cc_start: 0.7992 (ttm170) cc_final: 0.7694 (mtt90) REVERT: C 669 GLN cc_start: 0.7580 (mp10) cc_final: 0.7054 (mp10) REVERT: C 676 LYS cc_start: 0.8807 (mttt) cc_final: 0.8501 (mttm) REVERT: C 683 ARG cc_start: 0.7896 (mpt180) cc_final: 0.7471 (mmt90) REVERT: C 721 GLN cc_start: 0.7700 (tt0) cc_final: 0.7217 (tp40) REVERT: C 842 PHE cc_start: 0.7457 (m-80) cc_final: 0.6762 (m-80) REVERT: C 860 HIS cc_start: 0.6917 (t70) cc_final: 0.6668 (t-170) outliers start: 85 outliers final: 65 residues processed: 620 average time/residue: 0.3117 time to fit residues: 277.1063 Evaluate side-chains 652 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 582 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 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 478 PHE Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 591 GLN Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 719 ASN Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 462 ASN Chi-restraints excluded: chain B residue 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 795 VAL Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain C residue 140 VAL 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 318 CYS 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 488 SER Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 619 MET Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 719 ASN Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 762 CYS Chi-restraints excluded: chain C residue 825 VAL 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: 1.9990 chunk 111 optimal weight: 0.7980 chunk 147 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 70 optimal weight: 0.0070 chunk 167 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 84 optimal weight: 0.0470 chunk 81 optimal weight: 0.0030 chunk 153 optimal weight: 0.0970 overall best weight: 0.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 643 ASN C 197 ASN C 591 GLN ** C 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.118535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.100522 restraints weight = 28206.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.104179 restraints weight = 13655.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.106602 restraints weight = 7959.174| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 16782 Z= 0.120 Angle : 0.714 15.240 23079 Z= 0.338 Chirality : 0.047 0.299 2763 Planarity : 0.005 0.045 2880 Dihedral : 10.214 92.706 3246 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.98 % Allowed : 24.52 % Favored : 70.50 % 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: -0.78 (0.19), residues: 2052 helix: 0.14 (0.23), residues: 552 sheet: 0.20 (0.28), residues: 390 loop : -1.13 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 326 HIS 0.002 0.001 HIS A 860 PHE 0.016 0.001 PHE C 232 TYR 0.027 0.001 TYR B 276 ARG 0.016 0.001 ARG B 612 Details of bonding type rmsd link_NAG-ASN : bond 0.00356 ( 27) link_NAG-ASN : angle 2.26465 ( 81) link_ALPHA1-6 : bond 0.01457 ( 3) link_ALPHA1-6 : angle 3.15000 ( 9) link_BETA1-4 : bond 0.01000 ( 15) link_BETA1-4 : angle 2.38280 ( 45) link_ALPHA1-3 : bond 0.00036 ( 3) link_ALPHA1-3 : angle 4.10859 ( 9) hydrogen bonds : bond 0.03255 ( 482) hydrogen bonds : angle 4.82833 ( 1278) SS BOND : bond 0.00735 ( 27) SS BOND : angle 1.80083 ( 54) covalent geometry : bond 0.00278 (16707) covalent geometry : angle 0.68339 (22881) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 595 time to evaluate : 1.783 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 147 GLN cc_start: 0.7995 (tm-30) cc_final: 0.7477 (tm-30) REVERT: A 194 GLU cc_start: 0.7463 (tp30) cc_final: 0.6851 (tp30) REVERT: A 198 GLU cc_start: 0.7072 (mt-10) cc_final: 0.6709 (mt-10) REVERT: A 211 GLU cc_start: 0.8181 (tp30) cc_final: 0.7854 (tp30) REVERT: A 212 ILE cc_start: 0.8653 (mm) cc_final: 0.8340 (mm) REVERT: A 251 LEU cc_start: 0.8233 (tp) cc_final: 0.7712 (tt) REVERT: A 252 ILE cc_start: 0.8782 (mt) cc_final: 0.8417 (tt) REVERT: A 258 LEU cc_start: 0.8721 (mt) cc_final: 0.8468 (mm) REVERT: A 276 TYR cc_start: 0.8253 (t80) cc_final: 0.7975 (t80) REVERT: A 339 GLU cc_start: 0.7749 (tp30) cc_final: 0.7430 (tp30) REVERT: A 340 LEU cc_start: 0.8490 (tp) cc_final: 0.8273 (tt) REVERT: A 382 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7920 (mtt-85) REVERT: A 468 ASP cc_start: 0.7396 (t70) cc_final: 0.6861 (t70) REVERT: A 500 TYR cc_start: 0.8163 (t80) cc_final: 0.7805 (t80) REVERT: A 510 TYR cc_start: 0.7684 (m-80) cc_final: 0.7083 (m-80) REVERT: A 520 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8152 (mtmm) REVERT: A 651 GLU cc_start: 0.7388 (tt0) cc_final: 0.7186 (tt0) REVERT: A 653 ARG cc_start: 0.7840 (ttm170) cc_final: 0.7485 (mtm-85) REVERT: A 665 GLN cc_start: 0.8462 (tt0) cc_final: 0.8206 (tp40) REVERT: A 675 MET cc_start: 0.8005 (mmm) cc_final: 0.7515 (mmm) REVERT: A 676 LYS cc_start: 0.8638 (mttt) cc_final: 0.8374 (mttp) REVERT: A 690 LYS cc_start: 0.7747 (ttpp) cc_final: 0.7530 (ttpp) REVERT: A 702 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6935 (mt-10) REVERT: A 721 GLN cc_start: 0.7755 (tm-30) cc_final: 0.7417 (tm-30) REVERT: A 764 ARG cc_start: 0.7422 (ttt90) cc_final: 0.7082 (tpt90) REVERT: B 170 VAL cc_start: 0.8499 (OUTLIER) cc_final: 0.8277 (m) REVERT: B 194 GLU cc_start: 0.7548 (tp30) cc_final: 0.7001 (tp30) REVERT: B 249 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7275 (mm-30) REVERT: B 252 ILE cc_start: 0.8606 (mt) cc_final: 0.8316 (tp) REVERT: B 495 GLU cc_start: 0.7257 (pt0) cc_final: 0.7003 (pt0) REVERT: B 500 TYR cc_start: 0.8341 (t80) cc_final: 0.7906 (t80) REVERT: B 504 LYS cc_start: 0.8009 (mtpp) cc_final: 0.7788 (mtpp) REVERT: B 551 TYR cc_start: 0.8104 (m-80) cc_final: 0.7793 (m-80) REVERT: B 658 TYR cc_start: 0.8415 (m-80) cc_final: 0.8125 (m-80) REVERT: B 665 GLN cc_start: 0.8359 (tt0) cc_final: 0.8016 (tm-30) REVERT: B 676 LYS cc_start: 0.8635 (mttt) cc_final: 0.8365 (mttp) REVERT: B 680 ARG cc_start: 0.8391 (tpt-90) cc_final: 0.8183 (tpt-90) REVERT: C 194 GLU cc_start: 0.7431 (tp30) cc_final: 0.6895 (tp30) REVERT: C 197 ASN cc_start: 0.7547 (m110) cc_final: 0.7047 (m-40) REVERT: C 206 VAL cc_start: 0.8031 (m) cc_final: 0.7749 (p) REVERT: C 249 GLU cc_start: 0.7354 (mm-30) cc_final: 0.6697 (mm-30) REVERT: C 251 LEU cc_start: 0.8383 (tp) cc_final: 0.7996 (tt) REVERT: C 252 ILE cc_start: 0.8761 (tp) cc_final: 0.8502 (tt) REVERT: C 295 LYS cc_start: 0.8753 (mptt) cc_final: 0.8456 (mptt) REVERT: C 347 LEU cc_start: 0.8389 (mt) cc_final: 0.8021 (tp) REVERT: C 382 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7913 (mtt-85) REVERT: C 468 ASP cc_start: 0.7402 (t70) cc_final: 0.6885 (t70) REVERT: C 500 TYR cc_start: 0.8178 (t80) cc_final: 0.7769 (t80) REVERT: C 504 LYS cc_start: 0.8064 (ttmm) cc_final: 0.7683 (ttmm) REVERT: C 510 TYR cc_start: 0.7662 (m-80) cc_final: 0.7107 (m-80) REVERT: C 516 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7626 (mt) REVERT: C 519 LEU cc_start: 0.8364 (mm) cc_final: 0.8072 (mp) REVERT: C 544 ASP cc_start: 0.8347 (t70) cc_final: 0.8145 (t0) REVERT: C 599 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8162 (tt) REVERT: C 601 ASP cc_start: 0.7069 (m-30) cc_final: 0.6645 (m-30) REVERT: C 604 LEU cc_start: 0.8619 (mp) cc_final: 0.8413 (mm) REVERT: C 642 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7820 (mm) REVERT: C 648 MET cc_start: 0.7895 (mmp) cc_final: 0.7692 (mmt) REVERT: C 653 ARG cc_start: 0.8039 (ttm170) cc_final: 0.7638 (mtt90) REVERT: C 665 GLN cc_start: 0.8396 (tt0) cc_final: 0.8079 (tp40) REVERT: C 669 GLN cc_start: 0.7558 (mp10) cc_final: 0.7025 (mp10) REVERT: C 676 LYS cc_start: 0.8774 (mttt) cc_final: 0.8459 (mttm) REVERT: C 679 LYS cc_start: 0.8511 (mtpt) cc_final: 0.8291 (mtpt) REVERT: C 683 ARG cc_start: 0.7862 (mpt180) cc_final: 0.7449 (mmt90) REVERT: C 842 PHE cc_start: 0.7451 (m-80) cc_final: 0.6840 (m-80) outliers start: 78 outliers final: 51 residues processed: 627 average time/residue: 0.3005 time to fit residues: 267.2154 Evaluate side-chains 647 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 589 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 TYR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 719 ASN Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 376 VAL 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 664 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 809 SER 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 356 ARG Chi-restraints excluded: chain C residue 382 ARG Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain C residue 591 GLN 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 719 ASN Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 759 LEU 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: 0.0050 chunk 138 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 100 optimal weight: 0.0870 chunk 112 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.9374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN A 836 GLN A 862 GLN B 492 GLN B 643 ASN C 591 GLN ** C 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.116599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.098438 restraints weight = 28564.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.102087 restraints weight = 13845.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.104470 restraints weight = 8100.596| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 16782 Z= 0.157 Angle : 0.745 17.597 23079 Z= 0.352 Chirality : 0.049 0.298 2763 Planarity : 0.005 0.045 2880 Dihedral : 10.115 90.946 3246 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.66 % Allowed : 25.99 % Favored : 69.35 % 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: -0.78 (0.19), residues: 2052 helix: 0.18 (0.23), residues: 549 sheet: 0.21 (0.29), residues: 390 loop : -1.14 (0.19), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 273 HIS 0.007 0.001 HIS C 639 PHE 0.019 0.001 PHE B 396 TYR 0.032 0.002 TYR B 276 ARG 0.011 0.001 ARG B 764 Details of bonding type rmsd link_NAG-ASN : bond 0.00273 ( 27) link_NAG-ASN : angle 2.24231 ( 81) link_ALPHA1-6 : bond 0.01303 ( 3) link_ALPHA1-6 : angle 3.35560 ( 9) link_BETA1-4 : bond 0.00933 ( 15) link_BETA1-4 : angle 2.42323 ( 45) link_ALPHA1-3 : bond 0.00115 ( 3) link_ALPHA1-3 : angle 3.97297 ( 9) hydrogen bonds : bond 0.04159 ( 482) hydrogen bonds : angle 4.88458 ( 1278) SS BOND : bond 0.00997 ( 27) SS BOND : angle 2.19109 ( 54) covalent geometry : bond 0.00360 (16707) covalent geometry : angle 0.71333 (22881) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 600 time to evaluate : 1.727 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: 0.7978 (OUTLIER) cc_final: 0.7424 (tm-30) REVERT: A 194 GLU cc_start: 0.7494 (tp30) cc_final: 0.6887 (tp30) REVERT: A 198 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6721 (mt-10) REVERT: A 211 GLU cc_start: 0.8203 (tp30) cc_final: 0.7848 (tp30) REVERT: A 212 ILE cc_start: 0.8690 (mm) cc_final: 0.8356 (mm) REVERT: A 251 LEU cc_start: 0.8272 (tp) cc_final: 0.7764 (tt) REVERT: A 252 ILE cc_start: 0.8816 (mt) cc_final: 0.8419 (tt) REVERT: A 258 LEU cc_start: 0.8711 (mt) cc_final: 0.8442 (mm) REVERT: A 339 GLU cc_start: 0.7799 (tp30) cc_final: 0.7482 (tp30) REVERT: A 382 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7964 (mtt-85) REVERT: A 468 ASP cc_start: 0.7445 (t70) cc_final: 0.6903 (t70) REVERT: A 500 TYR cc_start: 0.8216 (t80) cc_final: 0.7807 (t80) REVERT: A 510 TYR cc_start: 0.7832 (m-80) cc_final: 0.7192 (m-80) REVERT: A 520 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8119 (mtmm) REVERT: A 648 MET cc_start: 0.8023 (mmp) cc_final: 0.7822 (mmp) REVERT: A 653 ARG cc_start: 0.7897 (ttm170) cc_final: 0.7460 (mtm-85) REVERT: A 665 GLN cc_start: 0.8496 (tt0) cc_final: 0.8243 (tp40) REVERT: A 675 MET cc_start: 0.7969 (mmm) cc_final: 0.7543 (mmm) REVERT: A 676 LYS cc_start: 0.8674 (mttt) cc_final: 0.8278 (mttm) REVERT: A 702 GLU cc_start: 0.7314 (mt-10) cc_final: 0.7021 (mt-10) REVERT: A 764 ARG cc_start: 0.7483 (ttt90) cc_final: 0.7098 (tpt90) REVERT: B 194 GLU cc_start: 0.7552 (tp30) cc_final: 0.7012 (tp30) REVERT: B 235 CYS cc_start: 0.5848 (m) cc_final: 0.5598 (m) REVERT: B 249 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7393 (mm-30) REVERT: B 252 ILE cc_start: 0.8624 (mt) cc_final: 0.8365 (tp) REVERT: B 273 TRP cc_start: 0.8815 (m-10) cc_final: 0.8539 (m-10) REVERT: B 308 ARG cc_start: 0.8119 (ptt180) cc_final: 0.7831 (ptt-90) REVERT: B 318 CYS cc_start: 0.5441 (p) cc_final: 0.4701 (p) REVERT: B 495 GLU cc_start: 0.7302 (pt0) cc_final: 0.7032 (pt0) REVERT: B 504 LYS cc_start: 0.8001 (mtpp) cc_final: 0.7788 (mtpp) REVERT: B 551 TYR cc_start: 0.8122 (m-80) cc_final: 0.7805 (m-80) REVERT: B 658 TYR cc_start: 0.8424 (m-80) cc_final: 0.8141 (m-80) REVERT: B 665 GLN cc_start: 0.8371 (tt0) cc_final: 0.8076 (tm-30) REVERT: B 676 LYS cc_start: 0.8621 (mttt) cc_final: 0.8378 (mttp) REVERT: C 147 GLN cc_start: 0.8083 (tm-30) cc_final: 0.7438 (tm-30) REVERT: C 194 GLU cc_start: 0.7461 (tp30) cc_final: 0.6957 (tp30) REVERT: C 249 GLU cc_start: 0.7392 (mm-30) cc_final: 0.6718 (mm-30) REVERT: C 251 LEU cc_start: 0.8413 (tp) cc_final: 0.8005 (tt) REVERT: C 252 ILE cc_start: 0.8779 (tp) cc_final: 0.8520 (tt) REVERT: C 295 LYS cc_start: 0.8744 (mptt) cc_final: 0.8444 (mptt) REVERT: C 318 CYS cc_start: 0.5595 (OUTLIER) cc_final: 0.4802 (p) REVERT: C 382 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7939 (mtt-85) REVERT: C 510 TYR cc_start: 0.7796 (m-80) cc_final: 0.7175 (m-80) REVERT: C 519 LEU cc_start: 0.8384 (mm) cc_final: 0.8102 (mp) REVERT: C 544 ASP cc_start: 0.8357 (t70) cc_final: 0.8151 (t0) REVERT: C 599 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8228 (tt) REVERT: C 601 ASP cc_start: 0.7063 (m-30) cc_final: 0.6642 (m-30) REVERT: C 604 LEU cc_start: 0.8658 (mp) cc_final: 0.8442 (mm) REVERT: C 642 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7861 (mm) REVERT: C 648 MET cc_start: 0.8044 (mmp) cc_final: 0.7656 (mmt) REVERT: C 653 ARG cc_start: 0.8049 (ttm170) cc_final: 0.7704 (mtt90) REVERT: C 669 GLN cc_start: 0.7585 (mp10) cc_final: 0.7044 (mp10) REVERT: C 676 LYS cc_start: 0.8810 (mttt) cc_final: 0.8545 (mttm) REVERT: C 683 ARG cc_start: 0.7915 (mpt180) cc_final: 0.7462 (mmt90) REVERT: C 764 ARG cc_start: 0.7356 (ttt90) cc_final: 0.6933 (tpt90) REVERT: C 842 PHE cc_start: 0.7517 (m-80) cc_final: 0.6847 (m-80) outliers start: 73 outliers final: 56 residues processed: 628 average time/residue: 0.3122 time to fit residues: 275.2468 Evaluate side-chains 652 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 589 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 151 TYR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 462 ASN Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 591 GLN Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 762 CYS Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 795 VAL 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 279 ILE Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 318 CYS 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 526 THR Chi-restraints excluded: chain C residue 591 GLN 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 750 GLU Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 763 ARG Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 837 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 35 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 200 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 179 optimal weight: 0.0570 chunk 201 optimal weight: 0.0670 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 ASN C 180 ASN C 197 ASN C 591 GLN ** C 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.117459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.099353 restraints weight = 28480.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.102990 restraints weight = 13837.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.105391 restraints weight = 8117.958| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 16782 Z= 0.131 Angle : 0.747 16.260 23079 Z= 0.352 Chirality : 0.048 0.298 2763 Planarity : 0.005 0.045 2880 Dihedral : 9.945 88.878 3246 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.28 % Allowed : 27.01 % Favored : 68.71 % 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: -0.75 (0.19), residues: 2052 helix: 0.13 (0.23), residues: 555 sheet: 0.26 (0.28), residues: 390 loop : -1.11 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 273 HIS 0.005 0.001 HIS C 639 PHE 0.018 0.001 PHE B 396 TYR 0.033 0.001 TYR A 276 ARG 0.010 0.001 ARG A 407 Details of bonding type rmsd link_NAG-ASN : bond 0.00279 ( 27) link_NAG-ASN : angle 2.19008 ( 81) link_ALPHA1-6 : bond 0.01396 ( 3) link_ALPHA1-6 : angle 3.34936 ( 9) link_BETA1-4 : bond 0.00952 ( 15) link_BETA1-4 : angle 2.37983 ( 45) link_ALPHA1-3 : bond 0.00019 ( 3) link_ALPHA1-3 : angle 3.98607 ( 9) hydrogen bonds : bond 0.03833 ( 482) hydrogen bonds : angle 4.84018 ( 1278) SS BOND : bond 0.00861 ( 27) SS BOND : angle 2.46623 ( 54) covalent geometry : bond 0.00307 (16707) covalent geometry : angle 0.71418 (22881) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 583 time to evaluate : 1.672 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: 0.7976 (OUTLIER) cc_final: 0.7423 (tm-30) REVERT: A 194 GLU cc_start: 0.7482 (tp30) cc_final: 0.6884 (tp30) REVERT: A 198 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6745 (mt-10) REVERT: A 211 GLU cc_start: 0.8193 (tp30) cc_final: 0.7845 (tp30) REVERT: A 212 ILE cc_start: 0.8677 (mm) cc_final: 0.8343 (mm) REVERT: A 251 LEU cc_start: 0.8259 (tp) cc_final: 0.7785 (tt) REVERT: A 252 ILE cc_start: 0.8813 (mt) cc_final: 0.8425 (tt) REVERT: A 339 GLU cc_start: 0.7793 (tp30) cc_final: 0.7468 (tp30) REVERT: A 382 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7960 (mtt-85) REVERT: A 468 ASP cc_start: 0.7415 (t70) cc_final: 0.6867 (t70) REVERT: A 500 TYR cc_start: 0.8182 (t80) cc_final: 0.7801 (t80) REVERT: A 510 TYR cc_start: 0.7789 (m-80) cc_final: 0.7172 (m-80) REVERT: A 520 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8117 (mtmm) REVERT: A 653 ARG cc_start: 0.7852 (ttm170) cc_final: 0.7427 (mtm-85) REVERT: A 665 GLN cc_start: 0.8497 (tt0) cc_final: 0.8089 (tp40) REVERT: A 675 MET cc_start: 0.7973 (mmm) cc_final: 0.7548 (mmm) REVERT: A 676 LYS cc_start: 0.8652 (mttt) cc_final: 0.8389 (mttp) REVERT: A 702 GLU cc_start: 0.7286 (mt-10) cc_final: 0.6982 (mt-10) REVERT: A 764 ARG cc_start: 0.7491 (ttt90) cc_final: 0.7122 (tpt90) REVERT: B 194 GLU cc_start: 0.7542 (tp30) cc_final: 0.7002 (tp30) REVERT: B 207 MET cc_start: 0.7684 (mmm) cc_final: 0.7466 (mmp) REVERT: B 249 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7270 (mm-30) REVERT: B 252 ILE cc_start: 0.8625 (mt) cc_final: 0.8344 (tp) REVERT: B 273 TRP cc_start: 0.8813 (m-10) cc_final: 0.8556 (m-10) REVERT: B 318 CYS cc_start: 0.5511 (p) cc_final: 0.4832 (p) REVERT: B 495 GLU cc_start: 0.7289 (pt0) cc_final: 0.7019 (pt0) REVERT: B 504 LYS cc_start: 0.7992 (mtpp) cc_final: 0.7779 (mtpp) REVERT: B 551 TYR cc_start: 0.8155 (m-80) cc_final: 0.7847 (m-80) REVERT: B 658 TYR cc_start: 0.8409 (m-80) cc_final: 0.8132 (m-80) REVERT: B 676 LYS cc_start: 0.8612 (mttt) cc_final: 0.8379 (mttp) REVERT: B 721 GLN cc_start: 0.8200 (tm-30) cc_final: 0.7947 (tm-30) REVERT: B 742 HIS cc_start: 0.7862 (m90) cc_final: 0.7519 (m90) REVERT: C 194 GLU cc_start: 0.7468 (tp30) cc_final: 0.6912 (tp30) REVERT: C 197 ASN cc_start: 0.7542 (m110) cc_final: 0.7060 (m-40) REVERT: C 249 GLU cc_start: 0.7326 (mm-30) cc_final: 0.6684 (mm-30) REVERT: C 251 LEU cc_start: 0.8414 (tp) cc_final: 0.8022 (tt) REVERT: C 252 ILE cc_start: 0.8760 (tp) cc_final: 0.8502 (tt) REVERT: C 295 LYS cc_start: 0.8744 (mptt) cc_final: 0.8444 (mptt) REVERT: C 347 LEU cc_start: 0.8365 (mt) cc_final: 0.8006 (tp) REVERT: C 382 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7960 (mtt-85) REVERT: C 510 TYR cc_start: 0.7781 (m-80) cc_final: 0.7152 (m-80) REVERT: C 519 LEU cc_start: 0.8380 (mm) cc_final: 0.8102 (mp) REVERT: C 544 ASP cc_start: 0.8349 (t70) cc_final: 0.8148 (t0) REVERT: C 599 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8203 (tt) REVERT: C 601 ASP cc_start: 0.7050 (m-30) cc_final: 0.6621 (m-30) REVERT: C 604 LEU cc_start: 0.8661 (mp) cc_final: 0.8452 (mm) REVERT: C 642 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7855 (mm) REVERT: C 648 MET cc_start: 0.8030 (mmp) cc_final: 0.7708 (mmt) REVERT: C 653 ARG cc_start: 0.8042 (ttm170) cc_final: 0.7616 (mtt90) REVERT: C 665 GLN cc_start: 0.8397 (tt0) cc_final: 0.8083 (tp40) REVERT: C 669 GLN cc_start: 0.7593 (mp10) cc_final: 0.7059 (mp10) REVERT: C 676 LYS cc_start: 0.8803 (mttt) cc_final: 0.8509 (mttm) REVERT: C 683 ARG cc_start: 0.7885 (mpt180) cc_final: 0.7525 (mmt90) REVERT: C 721 GLN cc_start: 0.8081 (tm-30) cc_final: 0.7527 (tp40) REVERT: C 842 PHE cc_start: 0.7505 (m-80) cc_final: 0.6844 (m-80) outliers start: 67 outliers final: 57 residues processed: 611 average time/residue: 0.3108 time to fit residues: 271.3595 Evaluate side-chains 647 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 584 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 151 TYR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 591 GLN Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 719 ASN Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 762 CYS Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 795 VAL 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 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 387 LEU Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 591 GLN 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 747 ILE 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 Chi-restraints excluded: chain C residue 837 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 206 optimal weight: 10.0000 chunk 203 optimal weight: 0.0870 chunk 135 optimal weight: 0.0670 chunk 146 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 24 optimal weight: 0.3980 chunk 20 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 178 optimal weight: 0.9980 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN ** B 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 ASN C 591 GLN ** C 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 636 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.117968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.099926 restraints weight = 28515.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.103575 restraints weight = 13848.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.105963 restraints weight = 8087.653| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 16782 Z= 0.128 Angle : 0.740 15.712 23079 Z= 0.346 Chirality : 0.048 0.351 2763 Planarity : 0.005 0.044 2880 Dihedral : 9.704 85.572 3246 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.09 % Allowed : 27.33 % Favored : 68.58 % 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: -0.72 (0.19), residues: 2052 helix: 0.16 (0.23), residues: 555 sheet: 0.32 (0.28), residues: 390 loop : -1.10 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 326 HIS 0.004 0.001 HIS C 639 PHE 0.016 0.001 PHE C 232 TYR 0.031 0.001 TYR A 276 ARG 0.009 0.001 ARG B 764 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 27) link_NAG-ASN : angle 2.14816 ( 81) link_ALPHA1-6 : bond 0.01457 ( 3) link_ALPHA1-6 : angle 3.38107 ( 9) link_BETA1-4 : bond 0.00953 ( 15) link_BETA1-4 : angle 2.39483 ( 45) link_ALPHA1-3 : bond 0.00062 ( 3) link_ALPHA1-3 : angle 3.97136 ( 9) hydrogen bonds : bond 0.03705 ( 482) hydrogen bonds : angle 4.78090 ( 1278) SS BOND : bond 0.00857 ( 27) SS BOND : angle 2.84972 ( 54) covalent geometry : bond 0.00302 (16707) covalent geometry : angle 0.70313 (22881) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6139.42 seconds wall clock time: 107 minutes 37.37 seconds (6457.37 seconds total)