Starting phenix.real_space_refine on Thu Sep 18 11:54:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rm0_19347/09_2025/8rm0_19347.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rm0_19347/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8rm0_19347/09_2025/8rm0_19347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rm0_19347/09_2025/8rm0_19347.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rm0_19347/09_2025/8rm0_19347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rm0_19347/09_2025/8rm0_19347.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 22, 'ARG:plan': 8, 'ASP:plan': 10, 'GLN:plan1': 8, 'PHE:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 3} 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: {'GLU:plan': 22, 'ARG:plan': 8, 'ASP:plan': 10, 'GLN:plan1': 8, 'PHE:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 3} 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: {'GLU:plan': 22, 'ARG:plan': 8, 'ASP:plan': 10, 'GLN:plan1': 8, 'PHE:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 3} 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: 3.81, per 1000 atoms: 0.23 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: 1.39 Conformation dependent library (CDL) restraints added in 769.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.41 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: 2.17 Time building geometry restraints manager: 1.86 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.940 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.420 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.010 0.000 ARG C 763 TYR 0.023 0.001 TYR C 327 PHE 0.014 0.001 PHE A 232 TRP 0.016 0.001 TRP C 791 HIS 0.009 0.001 HIS A 742 Details of bonding type rmsd covalent geometry : bond 0.00399 (16707) covalent geometry : angle 0.72451 (22881) SS BOND : bond 0.00352 ( 27) SS BOND : angle 1.64097 ( 54) hydrogen bonds : bond 0.19916 ( 482) hydrogen bonds : angle 7.25165 ( 1278) link_ALPHA1-3 : bond 0.00890 ( 3) link_ALPHA1-3 : angle 3.34429 ( 9) 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_NAG-ASN : bond 0.00439 ( 27) link_NAG-ASN : angle 3.29127 ( 81) *********************** 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 : 0.607 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: 0.7313 (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: 0.8144 (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: 0.7320 (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: 0.8233 (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: 0.8371 (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: 0.8304 (p) REVERT: A 349 ILE cc_start: 0.8576 (mt) cc_final: 0.8303 (mm) REVERT: A 384 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7718 (mp0) REVERT: A 468 ASP cc_start: 0.7204 (t70) cc_final: 0.6816 (t70) REVERT: A 495 GLU cc_start: 0.7222 (pt0) cc_final: 0.6950 (pt0) REVERT: A 500 TYR cc_start: 0.8349 (t80) cc_final: 0.7932 (t80) REVERT: A 510 TYR cc_start: 0.7943 (m-80) cc_final: 0.7374 (m-80) REVERT: A 537 ARG cc_start: 0.7428 (mtt-85) cc_final: 0.7145 (mtt-85) REVERT: A 540 VAL cc_start: 0.8284 (p) cc_final: 0.8069 (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: 0.7555 (mtp85) REVERT: A 653 ARG cc_start: 0.7901 (ttm170) cc_final: 0.7611 (mtm-85) REVERT: A 665 GLN cc_start: 0.8387 (tt0) cc_final: 0.8145 (tt0) REVERT: A 675 MET cc_start: 0.7928 (mmm) cc_final: 0.7709 (mmm) REVERT: A 676 LYS cc_start: 0.8632 (mttt) cc_final: 0.8292 (mttm) REVERT: A 680 ARG cc_start: 0.8402 (tpt-90) cc_final: 0.7945 (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: 0.8010 (tt) REVERT: B 194 GLU cc_start: 0.7396 (tp30) cc_final: 0.6816 (tp30) REVERT: B 198 GLU cc_start: 0.6961 (mt-10) cc_final: 0.6434 (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: 0.6660 (mm-30) REVERT: B 251 LEU cc_start: 0.8387 (tp) cc_final: 0.8019 (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: 0.8492 (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: 0.8440 (mptt) REVERT: B 308 ARG cc_start: 0.7883 (ptt-90) cc_final: 0.7619 (ptt-90) REVERT: B 338 ASN cc_start: 0.7648 (t0) cc_final: 0.7310 (t0) REVERT: B 339 GLU cc_start: 0.7623 (tp30) cc_final: 0.7247 (tp30) REVERT: B 341 THR cc_start: 0.8658 (m) cc_final: 0.8428 (p) REVERT: B 347 LEU cc_start: 0.8348 (mt) cc_final: 0.8144 (mp) REVERT: B 349 ILE cc_start: 0.8515 (mt) cc_final: 0.8275 (mm) REVERT: B 372 ARG cc_start: 0.7225 (ptt90) cc_final: 0.6966 (ptt90) REVERT: B 396 PHE cc_start: 0.7847 (t80) cc_final: 0.7575 (t80) REVERT: B 468 ASP cc_start: 0.7069 (t70) cc_final: 0.6708 (t0) REVERT: B 483 CYS cc_start: 0.4869 (t) cc_final: 0.4414 (t) REVERT: B 495 GLU cc_start: 0.7202 (pt0) cc_final: 0.6902 (pt0) REVERT: B 504 LYS cc_start: 0.8015 (mtpt) cc_final: 0.7810 (mtpp) REVERT: B 535 ASN cc_start: 0.7294 (t0) cc_final: 0.7040 (t0) REVERT: B 537 ARG cc_start: 0.7492 (mtt-85) cc_final: 0.7183 (mtt-85) REVERT: B 540 VAL cc_start: 0.8226 (p) cc_final: 0.8006 (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: 0.7544 (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: 0.8106 (m-80) REVERT: B 665 GLN cc_start: 0.8423 (tt0) cc_final: 0.7970 (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: 0.7706 (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: 0.7729 (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: 0.7700 (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: 0.7211 (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: 0.7881 (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: 0.8373 (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: 0.6933 (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: 0.7114 (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: 0.7493 (mpt180) REVERT: C 715 ILE cc_start: 0.8583 (tt) cc_final: 0.8367 (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: 0.1431 time to fit residues: 142.1220 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 : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.0870 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- 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 737 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** B 637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 753 ASN C 180 ASN C 225 HIS C 234 HIS C 314 HIS ** C 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 ASN C 836 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.113876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.096367 restraints weight = 28851.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.099906 restraints weight = 13874.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.102224 restraints weight = 8085.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.103762 restraints weight = 5375.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.104725 restraints weight = 3942.122| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 16782 Z= 0.256 Angle : 0.815 11.060 23079 Z= 0.398 Chirality : 0.053 0.340 2763 Planarity : 0.006 0.064 2880 Dihedral : 11.992 91.057 3246 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.00 % Allowed : 14.24 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.19), residues: 2052 helix: -0.27 (0.22), residues: 549 sheet: -0.07 (0.27), residues: 420 loop : -1.00 (0.19), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 407 TYR 0.026 0.002 TYR C 240 PHE 0.022 0.002 PHE B 539 TRP 0.019 0.002 TRP A 246 HIS 0.014 0.002 HIS C 639 Details of bonding type rmsd covalent geometry : bond 0.00556 (16707) covalent geometry : angle 0.78238 (22881) SS BOND : bond 0.00705 ( 27) SS BOND : angle 1.80172 ( 54) hydrogen bonds : bond 0.06143 ( 482) hydrogen bonds : angle 5.93993 ( 1278) link_ALPHA1-3 : bond 0.00388 ( 3) link_ALPHA1-3 : angle 3.72605 ( 9) link_ALPHA1-6 : bond 0.01361 ( 3) link_ALPHA1-6 : angle 3.11985 ( 9) link_BETA1-4 : bond 0.00833 ( 15) link_BETA1-4 : angle 2.55972 ( 45) link_NAG-ASN : bond 0.00449 ( 27) link_NAG-ASN : angle 2.83706 ( 81) *********************** 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 663 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 616 time to evaluate : 0.625 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: 0.7628 (t80) cc_final: 0.7293 (t80) REVERT: A 158 ILE cc_start: 0.8692 (mt) cc_final: 0.8311 (mm) REVERT: A 174 ASN cc_start: 0.8388 (t0) cc_final: 0.8170 (t0) REVERT: A 194 GLU cc_start: 0.7483 (tp30) cc_final: 0.6877 (tp30) REVERT: A 198 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6598 (mt-10) REVERT: A 211 GLU cc_start: 0.8192 (tp30) cc_final: 0.7832 (tp30) REVERT: A 251 LEU cc_start: 0.8182 (tp) cc_final: 0.7709 (tt) REVERT: A 252 ILE cc_start: 0.8777 (mt) cc_final: 0.8376 (tp) REVERT: A 258 LEU cc_start: 0.8693 (mt) cc_final: 0.8432 (mm) REVERT: A 315 ILE cc_start: 0.8519 (mm) cc_final: 0.8310 (mt) REVERT: A 334 LEU cc_start: 0.8721 (mt) cc_final: 0.8492 (mt) REVERT: A 438 ARG cc_start: 0.7553 (mmm160) cc_final: 0.7166 (tpt90) REVERT: A 444 VAL cc_start: 0.8326 (t) cc_final: 0.8005 (p) REVERT: A 468 ASP cc_start: 0.7307 (t70) cc_final: 0.6826 (t70) REVERT: A 495 GLU cc_start: 0.7000 (pt0) cc_final: 0.6763 (pt0) REVERT: A 500 TYR cc_start: 0.8397 (t80) cc_final: 0.7944 (t80) REVERT: A 510 TYR cc_start: 0.7876 (m-80) cc_final: 0.7338 (m-80) REVERT: A 540 VAL cc_start: 0.8309 (p) cc_final: 0.7866 (m) REVERT: A 591 GLN cc_start: 0.7272 (tt0) cc_final: 0.7049 (tt0) REVERT: A 624 HIS cc_start: 0.6382 (m-70) cc_final: 0.6114 (m-70) REVERT: A 635 VAL cc_start: 0.8052 (m) cc_final: 0.7772 (p) REVERT: A 675 MET cc_start: 0.7891 (mmm) cc_final: 0.7558 (mmm) REVERT: A 676 LYS cc_start: 0.8742 (mttt) cc_final: 0.8338 (mttm) REVERT: A 683 ARG cc_start: 0.7982 (mpt180) cc_final: 0.7740 (mmt-90) REVERT: A 702 GLU cc_start: 0.7286 (mt-10) cc_final: 0.6985 (mt-10) REVERT: A 803 SER cc_start: 0.8253 (t) cc_final: 0.7721 (p) REVERT: B 173 ILE cc_start: 0.8432 (mt) cc_final: 0.8225 (mt) REVERT: B 206 VAL cc_start: 0.8168 (m) cc_final: 0.7691 (p) REVERT: B 249 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7306 (mm-30) REVERT: B 252 ILE cc_start: 0.8669 (mt) cc_final: 0.8353 (tp) REVERT: B 273 TRP cc_start: 0.8853 (m-10) cc_final: 0.8594 (m-10) REVERT: B 298 MET cc_start: 0.7584 (mmm) cc_final: 0.7349 (mmm) REVERT: B 315 ILE cc_start: 0.8405 (mm) cc_final: 0.8198 (mt) REVERT: B 339 GLU cc_start: 0.7657 (tp30) cc_final: 0.7435 (tp30) REVERT: B 360 TYR cc_start: 0.8185 (t80) cc_final: 0.7759 (t80) REVERT: B 386 VAL cc_start: 0.8716 (m) cc_final: 0.8475 (t) REVERT: B 396 PHE cc_start: 0.7927 (t80) cc_final: 0.7669 (t80) REVERT: B 468 ASP cc_start: 0.7250 (t70) cc_final: 0.6738 (t0) REVERT: B 495 GLU cc_start: 0.7312 (pt0) cc_final: 0.7041 (pt0) REVERT: B 504 LYS cc_start: 0.8108 (mtpt) cc_final: 0.7801 (mtpp) REVERT: B 510 TYR cc_start: 0.7830 (m-80) cc_final: 0.7559 (m-80) REVERT: B 535 ASN cc_start: 0.7452 (t0) cc_final: 0.7185 (t0) REVERT: B 551 TYR cc_start: 0.8124 (m-80) cc_final: 0.7805 (m-80) REVERT: B 591 GLN cc_start: 0.7277 (tt0) cc_final: 0.7039 (tt0) REVERT: B 611 LEU cc_start: 0.7463 (tp) cc_final: 0.7099 (tp) REVERT: B 635 VAL cc_start: 0.8049 (m) cc_final: 0.7806 (p) REVERT: B 658 TYR cc_start: 0.8459 (m-80) cc_final: 0.8147 (m-80) REVERT: B 665 GLN cc_start: 0.8362 (tt0) cc_final: 0.7975 (tm-30) REVERT: B 672 ASP cc_start: 0.8102 (m-30) cc_final: 0.7891 (m-30) REVERT: B 676 LYS cc_start: 0.8701 (mttt) cc_final: 0.8325 (mttm) REVERT: C 191 LEU cc_start: 0.8530 (tp) cc_final: 0.8287 (tt) REVERT: C 193 THR cc_start: 0.8083 (t) cc_final: 0.7856 (t) REVERT: C 194 GLU cc_start: 0.7448 (tp30) cc_final: 0.6838 (tp30) REVERT: C 197 ASN cc_start: 0.7520 (m110) cc_final: 0.7193 (m-40) REVERT: C 198 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6429 (mt-10) REVERT: C 206 VAL cc_start: 0.8143 (p) cc_final: 0.7932 (m) REVERT: C 212 ILE cc_start: 0.8648 (mm) cc_final: 0.8444 (mm) REVERT: C 384 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7443 (mm-30) REVERT: C 468 ASP cc_start: 0.7386 (t70) cc_final: 0.6883 (t70) REVERT: C 489 ILE cc_start: 0.8618 (tt) cc_final: 0.8350 (tp) REVERT: C 500 TYR cc_start: 0.8248 (t80) cc_final: 0.7897 (t80) REVERT: C 510 TYR cc_start: 0.7885 (m-80) cc_final: 0.7316 (m-80) REVERT: C 540 VAL cc_start: 0.8358 (p) cc_final: 0.8104 (t) REVERT: C 544 ASP cc_start: 0.8308 (t70) cc_final: 0.8055 (t0) REVERT: C 551 TYR cc_start: 0.8286 (m-80) cc_final: 0.8032 (m-80) REVERT: C 591 GLN cc_start: 0.7248 (tt0) cc_final: 0.7010 (tt0) REVERT: C 599 ILE cc_start: 0.8297 (tp) cc_final: 0.8072 (mm) REVERT: C 601 ASP cc_start: 0.7116 (m-30) cc_final: 0.6805 (m-30) REVERT: C 611 LEU cc_start: 0.7637 (tp) cc_final: 0.7263 (tp) REVERT: C 648 MET cc_start: 0.8063 (mmt) cc_final: 0.7527 (mmp) REVERT: C 653 ARG cc_start: 0.7996 (ttm170) cc_final: 0.7553 (mtm-85) REVERT: C 654 ILE cc_start: 0.8550 (mt) cc_final: 0.7808 (mt) REVERT: C 656 TRP cc_start: 0.8610 (m100) cc_final: 0.8143 (m-90) REVERT: C 676 LYS cc_start: 0.8830 (mttt) cc_final: 0.8477 (mttm) REVERT: C 683 ARG cc_start: 0.7859 (mpt180) cc_final: 0.7629 (mpt180) REVERT: C 711 ILE cc_start: 0.8702 (pt) cc_final: 0.8493 (mp) REVERT: C 715 ILE cc_start: 0.8728 (tt) cc_final: 0.8510 (mt) REVERT: C 724 ASN cc_start: 0.7985 (t0) cc_final: 0.7726 (t0) REVERT: C 773 VAL cc_start: 0.8698 (t) cc_final: 0.8484 (m) REVERT: C 842 PHE cc_start: 0.7662 (m-10) cc_final: 0.7385 (m-80) outliers start: 47 outliers final: 25 residues processed: 632 average time/residue: 0.1388 time to fit residues: 124.8554 Evaluate side-chains 607 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 582 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 390 ASN 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 390 ASN Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 666 THR 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 128 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 172 optimal weight: 0.0570 chunk 30 optimal weight: 0.7980 chunk 105 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 184 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 HIS A 643 ASN B 451 HIS B 637 HIS B 643 ASN B 836 GLN C 225 HIS C 314 HIS C 535 ASN C 636 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.116442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.098467 restraints weight = 29289.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.102040 restraints weight = 14087.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.104394 restraints weight = 8231.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.105976 restraints weight = 5515.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.107001 restraints weight = 4075.475| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 16782 Z= 0.136 Angle : 0.714 11.577 23079 Z= 0.340 Chirality : 0.047 0.299 2763 Planarity : 0.005 0.062 2880 Dihedral : 11.409 91.472 3246 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.90 % Allowed : 18.58 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.19), residues: 2052 helix: 0.08 (0.23), residues: 546 sheet: 0.07 (0.28), residues: 399 loop : -1.02 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 407 TYR 0.020 0.001 TYR C 474 PHE 0.015 0.001 PHE A 396 TRP 0.018 0.001 TRP C 326 HIS 0.006 0.001 HIS C 639 Details of bonding type rmsd covalent geometry : bond 0.00315 (16707) covalent geometry : angle 0.67807 (22881) SS BOND : bond 0.00677 ( 27) SS BOND : angle 1.94973 ( 54) hydrogen bonds : bond 0.04506 ( 482) hydrogen bonds : angle 5.37466 ( 1278) link_ALPHA1-3 : bond 0.00151 ( 3) link_ALPHA1-3 : angle 4.05637 ( 9) link_ALPHA1-6 : bond 0.01283 ( 3) link_ALPHA1-6 : angle 3.05155 ( 9) link_BETA1-4 : bond 0.00971 ( 15) link_BETA1-4 : angle 2.30120 ( 45) link_NAG-ASN : bond 0.00310 ( 27) link_NAG-ASN : angle 2.62371 ( 81) *********************** 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 652 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 591 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 PHE cc_start: 0.7630 (t80) cc_final: 0.7288 (t80) REVERT: A 158 ILE cc_start: 0.8605 (mt) cc_final: 0.8261 (mm) REVERT: A 172 MET cc_start: 0.7793 (mtm) cc_final: 0.7587 (mtp) REVERT: A 194 GLU cc_start: 0.7443 (tp30) cc_final: 0.6806 (tp30) REVERT: A 197 ASN cc_start: 0.7743 (m-40) cc_final: 0.7531 (m-40) REVERT: A 198 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6468 (mt-10) REVERT: A 211 GLU cc_start: 0.8131 (tp30) cc_final: 0.7662 (tp30) REVERT: A 235 CYS cc_start: 0.5662 (m) cc_final: 0.5334 (m) REVERT: A 251 LEU cc_start: 0.8207 (tp) cc_final: 0.7709 (tt) REVERT: A 252 ILE cc_start: 0.8803 (mt) cc_final: 0.8397 (tp) REVERT: A 258 LEU cc_start: 0.8736 (mt) cc_final: 0.8475 (mm) REVERT: A 334 LEU cc_start: 0.8665 (mt) cc_final: 0.8401 (mt) REVERT: A 341 THR cc_start: 0.8681 (m) cc_final: 0.8287 (p) REVERT: A 444 VAL cc_start: 0.8284 (t) cc_final: 0.7992 (p) REVERT: A 468 ASP cc_start: 0.7301 (t70) cc_final: 0.6800 (t70) REVERT: A 500 TYR cc_start: 0.8321 (t80) cc_final: 0.7893 (t80) REVERT: A 510 TYR cc_start: 0.7733 (m-80) cc_final: 0.7211 (m-80) REVERT: A 591 GLN cc_start: 0.7253 (tt0) cc_final: 0.7041 (tt0) REVERT: A 624 HIS cc_start: 0.6348 (m-70) cc_final: 0.6118 (m-70) REVERT: A 653 ARG cc_start: 0.7854 (ttm170) cc_final: 0.7597 (mtm-85) REVERT: A 675 MET cc_start: 0.7876 (mmm) cc_final: 0.7542 (mmm) REVERT: A 676 LYS cc_start: 0.8650 (mttt) cc_final: 0.8296 (mttm) REVERT: A 702 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6898 (mt-10) REVERT: A 803 SER cc_start: 0.8241 (t) cc_final: 0.7737 (p) REVERT: B 173 ILE cc_start: 0.8441 (mt) cc_final: 0.8202 (mt) REVERT: B 206 VAL cc_start: 0.8281 (m) cc_final: 0.7877 (p) REVERT: B 207 MET cc_start: 0.7496 (mmm) cc_final: 0.7145 (mmm) REVERT: B 235 CYS cc_start: 0.5869 (m) cc_final: 0.5610 (m) REVERT: B 252 ILE cc_start: 0.8728 (mt) cc_final: 0.8356 (tp) REVERT: B 273 TRP cc_start: 0.8832 (m-10) cc_final: 0.8473 (m-10) REVERT: B 339 GLU cc_start: 0.7641 (tp30) cc_final: 0.7436 (tp30) REVERT: B 356 ARG cc_start: 0.7812 (tpp-160) cc_final: 0.7543 (tpp-160) REVERT: B 396 PHE cc_start: 0.7886 (t80) cc_final: 0.7640 (t80) REVERT: B 468 ASP cc_start: 0.7205 (t70) cc_final: 0.6687 (t0) REVERT: B 495 GLU cc_start: 0.7239 (pt0) cc_final: 0.6983 (pt0) REVERT: B 510 TYR cc_start: 0.7714 (m-80) cc_final: 0.7503 (m-80) REVERT: B 551 TYR cc_start: 0.8111 (m-80) cc_final: 0.7783 (m-80) REVERT: B 658 TYR cc_start: 0.8442 (m-80) cc_final: 0.8159 (m-80) REVERT: B 665 GLN cc_start: 0.8298 (tt0) cc_final: 0.7972 (tm-30) REVERT: B 676 LYS cc_start: 0.8696 (mttt) cc_final: 0.8423 (mttp) REVERT: B 707 TYR cc_start: 0.8312 (m-10) cc_final: 0.8039 (m-10) REVERT: B 721 GLN cc_start: 0.7963 (tm-30) cc_final: 0.7726 (tm-30) REVERT: B 810 TYR cc_start: 0.8026 (m-80) cc_final: 0.7824 (m-80) REVERT: C 191 LEU cc_start: 0.8508 (tp) cc_final: 0.8289 (tt) REVERT: C 193 THR cc_start: 0.8058 (t) cc_final: 0.7826 (t) REVERT: C 194 GLU cc_start: 0.7341 (tp30) cc_final: 0.6825 (tp30) REVERT: C 197 ASN cc_start: 0.7427 (m110) cc_final: 0.7160 (m-40) REVERT: C 198 GLU cc_start: 0.6863 (mt-10) cc_final: 0.6265 (mt-10) REVERT: C 231 GLU cc_start: 0.7219 (mt-10) cc_final: 0.7000 (mt-10) REVERT: C 252 ILE cc_start: 0.8756 (tp) cc_final: 0.8516 (tt) REVERT: C 295 LYS cc_start: 0.8710 (mptt) cc_final: 0.8411 (mptt) REVERT: C 384 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7373 (mm-30) REVERT: C 468 ASP cc_start: 0.7301 (t70) cc_final: 0.6773 (t70) REVERT: C 500 TYR cc_start: 0.8180 (t80) cc_final: 0.7585 (t80) REVERT: C 504 LYS cc_start: 0.8094 (ttmm) cc_final: 0.7786 (ttmm) REVERT: C 510 TYR cc_start: 0.7730 (m-80) cc_final: 0.7183 (m-80) REVERT: C 516 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7584 (mt) REVERT: C 540 VAL cc_start: 0.8260 (p) cc_final: 0.7968 (t) REVERT: C 544 ASP cc_start: 0.8292 (t70) cc_final: 0.8077 (t0) REVERT: C 551 TYR cc_start: 0.8259 (m-80) cc_final: 0.8015 (m-80) REVERT: C 591 GLN cc_start: 0.7147 (tt0) cc_final: 0.6864 (tt0) REVERT: C 599 ILE cc_start: 0.8327 (tp) cc_final: 0.8001 (mm) REVERT: C 601 ASP cc_start: 0.7108 (m-30) cc_final: 0.6743 (m-30) REVERT: C 642 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7926 (mm) REVERT: C 646 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7440 (tmm-80) REVERT: C 648 MET cc_start: 0.8093 (mmt) cc_final: 0.7415 (mmt) REVERT: C 654 ILE cc_start: 0.8569 (mt) cc_final: 0.8088 (mt) REVERT: C 656 TRP cc_start: 0.8498 (m100) cc_final: 0.8119 (m-90) REVERT: C 676 LYS cc_start: 0.8851 (mttt) cc_final: 0.8434 (mttm) REVERT: C 683 ARG cc_start: 0.7899 (mpt180) cc_final: 0.7413 (mmt90) REVERT: C 715 ILE cc_start: 0.8741 (tt) cc_final: 0.8505 (mt) REVERT: C 724 ASN cc_start: 0.7890 (t0) cc_final: 0.7655 (t0) REVERT: C 842 PHE cc_start: 0.7570 (m-10) cc_final: 0.7365 (m-80) outliers start: 61 outliers final: 45 residues processed: 613 average time/residue: 0.1371 time to fit residues: 120.5775 Evaluate side-chains 622 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 574 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 316 LEU Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 489 ILE 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 686 VAL Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 167 LEU 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 344 LEU Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 516 LEU 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 650 MET 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 837 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 177 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 141 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 156 optimal weight: 0.7980 chunk 168 optimal weight: 1.9990 chunk 206 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 HIS A 643 ASN A 665 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 535 ASN B 643 ASN C 314 HIS C 600 ASN C 637 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.111894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.094176 restraints weight = 29006.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.097659 restraints weight = 14136.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.099947 restraints weight = 8330.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.101502 restraints weight = 5590.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.102466 restraints weight = 4120.599| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 16782 Z= 0.320 Angle : 0.851 18.558 23079 Z= 0.417 Chirality : 0.054 0.399 2763 Planarity : 0.006 0.052 2880 Dihedral : 11.530 92.893 3246 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 6.00 % Allowed : 18.52 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.18), residues: 2052 helix: -0.30 (0.22), residues: 546 sheet: -0.31 (0.28), residues: 384 loop : -1.30 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 407 TYR 0.028 0.002 TYR C 706 PHE 0.020 0.002 PHE A 396 TRP 0.022 0.002 TRP A 720 HIS 0.018 0.002 HIS C 639 Details of bonding type rmsd covalent geometry : bond 0.00692 (16707) covalent geometry : angle 0.81152 (22881) SS BOND : bond 0.00824 ( 27) SS BOND : angle 2.86693 ( 54) hydrogen bonds : bond 0.06754 ( 482) hydrogen bonds : angle 5.77254 ( 1278) link_ALPHA1-3 : bond 0.00561 ( 3) link_ALPHA1-3 : angle 4.13033 ( 9) link_ALPHA1-6 : bond 0.00968 ( 3) link_ALPHA1-6 : angle 3.19437 ( 9) link_BETA1-4 : bond 0.00951 ( 15) link_BETA1-4 : angle 2.58534 ( 45) link_NAG-ASN : bond 0.00629 ( 27) link_NAG-ASN : angle 2.80504 ( 81) *********************** 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 685 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 591 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 PHE cc_start: 0.7654 (t80) cc_final: 0.7287 (t80) REVERT: A 194 GLU cc_start: 0.7522 (tp30) cc_final: 0.6944 (tp30) REVERT: A 198 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6714 (mt-10) REVERT: A 205 ASP cc_start: 0.7339 (t0) cc_final: 0.7127 (t0) REVERT: A 211 GLU cc_start: 0.8250 (tp30) cc_final: 0.7912 (tp30) REVERT: A 251 LEU cc_start: 0.8222 (tp) cc_final: 0.7753 (tt) REVERT: A 252 ILE cc_start: 0.8790 (mt) cc_final: 0.8389 (tp) REVERT: A 258 LEU cc_start: 0.8723 (mt) cc_final: 0.8449 (mm) REVERT: A 334 LEU cc_start: 0.8750 (mt) cc_final: 0.8532 (mt) REVERT: A 438 ARG cc_start: 0.7585 (mmm160) cc_final: 0.7214 (tpt90) REVERT: A 444 VAL cc_start: 0.8349 (t) cc_final: 0.8067 (p) REVERT: A 468 ASP cc_start: 0.7403 (t70) cc_final: 0.6866 (t70) REVERT: A 500 TYR cc_start: 0.8392 (t80) cc_final: 0.7747 (t80) REVERT: A 510 TYR cc_start: 0.7984 (m-80) cc_final: 0.7388 (m-80) REVERT: A 516 LEU cc_start: 0.7893 (mt) cc_final: 0.7679 (mp) REVERT: A 520 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8127 (mtmm) REVERT: A 586 LEU cc_start: 0.5879 (OUTLIER) cc_final: 0.5592 (mm) REVERT: A 599 ILE cc_start: 0.8775 (mm) cc_final: 0.8417 (tt) REVERT: A 624 HIS cc_start: 0.6394 (m-70) cc_final: 0.6189 (m-70) REVERT: A 675 MET cc_start: 0.7912 (mmm) cc_final: 0.7563 (mmm) REVERT: A 676 LYS cc_start: 0.8738 (mttt) cc_final: 0.8356 (mttm) REVERT: A 683 ARG cc_start: 0.8002 (mpt180) cc_final: 0.7768 (mmt-90) REVERT: A 702 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7055 (mt-10) REVERT: B 173 ILE cc_start: 0.8425 (mt) cc_final: 0.8195 (mt) REVERT: B 206 VAL cc_start: 0.8175 (m) cc_final: 0.7790 (p) REVERT: B 249 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7485 (mm-30) REVERT: B 252 ILE cc_start: 0.8743 (mt) cc_final: 0.8385 (tp) REVERT: B 273 TRP cc_start: 0.8840 (m-10) cc_final: 0.8558 (m-10) REVERT: B 384 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7433 (mp0) REVERT: B 386 VAL cc_start: 0.8715 (m) cc_final: 0.8440 (t) REVERT: B 396 PHE cc_start: 0.8012 (t80) cc_final: 0.7709 (t80) REVERT: B 495 GLU cc_start: 0.7356 (pt0) cc_final: 0.7092 (pt0) REVERT: B 510 TYR cc_start: 0.7954 (m-80) cc_final: 0.7662 (m-80) REVERT: B 551 TYR cc_start: 0.8156 (m-80) cc_final: 0.7865 (m-80) REVERT: B 586 LEU cc_start: 0.5885 (OUTLIER) cc_final: 0.5668 (mm) REVERT: B 611 LEU cc_start: 0.7546 (tp) cc_final: 0.7005 (tp) REVERT: B 618 LEU cc_start: 0.8240 (mp) cc_final: 0.7973 (mt) REVERT: B 624 HIS cc_start: 0.6396 (m-70) cc_final: 0.6177 (m-70) REVERT: B 635 VAL cc_start: 0.8266 (m) cc_final: 0.7942 (t) REVERT: B 658 TYR cc_start: 0.8445 (m-80) cc_final: 0.8153 (m-80) REVERT: B 665 GLN cc_start: 0.8339 (tt0) cc_final: 0.8043 (tm-30) REVERT: B 676 LYS cc_start: 0.8713 (mttt) cc_final: 0.8333 (mttm) REVERT: C 191 LEU cc_start: 0.8619 (tp) cc_final: 0.8326 (tt) REVERT: C 193 THR cc_start: 0.8125 (t) cc_final: 0.7902 (t) REVERT: C 194 GLU cc_start: 0.7476 (tp30) cc_final: 0.6964 (tp30) REVERT: C 197 ASN cc_start: 0.7578 (m110) cc_final: 0.7304 (m-40) REVERT: C 198 GLU cc_start: 0.6879 (mt-10) cc_final: 0.6553 (mt-10) REVERT: C 211 GLU cc_start: 0.8113 (tp30) cc_final: 0.7881 (tp30) REVERT: C 252 ILE cc_start: 0.8753 (tp) cc_final: 0.8520 (tt) REVERT: C 386 VAL cc_start: 0.8773 (m) cc_final: 0.8438 (t) REVERT: C 468 ASP cc_start: 0.7487 (t70) cc_final: 0.6958 (t70) REVERT: C 495 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6897 (pm20) REVERT: C 510 TYR cc_start: 0.8021 (m-80) cc_final: 0.7444 (m-80) REVERT: C 516 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7802 (mt) REVERT: C 520 LYS cc_start: 0.8419 (mttt) cc_final: 0.8150 (mtpt) REVERT: C 540 VAL cc_start: 0.8355 (p) cc_final: 0.8126 (t) REVERT: C 544 ASP cc_start: 0.8298 (t70) cc_final: 0.8057 (t0) REVERT: C 600 ASN cc_start: 0.7683 (m-40) cc_final: 0.7423 (m-40) REVERT: C 601 ASP cc_start: 0.7072 (m-30) cc_final: 0.6752 (m-30) REVERT: C 611 LEU cc_start: 0.7709 (tp) cc_final: 0.7440 (tp) REVERT: C 629 MET cc_start: 0.7992 (mmm) cc_final: 0.7556 (mtp) REVERT: C 635 VAL cc_start: 0.8129 (m) cc_final: 0.7854 (t) REVERT: C 648 MET cc_start: 0.8055 (mmt) cc_final: 0.7516 (mmp) REVERT: C 653 ARG cc_start: 0.8037 (ttm170) cc_final: 0.7693 (mtm-85) REVERT: C 676 LYS cc_start: 0.8872 (mttt) cc_final: 0.8575 (mttm) REVERT: C 683 ARG cc_start: 0.7861 (mpt180) cc_final: 0.7579 (mpt180) REVERT: C 842 PHE cc_start: 0.7673 (m-10) cc_final: 0.7365 (m-80) outliers start: 94 outliers final: 65 residues processed: 630 average time/residue: 0.1411 time to fit residues: 127.1262 Evaluate side-chains 644 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 574 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 462 ASN Chi-restraints excluded: chain A residue 478 PHE Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 586 LEU 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 708 GLU 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 272 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 333 ILE 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 488 SER Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 586 LEU 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 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 825 VAL Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 321 VAL 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 509 THR Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 721 GLN Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 762 CYS Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 837 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 156 optimal weight: 2.9990 chunk 167 optimal weight: 0.6980 chunk 43 optimal weight: 0.1980 chunk 109 optimal weight: 1.9990 chunk 199 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN A 643 ASN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 GLN B 535 ASN B 643 ASN C 180 ASN C 225 HIS C 600 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.113034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.095329 restraints weight = 28857.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.098860 restraints weight = 14039.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.101183 restraints weight = 8227.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.102712 restraints weight = 5520.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.103756 restraints weight = 4078.145| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 16782 Z= 0.204 Angle : 0.780 19.895 23079 Z= 0.373 Chirality : 0.050 0.319 2763 Planarity : 0.005 0.050 2880 Dihedral : 11.185 93.646 3246 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 5.24 % Allowed : 22.22 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.18), residues: 2052 helix: -0.18 (0.22), residues: 546 sheet: -0.13 (0.29), residues: 372 loop : -1.30 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 612 TYR 0.022 0.002 TYR A 474 PHE 0.020 0.002 PHE A 396 TRP 0.022 0.002 TRP A 326 HIS 0.010 0.001 HIS C 639 Details of bonding type rmsd covalent geometry : bond 0.00451 (16707) covalent geometry : angle 0.74276 (22881) SS BOND : bond 0.00678 ( 27) SS BOND : angle 2.48558 ( 54) hydrogen bonds : bond 0.05175 ( 482) hydrogen bonds : angle 5.42484 ( 1278) link_ALPHA1-3 : bond 0.00468 ( 3) link_ALPHA1-3 : angle 4.31725 ( 9) link_ALPHA1-6 : bond 0.01176 ( 3) link_ALPHA1-6 : angle 3.19985 ( 9) link_BETA1-4 : bond 0.00999 ( 15) link_BETA1-4 : angle 2.47100 ( 45) link_NAG-ASN : bond 0.00390 ( 27) link_NAG-ASN : angle 2.60891 ( 81) *********************** 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 664 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 582 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 PHE cc_start: 0.7604 (t80) cc_final: 0.7289 (t80) REVERT: A 194 GLU cc_start: 0.7515 (tp30) cc_final: 0.6938 (tp30) REVERT: A 198 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6633 (mt-10) REVERT: A 205 ASP cc_start: 0.7345 (t0) cc_final: 0.7095 (t0) REVERT: A 211 GLU cc_start: 0.8173 (tp30) cc_final: 0.7861 (tp30) REVERT: A 251 LEU cc_start: 0.8176 (tp) cc_final: 0.7681 (tt) REVERT: A 252 ILE cc_start: 0.8795 (mt) cc_final: 0.8389 (tp) REVERT: A 258 LEU cc_start: 0.8744 (mt) cc_final: 0.8472 (mm) REVERT: A 334 LEU cc_start: 0.8701 (mt) cc_final: 0.8473 (mt) REVERT: A 382 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.8015 (mtt-85) REVERT: A 438 ARG cc_start: 0.7511 (mmm160) cc_final: 0.7095 (tpt90) REVERT: A 444 VAL cc_start: 0.8321 (t) cc_final: 0.8013 (p) REVERT: A 468 ASP cc_start: 0.7386 (t70) cc_final: 0.6875 (t70) REVERT: A 500 TYR cc_start: 0.8305 (t80) cc_final: 0.7718 (t80) REVERT: A 510 TYR cc_start: 0.7883 (m-80) cc_final: 0.7324 (m-80) REVERT: A 520 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8124 (mtmm) REVERT: A 653 ARG cc_start: 0.7927 (ttm170) cc_final: 0.7612 (mtt90) REVERT: A 675 MET cc_start: 0.7902 (mmm) cc_final: 0.7523 (mmm) REVERT: A 676 LYS cc_start: 0.8703 (mttt) cc_final: 0.8291 (mttm) REVERT: A 683 ARG cc_start: 0.8018 (mpt180) cc_final: 0.7775 (mmt-90) REVERT: A 702 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6988 (mt-10) REVERT: B 249 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7398 (mm-30) REVERT: B 252 ILE cc_start: 0.8706 (mt) cc_final: 0.8396 (tp) REVERT: B 273 TRP cc_start: 0.8842 (m-10) cc_final: 0.8572 (m-10) REVERT: B 356 ARG cc_start: 0.7823 (tpp-160) cc_final: 0.7562 (tpp-160) REVERT: B 386 VAL cc_start: 0.8707 (m) cc_final: 0.8403 (t) REVERT: B 396 PHE cc_start: 0.7938 (t80) cc_final: 0.7668 (t80) REVERT: B 408 TYR cc_start: 0.7618 (p90) cc_final: 0.7408 (p90) REVERT: B 495 GLU cc_start: 0.7327 (pt0) cc_final: 0.7085 (pt0) REVERT: B 510 TYR cc_start: 0.7843 (m-80) cc_final: 0.7574 (m-80) REVERT: B 551 TYR cc_start: 0.8164 (m-80) cc_final: 0.7866 (m-80) REVERT: B 618 LEU cc_start: 0.8243 (mp) cc_final: 0.7999 (mt) REVERT: B 635 VAL cc_start: 0.8071 (m) cc_final: 0.7742 (t) REVERT: B 658 TYR cc_start: 0.8453 (m-80) cc_final: 0.8173 (m-80) REVERT: B 665 GLN cc_start: 0.8324 (tt0) cc_final: 0.8043 (tm-30) REVERT: B 676 LYS cc_start: 0.8679 (mttt) cc_final: 0.8385 (mttp) REVERT: B 810 TYR cc_start: 0.8006 (m-80) cc_final: 0.7671 (m-10) REVERT: B 825 VAL cc_start: 0.8254 (OUTLIER) cc_final: 0.7841 (p) REVERT: C 191 LEU cc_start: 0.8519 (tp) cc_final: 0.8213 (tt) REVERT: C 194 GLU cc_start: 0.7428 (tp30) cc_final: 0.6938 (tp30) REVERT: C 198 GLU cc_start: 0.6854 (mt-10) cc_final: 0.6539 (mt-10) REVERT: C 211 GLU cc_start: 0.8073 (tp30) cc_final: 0.7842 (tp30) REVERT: C 252 ILE cc_start: 0.8791 (tp) cc_final: 0.8577 (tt) REVERT: C 382 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7909 (mtt-85) REVERT: C 468 ASP cc_start: 0.7336 (t70) cc_final: 0.6823 (t70) REVERT: C 510 TYR cc_start: 0.7931 (m-80) cc_final: 0.7281 (m-80) REVERT: C 516 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7723 (mt) REVERT: C 520 LYS cc_start: 0.8322 (mttt) cc_final: 0.8039 (mtpt) REVERT: C 526 THR cc_start: 0.8682 (t) cc_final: 0.8477 (p) REVERT: C 540 VAL cc_start: 0.8210 (p) cc_final: 0.8005 (t) REVERT: C 544 ASP cc_start: 0.8323 (t70) cc_final: 0.8083 (t0) REVERT: C 600 ASN cc_start: 0.7666 (m110) cc_final: 0.7410 (m110) REVERT: C 601 ASP cc_start: 0.7039 (m-30) cc_final: 0.6663 (m-30) REVERT: C 604 LEU cc_start: 0.8668 (mp) cc_final: 0.8463 (mp) REVERT: C 629 MET cc_start: 0.8099 (mmm) cc_final: 0.7858 (mtp) REVERT: C 635 VAL cc_start: 0.7950 (m) cc_final: 0.7683 (t) REVERT: C 642 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7886 (mm) REVERT: C 648 MET cc_start: 0.8147 (mmt) cc_final: 0.7630 (mmp) REVERT: C 653 ARG cc_start: 0.7993 (ttm170) cc_final: 0.7656 (mtm-85) REVERT: C 656 TRP cc_start: 0.8594 (m100) cc_final: 0.8204 (m-90) REVERT: C 676 LYS cc_start: 0.8869 (mttt) cc_final: 0.8561 (mttm) REVERT: C 683 ARG cc_start: 0.7887 (mpt180) cc_final: 0.7570 (mpt180) REVERT: C 721 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7327 (tp-100) outliers start: 82 outliers final: 60 residues processed: 616 average time/residue: 0.1238 time to fit residues: 109.0009 Evaluate side-chains 649 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 582 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 341 THR 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 540 VAL 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 660 SER Chi-restraints excluded: chain A residue 686 VAL 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 214 LEU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 390 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 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 811 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 382 ARG Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 462 ASN Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 719 ASN Chi-restraints excluded: chain C residue 721 GLN Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 762 CYS Chi-restraints excluded: chain C residue 763 ARG Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 837 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 206 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 193 optimal weight: 0.0980 chunk 16 optimal weight: 1.9990 chunk 127 optimal weight: 0.0370 chunk 121 optimal weight: 0.1980 chunk 50 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 chunk 203 optimal weight: 0.9980 chunk 187 optimal weight: 3.9990 overall best weight: 0.3658 ------------------------------------------------------------------------------- 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 B 639 HIS B 643 ASN C 197 ASN C 314 HIS C 591 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.116519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.098922 restraints weight = 28753.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.102510 restraints weight = 13856.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.104866 restraints weight = 8056.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.106435 restraints weight = 5363.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.107358 restraints weight = 3925.222| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 16782 Z= 0.119 Angle : 0.710 15.700 23079 Z= 0.336 Chirality : 0.047 0.302 2763 Planarity : 0.005 0.047 2880 Dihedral : 10.732 93.854 3246 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 5.11 % Allowed : 23.24 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.19), residues: 2052 helix: 0.07 (0.23), residues: 546 sheet: 0.08 (0.29), residues: 372 loop : -1.19 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 407 TYR 0.023 0.001 TYR A 474 PHE 0.015 0.001 PHE A 396 TRP 0.022 0.001 TRP A 326 HIS 0.003 0.001 HIS C 639 Details of bonding type rmsd covalent geometry : bond 0.00275 (16707) covalent geometry : angle 0.67604 (22881) SS BOND : bond 0.00690 ( 27) SS BOND : angle 1.96852 ( 54) hydrogen bonds : bond 0.03734 ( 482) hydrogen bonds : angle 5.03628 ( 1278) link_ALPHA1-3 : bond 0.00120 ( 3) link_ALPHA1-3 : angle 4.19364 ( 9) link_ALPHA1-6 : bond 0.01413 ( 3) link_ALPHA1-6 : angle 3.11927 ( 9) link_BETA1-4 : bond 0.01075 ( 15) link_BETA1-4 : angle 2.44600 ( 45) link_NAG-ASN : bond 0.00340 ( 27) link_NAG-ASN : angle 2.38808 ( 81) *********************** 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 678 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 598 time to evaluate : 0.473 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: 0.7984 (tm-30) cc_final: 0.7489 (tm-30) REVERT: A 150 PHE cc_start: 0.7574 (t80) cc_final: 0.7318 (t80) REVERT: A 194 GLU cc_start: 0.7475 (tp30) cc_final: 0.6866 (tp30) REVERT: A 198 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6613 (mt-10) REVERT: A 205 ASP cc_start: 0.7451 (t0) cc_final: 0.7050 (t0) REVERT: A 211 GLU cc_start: 0.8149 (tp30) cc_final: 0.7725 (tp30) REVERT: A 251 LEU cc_start: 0.8160 (tp) cc_final: 0.7620 (tt) REVERT: A 252 ILE cc_start: 0.8780 (mt) cc_final: 0.8395 (tt) REVERT: A 258 LEU cc_start: 0.8734 (mt) cc_final: 0.8447 (mm) REVERT: A 276 TYR cc_start: 0.8216 (t80) cc_final: 0.8013 (t80) REVERT: A 334 LEU cc_start: 0.8621 (mt) cc_final: 0.8392 (mt) REVERT: A 340 LEU cc_start: 0.8560 (tp) cc_final: 0.8350 (tt) REVERT: A 382 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.8001 (mtt-85) REVERT: A 444 VAL cc_start: 0.8215 (t) cc_final: 0.7929 (p) REVERT: A 468 ASP cc_start: 0.7370 (t70) cc_final: 0.6860 (t70) REVERT: A 500 TYR cc_start: 0.8233 (t80) cc_final: 0.7680 (t80) REVERT: A 510 TYR cc_start: 0.7745 (m-80) cc_final: 0.7166 (m-80) REVERT: A 520 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8148 (mtmm) REVERT: A 653 ARG cc_start: 0.7909 (ttm170) cc_final: 0.7652 (mtm-85) REVERT: A 675 MET cc_start: 0.7862 (mmm) cc_final: 0.7502 (mmm) REVERT: A 676 LYS cc_start: 0.8643 (mttt) cc_final: 0.8289 (mttm) REVERT: A 702 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6880 (mt-10) REVERT: B 170 VAL cc_start: 0.8446 (OUTLIER) cc_final: 0.8231 (m) REVERT: B 249 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7224 (mm-30) REVERT: B 252 ILE cc_start: 0.8677 (mt) cc_final: 0.8344 (tp) REVERT: B 273 TRP cc_start: 0.8805 (m-10) cc_final: 0.8527 (m-10) REVERT: B 320 ASP cc_start: 0.7146 (t70) cc_final: 0.6795 (t0) REVERT: B 396 PHE cc_start: 0.7856 (t80) cc_final: 0.7635 (t80) REVERT: B 495 GLU cc_start: 0.7246 (pt0) cc_final: 0.6987 (pt0) REVERT: B 510 TYR cc_start: 0.7682 (m-80) cc_final: 0.7435 (m-80) REVERT: B 551 TYR cc_start: 0.8141 (m-80) cc_final: 0.7819 (m-80) REVERT: B 618 LEU cc_start: 0.8130 (mp) cc_final: 0.7910 (mt) REVERT: B 658 TYR cc_start: 0.8427 (m-80) cc_final: 0.8132 (m-80) REVERT: B 665 GLN cc_start: 0.8295 (tt0) cc_final: 0.7992 (tm-30) REVERT: B 676 LYS cc_start: 0.8666 (mttt) cc_final: 0.8378 (mttp) REVERT: B 772 VAL cc_start: 0.8313 (p) cc_final: 0.8021 (m) REVERT: C 191 LEU cc_start: 0.8389 (tp) cc_final: 0.8161 (tt) REVERT: C 194 GLU cc_start: 0.7456 (tp30) cc_final: 0.6917 (tp30) REVERT: C 198 GLU cc_start: 0.6870 (mt-10) cc_final: 0.6606 (mt-10) REVERT: C 211 GLU cc_start: 0.8034 (tp30) cc_final: 0.7767 (tp30) REVERT: C 347 LEU cc_start: 0.8382 (mt) cc_final: 0.8076 (tp) REVERT: C 382 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7929 (mtt-85) REVERT: C 468 ASP cc_start: 0.7321 (t70) cc_final: 0.6791 (t70) REVERT: C 510 TYR cc_start: 0.7729 (m-80) cc_final: 0.7157 (m-80) REVERT: C 516 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7637 (mt) REVERT: C 520 LYS cc_start: 0.8346 (mttt) cc_final: 0.8032 (mtpp) REVERT: C 526 THR cc_start: 0.8632 (t) cc_final: 0.8404 (p) REVERT: C 544 ASP cc_start: 0.8293 (t70) cc_final: 0.8083 (t0) REVERT: C 601 ASP cc_start: 0.7067 (m-30) cc_final: 0.6680 (m-30) REVERT: C 604 LEU cc_start: 0.8644 (mp) cc_final: 0.8394 (mp) REVERT: C 629 MET cc_start: 0.8017 (mmm) cc_final: 0.7684 (mtp) REVERT: C 642 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7846 (mm) REVERT: C 653 ARG cc_start: 0.7975 (ttm170) cc_final: 0.7582 (mtm-85) REVERT: C 656 TRP cc_start: 0.8517 (m100) cc_final: 0.8085 (m-90) REVERT: C 665 GLN cc_start: 0.8358 (tt0) cc_final: 0.8082 (tp40) REVERT: C 676 LYS cc_start: 0.8807 (mttt) cc_final: 0.8501 (mttm) REVERT: C 683 ARG cc_start: 0.7875 (mpt180) cc_final: 0.7525 (mpt180) REVERT: C 721 GLN cc_start: 0.7685 (tt0) cc_final: 0.7209 (tp40) outliers start: 80 outliers final: 56 residues processed: 631 average time/residue: 0.1315 time to fit residues: 117.4994 Evaluate side-chains 640 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 578 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 344 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 532 GLU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 710 ILE 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 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 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 710 ILE Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 221 GLU 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 533 MET 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 686 VAL Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 719 ASN Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 762 CYS Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 837 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 58 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 197 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 chunk 7 optimal weight: 0.1980 chunk 0 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 108 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN A 643 ASN B 535 ASN C 197 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.115095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.097573 restraints weight = 28712.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.101067 restraints weight = 13703.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.103366 restraints weight = 7969.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.104884 restraints weight = 5310.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.105929 restraints weight = 3920.679| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 16782 Z= 0.154 Angle : 0.728 14.580 23079 Z= 0.346 Chirality : 0.049 0.303 2763 Planarity : 0.005 0.046 2880 Dihedral : 10.591 93.665 3246 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 5.04 % Allowed : 24.20 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.19), residues: 2052 helix: 0.10 (0.23), residues: 546 sheet: 0.09 (0.28), residues: 390 loop : -1.12 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 407 TYR 0.026 0.002 TYR B 276 PHE 0.019 0.001 PHE B 232 TRP 0.022 0.001 TRP A 326 HIS 0.007 0.001 HIS C 639 Details of bonding type rmsd covalent geometry : bond 0.00350 (16707) covalent geometry : angle 0.69481 (22881) SS BOND : bond 0.00740 ( 27) SS BOND : angle 2.14395 ( 54) hydrogen bonds : bond 0.04364 ( 482) hydrogen bonds : angle 5.00039 ( 1278) link_ALPHA1-3 : bond 0.00183 ( 3) link_ALPHA1-3 : angle 4.05353 ( 9) link_ALPHA1-6 : bond 0.01263 ( 3) link_ALPHA1-6 : angle 3.22520 ( 9) link_BETA1-4 : bond 0.00970 ( 15) link_BETA1-4 : angle 2.42242 ( 45) link_NAG-ASN : bond 0.00301 ( 27) link_NAG-ASN : angle 2.34732 ( 81) *********************** 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 676 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 597 time to evaluate : 0.557 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: 0.7981 (OUTLIER) cc_final: 0.7479 (tm-30) REVERT: A 150 PHE cc_start: 0.7621 (t80) cc_final: 0.7364 (t80) REVERT: A 194 GLU cc_start: 0.7526 (tp30) cc_final: 0.6912 (tp30) REVERT: A 198 GLU cc_start: 0.7150 (mt-10) cc_final: 0.6666 (mt-10) REVERT: A 205 ASP cc_start: 0.7452 (t0) cc_final: 0.7087 (t0) REVERT: A 211 GLU cc_start: 0.8184 (tp30) cc_final: 0.7820 (tp30) REVERT: A 251 LEU cc_start: 0.8199 (tp) cc_final: 0.7717 (tt) REVERT: A 252 ILE cc_start: 0.8790 (mt) cc_final: 0.8405 (tt) REVERT: A 258 LEU cc_start: 0.8734 (mt) cc_final: 0.8448 (mm) REVERT: A 334 LEU cc_start: 0.8661 (mt) cc_final: 0.8424 (mt) REVERT: A 340 LEU cc_start: 0.8551 (tp) cc_final: 0.8348 (tt) REVERT: A 382 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8004 (mtt-85) REVERT: A 444 VAL cc_start: 0.8188 (t) cc_final: 0.7882 (p) REVERT: A 468 ASP cc_start: 0.7378 (t70) cc_final: 0.6855 (t70) REVERT: A 500 TYR cc_start: 0.8281 (t80) cc_final: 0.7642 (t80) REVERT: A 510 TYR cc_start: 0.7853 (m-80) cc_final: 0.7252 (m-80) REVERT: A 520 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8116 (mtmm) REVERT: A 653 ARG cc_start: 0.7911 (ttm170) cc_final: 0.7651 (mtm-85) REVERT: A 675 MET cc_start: 0.7895 (mmm) cc_final: 0.7539 (mmm) REVERT: A 676 LYS cc_start: 0.8668 (mttt) cc_final: 0.8292 (mttm) REVERT: A 702 GLU cc_start: 0.7246 (mt-10) cc_final: 0.6962 (mt-10) REVERT: A 721 GLN cc_start: 0.8062 (tm-30) cc_final: 0.7285 (tm-30) REVERT: B 170 VAL cc_start: 0.8450 (OUTLIER) cc_final: 0.8233 (m) REVERT: B 249 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7252 (mm-30) REVERT: B 252 ILE cc_start: 0.8675 (mt) cc_final: 0.8362 (tp) REVERT: B 273 TRP cc_start: 0.8797 (m-10) cc_final: 0.8517 (m-10) REVERT: B 320 ASP cc_start: 0.7147 (t70) cc_final: 0.6757 (t0) REVERT: B 386 VAL cc_start: 0.8644 (m) cc_final: 0.8403 (t) REVERT: B 396 PHE cc_start: 0.7879 (t80) cc_final: 0.7603 (t80) REVERT: B 495 GLU cc_start: 0.7299 (pt0) cc_final: 0.7045 (pt0) REVERT: B 510 TYR cc_start: 0.7748 (m-80) cc_final: 0.7465 (m-80) REVERT: B 535 ASN cc_start: 0.7785 (t0) cc_final: 0.7559 (t0) REVERT: B 551 TYR cc_start: 0.8160 (m-80) cc_final: 0.7842 (m-80) REVERT: B 658 TYR cc_start: 0.8457 (m-80) cc_final: 0.8104 (m-80) REVERT: B 665 GLN cc_start: 0.8315 (tt0) cc_final: 0.8003 (tm-30) REVERT: B 676 LYS cc_start: 0.8667 (mttt) cc_final: 0.8378 (mttp) REVERT: C 147 GLN cc_start: 0.8060 (tm-30) cc_final: 0.7484 (tm-30) REVERT: C 191 LEU cc_start: 0.8424 (tp) cc_final: 0.8164 (tt) REVERT: C 194 GLU cc_start: 0.7512 (tp30) cc_final: 0.6998 (tp30) REVERT: C 211 GLU cc_start: 0.8071 (tp30) cc_final: 0.7770 (tp30) REVERT: C 251 LEU cc_start: 0.8411 (tp) cc_final: 0.8048 (tt) REVERT: C 295 LYS cc_start: 0.8722 (mptt) cc_final: 0.8416 (mptt) REVERT: C 382 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7913 (mtt-85) REVERT: C 468 ASP cc_start: 0.7326 (t70) cc_final: 0.6827 (t70) REVERT: C 510 TYR cc_start: 0.7830 (m-80) cc_final: 0.7203 (m-80) REVERT: C 516 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7698 (mt) REVERT: C 520 LYS cc_start: 0.8353 (mttt) cc_final: 0.8030 (mtpt) REVERT: C 526 THR cc_start: 0.8616 (t) cc_final: 0.8378 (p) REVERT: C 544 ASP cc_start: 0.8328 (t70) cc_final: 0.8105 (t0) REVERT: C 601 ASP cc_start: 0.7076 (m-30) cc_final: 0.6679 (m-30) REVERT: C 604 LEU cc_start: 0.8647 (mp) cc_final: 0.8441 (mp) REVERT: C 629 MET cc_start: 0.8122 (mmm) cc_final: 0.7850 (mtp) REVERT: C 642 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7852 (mm) REVERT: C 648 MET cc_start: 0.8331 (tpp) cc_final: 0.7998 (mmp) REVERT: C 653 ARG cc_start: 0.7944 (ttm170) cc_final: 0.7681 (mtt90) REVERT: C 656 TRP cc_start: 0.8540 (m100) cc_final: 0.8173 (m-90) REVERT: C 676 LYS cc_start: 0.8823 (mttt) cc_final: 0.8528 (mttm) REVERT: C 683 ARG cc_start: 0.7853 (mpt180) cc_final: 0.7423 (mmt90) REVERT: C 842 PHE cc_start: 0.7468 (m-80) cc_final: 0.7159 (m-80) outliers start: 79 outliers final: 58 residues processed: 627 average time/residue: 0.1300 time to fit residues: 115.2539 Evaluate side-chains 652 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 587 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 188 THR 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 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 603 ASN Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 719 ASN Chi-restraints excluded: chain A residue 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 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 333 ILE 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 619 MET Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 757 LEU 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 300 SER Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain C residue 382 ARG Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 462 ASN Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain C residue 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 762 CYS Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 837 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 205 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 66 optimal weight: 0.0030 chunk 92 optimal weight: 0.8980 chunk 173 optimal weight: 0.9990 chunk 163 optimal weight: 0.7980 chunk 81 optimal weight: 0.0470 chunk 142 optimal weight: 0.4980 overall best weight: 0.4088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN A 591 GLN A 836 GLN B 492 GLN C 197 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.116693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.099167 restraints weight = 28768.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.102699 restraints weight = 13641.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.105034 restraints weight = 7908.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.106531 restraints weight = 5268.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.107556 restraints weight = 3900.305| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 16782 Z= 0.120 Angle : 0.720 17.946 23079 Z= 0.341 Chirality : 0.048 0.295 2763 Planarity : 0.005 0.045 2880 Dihedral : 10.341 92.588 3246 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.60 % Allowed : 25.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.19), residues: 2052 helix: 0.21 (0.23), residues: 537 sheet: 0.21 (0.28), residues: 390 loop : -1.10 (0.19), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 407 TYR 0.032 0.001 TYR A 276 PHE 0.023 0.001 PHE C 232 TRP 0.023 0.001 TRP A 326 HIS 0.012 0.001 HIS B 799 Details of bonding type rmsd covalent geometry : bond 0.00275 (16707) covalent geometry : angle 0.68629 (22881) SS BOND : bond 0.00823 ( 27) SS BOND : angle 2.27229 ( 54) hydrogen bonds : bond 0.03616 ( 482) hydrogen bonds : angle 4.83238 ( 1278) link_ALPHA1-3 : bond 0.00085 ( 3) link_ALPHA1-3 : angle 4.07841 ( 9) link_ALPHA1-6 : bond 0.01407 ( 3) link_ALPHA1-6 : angle 3.20214 ( 9) link_BETA1-4 : bond 0.01002 ( 15) link_BETA1-4 : angle 2.37873 ( 45) link_NAG-ASN : bond 0.00324 ( 27) link_NAG-ASN : angle 2.23782 ( 81) *********************** 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 668 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 596 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLN cc_start: 0.7983 (tm-30) cc_final: 0.7531 (tm-30) REVERT: A 194 GLU cc_start: 0.7493 (tp30) cc_final: 0.6900 (tp30) REVERT: A 198 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6671 (mt-10) REVERT: A 205 ASP cc_start: 0.7462 (t0) cc_final: 0.7058 (t0) REVERT: A 211 GLU cc_start: 0.8141 (tp30) cc_final: 0.7784 (tp30) REVERT: A 251 LEU cc_start: 0.8227 (tp) cc_final: 0.7737 (tt) REVERT: A 252 ILE cc_start: 0.8772 (mt) cc_final: 0.8405 (tt) REVERT: A 334 LEU cc_start: 0.8620 (mt) cc_final: 0.8393 (mt) REVERT: A 382 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8006 (mtt-85) REVERT: A 468 ASP cc_start: 0.7347 (t70) cc_final: 0.6797 (t70) REVERT: A 492 GLN cc_start: 0.7290 (mp10) cc_final: 0.7073 (mm110) REVERT: A 500 TYR cc_start: 0.8246 (t80) cc_final: 0.7646 (t80) REVERT: A 510 TYR cc_start: 0.7758 (m-80) cc_final: 0.7155 (m-80) REVERT: A 520 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8125 (mtmm) REVERT: A 604 LEU cc_start: 0.8681 (mp) cc_final: 0.8411 (mm) REVERT: A 653 ARG cc_start: 0.7918 (ttm170) cc_final: 0.7612 (mtm-85) REVERT: A 675 MET cc_start: 0.7865 (mmm) cc_final: 0.7521 (mmm) REVERT: A 676 LYS cc_start: 0.8632 (mttt) cc_final: 0.8249 (mttm) REVERT: A 702 GLU cc_start: 0.7301 (mt-10) cc_final: 0.6980 (mt-10) REVERT: A 721 GLN cc_start: 0.8062 (tm-30) cc_final: 0.7585 (tm-30) REVERT: A 764 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.7009 (tpt90) REVERT: B 170 VAL cc_start: 0.8456 (OUTLIER) cc_final: 0.8232 (m) REVERT: B 249 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7249 (mm-30) REVERT: B 252 ILE cc_start: 0.8633 (mt) cc_final: 0.8373 (tp) REVERT: B 273 TRP cc_start: 0.8791 (m-10) cc_final: 0.8506 (m-10) REVERT: B 320 ASP cc_start: 0.7142 (t70) cc_final: 0.6782 (t0) REVERT: B 396 PHE cc_start: 0.7874 (t80) cc_final: 0.7647 (t80) REVERT: B 408 TYR cc_start: 0.7837 (p90) cc_final: 0.7538 (p90) REVERT: B 495 GLU cc_start: 0.7252 (pt0) cc_final: 0.6996 (pt0) REVERT: B 500 TYR cc_start: 0.8392 (t80) cc_final: 0.8018 (t80) REVERT: B 510 TYR cc_start: 0.7673 (m-80) cc_final: 0.7416 (m-80) REVERT: B 551 TYR cc_start: 0.8149 (m-80) cc_final: 0.7837 (m-80) REVERT: B 658 TYR cc_start: 0.8422 (m-80) cc_final: 0.8153 (m-80) REVERT: B 665 GLN cc_start: 0.8329 (tt0) cc_final: 0.7979 (tm-30) REVERT: B 676 LYS cc_start: 0.8648 (mttt) cc_final: 0.8372 (mttp) REVERT: B 707 TYR cc_start: 0.8065 (m-10) cc_final: 0.7850 (m-10) REVERT: C 147 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7508 (tm-30) REVERT: C 194 GLU cc_start: 0.7470 (tp30) cc_final: 0.6918 (tp30) REVERT: C 197 ASN cc_start: 0.7570 (m110) cc_final: 0.7072 (m-40) REVERT: C 211 GLU cc_start: 0.8035 (tp30) cc_final: 0.7735 (tp30) REVERT: C 249 GLU cc_start: 0.7324 (mm-30) cc_final: 0.6743 (mm-30) REVERT: C 251 LEU cc_start: 0.8396 (tp) cc_final: 0.8003 (tt) REVERT: C 295 LYS cc_start: 0.8720 (mptt) cc_final: 0.8449 (mptt) REVERT: C 347 LEU cc_start: 0.8376 (mt) cc_final: 0.8044 (tp) REVERT: C 382 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7967 (mtt-85) REVERT: C 468 ASP cc_start: 0.7299 (t70) cc_final: 0.6810 (t70) REVERT: C 510 TYR cc_start: 0.7722 (m-80) cc_final: 0.7162 (m-80) REVERT: C 516 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7621 (mt) REVERT: C 520 LYS cc_start: 0.8373 (mttt) cc_final: 0.7897 (mtpp) REVERT: C 544 ASP cc_start: 0.8336 (t70) cc_final: 0.8122 (t0) REVERT: C 601 ASP cc_start: 0.7046 (m-30) cc_final: 0.6684 (m-30) REVERT: C 604 LEU cc_start: 0.8598 (mp) cc_final: 0.8396 (mp) REVERT: C 629 MET cc_start: 0.8107 (mmm) cc_final: 0.7786 (mtp) REVERT: C 642 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7818 (mm) REVERT: C 648 MET cc_start: 0.8294 (tpp) cc_final: 0.7456 (mmp) REVERT: C 653 ARG cc_start: 0.7962 (ttm170) cc_final: 0.7591 (mtt90) REVERT: C 656 TRP cc_start: 0.8523 (m100) cc_final: 0.8163 (m-90) REVERT: C 665 GLN cc_start: 0.8361 (tt0) cc_final: 0.8070 (tp40) REVERT: C 676 LYS cc_start: 0.8773 (mttt) cc_final: 0.8444 (mttm) REVERT: C 683 ARG cc_start: 0.7850 (mpt180) cc_final: 0.7418 (mmt90) REVERT: C 721 GLN cc_start: 0.7664 (tt0) cc_final: 0.7152 (tp40) REVERT: C 842 PHE cc_start: 0.7468 (m-80) cc_final: 0.7061 (m-80) outliers start: 72 outliers final: 50 residues processed: 627 average time/residue: 0.1231 time to fit residues: 110.5232 Evaluate side-chains 640 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 583 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 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 619 MET Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 719 ASN Chi-restraints excluded: chain A residue 764 ARG 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 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 375 SER Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain C residue 382 ARG Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 719 ASN Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 762 CYS Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 837 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 189 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 188 optimal weight: 0.0670 chunk 162 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 535 ASN B 600 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.115872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.097997 restraints weight = 28628.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.101554 restraints weight = 13769.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.103909 restraints weight = 8083.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.105549 restraints weight = 5363.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.106603 restraints weight = 3898.244| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 16782 Z= 0.174 Angle : 0.767 19.513 23079 Z= 0.362 Chirality : 0.049 0.306 2763 Planarity : 0.005 0.044 2880 Dihedral : 10.262 90.934 3246 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.47 % Allowed : 26.12 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.19), residues: 2052 helix: 0.14 (0.23), residues: 543 sheet: 0.18 (0.28), residues: 390 loop : -1.13 (0.19), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 612 TYR 0.034 0.002 TYR A 276 PHE 0.019 0.002 PHE C 232 TRP 0.020 0.001 TRP A 326 HIS 0.012 0.001 HIS B 799 Details of bonding type rmsd covalent geometry : bond 0.00389 (16707) covalent geometry : angle 0.73440 (22881) SS BOND : bond 0.00600 ( 27) SS BOND : angle 2.45507 ( 54) hydrogen bonds : bond 0.04518 ( 482) hydrogen bonds : angle 4.94037 ( 1278) link_ALPHA1-3 : bond 0.00123 ( 3) link_ALPHA1-3 : angle 3.93146 ( 9) link_ALPHA1-6 : bond 0.01236 ( 3) link_ALPHA1-6 : angle 3.37836 ( 9) link_BETA1-4 : bond 0.00947 ( 15) link_BETA1-4 : angle 2.44643 ( 45) link_NAG-ASN : bond 0.00315 ( 27) link_NAG-ASN : angle 2.26683 ( 81) *********************** 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 657 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 587 time to evaluate : 0.378 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: 0.8012 (OUTLIER) cc_final: 0.7461 (tm-30) REVERT: A 194 GLU cc_start: 0.7528 (tp30) cc_final: 0.6937 (tp30) REVERT: A 198 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6703 (mt-10) REVERT: A 205 ASP cc_start: 0.7453 (t0) cc_final: 0.7050 (t0) REVERT: A 211 GLU cc_start: 0.8191 (tp30) cc_final: 0.7805 (tp30) REVERT: A 251 LEU cc_start: 0.8226 (tp) cc_final: 0.7749 (tt) REVERT: A 252 ILE cc_start: 0.8802 (mt) cc_final: 0.8412 (tt) REVERT: A 334 LEU cc_start: 0.8603 (mt) cc_final: 0.8375 (mt) REVERT: A 382 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7984 (mtt-85) REVERT: A 510 TYR cc_start: 0.7875 (m-80) cc_final: 0.7252 (m-80) REVERT: A 520 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8103 (mtmm) REVERT: A 604 LEU cc_start: 0.8750 (mp) cc_final: 0.8488 (mm) REVERT: A 675 MET cc_start: 0.7883 (mmm) cc_final: 0.7530 (mmm) REVERT: A 676 LYS cc_start: 0.8658 (mttt) cc_final: 0.8267 (mttm) REVERT: A 702 GLU cc_start: 0.7289 (mt-10) cc_final: 0.6990 (mt-10) REVERT: A 721 GLN cc_start: 0.8087 (tm-30) cc_final: 0.7611 (tm-30) REVERT: A 764 ARG cc_start: 0.7400 (ttt90) cc_final: 0.7017 (tpt90) REVERT: B 170 VAL cc_start: 0.8481 (OUTLIER) cc_final: 0.8273 (m) REVERT: B 249 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7287 (mm-30) REVERT: B 252 ILE cc_start: 0.8640 (mt) cc_final: 0.8385 (tp) REVERT: B 273 TRP cc_start: 0.8791 (m-10) cc_final: 0.8540 (m-10) REVERT: B 320 ASP cc_start: 0.7150 (t70) cc_final: 0.6752 (t0) REVERT: B 396 PHE cc_start: 0.7920 (t80) cc_final: 0.7699 (t80) REVERT: B 495 GLU cc_start: 0.7297 (pt0) cc_final: 0.7031 (pt0) REVERT: B 510 TYR cc_start: 0.7750 (m-80) cc_final: 0.7494 (m-80) REVERT: B 551 TYR cc_start: 0.8162 (m-80) cc_final: 0.7864 (m-80) REVERT: B 658 TYR cc_start: 0.8426 (m-80) cc_final: 0.8111 (m-80) REVERT: B 665 GLN cc_start: 0.8347 (tt0) cc_final: 0.8052 (tm-30) REVERT: B 676 LYS cc_start: 0.8647 (mttt) cc_final: 0.8372 (mttp) REVERT: B 803 SER cc_start: 0.8172 (t) cc_final: 0.7744 (p) REVERT: C 147 GLN cc_start: 0.8067 (tm-30) cc_final: 0.7512 (tm-30) REVERT: C 194 GLU cc_start: 0.7451 (tp30) cc_final: 0.6974 (tp30) REVERT: C 211 GLU cc_start: 0.8069 (tp30) cc_final: 0.7778 (tp30) REVERT: C 249 GLU cc_start: 0.7365 (mm-30) cc_final: 0.6751 (mm-30) REVERT: C 251 LEU cc_start: 0.8418 (tp) cc_final: 0.8052 (tt) REVERT: C 295 LYS cc_start: 0.8727 (mptt) cc_final: 0.8410 (mptt) REVERT: C 347 LEU cc_start: 0.8336 (mt) cc_final: 0.8023 (tp) REVERT: C 382 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7944 (mtt-85) REVERT: C 510 TYR cc_start: 0.7877 (m-80) cc_final: 0.7242 (m-80) REVERT: C 516 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7698 (mt) REVERT: C 520 LYS cc_start: 0.8390 (mttt) cc_final: 0.8061 (mtpt) REVERT: C 544 ASP cc_start: 0.8342 (t70) cc_final: 0.8141 (t0) REVERT: C 601 ASP cc_start: 0.7010 (m-30) cc_final: 0.6635 (m-30) REVERT: C 629 MET cc_start: 0.8167 (mmm) cc_final: 0.7893 (mtp) REVERT: C 642 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7855 (mm) REVERT: C 648 MET cc_start: 0.8318 (tpp) cc_final: 0.7388 (mmp) REVERT: C 653 ARG cc_start: 0.8014 (ttm170) cc_final: 0.7734 (mtt90) REVERT: C 665 GLN cc_start: 0.8388 (tt0) cc_final: 0.8102 (tp40) REVERT: C 676 LYS cc_start: 0.8837 (mttt) cc_final: 0.8533 (mttm) REVERT: C 683 ARG cc_start: 0.7899 (mpt180) cc_final: 0.7573 (mmt90) REVERT: C 721 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7173 (tp40) REVERT: C 842 PHE cc_start: 0.7541 (m-80) cc_final: 0.7074 (m-80) outliers start: 70 outliers final: 56 residues processed: 618 average time/residue: 0.1156 time to fit residues: 103.0357 Evaluate side-chains 649 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 585 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 307 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 520 LYS Chi-restraints excluded: chain A residue 532 GLU 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 650 MET Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 719 ASN Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 318 CYS 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 488 SER Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain C residue 382 ARG Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 462 ASN Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 619 MET Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 719 ASN Chi-restraints excluded: chain C residue 721 GLN Chi-restraints excluded: chain C residue 747 ILE Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 762 CYS Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 837 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 182 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 118 optimal weight: 0.5980 chunk 196 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 202 optimal weight: 0.0370 chunk 52 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN B 492 GLN ** B 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.117845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.099888 restraints weight = 28463.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.103512 restraints weight = 13698.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.105882 restraints weight = 7979.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.107477 restraints weight = 5295.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.108524 restraints weight = 3873.696| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 16782 Z= 0.128 Angle : 0.747 17.219 23079 Z= 0.350 Chirality : 0.048 0.298 2763 Planarity : 0.005 0.044 2880 Dihedral : 9.947 88.321 3246 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.28 % Allowed : 26.63 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.19), residues: 2052 helix: 0.34 (0.23), residues: 519 sheet: 0.30 (0.28), residues: 390 loop : -1.10 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 438 TYR 0.029 0.001 TYR A 276 PHE 0.023 0.001 PHE C 232 TRP 0.025 0.001 TRP B 326 HIS 0.012 0.001 HIS B 799 Details of bonding type rmsd covalent geometry : bond 0.00293 (16707) covalent geometry : angle 0.71595 (22881) SS BOND : bond 0.00608 ( 27) SS BOND : angle 2.24540 ( 54) hydrogen bonds : bond 0.03710 ( 482) hydrogen bonds : angle 4.79055 ( 1278) link_ALPHA1-3 : bond 0.00107 ( 3) link_ALPHA1-3 : angle 4.03443 ( 9) link_ALPHA1-6 : bond 0.01499 ( 3) link_ALPHA1-6 : angle 3.40096 ( 9) link_BETA1-4 : bond 0.00958 ( 15) link_BETA1-4 : angle 2.39347 ( 45) link_NAG-ASN : bond 0.00287 ( 27) link_NAG-ASN : angle 2.15412 ( 81) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 590 time to evaluate : 0.583 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: 0.7956 (OUTLIER) cc_final: 0.7412 (tm-30) REVERT: A 194 GLU cc_start: 0.7493 (tp30) cc_final: 0.6902 (tp30) REVERT: A 198 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6700 (mt-10) REVERT: A 205 ASP cc_start: 0.7485 (t0) cc_final: 0.7058 (t0) REVERT: A 211 GLU cc_start: 0.8146 (tp30) cc_final: 0.7791 (tp30) REVERT: A 251 LEU cc_start: 0.8228 (tp) cc_final: 0.7752 (tt) REVERT: A 252 ILE cc_start: 0.8755 (mt) cc_final: 0.8349 (tt) REVERT: A 334 LEU cc_start: 0.8556 (mt) cc_final: 0.8353 (mt) REVERT: A 382 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7926 (ptp-170) REVERT: A 468 ASP cc_start: 0.7367 (t70) cc_final: 0.6853 (t70) REVERT: A 500 TYR cc_start: 0.8170 (t80) cc_final: 0.7660 (t80) REVERT: A 510 TYR cc_start: 0.7792 (m-80) cc_final: 0.7149 (m-80) REVERT: A 520 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8142 (mtmm) REVERT: A 604 LEU cc_start: 0.8718 (mp) cc_final: 0.8488 (mm) REVERT: A 653 ARG cc_start: 0.7937 (ttm170) cc_final: 0.7650 (mtm-85) REVERT: A 675 MET cc_start: 0.7864 (mmm) cc_final: 0.7512 (mmm) REVERT: A 676 LYS cc_start: 0.8628 (mttt) cc_final: 0.8251 (mttm) REVERT: A 702 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6994 (mt-10) REVERT: A 721 GLN cc_start: 0.8115 (tm-30) cc_final: 0.7601 (tm-30) REVERT: A 764 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.6955 (tpt90) REVERT: B 147 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7342 (tm-30) REVERT: B 170 VAL cc_start: 0.8431 (OUTLIER) cc_final: 0.8215 (m) REVERT: B 249 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7299 (mm-30) REVERT: B 252 ILE cc_start: 0.8637 (mt) cc_final: 0.8378 (tp) REVERT: B 273 TRP cc_start: 0.8775 (m-10) cc_final: 0.8514 (m-10) REVERT: B 320 ASP cc_start: 0.7124 (t70) cc_final: 0.6761 (t0) REVERT: B 396 PHE cc_start: 0.7867 (t80) cc_final: 0.7659 (t80) REVERT: B 495 GLU cc_start: 0.7247 (pt0) cc_final: 0.6998 (pt0) REVERT: B 510 TYR cc_start: 0.7687 (m-80) cc_final: 0.7441 (m-80) REVERT: B 551 TYR cc_start: 0.8145 (m-80) cc_final: 0.7848 (m-80) REVERT: B 658 TYR cc_start: 0.8417 (m-80) cc_final: 0.8114 (m-80) REVERT: B 665 GLN cc_start: 0.8327 (tt0) cc_final: 0.8040 (tm-30) REVERT: B 676 LYS cc_start: 0.8613 (mttt) cc_final: 0.8371 (mttp) REVERT: B 707 TYR cc_start: 0.8044 (m-10) cc_final: 0.7796 (m-10) REVERT: B 721 GLN cc_start: 0.8114 (tm-30) cc_final: 0.7848 (tp40) REVERT: B 764 ARG cc_start: 0.7279 (mmm160) cc_final: 0.7063 (mmm160) REVERT: B 776 VAL cc_start: 0.8067 (t) cc_final: 0.7716 (m) REVERT: B 803 SER cc_start: 0.8132 (t) cc_final: 0.7699 (p) REVERT: C 147 GLN cc_start: 0.8069 (tm-30) cc_final: 0.7488 (tm-30) REVERT: C 194 GLU cc_start: 0.7464 (tp30) cc_final: 0.6922 (tp30) REVERT: C 197 ASN cc_start: 0.7550 (m110) cc_final: 0.7068 (m-40) REVERT: C 211 GLU cc_start: 0.8021 (tp30) cc_final: 0.7734 (tp30) REVERT: C 249 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6738 (mm-30) REVERT: C 251 LEU cc_start: 0.8386 (tp) cc_final: 0.8019 (tt) REVERT: C 295 LYS cc_start: 0.8729 (mptt) cc_final: 0.8444 (mptt) REVERT: C 382 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8085 (ptp-170) REVERT: C 510 TYR cc_start: 0.7790 (m-80) cc_final: 0.7169 (m-80) REVERT: C 516 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7656 (mt) REVERT: C 520 LYS cc_start: 0.8332 (mttt) cc_final: 0.8024 (mtpt) REVERT: C 601 ASP cc_start: 0.7021 (m-30) cc_final: 0.6643 (m-30) REVERT: C 629 MET cc_start: 0.8126 (mmm) cc_final: 0.7819 (mtp) REVERT: C 642 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7841 (mm) REVERT: C 648 MET cc_start: 0.8333 (tpp) cc_final: 0.7415 (mmp) REVERT: C 653 ARG cc_start: 0.7985 (ttm170) cc_final: 0.7653 (mtt90) REVERT: C 665 GLN cc_start: 0.8365 (tt0) cc_final: 0.8069 (tp40) REVERT: C 676 LYS cc_start: 0.8793 (mttt) cc_final: 0.8481 (mttm) REVERT: C 683 ARG cc_start: 0.7874 (mpt180) cc_final: 0.7463 (mmt90) REVERT: C 721 GLN cc_start: 0.7664 (tt0) cc_final: 0.7186 (tp40) REVERT: C 842 PHE cc_start: 0.7523 (m-80) cc_final: 0.6988 (m-80) outliers start: 67 outliers final: 49 residues processed: 620 average time/residue: 0.1240 time to fit residues: 110.3822 Evaluate side-chains 643 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 585 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 214 LEU 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 532 GLU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 591 GLN Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 719 ASN Chi-restraints excluded: chain A residue 764 ARG Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 318 CYS 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 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 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 300 SER Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain C residue 382 ARG Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 516 LEU 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 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 157 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 81 optimal weight: 0.0270 chunk 46 optimal weight: 0.0980 chunk 44 optimal weight: 0.0980 chunk 48 optimal weight: 2.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.116791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.099238 restraints weight = 28840.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.102790 restraints weight = 13907.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.105094 restraints weight = 8115.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.106615 restraints weight = 5414.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.107653 restraints weight = 4008.959| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16782 Z= 0.130 Angle : 0.746 17.168 23079 Z= 0.348 Chirality : 0.048 0.300 2763 Planarity : 0.005 0.044 2880 Dihedral : 9.780 85.579 3246 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.09 % Allowed : 27.59 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.19), residues: 2052 helix: 0.35 (0.23), residues: 519 sheet: 0.31 (0.28), residues: 390 loop : -1.11 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 407 TYR 0.030 0.001 TYR A 276 PHE 0.023 0.001 PHE C 232 TRP 0.023 0.001 TRP B 326 HIS 0.015 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00300 (16707) covalent geometry : angle 0.71468 (22881) SS BOND : bond 0.00600 ( 27) SS BOND : angle 2.23776 ( 54) hydrogen bonds : bond 0.03781 ( 482) hydrogen bonds : angle 4.78477 ( 1278) link_ALPHA1-3 : bond 0.00041 ( 3) link_ALPHA1-3 : angle 3.96738 ( 9) link_ALPHA1-6 : bond 0.01428 ( 3) link_ALPHA1-6 : angle 3.41686 ( 9) link_BETA1-4 : bond 0.00963 ( 15) link_BETA1-4 : angle 2.40876 ( 45) link_NAG-ASN : bond 0.00278 ( 27) link_NAG-ASN : angle 2.12650 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2905.02 seconds wall clock time: 50 minutes 38.30 seconds (3038.30 seconds total)