Starting phenix.real_space_refine on Mon Nov 18 13:40:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rm0_19347/11_2024/8rm0_19347.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rm0_19347/11_2024/8rm0_19347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rm0_19347/11_2024/8rm0_19347.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rm0_19347/11_2024/8rm0_19347.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rm0_19347/11_2024/8rm0_19347.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rm0_19347/11_2024/8rm0_19347.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 237 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 10386 2.51 5 N 2721 2.21 5 O 3102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 16311 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 5222 Classifications: {'peptide': 696} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 651} Chain breaks: 5 Unresolved non-hydrogen bonds: 458 Unresolved non-hydrogen angles: 572 Unresolved non-hydrogen dihedrals: 373 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 3, 'ASP:plan': 10, 'PHE:plan': 4, 'GLU:plan': 22, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 273 Chain: "B" Number of atoms: 5222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 5222 Classifications: {'peptide': 696} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 651} Chain breaks: 5 Unresolved non-hydrogen bonds: 458 Unresolved non-hydrogen angles: 572 Unresolved non-hydrogen dihedrals: 373 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 3, 'ASP:plan': 10, 'PHE:plan': 4, 'GLU:plan': 22, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 273 Chain: "C" Number of atoms: 5222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 5222 Classifications: {'peptide': 696} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 651} Chain breaks: 5 Unresolved non-hydrogen bonds: 458 Unresolved non-hydrogen angles: 572 Unresolved non-hydrogen dihedrals: 373 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 3, 'ASP:plan': 10, 'PHE:plan': 4, 'GLU:plan': 22, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 273 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 7.77, per 1000 atoms: 0.48 Number of scatterers: 16311 At special positions: 0 Unit cell: (111.15, 111.15, 151.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 3102 8.00 N 2721 7.00 C 10386 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 503 " distance=2.04 Simple disulfide: pdb=" SG CYS A 235 " - pdb=" SG CYS A 318 " distance=2.03 Simple disulfide: pdb=" SG CYS A 256 " - pdb=" SG CYS A 380 " distance=2.03 Simple disulfide: pdb=" SG CYS A 403 " - pdb=" SG CYS A 483 " distance=2.03 Simple disulfide: pdb=" SG CYS A 417 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 446 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 762 " - pdb=" SG CYS A 770 " distance=2.02 Simple disulfide: pdb=" SG CYS A 779 " - pdb=" SG CYS A 788 " distance=2.03 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 837 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 503 " distance=2.04 Simple disulfide: pdb=" SG CYS B 235 " - pdb=" SG CYS B 318 " distance=2.03 Simple disulfide: pdb=" SG CYS B 256 " - pdb=" SG CYS B 380 " distance=2.03 Simple disulfide: pdb=" SG CYS B 403 " - pdb=" SG CYS B 483 " distance=2.03 Simple disulfide: pdb=" SG CYS B 417 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 446 " - pdb=" SG CYS B 454 " distance=2.03 Simple disulfide: pdb=" SG CYS B 762 " - pdb=" SG CYS B 770 " distance=2.02 Simple disulfide: pdb=" SG CYS B 779 " - pdb=" SG CYS B 788 " distance=2.03 Simple disulfide: pdb=" SG CYS B 819 " - pdb=" SG CYS B 837 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 503 " distance=2.04 Simple disulfide: pdb=" SG CYS C 235 " - pdb=" SG CYS C 318 " distance=2.03 Simple disulfide: pdb=" SG CYS C 256 " - pdb=" SG CYS C 380 " distance=2.03 Simple disulfide: pdb=" SG CYS C 403 " - pdb=" SG CYS C 483 " distance=2.03 Simple disulfide: pdb=" SG CYS C 417 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 446 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 762 " - pdb=" SG CYS C 770 " distance=2.02 Simple disulfide: pdb=" SG CYS C 779 " - pdb=" SG CYS C 788 " distance=2.03 Simple disulfide: pdb=" SG CYS C 819 " - pdb=" SG CYS C 837 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA J 3 " - " MAN J 4 " " BMA N 3 " - " MAN N 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA J 3 " - " MAN J 5 " " BMA N 3 " - " MAN N 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1001 " - " ASN A 311 " " NAG A1002 " - " ASN A 346 " " NAG A1003 " - " ASN A 404 " " NAG A1004 " - " ASN A 524 " " NAG A1005 " - " ASN A 141 " " NAG B1001 " - " ASN B 311 " " NAG B1002 " - " ASN B 346 " " NAG B1003 " - " ASN B 404 " " NAG B1004 " - " ASN B 524 " " NAG B1005 " - " ASN B 141 " " NAG C1001 " - " ASN C 311 " " NAG C1002 " - " ASN C 346 " " NAG C1003 " - " ASN C 404 " " NAG C1004 " - " ASN C 524 " " NAG C1005 " - " ASN C 141 " " NAG D 1 " - " ASN A 183 " " NAG E 1 " - " ASN A 373 " " NAG F 1 " - " ASN A 390 " " NAG G 1 " - " ASN A 807 " " NAG H 1 " - " ASN B 183 " " NAG I 1 " - " ASN B 373 " " NAG J 1 " - " ASN B 390 " " NAG K 1 " - " ASN B 807 " " NAG L 1 " - " ASN C 183 " " NAG M 1 " - " ASN C 373 " " NAG N 1 " - " ASN C 390 " " NAG O 1 " - " ASN C 807 " Time building additional restraints: 4.53 Conformation dependent library (CDL) restraints added in 2.2 seconds 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4014 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 30 sheets defined 29.5% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 145 through 147 No H-bonds generated for 'chain 'A' and resid 145 through 147' Processing helix chain 'A' and resid 175 through 183 removed outlier: 3.644A pdb=" N SER A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 206 removed outlier: 3.719A pdb=" N GLU A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A 199 " --> pdb=" O MET A 195 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 219 removed outlier: 3.780A pdb=" N ASP A 219 " --> pdb=" O ASP A 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 216 through 219' Processing helix chain 'A' and resid 220 through 233 removed outlier: 3.876A pdb=" N GLU A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA A 233 " --> pdb=" O TYR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 276 Processing helix chain 'A' and resid 288 through 293 removed outlier: 3.935A pdb=" N LEU A 292 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 347 removed outlier: 3.765A pdb=" N SER A 345 " --> pdb=" O THR A 341 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN A 346 " --> pdb=" O LYS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 390 removed outlier: 3.624A pdb=" N VAL A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN A 390 " --> pdb=" O VAL A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 414 Processing helix chain 'A' and resid 415 through 419 removed outlier: 4.012A pdb=" N ASP A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 475 removed outlier: 3.682A pdb=" N MET A 475 " --> pdb=" O PHE A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 511 removed outlier: 4.037A pdb=" N LYS A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR A 509 " --> pdb=" O LEU A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 524 Processing helix chain 'A' and resid 534 through 538 removed outlier: 3.628A pdb=" N ALA A 538 " --> pdb=" O ASN A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 599 Processing helix chain 'A' and resid 619 through 623 Processing helix chain 'A' and resid 632 through 650 removed outlier: 3.671A pdb=" N GLN A 636 " --> pdb=" O MET A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 659 removed outlier: 4.017A pdb=" N TYR A 658 " --> pdb=" O ASP A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 669 removed outlier: 3.667A pdb=" N LEU A 664 " --> pdb=" O SER A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 681 removed outlier: 3.572A pdb=" N THR A 681 " --> pdb=" O VAL A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 876 removed outlier: 4.060A pdb=" N ILE A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA A 873 " --> pdb=" O VAL A 869 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A 876 " --> pdb=" O ILE A 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 175 through 183 removed outlier: 3.644A pdb=" N SER B 181 " --> pdb=" O ASN B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 206 removed outlier: 3.717A pdb=" N GLU B 194 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU B 199 " --> pdb=" O MET B 195 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL B 206 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 219 removed outlier: 3.779A pdb=" N ASP B 219 " --> pdb=" O ASP B 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 216 through 219' Processing helix chain 'B' and resid 220 through 233 removed outlier: 3.876A pdb=" N GLU B 231 " --> pdb=" O LYS B 227 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA B 233 " --> pdb=" O TYR B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 276 Processing helix chain 'B' and resid 288 through 293 removed outlier: 3.935A pdb=" N LEU B 292 " --> pdb=" O THR B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 347 removed outlier: 3.764A pdb=" N SER B 345 " --> pdb=" O THR B 341 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN B 346 " --> pdb=" O LYS B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 390 removed outlier: 3.625A pdb=" N VAL B 386 " --> pdb=" O ARG B 382 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 414 Processing helix chain 'B' and resid 415 through 419 removed outlier: 4.012A pdb=" N ASP B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 475 removed outlier: 3.683A pdb=" N MET B 475 " --> pdb=" O PHE B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 511 removed outlier: 4.037A pdb=" N LYS B 508 " --> pdb=" O LYS B 504 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR B 509 " --> pdb=" O LEU B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 524 Processing helix chain 'B' and resid 534 through 538 removed outlier: 3.627A pdb=" N ALA B 538 " --> pdb=" O ASN B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 599 Processing helix chain 'B' and resid 619 through 623 Processing helix chain 'B' and resid 632 through 650 removed outlier: 3.671A pdb=" N GLN B 636 " --> pdb=" O MET B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 659 removed outlier: 4.017A pdb=" N TYR B 658 " --> pdb=" O ASP B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 669 removed outlier: 3.667A pdb=" N LEU B 664 " --> pdb=" O SER B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 681 removed outlier: 3.573A pdb=" N THR B 681 " --> pdb=" O VAL B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 876 removed outlier: 4.061A pdb=" N ILE B 872 " --> pdb=" O LEU B 868 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA B 873 " --> pdb=" O VAL B 869 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS B 876 " --> pdb=" O ILE B 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 147 No H-bonds generated for 'chain 'C' and resid 145 through 147' Processing helix chain 'C' and resid 175 through 183 removed outlier: 3.644A pdb=" N SER C 181 " --> pdb=" O ASN C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 206 removed outlier: 3.718A pdb=" N GLU C 194 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU C 199 " --> pdb=" O MET C 195 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL C 206 " --> pdb=" O GLY C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 219 removed outlier: 3.778A pdb=" N ASP C 219 " --> pdb=" O ASP C 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 216 through 219' Processing helix chain 'C' and resid 220 through 233 removed outlier: 3.877A pdb=" N GLU C 231 " --> pdb=" O LYS C 227 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA C 233 " --> pdb=" O TYR C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 276 Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.936A pdb=" N LEU C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 347 removed outlier: 3.765A pdb=" N SER C 345 " --> pdb=" O THR C 341 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN C 346 " --> pdb=" O LYS C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 390 removed outlier: 3.624A pdb=" N VAL C 386 " --> pdb=" O ARG C 382 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN C 390 " --> pdb=" O VAL C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 414 Processing helix chain 'C' and resid 415 through 419 removed outlier: 4.012A pdb=" N ASP C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 475 removed outlier: 3.683A pdb=" N MET C 475 " --> pdb=" O PHE C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 511 removed outlier: 4.037A pdb=" N LYS C 508 " --> pdb=" O LYS C 504 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR C 509 " --> pdb=" O LEU C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 524 Processing helix chain 'C' and resid 534 through 538 removed outlier: 3.628A pdb=" N ALA C 538 " --> pdb=" O ASN C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'C' and resid 619 through 623 Processing helix chain 'C' and resid 632 through 650 removed outlier: 3.670A pdb=" N GLN C 636 " --> pdb=" O MET C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 659 removed outlier: 4.017A pdb=" N TYR C 658 " --> pdb=" O ASP C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 669 removed outlier: 3.668A pdb=" N LEU C 664 " --> pdb=" O SER C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 681 removed outlier: 3.572A pdb=" N THR C 681 " --> pdb=" O VAL C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 876 removed outlier: 4.060A pdb=" N ILE C 872 " --> pdb=" O LEU C 868 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA C 873 " --> pdb=" O VAL C 869 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS C 876 " --> pdb=" O ILE C 872 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 141 through 143 removed outlier: 3.929A pdb=" N GLN A 801 " --> pdb=" O LEU A 813 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 153 removed outlier: 7.372A pdb=" N LEU A 757 " --> pdb=" O ILE A 775 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE A 775 " --> pdb=" O LEU A 757 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU A 759 " --> pdb=" O VAL A 773 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL A 773 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N GLU A 761 " --> pdb=" O ASP A 771 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASP A 771 " --> pdb=" O GLU A 761 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 769 " --> pdb=" O ARG A 763 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ILE A 159 " --> pdb=" O CYS A 770 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N VAL A 772 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N THR A 161 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 10.823A pdb=" N LYS A 774 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 18.308A pdb=" N ARG A 163 " --> pdb=" O LYS A 774 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE A 159 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE A 715 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N THR A 161 " --> pdb=" O ARG A 713 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ARG A 713 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ARG A 163 " --> pdb=" O ILE A 711 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE A 711 " --> pdb=" O ARG A 163 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N SER A 168 " --> pdb=" O ILE A 615 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N THR A 617 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL A 170 " --> pdb=" O THR A 617 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 608 through 610 removed outlier: 8.228A pdb=" N TYR A 609 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL A 164 " --> pdb=" O TYR A 609 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE A 159 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE A 715 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N THR A 161 " --> pdb=" O ARG A 713 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ARG A 713 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ARG A 163 " --> pdb=" O ILE A 711 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE A 711 " --> pdb=" O ARG A 163 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ALA A 700 " --> pdb=" O THR A 692 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TYR A 688 " --> pdb=" O GLY A 704 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N TYR A 706 " --> pdb=" O VAL A 686 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N VAL A 686 " --> pdb=" O TYR A 706 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLU A 708 " --> pdb=" O SER A 684 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N SER A 684 " --> pdb=" O GLU A 708 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 495 through 498 removed outlier: 3.528A pdb=" N TYR A 236 " --> pdb=" O PHE A 317 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A 317 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N HIS A 314 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 250 through 251 Processing sheet with id=AA6, first strand: chain 'A' and resid 282 through 283 Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 Processing sheet with id=AA8, first strand: chain 'A' and resid 392 through 396 removed outlier: 3.749A pdb=" N GLU A 485 " --> pdb=" O THR A 395 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 790 through 792 removed outlier: 3.609A pdb=" N VAL A 790 " --> pdb=" O VAL A 882 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA A 792 " --> pdb=" O ILE A 880 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE A 880 " --> pdb=" O ALA A 792 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 836 through 837 Processing sheet with id=AB2, first strand: chain 'B' and resid 141 through 143 removed outlier: 3.929A pdb=" N GLN B 801 " --> pdb=" O LEU B 813 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 149 through 153 removed outlier: 7.372A pdb=" N LEU B 757 " --> pdb=" O ILE B 775 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ILE B 775 " --> pdb=" O LEU B 757 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N LEU B 759 " --> pdb=" O VAL B 773 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL B 773 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N GLU B 761 " --> pdb=" O ASP B 771 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP B 771 " --> pdb=" O GLU B 761 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 769 " --> pdb=" O ARG B 763 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ILE B 159 " --> pdb=" O CYS B 770 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N VAL B 772 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N THR B 161 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N LYS B 774 " --> pdb=" O THR B 161 " (cutoff:3.500A) removed outlier: 18.307A pdb=" N ARG B 163 " --> pdb=" O LYS B 774 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE B 159 " --> pdb=" O ILE B 715 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE B 715 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N THR B 161 " --> pdb=" O ARG B 713 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ARG B 713 " --> pdb=" O THR B 161 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ARG B 163 " --> pdb=" O ILE B 711 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE B 711 " --> pdb=" O ARG B 163 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N SER B 168 " --> pdb=" O ILE B 615 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N THR B 617 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL B 170 " --> pdb=" O THR B 617 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 608 through 610 removed outlier: 8.228A pdb=" N TYR B 609 " --> pdb=" O GLU B 162 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL B 164 " --> pdb=" O TYR B 609 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE B 159 " --> pdb=" O ILE B 715 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE B 715 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N THR B 161 " --> pdb=" O ARG B 713 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ARG B 713 " --> pdb=" O THR B 161 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ARG B 163 " --> pdb=" O ILE B 711 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE B 711 " --> pdb=" O ARG B 163 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ALA B 700 " --> pdb=" O THR B 692 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N TYR B 688 " --> pdb=" O GLY B 704 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N TYR B 706 " --> pdb=" O VAL B 686 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N VAL B 686 " --> pdb=" O TYR B 706 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLU B 708 " --> pdb=" O SER B 684 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N SER B 684 " --> pdb=" O GLU B 708 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 495 through 498 removed outlier: 3.500A pdb=" N GLU B 495 " --> pdb=" O LYS B 239 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR B 236 " --> pdb=" O PHE B 317 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE B 317 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N HIS B 314 " --> pdb=" O LEU B 542 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 250 through 251 Processing sheet with id=AB7, first strand: chain 'B' and resid 282 through 283 Processing sheet with id=AB8, first strand: chain 'B' and resid 348 through 349 Processing sheet with id=AB9, first strand: chain 'B' and resid 392 through 396 removed outlier: 3.748A pdb=" N GLU B 485 " --> pdb=" O THR B 395 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 790 through 792 removed outlier: 3.609A pdb=" N VAL B 790 " --> pdb=" O VAL B 882 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA B 792 " --> pdb=" O ILE B 880 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE B 880 " --> pdb=" O ALA B 792 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 836 through 837 Processing sheet with id=AC3, first strand: chain 'C' and resid 141 through 143 removed outlier: 3.928A pdb=" N GLN C 801 " --> pdb=" O LEU C 813 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 149 through 153 removed outlier: 7.373A pdb=" N LEU C 757 " --> pdb=" O ILE C 775 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE C 775 " --> pdb=" O LEU C 757 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU C 759 " --> pdb=" O VAL C 773 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL C 773 " --> pdb=" O LEU C 759 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N GLU C 761 " --> pdb=" O ASP C 771 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP C 771 " --> pdb=" O GLU C 761 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 769 " --> pdb=" O ARG C 763 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ILE C 159 " --> pdb=" O CYS C 770 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N VAL C 772 " --> pdb=" O ILE C 159 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N THR C 161 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N LYS C 774 " --> pdb=" O THR C 161 " (cutoff:3.500A) removed outlier: 18.307A pdb=" N ARG C 163 " --> pdb=" O LYS C 774 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE C 159 " --> pdb=" O ILE C 715 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE C 715 " --> pdb=" O ILE C 159 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N THR C 161 " --> pdb=" O ARG C 713 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ARG C 713 " --> pdb=" O THR C 161 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ARG C 163 " --> pdb=" O ILE C 711 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE C 711 " --> pdb=" O ARG C 163 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N SER C 168 " --> pdb=" O ILE C 615 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N THR C 617 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL C 170 " --> pdb=" O THR C 617 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 608 through 610 removed outlier: 8.228A pdb=" N TYR C 609 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL C 164 " --> pdb=" O TYR C 609 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE C 159 " --> pdb=" O ILE C 715 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE C 715 " --> pdb=" O ILE C 159 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N THR C 161 " --> pdb=" O ARG C 713 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ARG C 713 " --> pdb=" O THR C 161 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ARG C 163 " --> pdb=" O ILE C 711 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE C 711 " --> pdb=" O ARG C 163 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA C 700 " --> pdb=" O THR C 692 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N TYR C 688 " --> pdb=" O GLY C 704 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N TYR C 706 " --> pdb=" O VAL C 686 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N VAL C 686 " --> pdb=" O TYR C 706 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLU C 708 " --> pdb=" O SER C 684 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N SER C 684 " --> pdb=" O GLU C 708 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 495 through 498 removed outlier: 3.528A pdb=" N TYR C 236 " --> pdb=" O PHE C 317 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE C 317 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N HIS C 314 " --> pdb=" O LEU C 542 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 250 through 251 Processing sheet with id=AC8, first strand: chain 'C' and resid 282 through 283 Processing sheet with id=AC9, first strand: chain 'C' and resid 348 through 349 Processing sheet with id=AD1, first strand: chain 'C' and resid 392 through 396 removed outlier: 3.748A pdb=" N GLU C 485 " --> pdb=" O THR C 395 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 790 through 792 removed outlier: 3.609A pdb=" N VAL C 790 " --> pdb=" O VAL C 882 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA C 792 " --> pdb=" O ILE C 880 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE C 880 " --> pdb=" O ALA C 792 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 836 through 837 488 hydrogen bonds defined for protein. 1278 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.63 Time building geometry restraints manager: 5.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5190 1.35 - 1.47: 4178 1.47 - 1.59: 7192 1.59 - 1.71: 0 1.71 - 1.83: 147 Bond restraints: 16707 Sorted by residual: bond pdb=" C3 BMA F 3 " pdb=" O3 BMA F 3 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.37e+00 bond pdb=" C3 BMA N 3 " pdb=" O3 BMA N 3 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.09e+00 bond pdb=" C3 BMA J 3 " pdb=" O3 BMA J 3 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.05e+00 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.30e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.23e+00 ... (remaining 16702 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 21786 1.50 - 3.01: 892 3.01 - 4.51: 145 4.51 - 6.01: 40 6.01 - 7.52: 18 Bond angle restraints: 22881 Sorted by residual: angle pdb=" N LEU C 865 " pdb=" CA LEU C 865 " pdb=" C LEU C 865 " ideal model delta sigma weight residual 109.81 117.33 -7.52 2.21e+00 2.05e-01 1.16e+01 angle pdb=" N LEU A 865 " pdb=" CA LEU A 865 " pdb=" C LEU A 865 " ideal model delta sigma weight residual 109.81 117.29 -7.48 2.21e+00 2.05e-01 1.15e+01 angle pdb=" N LEU B 865 " pdb=" CA LEU B 865 " pdb=" C LEU B 865 " ideal model delta sigma weight residual 109.81 117.29 -7.48 2.21e+00 2.05e-01 1.15e+01 angle pdb=" N GLU B 439 " pdb=" CA GLU B 439 " pdb=" C GLU B 439 " ideal model delta sigma weight residual 107.23 112.61 -5.38 1.67e+00 3.59e-01 1.04e+01 angle pdb=" N GLU A 439 " pdb=" CA GLU A 439 " pdb=" C GLU A 439 " ideal model delta sigma weight residual 107.23 112.59 -5.36 1.67e+00 3.59e-01 1.03e+01 ... (remaining 22876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.30: 10143 21.30 - 42.60: 345 42.60 - 63.90: 87 63.90 - 85.20: 51 85.20 - 106.50: 21 Dihedral angle restraints: 10647 sinusoidal: 4446 harmonic: 6201 Sorted by residual: dihedral pdb=" CB CYS B 819 " pdb=" SG CYS B 819 " pdb=" SG CYS B 837 " pdb=" CB CYS B 837 " ideal model delta sinusoidal sigma weight residual -86.00 -156.13 70.13 1 1.00e+01 1.00e-02 6.34e+01 dihedral pdb=" CB CYS A 819 " pdb=" SG CYS A 819 " pdb=" SG CYS A 837 " pdb=" CB CYS A 837 " ideal model delta sinusoidal sigma weight residual -86.00 -156.13 70.13 1 1.00e+01 1.00e-02 6.34e+01 dihedral pdb=" CB CYS C 819 " pdb=" SG CYS C 819 " pdb=" SG CYS C 837 " pdb=" CB CYS C 837 " ideal model delta sinusoidal sigma weight residual -86.00 -156.11 70.11 1 1.00e+01 1.00e-02 6.33e+01 ... (remaining 10644 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2413 0.069 - 0.138: 326 0.138 - 0.207: 18 0.207 - 0.276: 3 0.276 - 0.345: 3 Chirality restraints: 2763 Sorted by residual: chirality pdb=" C1 NAG A1001 " pdb=" ND2 ASN A 311 " pdb=" C2 NAG A1001 " pdb=" O5 NAG A1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" C1 NAG B1001 " pdb=" ND2 ASN B 311 " pdb=" C2 NAG B1001 " pdb=" O5 NAG B1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" C1 NAG C1001 " pdb=" ND2 ASN C 311 " pdb=" C2 NAG C1001 " pdb=" O5 NAG C1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 2760 not shown) Planarity restraints: 2907 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 480 " 0.047 5.00e-02 4.00e+02 7.22e-02 8.35e+00 pdb=" N PRO C 481 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO C 481 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 481 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 480 " 0.047 5.00e-02 4.00e+02 7.18e-02 8.25e+00 pdb=" N PRO B 481 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 481 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 481 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 480 " 0.047 5.00e-02 4.00e+02 7.18e-02 8.25e+00 pdb=" N PRO A 481 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 481 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 481 " 0.039 5.00e-02 4.00e+02 ... (remaining 2904 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3184 2.78 - 3.31: 14691 3.31 - 3.84: 23999 3.84 - 4.37: 25386 4.37 - 4.90: 45685 Nonbonded interactions: 112945 Sorted by model distance: nonbonded pdb=" NH1 ARG A 438 " pdb=" O GLY A 440 " model vdw 2.251 3.120 nonbonded pdb=" NH1 ARG C 438 " pdb=" O GLY C 440 " model vdw 2.251 3.120 nonbonded pdb=" NH1 ARG B 438 " pdb=" O GLY B 440 " model vdw 2.252 3.120 nonbonded pdb=" O THR B 143 " pdb=" OG SER B 827 " model vdw 2.360 3.040 nonbonded pdb=" O THR A 143 " pdb=" OG SER A 827 " model vdw 2.360 3.040 ... (remaining 112940 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 36.530 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16707 Z= 0.272 Angle : 0.725 7.517 22881 Z= 0.375 Chirality : 0.048 0.345 2763 Planarity : 0.006 0.072 2880 Dihedral : 13.696 106.497 6552 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.19 % Allowed : 0.00 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.19), residues: 2052 helix: -0.53 (0.22), residues: 546 sheet: 0.62 (0.30), residues: 360 loop : -0.90 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 791 HIS 0.009 0.001 HIS A 742 PHE 0.014 0.001 PHE A 232 TYR 0.023 0.001 TYR C 327 ARG 0.010 0.000 ARG C 763 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 699 time to evaluate : 1.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 PHE cc_start: 0.7694 (t80) cc_final: 0.7314 (t80) REVERT: A 158 ILE cc_start: 0.8398 (mt) cc_final: 0.8189 (mm) REVERT: A 173 ILE cc_start: 0.8357 (mt) cc_final: 0.8145 (tt) REVERT: A 194 GLU cc_start: 0.7461 (tp30) cc_final: 0.6817 (tp30) REVERT: A 198 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6518 (mt-10) REVERT: A 211 GLU cc_start: 0.8202 (tp30) cc_final: 0.7913 (tp30) REVERT: A 221 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7321 (mt-10) REVERT: A 249 GLU cc_start: 0.7376 (mm-30) cc_final: 0.6839 (mm-30) REVERT: A 251 LEU cc_start: 0.8593 (tp) cc_final: 0.8234 (tt) REVERT: A 252 ILE cc_start: 0.8785 (mt) cc_final: 0.8210 (tp) REVERT: A 258 LEU cc_start: 0.8647 (mt) cc_final: 0.8442 (mm) REVERT: A 295 LYS cc_start: 0.8638 (mptt) cc_final: 0.8323 (mptt) REVERT: A 334 LEU cc_start: 0.8661 (mt) cc_final: 0.8369 (mt) REVERT: A 339 GLU cc_start: 0.7643 (tp30) cc_final: 0.7181 (tp30) REVERT: A 341 THR cc_start: 0.8675 (m) cc_final: 0.8302 (p) REVERT: A 349 ILE cc_start: 0.8576 (mt) cc_final: 0.8305 (mm) REVERT: A 384 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7719 (mp0) REVERT: A 468 ASP cc_start: 0.7204 (t70) cc_final: 0.6814 (t70) REVERT: A 495 GLU cc_start: 0.7222 (pt0) cc_final: 0.6948 (pt0) REVERT: A 500 TYR cc_start: 0.8349 (t80) cc_final: 0.7930 (t80) REVERT: A 510 TYR cc_start: 0.7943 (m-80) cc_final: 0.7375 (m-80) REVERT: A 537 ARG cc_start: 0.7428 (mtt-85) cc_final: 0.7146 (mtt-85) REVERT: A 540 VAL cc_start: 0.8284 (p) cc_final: 0.8067 (t) REVERT: A 591 GLN cc_start: 0.7405 (tt0) cc_final: 0.7096 (tt0) REVERT: A 652 ARG cc_start: 0.7796 (mtp85) cc_final: 0.7554 (mtp85) REVERT: A 653 ARG cc_start: 0.7901 (ttm170) cc_final: 0.7610 (mtm-85) REVERT: A 665 GLN cc_start: 0.8387 (tt0) cc_final: 0.8146 (tt0) REVERT: A 675 MET cc_start: 0.7928 (mmm) cc_final: 0.7710 (mmm) REVERT: A 676 LYS cc_start: 0.8632 (mttt) cc_final: 0.8293 (mttm) REVERT: A 680 ARG cc_start: 0.8402 (tpt-90) cc_final: 0.7944 (tpt-90) REVERT: A 702 GLU cc_start: 0.7403 (mt-10) cc_final: 0.7082 (mt-10) REVERT: A 803 SER cc_start: 0.8058 (t) cc_final: 0.7590 (p) REVERT: B 151 TYR cc_start: 0.7296 (p90) cc_final: 0.6872 (p90) REVERT: B 158 ILE cc_start: 0.8421 (mt) cc_final: 0.8131 (mm) REVERT: B 173 ILE cc_start: 0.8291 (mt) cc_final: 0.8011 (tt) REVERT: B 194 GLU cc_start: 0.7396 (tp30) cc_final: 0.6815 (tp30) REVERT: B 198 GLU cc_start: 0.6961 (mt-10) cc_final: 0.6435 (mt-10) REVERT: B 206 VAL cc_start: 0.8163 (m) cc_final: 0.7774 (p) REVERT: B 226 ARG cc_start: 0.8018 (mmt90) cc_final: 0.7555 (mmt90) REVERT: B 249 GLU cc_start: 0.7295 (mm-30) cc_final: 0.6659 (mm-30) REVERT: B 251 LEU cc_start: 0.8387 (tp) cc_final: 0.8020 (tt) REVERT: B 252 ILE cc_start: 0.8706 (mt) cc_final: 0.8251 (tp) REVERT: B 258 LEU cc_start: 0.8697 (mt) cc_final: 0.8491 (mm) REVERT: B 273 TRP cc_start: 0.8918 (m-10) cc_final: 0.8530 (m-10) REVERT: B 295 LYS cc_start: 0.8794 (mptt) cc_final: 0.8441 (mptt) REVERT: B 308 ARG cc_start: 0.7883 (ptt-90) cc_final: 0.7618 (ptt-90) REVERT: B 338 ASN cc_start: 0.7648 (t0) cc_final: 0.7309 (t0) REVERT: B 339 GLU cc_start: 0.7623 (tp30) cc_final: 0.7245 (tp30) REVERT: B 341 THR cc_start: 0.8658 (m) cc_final: 0.8427 (p) REVERT: B 347 LEU cc_start: 0.8348 (mt) cc_final: 0.8146 (mp) REVERT: B 349 ILE cc_start: 0.8515 (mt) cc_final: 0.8278 (mm) REVERT: B 360 TYR cc_start: 0.8055 (t80) cc_final: 0.7752 (t80) REVERT: B 372 ARG cc_start: 0.7225 (ptt90) cc_final: 0.6964 (ptt90) REVERT: B 396 PHE cc_start: 0.7847 (t80) cc_final: 0.7576 (t80) REVERT: B 468 ASP cc_start: 0.7069 (t70) cc_final: 0.6706 (t0) REVERT: B 483 CYS cc_start: 0.4869 (t) cc_final: 0.4413 (t) REVERT: B 495 GLU cc_start: 0.7202 (pt0) cc_final: 0.6899 (pt0) REVERT: B 504 LYS cc_start: 0.8015 (mtpt) cc_final: 0.7809 (mtpp) REVERT: B 535 ASN cc_start: 0.7294 (t0) cc_final: 0.7039 (t0) REVERT: B 537 ARG cc_start: 0.7492 (mtt-85) cc_final: 0.7184 (mtt-85) REVERT: B 540 VAL cc_start: 0.8226 (p) cc_final: 0.8005 (t) REVERT: B 551 TYR cc_start: 0.7994 (m-80) cc_final: 0.7771 (m-80) REVERT: B 590 VAL cc_start: 0.7744 (p) cc_final: 0.7542 (m) REVERT: B 591 GLN cc_start: 0.7359 (tt0) cc_final: 0.7022 (tt0) REVERT: B 658 TYR cc_start: 0.8442 (m-80) cc_final: 0.8105 (m-80) REVERT: B 665 GLN cc_start: 0.8423 (tt0) cc_final: 0.7971 (tm-30) REVERT: B 667 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7908 (mm-40) REVERT: B 676 LYS cc_start: 0.8622 (mttt) cc_final: 0.8372 (mttp) REVERT: B 772 VAL cc_start: 0.7915 (t) cc_final: 0.7707 (t) REVERT: B 776 VAL cc_start: 0.8086 (t) cc_final: 0.7852 (m) REVERT: B 810 TYR cc_start: 0.7960 (m-80) cc_final: 0.7728 (m-80) REVERT: C 158 ILE cc_start: 0.8453 (mt) cc_final: 0.8241 (mm) REVERT: C 173 ILE cc_start: 0.8534 (mt) cc_final: 0.8300 (tt) REVERT: C 191 LEU cc_start: 0.8393 (tp) cc_final: 0.8176 (tt) REVERT: C 193 THR cc_start: 0.7919 (t) cc_final: 0.7701 (t) REVERT: C 194 GLU cc_start: 0.7435 (tp30) cc_final: 0.6743 (tp30) REVERT: C 197 ASN cc_start: 0.7438 (m110) cc_final: 0.7212 (m-40) REVERT: C 198 GLU cc_start: 0.6914 (mt-10) cc_final: 0.6298 (mt-10) REVERT: C 275 TYR cc_start: 0.8084 (m-10) cc_final: 0.7882 (m-10) REVERT: C 295 LYS cc_start: 0.8643 (mptt) cc_final: 0.8367 (mptt) REVERT: C 305 LYS cc_start: 0.8255 (pttp) cc_final: 0.8020 (pttp) REVERT: C 339 GLU cc_start: 0.7663 (tp30) cc_final: 0.7459 (tp30) REVERT: C 349 ILE cc_start: 0.8605 (mt) cc_final: 0.8372 (mm) REVERT: C 384 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7391 (mm-30) REVERT: C 451 HIS cc_start: 0.7876 (m-70) cc_final: 0.7642 (m-70) REVERT: C 468 ASP cc_start: 0.7315 (t70) cc_final: 0.6932 (t70) REVERT: C 500 TYR cc_start: 0.8326 (t80) cc_final: 0.8020 (t80) REVERT: C 510 TYR cc_start: 0.7972 (m-80) cc_final: 0.7245 (m-80) REVERT: C 537 ARG cc_start: 0.7413 (mtt-85) cc_final: 0.7179 (mtt-85) REVERT: C 540 VAL cc_start: 0.8334 (p) cc_final: 0.8032 (t) REVERT: C 544 ASP cc_start: 0.8347 (t70) cc_final: 0.8114 (t0) REVERT: C 591 GLN cc_start: 0.7312 (tt0) cc_final: 0.6804 (tt0) REVERT: C 624 HIS cc_start: 0.6220 (m-70) cc_final: 0.6003 (m-70) REVERT: C 635 VAL cc_start: 0.7556 (m) cc_final: 0.7115 (t) REVERT: C 648 MET cc_start: 0.7955 (mmt) cc_final: 0.7550 (mmt) REVERT: C 652 ARG cc_start: 0.7827 (mtp85) cc_final: 0.7585 (mtp85) REVERT: C 653 ARG cc_start: 0.7947 (ttm170) cc_final: 0.7612 (mtm-85) REVERT: C 654 ILE cc_start: 0.8523 (mt) cc_final: 0.7931 (mt) REVERT: C 656 TRP cc_start: 0.8602 (m100) cc_final: 0.8230 (m-90) REVERT: C 676 LYS cc_start: 0.8745 (mttt) cc_final: 0.8460 (mttm) REVERT: C 683 ARG cc_start: 0.7783 (mpt180) cc_final: 0.7494 (mpt180) REVERT: C 715 ILE cc_start: 0.8583 (tt) cc_final: 0.8368 (mt) REVERT: C 763 ARG cc_start: 0.7390 (ptp-170) cc_final: 0.7176 (ptp-170) REVERT: C 773 VAL cc_start: 0.8777 (t) cc_final: 0.8576 (m) REVERT: C 842 PHE cc_start: 0.7569 (m-10) cc_final: 0.7224 (m-80) outliers start: 3 outliers final: 0 residues processed: 701 average time/residue: 0.3283 time to fit residues: 323.1532 Evaluate side-chains 594 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 594 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 2.9990 chunk 156 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 162 optimal weight: 0.6980 chunk 62 optimal weight: 0.0470 chunk 98 optimal weight: 0.1980 chunk 120 optimal weight: 2.9990 chunk 187 optimal weight: 0.8980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 600 ASN A 637 HIS A 643 ASN A 737 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN B 753 ASN C 180 ASN C 643 ASN C 836 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 16707 Z= 0.201 Angle : 0.678 10.310 22881 Z= 0.334 Chirality : 0.047 0.272 2763 Planarity : 0.006 0.063 2880 Dihedral : 11.978 94.612 3246 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.85 % Allowed : 15.26 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.19), residues: 2052 helix: -0.06 (0.22), residues: 546 sheet: 0.59 (0.30), residues: 369 loop : -0.95 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 326 HIS 0.007 0.001 HIS C 234 PHE 0.019 0.001 PHE C 150 TYR 0.025 0.001 TYR A 474 ARG 0.006 0.001 ARG C 407 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 612 time to evaluate : 1.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 PHE cc_start: 0.7624 (t80) cc_final: 0.7323 (t80) REVERT: A 151 TYR cc_start: 0.7449 (p90) cc_final: 0.7156 (p90) REVERT: A 158 ILE cc_start: 0.8551 (mt) cc_final: 0.8282 (mm) REVERT: A 186 GLN cc_start: 0.7111 (mm110) cc_final: 0.6842 (mm110) REVERT: A 194 GLU cc_start: 0.7411 (tp30) cc_final: 0.6746 (tp30) REVERT: A 198 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6466 (mt-10) REVERT: A 211 GLU cc_start: 0.8141 (tp30) cc_final: 0.7626 (tp30) REVERT: A 227 LYS cc_start: 0.8590 (tptm) cc_final: 0.8324 (tppt) REVERT: A 249 GLU cc_start: 0.7525 (mm-30) cc_final: 0.6866 (mm-30) REVERT: A 251 LEU cc_start: 0.8316 (tp) cc_final: 0.7805 (tt) REVERT: A 252 ILE cc_start: 0.8785 (mt) cc_final: 0.8384 (tp) REVERT: A 258 LEU cc_start: 0.8665 (mt) cc_final: 0.8462 (mm) REVERT: A 295 LYS cc_start: 0.8675 (mptt) cc_final: 0.8378 (mptt) REVERT: A 334 LEU cc_start: 0.8630 (mt) cc_final: 0.8401 (mt) REVERT: A 339 GLU cc_start: 0.7625 (tp30) cc_final: 0.7359 (tp30) REVERT: A 438 ARG cc_start: 0.7536 (mmm160) cc_final: 0.7004 (tpt90) REVERT: A 468 ASP cc_start: 0.7300 (t70) cc_final: 0.6832 (t70) REVERT: A 495 GLU cc_start: 0.6929 (pt0) cc_final: 0.6707 (pt0) REVERT: A 500 TYR cc_start: 0.8330 (t80) cc_final: 0.7990 (t80) REVERT: A 510 TYR cc_start: 0.7609 (m-80) cc_final: 0.7167 (m-80) REVERT: A 519 LEU cc_start: 0.8242 (mm) cc_final: 0.7928 (mp) REVERT: A 533 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.7850 (tpp) REVERT: A 540 VAL cc_start: 0.8116 (p) cc_final: 0.7509 (m) REVERT: A 591 GLN cc_start: 0.7365 (tt0) cc_final: 0.7136 (tt0) REVERT: A 599 ILE cc_start: 0.8423 (tp) cc_final: 0.8211 (mm) REVERT: A 612 ARG cc_start: 0.7429 (tpp80) cc_final: 0.7000 (mmm-85) REVERT: A 624 HIS cc_start: 0.6362 (m-70) cc_final: 0.6099 (m-70) REVERT: A 652 ARG cc_start: 0.7815 (mtp85) cc_final: 0.7455 (mtp-110) REVERT: A 675 MET cc_start: 0.8021 (mmm) cc_final: 0.7608 (mmm) REVERT: A 676 LYS cc_start: 0.8668 (mttt) cc_final: 0.8332 (mttm) REVERT: A 702 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7023 (mt-10) REVERT: A 724 ASN cc_start: 0.8091 (t0) cc_final: 0.7839 (t0) REVERT: A 803 SER cc_start: 0.8145 (t) cc_final: 0.7634 (p) REVERT: B 158 ILE cc_start: 0.8453 (mt) cc_final: 0.8234 (mm) REVERT: B 194 GLU cc_start: 0.7472 (tp30) cc_final: 0.6783 (tp30) REVERT: B 198 GLU cc_start: 0.6968 (mt-10) cc_final: 0.6390 (mt-10) REVERT: B 206 VAL cc_start: 0.8234 (m) cc_final: 0.7866 (p) REVERT: B 252 ILE cc_start: 0.8713 (mt) cc_final: 0.8382 (tp) REVERT: B 258 LEU cc_start: 0.8715 (mt) cc_final: 0.8495 (mm) REVERT: B 273 TRP cc_start: 0.8826 (m-10) cc_final: 0.8460 (m-10) REVERT: B 297 ARG cc_start: 0.8301 (mtm-85) cc_final: 0.7785 (mtm180) REVERT: B 298 MET cc_start: 0.7627 (mmm) cc_final: 0.7425 (mmm) REVERT: B 338 ASN cc_start: 0.7667 (t0) cc_final: 0.7361 (t0) REVERT: B 339 GLU cc_start: 0.7639 (tp30) cc_final: 0.7305 (tp30) REVERT: B 341 THR cc_start: 0.8736 (m) cc_final: 0.8464 (p) REVERT: B 356 ARG cc_start: 0.7897 (tpp-160) cc_final: 0.7513 (tpp-160) REVERT: B 396 PHE cc_start: 0.7766 (t80) cc_final: 0.7562 (t80) REVERT: B 468 ASP cc_start: 0.7183 (t70) cc_final: 0.6710 (t0) REVERT: B 495 GLU cc_start: 0.7187 (pt0) cc_final: 0.6967 (pt0) REVERT: B 535 ASN cc_start: 0.7188 (t0) cc_final: 0.6762 (t0) REVERT: B 551 TYR cc_start: 0.8053 (m-80) cc_final: 0.7720 (m-80) REVERT: B 591 GLN cc_start: 0.7324 (tt0) cc_final: 0.7106 (tt0) REVERT: B 611 LEU cc_start: 0.7235 (tp) cc_final: 0.6735 (tp) REVERT: B 635 VAL cc_start: 0.7704 (m) cc_final: 0.7476 (p) REVERT: B 658 TYR cc_start: 0.8411 (m-80) cc_final: 0.8105 (m-80) REVERT: B 665 GLN cc_start: 0.8413 (tt0) cc_final: 0.7957 (tm-30) REVERT: B 667 GLN cc_start: 0.8204 (mm-40) cc_final: 0.8002 (mm-40) REVERT: B 669 GLN cc_start: 0.7958 (mt0) cc_final: 0.7717 (mm110) REVERT: B 676 LYS cc_start: 0.8678 (mttt) cc_final: 0.8405 (mttp) REVERT: B 711 ILE cc_start: 0.8653 (pt) cc_final: 0.8441 (mt) REVERT: B 776 VAL cc_start: 0.8084 (t) cc_final: 0.7829 (m) REVERT: B 810 TYR cc_start: 0.7942 (m-80) cc_final: 0.7666 (m-80) REVERT: C 193 THR cc_start: 0.7930 (t) cc_final: 0.7718 (t) REVERT: C 194 GLU cc_start: 0.7383 (tp30) cc_final: 0.6720 (tp30) REVERT: C 197 ASN cc_start: 0.7469 (m110) cc_final: 0.7211 (m-40) REVERT: C 198 GLU cc_start: 0.6917 (mt-10) cc_final: 0.6381 (mt-10) REVERT: C 207 MET cc_start: 0.6918 (mtt) cc_final: 0.6322 (mtm) REVERT: C 295 LYS cc_start: 0.8668 (mptt) cc_final: 0.8358 (mptt) REVERT: C 305 LYS cc_start: 0.8252 (pttp) cc_final: 0.8032 (pttp) REVERT: C 384 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7399 (mm-30) REVERT: C 451 HIS cc_start: 0.7877 (m-70) cc_final: 0.7540 (m90) REVERT: C 500 TYR cc_start: 0.8162 (t80) cc_final: 0.7897 (t80) REVERT: C 510 TYR cc_start: 0.7576 (m-80) cc_final: 0.7130 (m-80) REVERT: C 544 ASP cc_start: 0.8372 (t70) cc_final: 0.8008 (t70) REVERT: C 591 GLN cc_start: 0.7271 (tt0) cc_final: 0.7049 (tt0) REVERT: C 601 ASP cc_start: 0.7093 (m-30) cc_final: 0.6780 (m-30) REVERT: C 646 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7487 (tmm-80) REVERT: C 654 ILE cc_start: 0.8538 (mt) cc_final: 0.7924 (mt) REVERT: C 656 TRP cc_start: 0.8515 (m100) cc_final: 0.8124 (m-90) REVERT: C 665 GLN cc_start: 0.8367 (tt0) cc_final: 0.8098 (tp40) REVERT: C 672 ASP cc_start: 0.8128 (m-30) cc_final: 0.7843 (m-30) REVERT: C 676 LYS cc_start: 0.8776 (mttt) cc_final: 0.8384 (mttm) REVERT: C 683 ARG cc_start: 0.7826 (mpt180) cc_final: 0.7395 (mmt90) REVERT: C 763 ARG cc_start: 0.7279 (ptp-170) cc_final: 0.7071 (ptp-170) REVERT: C 773 VAL cc_start: 0.8690 (t) cc_final: 0.8468 (m) REVERT: C 842 PHE cc_start: 0.7593 (m-10) cc_final: 0.7293 (m-80) outliers start: 29 outliers final: 17 residues processed: 621 average time/residue: 0.3435 time to fit residues: 307.8725 Evaluate side-chains 590 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 571 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 650 MET Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 837 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 156 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 chunk 203 optimal weight: 0.8980 chunk 167 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 151 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 643 ASN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 HIS B 637 HIS C 600 ASN C 636 GLN C 637 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 16707 Z= 0.224 Angle : 0.672 10.645 22881 Z= 0.330 Chirality : 0.048 0.297 2763 Planarity : 0.005 0.053 2880 Dihedral : 11.343 90.756 3246 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.58 % Allowed : 17.37 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.19), residues: 2052 helix: 0.06 (0.23), residues: 543 sheet: 0.50 (0.29), residues: 366 loop : -1.04 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 326 HIS 0.008 0.001 HIS C 639 PHE 0.017 0.002 PHE B 539 TYR 0.028 0.002 TYR B 360 ARG 0.008 0.001 ARG B 612 *********************** 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 632 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 576 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 PHE cc_start: 0.7581 (t80) cc_final: 0.7286 (t80) REVERT: A 158 ILE cc_start: 0.8655 (mt) cc_final: 0.8289 (mm) REVERT: A 174 ASN cc_start: 0.8382 (t0) cc_final: 0.8180 (t0) REVERT: A 194 GLU cc_start: 0.7518 (tp30) cc_final: 0.6820 (tp30) REVERT: A 198 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6578 (mt-10) REVERT: A 211 GLU cc_start: 0.8203 (tp30) cc_final: 0.7792 (tp30) REVERT: A 251 LEU cc_start: 0.8231 (tp) cc_final: 0.7728 (tt) REVERT: A 252 ILE cc_start: 0.8832 (mt) cc_final: 0.8397 (tp) REVERT: A 258 LEU cc_start: 0.8659 (mt) cc_final: 0.8422 (mm) REVERT: A 334 LEU cc_start: 0.8692 (mt) cc_final: 0.8416 (mt) REVERT: A 384 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7709 (mp0) REVERT: A 438 ARG cc_start: 0.7531 (mmm160) cc_final: 0.7087 (tpt90) REVERT: A 468 ASP cc_start: 0.7414 (t70) cc_final: 0.6921 (t70) REVERT: A 495 GLU cc_start: 0.6912 (pt0) cc_final: 0.6673 (pt0) REVERT: A 500 TYR cc_start: 0.8387 (t80) cc_final: 0.7901 (t80) REVERT: A 510 TYR cc_start: 0.7758 (m-80) cc_final: 0.7193 (m-80) REVERT: A 591 GLN cc_start: 0.7329 (tt0) cc_final: 0.7061 (tt0) REVERT: A 624 HIS cc_start: 0.6354 (m-70) cc_final: 0.6023 (m-70) REVERT: A 636 GLN cc_start: 0.7693 (tp40) cc_final: 0.7467 (tp40) REVERT: A 648 MET cc_start: 0.8164 (mmt) cc_final: 0.7504 (mmt) REVERT: A 652 ARG cc_start: 0.7794 (mtp85) cc_final: 0.7464 (mtp-110) REVERT: A 665 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8316 (tp-100) REVERT: A 675 MET cc_start: 0.8013 (mmm) cc_final: 0.7607 (mmm) REVERT: A 676 LYS cc_start: 0.8678 (mttt) cc_final: 0.8291 (mttm) REVERT: A 702 GLU cc_start: 0.7310 (mt-10) cc_final: 0.7039 (mt-10) REVERT: A 803 SER cc_start: 0.8204 (t) cc_final: 0.7699 (p) REVERT: B 158 ILE cc_start: 0.8518 (mt) cc_final: 0.8219 (mm) REVERT: B 206 VAL cc_start: 0.8286 (m) cc_final: 0.8036 (p) REVERT: B 249 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7196 (mm-30) REVERT: B 252 ILE cc_start: 0.8801 (mt) cc_final: 0.8352 (tp) REVERT: B 273 TRP cc_start: 0.8806 (m-10) cc_final: 0.8466 (m-10) REVERT: B 318 CYS cc_start: 0.5333 (OUTLIER) cc_final: 0.5009 (p) REVERT: B 338 ASN cc_start: 0.7757 (t0) cc_final: 0.7421 (t0) REVERT: B 339 GLU cc_start: 0.7650 (tp30) cc_final: 0.7347 (tp30) REVERT: B 340 LEU cc_start: 0.8686 (tp) cc_final: 0.8469 (tt) REVERT: B 341 THR cc_start: 0.8729 (m) cc_final: 0.8410 (p) REVERT: B 356 ARG cc_start: 0.7898 (tpp-160) cc_final: 0.7556 (tpp-160) REVERT: B 396 PHE cc_start: 0.7860 (t80) cc_final: 0.7601 (t80) REVERT: B 468 ASP cc_start: 0.7266 (t70) cc_final: 0.6758 (t0) REVERT: B 495 GLU cc_start: 0.7285 (pt0) cc_final: 0.7005 (pt0) REVERT: B 520 LYS cc_start: 0.8281 (mmmm) cc_final: 0.7937 (mtpp) REVERT: B 535 ASN cc_start: 0.7283 (t0) cc_final: 0.7035 (t0) REVERT: B 551 TYR cc_start: 0.8054 (m-80) cc_final: 0.7728 (m-80) REVERT: B 611 LEU cc_start: 0.7343 (tp) cc_final: 0.6865 (tp) REVERT: B 612 ARG cc_start: 0.7737 (tpp80) cc_final: 0.7265 (mmm-85) REVERT: B 635 VAL cc_start: 0.7916 (m) cc_final: 0.7638 (p) REVERT: B 658 TYR cc_start: 0.8471 (m-80) cc_final: 0.8185 (m-80) REVERT: B 665 GLN cc_start: 0.8385 (tt0) cc_final: 0.7961 (tm-30) REVERT: B 667 GLN cc_start: 0.8204 (mm-40) cc_final: 0.7957 (mm-40) REVERT: B 669 GLN cc_start: 0.8017 (mt0) cc_final: 0.7764 (mm110) REVERT: B 676 LYS cc_start: 0.8691 (mttt) cc_final: 0.8420 (mttp) REVERT: B 688 TYR cc_start: 0.8475 (p90) cc_final: 0.8224 (p90) REVERT: B 776 VAL cc_start: 0.8019 (t) cc_final: 0.7737 (m) REVERT: C 180 ASN cc_start: 0.7656 (m110) cc_final: 0.7451 (m110) REVERT: C 193 THR cc_start: 0.8022 (t) cc_final: 0.7798 (t) REVERT: C 194 GLU cc_start: 0.7354 (tp30) cc_final: 0.6726 (tp30) REVERT: C 197 ASN cc_start: 0.7490 (m110) cc_final: 0.7189 (m-40) REVERT: C 198 GLU cc_start: 0.6916 (mt-10) cc_final: 0.6517 (mt-10) REVERT: C 252 ILE cc_start: 0.8830 (tp) cc_final: 0.8597 (tt) REVERT: C 295 LYS cc_start: 0.8658 (mptt) cc_final: 0.8411 (mptt) REVERT: C 305 LYS cc_start: 0.8242 (pttp) cc_final: 0.8019 (pttp) REVERT: C 384 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7362 (mm-30) REVERT: C 451 HIS cc_start: 0.7899 (m-70) cc_final: 0.7685 (m-70) REVERT: C 495 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6782 (pm20) REVERT: C 500 TYR cc_start: 0.8253 (t80) cc_final: 0.7643 (t80) REVERT: C 504 LYS cc_start: 0.8080 (ttmm) cc_final: 0.7858 (ttmm) REVERT: C 510 TYR cc_start: 0.7775 (m-80) cc_final: 0.7216 (m-80) REVERT: C 516 LEU cc_start: 0.7678 (tt) cc_final: 0.7430 (mt) REVERT: C 544 ASP cc_start: 0.8381 (t70) cc_final: 0.8135 (t0) REVERT: C 591 GLN cc_start: 0.7202 (tt0) cc_final: 0.6954 (tt0) REVERT: C 601 ASP cc_start: 0.7093 (m-30) cc_final: 0.6665 (m-30) REVERT: C 611 LEU cc_start: 0.7516 (tp) cc_final: 0.6983 (tp) REVERT: C 646 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7435 (tmm-80) REVERT: C 648 MET cc_start: 0.8093 (mmt) cc_final: 0.7546 (mmt) REVERT: C 654 ILE cc_start: 0.8518 (mt) cc_final: 0.8027 (mt) REVERT: C 656 TRP cc_start: 0.8532 (m100) cc_final: 0.8163 (m-90) REVERT: C 669 GLN cc_start: 0.7651 (mp10) cc_final: 0.7332 (mp10) REVERT: C 672 ASP cc_start: 0.8096 (m-30) cc_final: 0.7856 (m-30) REVERT: C 675 MET cc_start: 0.8076 (mmm) cc_final: 0.7834 (mmm) REVERT: C 676 LYS cc_start: 0.8826 (mttt) cc_final: 0.8418 (mttm) REVERT: C 683 ARG cc_start: 0.7865 (mpt180) cc_final: 0.7403 (mmt90) REVERT: C 724 ASN cc_start: 0.7868 (t0) cc_final: 0.7662 (t0) REVERT: C 842 PHE cc_start: 0.7649 (m-10) cc_final: 0.7408 (m-80) outliers start: 56 outliers final: 34 residues processed: 597 average time/residue: 0.3083 time to fit residues: 263.4431 Evaluate side-chains 610 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 572 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 665 GLN Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 650 MET Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 495 GLU Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 837 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 0.0050 chunk 141 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 200 optimal weight: 5.9990 chunk 98 optimal weight: 0.0040 chunk 179 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 overall best weight: 0.7008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 643 ASN C 535 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 16707 Z= 0.202 Angle : 0.679 20.133 22881 Z= 0.330 Chirality : 0.048 0.283 2763 Planarity : 0.005 0.048 2880 Dihedral : 10.867 92.984 3246 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.34 % Allowed : 18.97 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.19), residues: 2052 helix: 0.14 (0.23), residues: 543 sheet: 0.19 (0.28), residues: 399 loop : -1.00 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 326 HIS 0.006 0.001 HIS C 639 PHE 0.017 0.001 PHE C 317 TYR 0.029 0.001 TYR A 276 ARG 0.008 0.001 ARG B 407 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 574 time to evaluate : 1.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 PHE cc_start: 0.7580 (t80) cc_final: 0.7353 (t80) REVERT: A 158 ILE cc_start: 0.8624 (mt) cc_final: 0.8242 (mm) REVERT: A 172 MET cc_start: 0.7793 (mtm) cc_final: 0.7587 (mtp) REVERT: A 194 GLU cc_start: 0.7501 (tp30) cc_final: 0.6823 (tp30) REVERT: A 198 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6529 (mt-10) REVERT: A 211 GLU cc_start: 0.8180 (tp30) cc_final: 0.7640 (tp30) REVERT: A 251 LEU cc_start: 0.8208 (tp) cc_final: 0.7684 (tt) REVERT: A 252 ILE cc_start: 0.8779 (mt) cc_final: 0.8388 (tp) REVERT: A 334 LEU cc_start: 0.8613 (mt) cc_final: 0.8376 (mt) REVERT: A 438 ARG cc_start: 0.7522 (mmm160) cc_final: 0.7064 (tpt90) REVERT: A 468 ASP cc_start: 0.7357 (t70) cc_final: 0.6879 (t70) REVERT: A 500 TYR cc_start: 0.8351 (t80) cc_final: 0.7850 (t80) REVERT: A 510 TYR cc_start: 0.7742 (m-80) cc_final: 0.7184 (m-80) REVERT: A 591 GLN cc_start: 0.7267 (tt0) cc_final: 0.7032 (tt0) REVERT: A 636 GLN cc_start: 0.7558 (tp40) cc_final: 0.7337 (tp40) REVERT: A 652 ARG cc_start: 0.7832 (mtp85) cc_final: 0.7561 (mtp85) REVERT: A 675 MET cc_start: 0.8022 (mmm) cc_final: 0.7628 (mmm) REVERT: A 676 LYS cc_start: 0.8654 (mttt) cc_final: 0.8290 (mttm) REVERT: A 702 GLU cc_start: 0.7323 (mt-10) cc_final: 0.6958 (mt-10) REVERT: A 772 VAL cc_start: 0.8216 (p) cc_final: 0.8011 (m) REVERT: B 206 VAL cc_start: 0.8313 (m) cc_final: 0.8044 (p) REVERT: B 249 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7068 (mm-30) REVERT: B 252 ILE cc_start: 0.8739 (mt) cc_final: 0.8383 (tp) REVERT: B 273 TRP cc_start: 0.8840 (m-10) cc_final: 0.8504 (m-10) REVERT: B 338 ASN cc_start: 0.7779 (t0) cc_final: 0.7432 (t0) REVERT: B 339 GLU cc_start: 0.7655 (tp30) cc_final: 0.7413 (tp30) REVERT: B 341 THR cc_start: 0.8723 (m) cc_final: 0.8410 (p) REVERT: B 396 PHE cc_start: 0.7867 (t80) cc_final: 0.7625 (t80) REVERT: B 495 GLU cc_start: 0.7254 (pt0) cc_final: 0.6955 (pt0) REVERT: B 504 LYS cc_start: 0.8039 (mtpp) cc_final: 0.7824 (mtpp) REVERT: B 520 LYS cc_start: 0.8283 (mmmm) cc_final: 0.7968 (mtpp) REVERT: B 551 TYR cc_start: 0.8051 (m-80) cc_final: 0.7722 (m-80) REVERT: B 635 VAL cc_start: 0.7846 (m) cc_final: 0.7592 (p) REVERT: B 658 TYR cc_start: 0.8484 (m-80) cc_final: 0.8202 (m-80) REVERT: B 665 GLN cc_start: 0.8393 (tt0) cc_final: 0.7986 (tm-30) REVERT: B 676 LYS cc_start: 0.8679 (mttt) cc_final: 0.8414 (mttp) REVERT: B 688 TYR cc_start: 0.8465 (p90) cc_final: 0.8195 (p90) REVERT: B 707 TYR cc_start: 0.8297 (m-10) cc_final: 0.8073 (m-10) REVERT: B 776 VAL cc_start: 0.8061 (t) cc_final: 0.7761 (m) REVERT: C 193 THR cc_start: 0.8009 (t) cc_final: 0.7725 (t) REVERT: C 194 GLU cc_start: 0.7334 (tp30) cc_final: 0.6807 (tp30) REVERT: C 197 ASN cc_start: 0.7470 (m110) cc_final: 0.7179 (m-40) REVERT: C 198 GLU cc_start: 0.6882 (mt-10) cc_final: 0.6380 (mt-10) REVERT: C 295 LYS cc_start: 0.8679 (mptt) cc_final: 0.8397 (mptt) REVERT: C 305 LYS cc_start: 0.8224 (pttp) cc_final: 0.8008 (pttp) REVERT: C 384 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7417 (mm-30) REVERT: C 468 ASP cc_start: 0.7388 (t70) cc_final: 0.6871 (t70) REVERT: C 500 TYR cc_start: 0.8247 (t80) cc_final: 0.7544 (t80) REVERT: C 504 LYS cc_start: 0.8070 (ttmm) cc_final: 0.7708 (ttmm) REVERT: C 510 TYR cc_start: 0.7728 (m-80) cc_final: 0.7219 (m-80) REVERT: C 516 LEU cc_start: 0.7666 (tt) cc_final: 0.7442 (mt) REVERT: C 544 ASP cc_start: 0.8379 (t70) cc_final: 0.8119 (t0) REVERT: C 591 GLN cc_start: 0.7247 (tt0) cc_final: 0.7028 (tt0) REVERT: C 601 ASP cc_start: 0.7059 (m-30) cc_final: 0.6750 (m-30) REVERT: C 646 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7429 (tmm-80) REVERT: C 648 MET cc_start: 0.7990 (mmt) cc_final: 0.7577 (mmp) REVERT: C 651 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7128 (tt0) REVERT: C 654 ILE cc_start: 0.8528 (mt) cc_final: 0.8058 (mt) REVERT: C 656 TRP cc_start: 0.8542 (m100) cc_final: 0.8174 (m-90) REVERT: C 669 GLN cc_start: 0.7601 (mp10) cc_final: 0.7174 (mp10) REVERT: C 672 ASP cc_start: 0.8069 (m-30) cc_final: 0.7856 (m-30) REVERT: C 676 LYS cc_start: 0.8826 (mttt) cc_final: 0.8441 (mttm) REVERT: C 683 ARG cc_start: 0.7872 (mpt180) cc_final: 0.7413 (mmt90) REVERT: C 842 PHE cc_start: 0.7679 (m-10) cc_final: 0.7461 (m-80) outliers start: 68 outliers final: 43 residues processed: 602 average time/residue: 0.3157 time to fit residues: 273.7987 Evaluate side-chains 606 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 562 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 650 MET Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 646 ARG 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 809 SER 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 166 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 170 optimal weight: 0.7980 chunk 138 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 179 optimal weight: 0.1980 chunk 50 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 643 ASN ** B 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 GLN B 535 ASN B 600 ASN C 314 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 16707 Z= 0.436 Angle : 0.810 19.090 22881 Z= 0.403 Chirality : 0.053 0.363 2763 Planarity : 0.005 0.050 2880 Dihedral : 11.137 94.626 3246 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 5.62 % Allowed : 19.86 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.18), residues: 2052 helix: -0.16 (0.22), residues: 546 sheet: -0.13 (0.28), residues: 384 loop : -1.22 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 720 HIS 0.018 0.002 HIS C 639 PHE 0.022 0.002 PHE A 396 TYR 0.035 0.002 TYR A 276 ARG 0.008 0.001 ARG B 407 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 592 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLN cc_start: 0.8070 (tm-30) cc_final: 0.7658 (tm-30) REVERT: A 172 MET cc_start: 0.7899 (mtm) cc_final: 0.7691 (mtp) REVERT: A 194 GLU cc_start: 0.7597 (tp30) cc_final: 0.6961 (tp30) REVERT: A 198 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6603 (mt-10) REVERT: A 211 GLU cc_start: 0.8274 (tp30) cc_final: 0.7894 (tp30) REVERT: A 251 LEU cc_start: 0.8235 (tp) cc_final: 0.7743 (tt) REVERT: A 252 ILE cc_start: 0.8792 (mt) cc_final: 0.8387 (tt) REVERT: A 334 LEU cc_start: 0.8728 (mt) cc_final: 0.8487 (mt) REVERT: A 339 GLU cc_start: 0.7716 (tp30) cc_final: 0.7506 (tp30) REVERT: A 389 LEU cc_start: 0.8665 (mm) cc_final: 0.8459 (mt) REVERT: A 468 ASP cc_start: 0.7493 (t70) cc_final: 0.6973 (t70) REVERT: A 510 TYR cc_start: 0.7962 (m-80) cc_final: 0.7343 (m-80) REVERT: A 520 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8166 (mtmm) REVERT: A 591 GLN cc_start: 0.7161 (tt0) cc_final: 0.6945 (tt0) REVERT: A 635 VAL cc_start: 0.8097 (m) cc_final: 0.7775 (p) REVERT: A 636 GLN cc_start: 0.7777 (tp40) cc_final: 0.7533 (tp40) REVERT: A 653 ARG cc_start: 0.7826 (ttm170) cc_final: 0.7541 (mtt90) REVERT: A 675 MET cc_start: 0.8021 (mmm) cc_final: 0.7659 (mmm) REVERT: A 676 LYS cc_start: 0.8718 (mttt) cc_final: 0.8335 (mttm) REVERT: A 702 GLU cc_start: 0.7289 (mt-10) cc_final: 0.6960 (mt-10) REVERT: A 772 VAL cc_start: 0.8219 (p) cc_final: 0.8008 (m) REVERT: B 173 ILE cc_start: 0.8389 (mt) cc_final: 0.7975 (mm) REVERT: B 206 VAL cc_start: 0.8187 (m) cc_final: 0.7872 (p) REVERT: B 249 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7324 (mm-30) REVERT: B 252 ILE cc_start: 0.8759 (mt) cc_final: 0.8386 (tp) REVERT: B 384 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7469 (mp0) REVERT: B 386 VAL cc_start: 0.8738 (m) cc_final: 0.8486 (t) REVERT: B 396 PHE cc_start: 0.8002 (t80) cc_final: 0.7705 (t80) REVERT: B 495 GLU cc_start: 0.7380 (pt0) cc_final: 0.7100 (pt0) REVERT: B 551 TYR cc_start: 0.8120 (m-80) cc_final: 0.7783 (m-80) REVERT: B 611 LEU cc_start: 0.7616 (tp) cc_final: 0.6968 (tp) REVERT: B 625 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7969 (p0) REVERT: B 635 VAL cc_start: 0.8205 (m) cc_final: 0.7948 (t) REVERT: B 658 TYR cc_start: 0.8475 (m-80) cc_final: 0.8187 (m-80) REVERT: B 665 GLN cc_start: 0.8408 (tt0) cc_final: 0.8069 (tm-30) REVERT: B 672 ASP cc_start: 0.8237 (m-30) cc_final: 0.7984 (m-30) REVERT: B 676 LYS cc_start: 0.8681 (mttt) cc_final: 0.8311 (mttm) REVERT: B 721 GLN cc_start: 0.8128 (tm-30) cc_final: 0.7909 (tm-30) REVERT: C 193 THR cc_start: 0.8127 (t) cc_final: 0.7840 (t) REVERT: C 194 GLU cc_start: 0.7487 (tp30) cc_final: 0.6920 (tp30) REVERT: C 197 ASN cc_start: 0.7635 (m110) cc_final: 0.7253 (m-40) REVERT: C 198 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6621 (mt-10) REVERT: C 251 LEU cc_start: 0.8400 (tp) cc_final: 0.8023 (tt) REVERT: C 295 LYS cc_start: 0.8696 (mptt) cc_final: 0.8364 (mptt) REVERT: C 468 ASP cc_start: 0.7496 (t70) cc_final: 0.6964 (t70) REVERT: C 495 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6806 (pm20) REVERT: C 510 TYR cc_start: 0.8023 (m-80) cc_final: 0.7352 (m-80) REVERT: C 516 LEU cc_start: 0.7941 (tt) cc_final: 0.7710 (mt) REVERT: C 540 VAL cc_start: 0.8485 (p) cc_final: 0.8223 (t) REVERT: C 544 ASP cc_start: 0.8389 (t70) cc_final: 0.8129 (t0) REVERT: C 601 ASP cc_start: 0.7122 (m-30) cc_final: 0.6770 (m-30) REVERT: C 635 VAL cc_start: 0.8117 (m) cc_final: 0.7886 (t) REVERT: C 653 ARG cc_start: 0.8019 (ttm170) cc_final: 0.7708 (mtm-85) REVERT: C 669 GLN cc_start: 0.7677 (mp10) cc_final: 0.7196 (mp10) REVERT: C 676 LYS cc_start: 0.8847 (mttt) cc_final: 0.8573 (mttm) REVERT: C 683 ARG cc_start: 0.7902 (mpt180) cc_final: 0.7607 (mpt180) REVERT: C 711 ILE cc_start: 0.8810 (pt) cc_final: 0.8606 (mt) REVERT: C 773 VAL cc_start: 0.8627 (t) cc_final: 0.8416 (m) REVERT: C 842 PHE cc_start: 0.7729 (m-10) cc_final: 0.7439 (m-80) outliers start: 88 outliers final: 65 residues processed: 627 average time/residue: 0.3562 time to fit residues: 321.8892 Evaluate side-chains 633 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 565 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 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 488 SER 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 540 VAL 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 666 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 462 ASN Chi-restraints excluded: chain B residue 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 741 SER Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 462 ASN Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain C residue 495 GLU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain C residue 619 MET Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 719 ASN Chi-restraints excluded: chain C residue 721 GLN Chi-restraints excluded: chain C residue 762 CYS 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 67 optimal weight: 0.0060 chunk 180 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 200 optimal weight: 7.9990 chunk 166 optimal weight: 9.9990 chunk 92 optimal weight: 0.0770 chunk 16 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 105 optimal weight: 2.9990 overall best weight: 0.5354 ------------------------------------------------------------------------------- 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 600 ASN B 643 ASN C 180 ASN C 314 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 16707 Z= 0.192 Angle : 0.708 16.390 22881 Z= 0.343 Chirality : 0.048 0.305 2763 Planarity : 0.005 0.047 2880 Dihedral : 10.656 95.399 3246 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.15 % Allowed : 24.07 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.19), residues: 2052 helix: 0.04 (0.23), residues: 552 sheet: 0.16 (0.29), residues: 369 loop : -1.09 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 326 HIS 0.004 0.001 HIS C 639 PHE 0.018 0.001 PHE C 232 TYR 0.028 0.001 TYR B 474 ARG 0.010 0.001 ARG A 407 *********************** 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 657 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 592 time to evaluate : 1.840 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: 0.8053 (tm-30) cc_final: 0.7580 (tm-30) REVERT: A 150 PHE cc_start: 0.7589 (t80) cc_final: 0.7366 (t80) REVERT: A 194 GLU cc_start: 0.7514 (tp30) cc_final: 0.6900 (tp30) REVERT: A 198 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6553 (mt-10) REVERT: A 211 GLU cc_start: 0.8234 (tp30) cc_final: 0.7909 (tp30) REVERT: A 251 LEU cc_start: 0.8206 (tp) cc_final: 0.7705 (tt) REVERT: A 252 ILE cc_start: 0.8780 (mt) cc_final: 0.8404 (tt) REVERT: A 334 LEU cc_start: 0.8584 (mt) cc_final: 0.8359 (mt) REVERT: A 339 GLU cc_start: 0.7644 (tp30) cc_final: 0.7416 (tp30) REVERT: A 341 THR cc_start: 0.8628 (m) cc_final: 0.8265 (p) REVERT: A 382 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8047 (mtt-85) REVERT: A 389 LEU cc_start: 0.8696 (mm) cc_final: 0.8493 (mt) REVERT: A 438 ARG cc_start: 0.7522 (mmm160) cc_final: 0.6985 (tpt90) REVERT: A 468 ASP cc_start: 0.7428 (t70) cc_final: 0.6925 (t70) REVERT: A 500 TYR cc_start: 0.8297 (t80) cc_final: 0.7904 (t80) REVERT: A 502 GLU cc_start: 0.7915 (tp30) cc_final: 0.7714 (tp30) REVERT: A 510 TYR cc_start: 0.7756 (m-80) cc_final: 0.7166 (m-80) REVERT: A 599 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8457 (mm) REVERT: A 653 ARG cc_start: 0.7838 (ttm170) cc_final: 0.7577 (mtt90) REVERT: A 675 MET cc_start: 0.8013 (mmm) cc_final: 0.7616 (mmm) REVERT: A 676 LYS cc_start: 0.8653 (mttt) cc_final: 0.8278 (mttm) REVERT: A 702 GLU cc_start: 0.7298 (mt-10) cc_final: 0.6886 (mt-10) REVERT: B 206 VAL cc_start: 0.8281 (m) cc_final: 0.8019 (p) REVERT: B 249 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7257 (mm-30) REVERT: B 252 ILE cc_start: 0.8688 (mt) cc_final: 0.8388 (tp) REVERT: B 273 TRP cc_start: 0.8803 (m-10) cc_final: 0.8586 (m-10) REVERT: B 341 THR cc_start: 0.8731 (m) cc_final: 0.8420 (p) REVERT: B 396 PHE cc_start: 0.7898 (t80) cc_final: 0.7627 (t80) REVERT: B 495 GLU cc_start: 0.7273 (pt0) cc_final: 0.7012 (pt0) REVERT: B 520 LYS cc_start: 0.8331 (mmmm) cc_final: 0.8008 (mtpp) REVERT: B 535 ASN cc_start: 0.7547 (t0) cc_final: 0.7296 (t0) REVERT: B 551 TYR cc_start: 0.8103 (m-80) cc_final: 0.7761 (m-80) REVERT: B 658 TYR cc_start: 0.8435 (m-80) cc_final: 0.8115 (m-80) REVERT: B 665 GLN cc_start: 0.8348 (tt0) cc_final: 0.8082 (tm-30) REVERT: B 676 LYS cc_start: 0.8663 (mttt) cc_final: 0.8381 (mttp) REVERT: B 776 VAL cc_start: 0.8048 (t) cc_final: 0.7744 (m) REVERT: B 825 VAL cc_start: 0.8060 (OUTLIER) cc_final: 0.7741 (p) REVERT: C 147 GLN cc_start: 0.8150 (tm-30) cc_final: 0.7603 (tm-30) REVERT: C 194 GLU cc_start: 0.7429 (tp30) cc_final: 0.6918 (tp30) REVERT: C 198 GLU cc_start: 0.6829 (mt-10) cc_final: 0.6486 (mt-10) REVERT: C 211 GLU cc_start: 0.8078 (tp30) cc_final: 0.7844 (tp30) REVERT: C 251 LEU cc_start: 0.8352 (tp) cc_final: 0.8007 (tt) REVERT: C 295 LYS cc_start: 0.8712 (mptt) cc_final: 0.8419 (mptt) REVERT: C 347 LEU cc_start: 0.8432 (mt) cc_final: 0.8108 (tp) REVERT: C 382 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.8008 (ptp-170) REVERT: C 468 ASP cc_start: 0.7378 (t70) cc_final: 0.6829 (t70) REVERT: C 510 TYR cc_start: 0.7787 (m-80) cc_final: 0.7238 (m-80) REVERT: C 516 LEU cc_start: 0.7873 (tt) cc_final: 0.7634 (mt) REVERT: C 526 THR cc_start: 0.8712 (t) cc_final: 0.8470 (p) REVERT: C 544 ASP cc_start: 0.8365 (t70) cc_final: 0.8136 (t0) REVERT: C 601 ASP cc_start: 0.7040 (m-30) cc_final: 0.6583 (m-30) REVERT: C 604 LEU cc_start: 0.8662 (mp) cc_final: 0.8406 (mp) REVERT: C 642 LEU cc_start: 0.8213 (tp) cc_final: 0.8002 (mm) REVERT: C 653 ARG cc_start: 0.7957 (ttm170) cc_final: 0.7638 (mtm-85) REVERT: C 656 TRP cc_start: 0.8535 (m100) cc_final: 0.8144 (m-90) REVERT: C 669 GLN cc_start: 0.7674 (mp10) cc_final: 0.7139 (mp10) REVERT: C 676 LYS cc_start: 0.8806 (mttt) cc_final: 0.8511 (mttm) REVERT: C 683 ARG cc_start: 0.7901 (mpt180) cc_final: 0.7614 (mpt180) REVERT: C 711 ILE cc_start: 0.8703 (pt) cc_final: 0.8487 (mt) REVERT: C 721 GLN cc_start: 0.7689 (tt0) cc_final: 0.7342 (tp-100) outliers start: 65 outliers final: 47 residues processed: 617 average time/residue: 0.3314 time to fit residues: 287.2281 Evaluate side-chains 625 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 574 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 235 CYS 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 540 VAL Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 235 CYS Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 625 ASP 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 696 LEU Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 382 ARG Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 619 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 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 193 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 chunk 146 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 199 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 121 optimal weight: 0.6980 chunk 92 optimal weight: 0.0770 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN B 643 ASN C 197 ASN C 591 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 16707 Z= 0.191 Angle : 0.704 17.461 22881 Z= 0.339 Chirality : 0.048 0.294 2763 Planarity : 0.005 0.045 2880 Dihedral : 10.407 95.065 3246 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.85 % Allowed : 24.01 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.19), residues: 2052 helix: 0.15 (0.23), residues: 552 sheet: 0.25 (0.29), residues: 372 loop : -1.06 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 326 HIS 0.005 0.001 HIS C 639 PHE 0.019 0.001 PHE A 396 TYR 0.039 0.001 TYR B 276 ARG 0.010 0.001 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 588 time to evaluate : 1.849 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: 0.8075 (tm-30) cc_final: 0.7609 (tm-30) REVERT: A 194 GLU cc_start: 0.7542 (tp30) cc_final: 0.6897 (tp30) REVERT: A 198 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6640 (mt-10) REVERT: A 211 GLU cc_start: 0.8219 (tp30) cc_final: 0.7827 (tp30) REVERT: A 251 LEU cc_start: 0.8199 (tp) cc_final: 0.7710 (tt) REVERT: A 252 ILE cc_start: 0.8778 (mt) cc_final: 0.8417 (tt) REVERT: A 334 LEU cc_start: 0.8570 (mt) cc_final: 0.8357 (mt) REVERT: A 339 GLU cc_start: 0.7697 (tp30) cc_final: 0.7423 (tp30) REVERT: A 382 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.8018 (mtt-85) REVERT: A 389 LEU cc_start: 0.8710 (mm) cc_final: 0.8498 (mt) REVERT: A 468 ASP cc_start: 0.7463 (t70) cc_final: 0.6950 (t70) REVERT: A 500 TYR cc_start: 0.8296 (t80) cc_final: 0.7915 (t80) REVERT: A 502 GLU cc_start: 0.7938 (tp30) cc_final: 0.7735 (tp30) REVERT: A 510 TYR cc_start: 0.7763 (m-80) cc_final: 0.7153 (m-80) REVERT: A 599 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8353 (tt) REVERT: A 653 ARG cc_start: 0.7833 (ttm170) cc_final: 0.7532 (mtm-85) REVERT: A 675 MET cc_start: 0.7990 (mmm) cc_final: 0.7600 (mmm) REVERT: A 676 LYS cc_start: 0.8642 (mttt) cc_final: 0.8270 (mttm) REVERT: B 206 VAL cc_start: 0.8283 (m) cc_final: 0.8025 (p) REVERT: B 249 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7291 (mm-30) REVERT: B 252 ILE cc_start: 0.8643 (mt) cc_final: 0.8366 (tp) REVERT: B 273 TRP cc_start: 0.8816 (m-10) cc_final: 0.8599 (m-10) REVERT: B 396 PHE cc_start: 0.7843 (t80) cc_final: 0.7586 (t80) REVERT: B 495 GLU cc_start: 0.7289 (pt0) cc_final: 0.7017 (pt0) REVERT: B 504 LYS cc_start: 0.7979 (mtpp) cc_final: 0.7727 (mttm) REVERT: B 520 LYS cc_start: 0.8321 (mmmm) cc_final: 0.8005 (mtpp) REVERT: B 535 ASN cc_start: 0.7520 (t0) cc_final: 0.7254 (t0) REVERT: B 551 TYR cc_start: 0.8105 (m-80) cc_final: 0.7763 (m-80) REVERT: B 646 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7307 (tmm-80) REVERT: B 658 TYR cc_start: 0.8438 (m-80) cc_final: 0.8119 (m-80) REVERT: B 665 GLN cc_start: 0.8379 (tt0) cc_final: 0.8036 (tm-30) REVERT: B 676 LYS cc_start: 0.8655 (mttt) cc_final: 0.8386 (mttp) REVERT: B 776 VAL cc_start: 0.8057 (t) cc_final: 0.7719 (m) REVERT: C 147 GLN cc_start: 0.8115 (tm-30) cc_final: 0.7491 (tm-30) REVERT: C 194 GLU cc_start: 0.7470 (tp30) cc_final: 0.6875 (tp30) REVERT: C 197 ASN cc_start: 0.7560 (m110) cc_final: 0.7118 (m-40) REVERT: C 198 GLU cc_start: 0.6844 (mt-10) cc_final: 0.6582 (mt-10) REVERT: C 211 GLU cc_start: 0.8066 (tp30) cc_final: 0.7791 (tp30) REVERT: C 249 GLU cc_start: 0.7383 (mm-30) cc_final: 0.6738 (mm-30) REVERT: C 251 LEU cc_start: 0.8358 (tp) cc_final: 0.8004 (tt) REVERT: C 295 LYS cc_start: 0.8697 (mptt) cc_final: 0.8410 (mptt) REVERT: C 382 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.8002 (ptp-170) REVERT: C 468 ASP cc_start: 0.7398 (t70) cc_final: 0.6861 (t70) REVERT: C 510 TYR cc_start: 0.7762 (m-80) cc_final: 0.7166 (m-80) REVERT: C 516 LEU cc_start: 0.7838 (tt) cc_final: 0.7608 (mt) REVERT: C 544 ASP cc_start: 0.8361 (t70) cc_final: 0.8131 (t0) REVERT: C 601 ASP cc_start: 0.7067 (m-30) cc_final: 0.6637 (m-30) REVERT: C 604 LEU cc_start: 0.8650 (mp) cc_final: 0.8400 (mp) REVERT: C 642 LEU cc_start: 0.8174 (tp) cc_final: 0.7860 (mm) REVERT: C 653 ARG cc_start: 0.7963 (ttm170) cc_final: 0.7594 (mtt90) REVERT: C 656 TRP cc_start: 0.8541 (m100) cc_final: 0.8163 (m-90) REVERT: C 669 GLN cc_start: 0.7669 (mp10) cc_final: 0.7117 (mp10) REVERT: C 676 LYS cc_start: 0.8786 (mttt) cc_final: 0.8518 (mttm) REVERT: C 683 ARG cc_start: 0.7891 (mpt180) cc_final: 0.7391 (mmt90) REVERT: C 711 ILE cc_start: 0.8732 (pt) cc_final: 0.8501 (mt) REVERT: C 721 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7361 (tp-100) REVERT: C 842 PHE cc_start: 0.7496 (m-80) cc_final: 0.7189 (m-80) outliers start: 76 outliers final: 53 residues processed: 616 average time/residue: 0.3373 time to fit residues: 290.6606 Evaluate side-chains 638 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 580 time to evaluate : 2.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 462 ASN Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 591 GLN Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 719 ASN Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 462 ASN Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 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 462 ASN Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain C residue 591 GLN Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 619 MET Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 719 ASN Chi-restraints excluded: chain C residue 721 GLN Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 762 CYS Chi-restraints excluded: chain C residue 825 VAL 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 123 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 156 optimal weight: 0.3980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN B 643 ASN C 535 ASN C 591 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 16707 Z= 0.231 Angle : 0.715 18.343 22881 Z= 0.345 Chirality : 0.049 0.300 2763 Planarity : 0.005 0.044 2880 Dihedral : 10.334 94.548 3246 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.60 % Allowed : 24.46 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.19), residues: 2052 helix: 0.13 (0.22), residues: 552 sheet: 0.21 (0.29), residues: 372 loop : -1.07 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 326 HIS 0.008 0.001 HIS B 639 PHE 0.019 0.001 PHE A 396 TYR 0.033 0.002 TYR B 276 ARG 0.012 0.001 ARG B 407 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 588 time to evaluate : 1.863 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: 0.8040 (tm-30) cc_final: 0.7527 (tm-30) REVERT: A 194 GLU cc_start: 0.7558 (tp30) cc_final: 0.6943 (tp30) REVERT: A 198 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6637 (mt-10) REVERT: A 211 GLU cc_start: 0.8216 (tp30) cc_final: 0.7824 (tp30) REVERT: A 251 LEU cc_start: 0.8204 (tp) cc_final: 0.7725 (tt) REVERT: A 252 ILE cc_start: 0.8794 (mt) cc_final: 0.8413 (tt) REVERT: A 334 LEU cc_start: 0.8600 (mt) cc_final: 0.8382 (mt) REVERT: A 339 GLU cc_start: 0.7707 (tp30) cc_final: 0.7455 (tp30) REVERT: A 382 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8029 (mtt-85) REVERT: A 389 LEU cc_start: 0.8703 (mm) cc_final: 0.8492 (mt) REVERT: A 468 ASP cc_start: 0.7496 (t70) cc_final: 0.6962 (t70) REVERT: A 500 TYR cc_start: 0.8313 (t80) cc_final: 0.7902 (t80) REVERT: A 510 TYR cc_start: 0.7814 (m-80) cc_final: 0.7203 (m-80) REVERT: A 535 ASN cc_start: 0.7603 (t0) cc_final: 0.7131 (t0) REVERT: A 599 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8407 (tt) REVERT: A 653 ARG cc_start: 0.7885 (ttm170) cc_final: 0.7576 (mtm-85) REVERT: A 675 MET cc_start: 0.7972 (mmm) cc_final: 0.7586 (mmm) REVERT: A 676 LYS cc_start: 0.8648 (mttt) cc_final: 0.8279 (mttm) REVERT: B 206 VAL cc_start: 0.8248 (m) cc_final: 0.8004 (p) REVERT: B 249 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7290 (mm-30) REVERT: B 252 ILE cc_start: 0.8640 (mt) cc_final: 0.8422 (tp) REVERT: B 273 TRP cc_start: 0.8813 (m-10) cc_final: 0.8600 (m-10) REVERT: B 298 MET cc_start: 0.7324 (mmm) cc_final: 0.7100 (mmm) REVERT: B 396 PHE cc_start: 0.7849 (t80) cc_final: 0.7620 (t80) REVERT: B 495 GLU cc_start: 0.7313 (pt0) cc_final: 0.7067 (pt0) REVERT: B 504 LYS cc_start: 0.7988 (mtpp) cc_final: 0.7676 (mttm) REVERT: B 520 LYS cc_start: 0.8354 (mmmm) cc_final: 0.8022 (mtpp) REVERT: B 535 ASN cc_start: 0.7554 (t0) cc_final: 0.7310 (t0) REVERT: B 551 TYR cc_start: 0.8123 (m-80) cc_final: 0.7785 (m-80) REVERT: B 658 TYR cc_start: 0.8430 (m-80) cc_final: 0.8094 (m-80) REVERT: B 665 GLN cc_start: 0.8358 (tt0) cc_final: 0.8090 (tm-30) REVERT: B 676 LYS cc_start: 0.8652 (mttt) cc_final: 0.8385 (mttp) REVERT: B 721 GLN cc_start: 0.8134 (tm-30) cc_final: 0.7894 (tm-30) REVERT: C 147 GLN cc_start: 0.8143 (tm-30) cc_final: 0.7547 (tm-30) REVERT: C 194 GLU cc_start: 0.7481 (tp30) cc_final: 0.6925 (tp30) REVERT: C 198 GLU cc_start: 0.6856 (mt-10) cc_final: 0.6615 (mt-10) REVERT: C 211 GLU cc_start: 0.8071 (tp30) cc_final: 0.7800 (tp30) REVERT: C 249 GLU cc_start: 0.7383 (mm-30) cc_final: 0.6722 (mm-30) REVERT: C 251 LEU cc_start: 0.8392 (tp) cc_final: 0.8021 (tt) REVERT: C 295 LYS cc_start: 0.8705 (mptt) cc_final: 0.8412 (mptt) REVERT: C 382 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7956 (mtt-85) REVERT: C 468 ASP cc_start: 0.7402 (t70) cc_final: 0.6891 (t70) REVERT: C 510 TYR cc_start: 0.7799 (m-80) cc_final: 0.7179 (m-80) REVERT: C 516 LEU cc_start: 0.7841 (tt) cc_final: 0.7627 (mt) REVERT: C 544 ASP cc_start: 0.8370 (t70) cc_final: 0.8146 (t0) REVERT: C 601 ASP cc_start: 0.7092 (m-30) cc_final: 0.6653 (m-30) REVERT: C 604 LEU cc_start: 0.8647 (mp) cc_final: 0.8414 (mp) REVERT: C 642 LEU cc_start: 0.8187 (tp) cc_final: 0.7980 (mm) REVERT: C 648 MET cc_start: 0.8193 (mmt) cc_final: 0.7855 (mmt) REVERT: C 653 ARG cc_start: 0.7995 (ttm170) cc_final: 0.7601 (mtt90) REVERT: C 669 GLN cc_start: 0.7671 (mp10) cc_final: 0.7121 (mp10) REVERT: C 676 LYS cc_start: 0.8815 (mttt) cc_final: 0.8390 (mttm) REVERT: C 683 ARG cc_start: 0.7900 (mpt180) cc_final: 0.7435 (mmt90) REVERT: C 711 ILE cc_start: 0.8760 (pt) cc_final: 0.8536 (mt) REVERT: C 721 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7353 (tp-100) REVERT: C 842 PHE cc_start: 0.7574 (m-80) cc_final: 0.7106 (m-80) outliers start: 72 outliers final: 55 residues processed: 615 average time/residue: 0.3277 time to fit residues: 284.4744 Evaluate side-chains 647 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 588 time to evaluate : 1.965 ------------------------------------------------------------------------------- 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 462 ASN Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 591 GLN Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 462 ASN Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 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 214 LEU 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 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 591 GLN Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 619 MET Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 719 ASN Chi-restraints excluded: chain C residue 721 GLN Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 762 CYS Chi-restraints excluded: chain C residue 763 ARG Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 837 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 0.0770 chunk 191 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 80 optimal weight: 0.0670 chunk 145 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 GLN B 643 ASN C 197 ASN C 591 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 16707 Z= 0.296 Angle : 0.753 19.326 22881 Z= 0.365 Chirality : 0.050 0.326 2763 Planarity : 0.005 0.045 2880 Dihedral : 10.356 93.533 3246 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 4.41 % Allowed : 24.78 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.19), residues: 2052 helix: 0.13 (0.22), residues: 543 sheet: 0.12 (0.29), residues: 372 loop : -1.17 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 326 HIS 0.011 0.001 HIS B 639 PHE 0.021 0.002 PHE A 396 TYR 0.034 0.002 TYR B 276 ARG 0.011 0.001 ARG B 764 *********************** 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 664 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 595 time to evaluate : 1.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLN cc_start: 0.8005 (tm-30) cc_final: 0.7470 (tm-30) REVERT: A 194 GLU cc_start: 0.7581 (tp30) cc_final: 0.6977 (tp30) REVERT: A 198 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6634 (mt-10) REVERT: A 211 GLU cc_start: 0.8243 (tp30) cc_final: 0.7847 (tp30) REVERT: A 251 LEU cc_start: 0.8217 (tp) cc_final: 0.7736 (tt) REVERT: A 252 ILE cc_start: 0.8807 (mt) cc_final: 0.8418 (tt) REVERT: A 334 LEU cc_start: 0.8645 (mt) cc_final: 0.8421 (mt) REVERT: A 339 GLU cc_start: 0.7730 (tp30) cc_final: 0.7453 (tp30) REVERT: A 382 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.8035 (mtt-85) REVERT: A 389 LEU cc_start: 0.8705 (mm) cc_final: 0.8501 (mt) REVERT: A 468 ASP cc_start: 0.7539 (t70) cc_final: 0.6981 (t70) REVERT: A 500 TYR cc_start: 0.8286 (t80) cc_final: 0.7845 (t80) REVERT: A 510 TYR cc_start: 0.7902 (m-80) cc_final: 0.7276 (m-80) REVERT: A 535 ASN cc_start: 0.7626 (t0) cc_final: 0.7154 (t0) REVERT: A 599 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8482 (tt) REVERT: A 653 ARG cc_start: 0.7927 (ttm170) cc_final: 0.7615 (mtm-85) REVERT: A 675 MET cc_start: 0.7970 (mmm) cc_final: 0.7608 (mmm) REVERT: A 676 LYS cc_start: 0.8675 (mttt) cc_final: 0.8295 (mttm) REVERT: A 721 GLN cc_start: 0.7999 (tm-30) cc_final: 0.7276 (tm-30) REVERT: B 147 GLN cc_start: 0.7914 (tm-30) cc_final: 0.7403 (tm-30) REVERT: B 206 VAL cc_start: 0.8162 (m) cc_final: 0.7930 (p) REVERT: B 249 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7301 (mm-30) REVERT: B 252 ILE cc_start: 0.8692 (mt) cc_final: 0.8370 (tp) REVERT: B 273 TRP cc_start: 0.8821 (m-10) cc_final: 0.8582 (m-10) REVERT: B 298 MET cc_start: 0.7261 (mmm) cc_final: 0.6973 (mmm) REVERT: B 396 PHE cc_start: 0.7893 (t80) cc_final: 0.7656 (t80) REVERT: B 495 GLU cc_start: 0.7362 (pt0) cc_final: 0.7085 (pt0) REVERT: B 504 LYS cc_start: 0.8008 (mtpp) cc_final: 0.7772 (mtpp) REVERT: B 551 TYR cc_start: 0.8146 (m-80) cc_final: 0.7800 (m-80) REVERT: B 635 VAL cc_start: 0.8003 (m) cc_final: 0.7663 (t) REVERT: B 658 TYR cc_start: 0.8426 (m-80) cc_final: 0.8094 (m-80) REVERT: B 676 LYS cc_start: 0.8660 (mttt) cc_final: 0.8380 (mttp) REVERT: B 721 GLN cc_start: 0.8140 (tm-30) cc_final: 0.7872 (tm-30) REVERT: C 147 GLN cc_start: 0.8115 (tm-30) cc_final: 0.7566 (tm-30) REVERT: C 194 GLU cc_start: 0.7509 (tp30) cc_final: 0.6958 (tp30) REVERT: C 197 ASN cc_start: 0.7551 (m110) cc_final: 0.7155 (m-40) REVERT: C 211 GLU cc_start: 0.8093 (tp30) cc_final: 0.7818 (tp30) REVERT: C 251 LEU cc_start: 0.8399 (tp) cc_final: 0.8030 (tt) REVERT: C 295 LYS cc_start: 0.8706 (mptt) cc_final: 0.8375 (mptt) REVERT: C 319 SER cc_start: 0.8247 (p) cc_final: 0.8006 (t) REVERT: C 382 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7953 (mtt-85) REVERT: C 510 TYR cc_start: 0.7898 (m-80) cc_final: 0.7266 (m-80) REVERT: C 516 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7667 (mt) REVERT: C 535 ASN cc_start: 0.7899 (t0) cc_final: 0.7560 (t0) REVERT: C 544 ASP cc_start: 0.8371 (t70) cc_final: 0.8152 (t0) REVERT: C 601 ASP cc_start: 0.7073 (m-30) cc_final: 0.6637 (m-30) REVERT: C 604 LEU cc_start: 0.8683 (mp) cc_final: 0.8467 (mp) REVERT: C 653 ARG cc_start: 0.8026 (ttm170) cc_final: 0.7632 (mtt90) REVERT: C 669 GLN cc_start: 0.7681 (mp10) cc_final: 0.7117 (mp10) REVERT: C 676 LYS cc_start: 0.8834 (mttt) cc_final: 0.8408 (mttm) REVERT: C 683 ARG cc_start: 0.7894 (mpt180) cc_final: 0.7447 (mmt90) REVERT: C 711 ILE cc_start: 0.8762 (pt) cc_final: 0.8555 (mt) REVERT: C 721 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7365 (tp-100) REVERT: C 842 PHE cc_start: 0.7577 (m-80) cc_final: 0.6998 (m-80) outliers start: 69 outliers final: 54 residues processed: 623 average time/residue: 0.3309 time to fit residues: 290.4141 Evaluate side-chains 646 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 587 time to evaluate : 1.896 ------------------------------------------------------------------------------- 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 462 ASN Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 719 ASN Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 462 ASN Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 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 825 VAL Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 214 LEU 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 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 591 GLN Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 619 MET Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 719 ASN Chi-restraints excluded: chain C residue 721 GLN Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 762 CYS Chi-restraints excluded: chain C residue 825 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 136 optimal weight: 0.6980 chunk 206 optimal weight: 8.9990 chunk 189 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 ASN C 591 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 16707 Z= 0.286 Angle : 0.766 19.054 22881 Z= 0.370 Chirality : 0.050 0.320 2763 Planarity : 0.005 0.048 2880 Dihedral : 10.310 92.488 3246 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.65 % Favored : 94.30 % Rotamer: Outliers : 4.41 % Allowed : 25.03 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.19), residues: 2052 helix: 0.03 (0.22), residues: 552 sheet: 0.11 (0.29), residues: 372 loop : -1.18 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 326 HIS 0.010 0.001 HIS C 639 PHE 0.021 0.001 PHE A 396 TYR 0.035 0.002 TYR B 276 ARG 0.014 0.001 ARG B 612 ********************** 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 655 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 586 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLN cc_start: 0.8010 (tm-30) cc_final: 0.7453 (tm-30) REVERT: A 150 PHE cc_start: 0.7652 (t80) cc_final: 0.7429 (t80) REVERT: A 194 GLU cc_start: 0.7583 (tp30) cc_final: 0.6980 (tp30) REVERT: A 198 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6654 (mt-10) REVERT: A 211 GLU cc_start: 0.8241 (tp30) cc_final: 0.7828 (tp30) REVERT: A 212 ILE cc_start: 0.8701 (mm) cc_final: 0.8356 (mm) REVERT: A 251 LEU cc_start: 0.8227 (tp) cc_final: 0.7742 (tt) REVERT: A 252 ILE cc_start: 0.8812 (mt) cc_final: 0.8417 (tt) REVERT: A 334 LEU cc_start: 0.8643 (mt) cc_final: 0.8430 (mt) REVERT: A 339 GLU cc_start: 0.7731 (tp30) cc_final: 0.7463 (tp30) REVERT: A 382 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8064 (mtt-85) REVERT: A 389 LEU cc_start: 0.8709 (mm) cc_final: 0.8506 (mt) REVERT: A 468 ASP cc_start: 0.7536 (t70) cc_final: 0.6961 (t70) REVERT: A 510 TYR cc_start: 0.7917 (m-80) cc_final: 0.7313 (m-80) REVERT: A 535 ASN cc_start: 0.7664 (t0) cc_final: 0.7195 (t0) REVERT: A 599 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8492 (tt) REVERT: A 653 ARG cc_start: 0.7928 (ttm170) cc_final: 0.7625 (mtm-85) REVERT: A 675 MET cc_start: 0.7960 (mmm) cc_final: 0.7591 (mmm) REVERT: A 676 LYS cc_start: 0.8669 (mttt) cc_final: 0.8286 (mttm) REVERT: A 721 GLN cc_start: 0.8095 (tm-30) cc_final: 0.7267 (tm-30) REVERT: B 147 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7282 (tm-30) REVERT: B 206 VAL cc_start: 0.8183 (m) cc_final: 0.7940 (p) REVERT: B 249 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7287 (mm-30) REVERT: B 252 ILE cc_start: 0.8651 (mt) cc_final: 0.8368 (tp) REVERT: B 273 TRP cc_start: 0.8817 (m-10) cc_final: 0.8556 (m-10) REVERT: B 298 MET cc_start: 0.7265 (mmm) cc_final: 0.6968 (mmm) REVERT: B 396 PHE cc_start: 0.7887 (t80) cc_final: 0.7651 (t80) REVERT: B 495 GLU cc_start: 0.7355 (pt0) cc_final: 0.7097 (pt0) REVERT: B 504 LYS cc_start: 0.8023 (mtpp) cc_final: 0.7806 (mtpp) REVERT: B 551 TYR cc_start: 0.8143 (m-80) cc_final: 0.7807 (m-80) REVERT: B 599 ILE cc_start: 0.8560 (tp) cc_final: 0.8330 (mm) REVERT: B 635 VAL cc_start: 0.8023 (m) cc_final: 0.7697 (t) REVERT: B 658 TYR cc_start: 0.8405 (m-80) cc_final: 0.8142 (m-80) REVERT: B 676 LYS cc_start: 0.8648 (mttt) cc_final: 0.8384 (mttp) REVERT: C 147 GLN cc_start: 0.8114 (tm-30) cc_final: 0.7563 (tm-30) REVERT: C 194 GLU cc_start: 0.7452 (tp30) cc_final: 0.6969 (tp30) REVERT: C 211 GLU cc_start: 0.8099 (tp30) cc_final: 0.7820 (tp30) REVERT: C 249 GLU cc_start: 0.7372 (mm-30) cc_final: 0.6725 (mm-30) REVERT: C 251 LEU cc_start: 0.8406 (tp) cc_final: 0.8036 (tt) REVERT: C 295 LYS cc_start: 0.8714 (mptt) cc_final: 0.8389 (mptt) REVERT: C 319 SER cc_start: 0.8313 (p) cc_final: 0.8095 (t) REVERT: C 382 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7948 (mtt-85) REVERT: C 510 TYR cc_start: 0.7895 (m-80) cc_final: 0.7245 (m-80) REVERT: C 516 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7661 (mt) REVERT: C 535 ASN cc_start: 0.7938 (t0) cc_final: 0.7592 (t0) REVERT: C 544 ASP cc_start: 0.8372 (t70) cc_final: 0.8154 (t0) REVERT: C 601 ASP cc_start: 0.7016 (m-30) cc_final: 0.6541 (m-30) REVERT: C 648 MET cc_start: 0.8143 (mmt) cc_final: 0.7606 (mmt) REVERT: C 653 ARG cc_start: 0.8010 (ttm170) cc_final: 0.7646 (mtt90) REVERT: C 669 GLN cc_start: 0.7681 (mp10) cc_final: 0.7108 (mp10) REVERT: C 676 LYS cc_start: 0.8828 (mttt) cc_final: 0.8406 (mttm) REVERT: C 683 ARG cc_start: 0.7902 (mpt180) cc_final: 0.7468 (mmt90) REVERT: C 711 ILE cc_start: 0.8750 (pt) cc_final: 0.8545 (mt) REVERT: C 721 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7223 (tp40) REVERT: C 842 PHE cc_start: 0.7546 (m-80) cc_final: 0.6910 (m-80) outliers start: 69 outliers final: 55 residues processed: 612 average time/residue: 0.3232 time to fit residues: 278.8787 Evaluate side-chains 642 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 581 time to evaluate : 1.778 ------------------------------------------------------------------------------- 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 462 ASN Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 719 ASN Chi-restraints excluded: chain A residue 762 CYS Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 462 ASN Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 526 THR 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 825 VAL Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 305 LYS 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 619 MET Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 719 ASN Chi-restraints excluded: chain C residue 721 GLN Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 762 CYS Chi-restraints excluded: chain C residue 825 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 151 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 45 optimal weight: 0.0980 chunk 164 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 168 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 GLN B 492 GLN B 643 ASN C 197 ASN ** C 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.117494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.099656 restraints weight = 28477.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.103285 restraints weight = 13918.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.105671 restraints weight = 8180.129| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 16707 Z= 0.195 Angle : 0.725 17.541 22881 Z= 0.347 Chirality : 0.048 0.294 2763 Planarity : 0.005 0.044 2880 Dihedral : 9.935 89.686 3246 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.17 % Favored : 94.79 % Rotamer: Outliers : 3.96 % Allowed : 26.25 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.19), residues: 2052 helix: 0.15 (0.23), residues: 555 sheet: 0.25 (0.28), residues: 390 loop : -1.06 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 326 HIS 0.005 0.001 HIS C 639 PHE 0.020 0.001 PHE A 396 TYR 0.030 0.002 TYR B 276 ARG 0.011 0.001 ARG B 612 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4835.50 seconds wall clock time: 88 minutes 16.20 seconds (5296.20 seconds total)