Starting phenix.real_space_refine on Fri Feb 6 23:43:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n4r_48903/02_2026/9n4r_48903.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n4r_48903/02_2026/9n4r_48903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n4r_48903/02_2026/9n4r_48903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n4r_48903/02_2026/9n4r_48903.map" model { file = "/net/cci-nas-00/data/ceres_data/9n4r_48903/02_2026/9n4r_48903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n4r_48903/02_2026/9n4r_48903.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.037 sd= 1.295 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 S 164 5.16 5 C 18256 2.51 5 N 4532 2.21 5 O 5384 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28356 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6680 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 808} Conformer: "B" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 808} bond proxies already assigned to first conformer: 6823 Chain: "B" Number of atoms: 6680 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 808} Conformer: "B" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 808} bond proxies already assigned to first conformer: 6823 Chain: "C" Number of atoms: 6680 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 808} Conformer: "B" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 808} bond proxies already assigned to first conformer: 6823 Chain: "D" Number of atoms: 6680 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 808} Conformer: "B" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 808} bond proxies already assigned to first conformer: 6823 Chain: "E" 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: "F" 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: "G" 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: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" 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: "J" 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: "K" 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: "L" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 427 Unusual residues: {'2J9': 1, 'NAG': 6, 'POV': 6} Classifications: {'peptide': 1, 'undetermined': 13} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 207 Unusual residues: {'2J9': 2, 'NAG': 4, 'POV': 2} Classifications: {'peptide': 1, 'undetermined': 8} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 307 Unusual residues: {'NAG': 6, 'POV': 4} Classifications: {'peptide': 1, 'undetermined': 10} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "D" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 295 Unusual residues: {'2J9': 1, 'NAG': 4, 'POV': 4} Classifications: {'peptide': 1, 'undetermined': 9} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 12.09, per 1000 atoms: 0.43 Number of scatterers: 28356 At special positions: 0 Unit cell: (157.7, 118.69, 216.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 164 16.00 P 16 15.00 F 4 9.00 O 5384 8.00 N 4532 7.00 C 18256 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.03 Simple disulfide: pdb=" SG CYS A 750 " - pdb=" SG CYS A 804 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.04 Simple disulfide: pdb=" SG CYS B 750 " - pdb=" SG CYS B 804 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.03 Simple disulfide: pdb=" SG CYS C 750 " - pdb=" SG CYS C 804 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " distance=2.04 Simple disulfide: pdb=" SG CYS D 750 " - pdb=" SG CYS D 804 " 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 E 3 " - " MAN E 4 " " BMA G 3 " - " MAN G 4 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA G 3 " - " MAN G 5 " " BMA I 3 " - " MAN I 5 " " BMA K 3 " - " MAN K 5 " BETA1-3 " BMA H 3 " - " BMA H 4 " " BMA L 3 " - " BMA L 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG A1006 " - " ASN A 67 " " NAG A1007 " - " ASN A 73 " " NAG A1008 " - " ASN A 275 " " NAG A1009 " - " ASN A 412 " " NAG A1010 " - " ASN A 546 " " NAG A1011 " - " ASN A 751 " " NAG B1005 " - " ASN B 67 " " NAG B1006 " - " ASN B 73 " " NAG B1007 " - " ASN B 412 " " NAG B1008 " - " ASN B 751 " " NAG C1006 " - " ASN C 67 " " NAG C1007 " - " ASN C 73 " " NAG C1008 " - " ASN C 275 " " NAG C1009 " - " ASN C 412 " " NAG C1010 " - " ASN C 546 " " NAG C1011 " - " ASN C 751 " " NAG D1007 " - " ASN D 67 " " NAG D1008 " - " ASN D 73 " " NAG D1009 " - " ASN D 412 " " NAG D1010 " - " ASN D 751 " " NAG E 1 " - " ASN A 378 " " NAG F 1 " - " ASN B 275 " " NAG G 1 " - " ASN B 378 " " NAG H 1 " - " ASN B 546 " " NAG I 1 " - " ASN C 378 " " NAG J 1 " - " ASN D 275 " " NAG K 1 " - " ASN D 378 " " NAG L 1 " - " ASN D 546 " Time building additional restraints: 2.77 Conformation dependent library (CDL) restraints added in 2.1 seconds 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6304 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 40 sheets defined 42.8% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 Processing helix chain 'A' and resid 87 through 102 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.711A pdb=" N ASN A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 167 Processing helix chain 'A' and resid 180 through 185 removed outlier: 3.545A pdb=" N ARG A 184 " --> pdb=" O THR A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 191 through 194 Processing helix chain 'A' and resid 211 through 220 Processing helix chain 'A' and resid 231 through 245 removed outlier: 3.878A pdb=" N GLY A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE A 238 " --> pdb=" O MET A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 298 removed outlier: 3.535A pdb=" N ILE A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 337 removed outlier: 3.694A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 332 " --> pdb=" O HIS A 328 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA A 333 " --> pdb=" O VAL A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 365 removed outlier: 3.657A pdb=" N SER A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 458 removed outlier: 3.978A pdb=" N ASP A 457 " --> pdb=" O TYR A 454 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG A 458 " --> pdb=" O GLY A 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 454 through 458' Processing helix chain 'A' and resid 461 through 474 removed outlier: 4.055A pdb=" N LEU A 467 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.929A pdb=" N LYS A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 removed outlier: 3.682A pdb=" N LEU A 556 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 572 removed outlier: 3.666A pdb=" N LEU A 568 " --> pdb=" O TRP A 564 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 569 " --> pdb=" O MET A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 585 removed outlier: 3.747A pdb=" N PHE A 579 " --> pdb=" O SER A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 618 removed outlier: 3.546A pdb=" N TRP A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 660 removed outlier: 3.556A pdb=" N ILE A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE A 642 " --> pdb=" O GLY A 638 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 646 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE A 648 " --> pdb=" O THR A 644 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA A 656 " --> pdb=" O THR A 652 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA A 657 " --> pdb=" O ALA A 653 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 677 Processing helix chain 'A' and resid 690 through 696 Processing helix chain 'A' and resid 701 through 710 removed outlier: 3.948A pdb=" N MET A 709 " --> pdb=" O MET A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 731 removed outlier: 3.655A pdb=" N VAL A 728 " --> pdb=" O GLY A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 746 removed outlier: 4.171A pdb=" N PHE A 744 " --> pdb=" O THR A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 774 No H-bonds generated for 'chain 'A' and resid 772 through 774' Processing helix chain 'A' and resid 775 through 788 removed outlier: 3.841A pdb=" N THR A 779 " --> pdb=" O ARG A 775 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA A 781 " --> pdb=" O LYS A 777 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 785 " --> pdb=" O ALA A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 799 removed outlier: 4.011A pdb=" N LYS A 795 " --> pdb=" O LEU A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 853 removed outlier: 3.600A pdb=" N SER A 846 " --> pdb=" O PHE A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 866 Processing helix chain 'B' and resid 51 through 67 removed outlier: 3.556A pdb=" N ASN B 62 " --> pdb=" O ARG B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 102 Processing helix chain 'B' and resid 111 through 125 removed outlier: 3.736A pdb=" N ASN B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 167 removed outlier: 3.982A pdb=" N ARG B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 191 through 194 Processing helix chain 'B' and resid 211 through 220 removed outlier: 3.654A pdb=" N GLU B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG B 220 " --> pdb=" O LYS B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 245 removed outlier: 3.654A pdb=" N ALA B 236 " --> pdb=" O HIS B 232 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 301 removed outlier: 3.795A pdb=" N ILE B 292 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE B 293 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 294 " --> pdb=" O SER B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 336 removed outlier: 3.864A pdb=" N MET B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N HIS B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 365 removed outlier: 3.562A pdb=" N SER B 361 " --> pdb=" O THR B 357 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 362 " --> pdb=" O ARG B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 474 Processing helix chain 'B' and resid 499 through 507 Processing helix chain 'B' and resid 520 through 525 removed outlier: 3.578A pdb=" N LYS B 525 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 585 removed outlier: 3.846A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS B 576 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG B 583 " --> pdb=" O PHE B 579 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 618 Processing helix chain 'B' and resid 631 through 655 removed outlier: 3.971A pdb=" N VAL B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY B 637 " --> pdb=" O THR B 633 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE B 642 " --> pdb=" O GLY B 638 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 696 removed outlier: 3.538A pdb=" N PHE B 694 " --> pdb=" O THR B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 712 removed outlier: 3.881A pdb=" N TRP B 706 " --> pdb=" O TYR B 702 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N MET B 709 " --> pdb=" O MET B 705 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER B 711 " --> pdb=" O ALA B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 730 removed outlier: 3.581A pdb=" N ARG B 727 " --> pdb=" O GLU B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 749 removed outlier: 3.569A pdb=" N PHE B 744 " --> pdb=" O THR B 740 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLN B 747 " --> pdb=" O GLU B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 788 removed outlier: 3.595A pdb=" N LYS B 777 " --> pdb=" O PRO B 773 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA B 781 " --> pdb=" O LYS B 777 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 783 " --> pdb=" O THR B 779 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU B 788 " --> pdb=" O GLN B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 800 removed outlier: 3.562A pdb=" N ARG B 800 " --> pdb=" O GLU B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 850 removed outlier: 3.612A pdb=" N GLY B 830 " --> pdb=" O VAL B 826 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL B 832 " --> pdb=" O ALA B 828 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU B 833 " --> pdb=" O ALA B 829 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER B 846 " --> pdb=" O PHE B 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 870 removed outlier: 3.579A pdb=" N ALA B 860 " --> pdb=" O SER B 856 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL B 862 " --> pdb=" O CYS B 858 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU B 863 " --> pdb=" O SER B 859 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS B 870 " --> pdb=" O ARG B 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 67 Processing helix chain 'C' and resid 87 through 102 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.711A pdb=" N ASN C 116 " --> pdb=" O SER C 112 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE C 121 " --> pdb=" O ALA C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 167 Processing helix chain 'C' and resid 180 through 185 removed outlier: 3.545A pdb=" N ARG C 184 " --> pdb=" O THR C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 191 through 194 Processing helix chain 'C' and resid 211 through 220 Processing helix chain 'C' and resid 231 through 245 removed outlier: 3.878A pdb=" N GLY C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE C 238 " --> pdb=" O MET C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 298 removed outlier: 3.535A pdb=" N ILE C 292 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 337 removed outlier: 3.693A pdb=" N MET C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N HIS C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL C 332 " --> pdb=" O HIS C 328 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA C 333 " --> pdb=" O VAL C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 365 removed outlier: 3.658A pdb=" N SER C 361 " --> pdb=" O THR C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 458 removed outlier: 3.978A pdb=" N ASP C 457 " --> pdb=" O TYR C 454 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG C 458 " --> pdb=" O GLY C 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 454 through 458' Processing helix chain 'C' and resid 461 through 474 removed outlier: 4.055A pdb=" N LEU C 467 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE C 473 " --> pdb=" O GLU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 507 Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.929A pdb=" N LYS C 525 " --> pdb=" O TYR C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 557 removed outlier: 3.682A pdb=" N LEU C 556 " --> pdb=" O PHE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 572 removed outlier: 3.666A pdb=" N LEU C 568 " --> pdb=" O TRP C 564 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 569 " --> pdb=" O MET C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 585 removed outlier: 3.748A pdb=" N PHE C 579 " --> pdb=" O SER C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 618 removed outlier: 3.546A pdb=" N TRP C 613 " --> pdb=" O LEU C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 660 removed outlier: 3.555A pdb=" N ILE C 635 " --> pdb=" O LEU C 631 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE C 642 " --> pdb=" O GLY C 638 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE C 646 " --> pdb=" O PHE C 642 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE C 648 " --> pdb=" O THR C 644 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA C 656 " --> pdb=" O THR C 652 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR C 660 " --> pdb=" O ALA C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 677 Processing helix chain 'C' and resid 690 through 696 Processing helix chain 'C' and resid 701 through 708 Processing helix chain 'C' and resid 721 through 731 removed outlier: 3.654A pdb=" N VAL C 728 " --> pdb=" O GLY C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 746 removed outlier: 4.172A pdb=" N PHE C 744 " --> pdb=" O THR C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 774 No H-bonds generated for 'chain 'C' and resid 772 through 774' Processing helix chain 'C' and resid 775 through 788 removed outlier: 3.842A pdb=" N THR C 779 " --> pdb=" O ARG C 775 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA C 781 " --> pdb=" O LYS C 777 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU C 785 " --> pdb=" O ALA C 781 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 799 removed outlier: 4.011A pdb=" N LYS C 795 " --> pdb=" O LEU C 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 853 removed outlier: 3.600A pdb=" N SER C 846 " --> pdb=" O PHE C 842 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 866 Processing helix chain 'D' and resid 51 through 67 removed outlier: 3.556A pdb=" N ASN D 62 " --> pdb=" O ARG D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 102 Processing helix chain 'D' and resid 111 through 125 removed outlier: 3.736A pdb=" N ASN D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 167 removed outlier: 3.982A pdb=" N ARG D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 185 Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 191 through 194 Processing helix chain 'D' and resid 211 through 220 removed outlier: 3.654A pdb=" N GLU D 217 " --> pdb=" O PRO D 213 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 245 removed outlier: 3.654A pdb=" N ALA D 236 " --> pdb=" O HIS D 232 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 301 removed outlier: 3.795A pdb=" N ILE D 292 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE D 293 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU D 294 " --> pdb=" O SER D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 336 removed outlier: 3.863A pdb=" N MET D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 365 removed outlier: 3.561A pdb=" N SER D 361 " --> pdb=" O THR D 357 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU D 362 " --> pdb=" O ARG D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 474 Processing helix chain 'D' and resid 499 through 507 Processing helix chain 'D' and resid 520 through 525 removed outlier: 3.579A pdb=" N LYS D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 585 removed outlier: 3.846A pdb=" N LEU D 568 " --> pdb=" O TRP D 564 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS D 576 " --> pdb=" O LEU D 572 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG D 583 " --> pdb=" O PHE D 579 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE D 584 " --> pdb=" O VAL D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 618 Processing helix chain 'D' and resid 631 through 655 removed outlier: 3.970A pdb=" N VAL D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY D 637 " --> pdb=" O THR D 633 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE D 642 " --> pdb=" O GLY D 638 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 696 removed outlier: 3.538A pdb=" N PHE D 694 " --> pdb=" O THR D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 712 removed outlier: 3.881A pdb=" N TRP D 706 " --> pdb=" O TYR D 702 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N MET D 709 " --> pdb=" O MET D 705 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER D 711 " --> pdb=" O ALA D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 730 removed outlier: 3.581A pdb=" N ARG D 727 " --> pdb=" O GLU D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 749 removed outlier: 3.570A pdb=" N PHE D 744 " --> pdb=" O THR D 740 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLN D 747 " --> pdb=" O GLU D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 773 through 788 removed outlier: 3.595A pdb=" N LYS D 777 " --> pdb=" O PRO D 773 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA D 781 " --> pdb=" O LYS D 777 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU D 783 " --> pdb=" O THR D 779 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU D 788 " --> pdb=" O GLN D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 800 removed outlier: 3.562A pdb=" N ARG D 800 " --> pdb=" O GLU D 796 " (cutoff:3.500A) Processing helix chain 'D' and resid 822 through 850 removed outlier: 3.612A pdb=" N GLY D 830 " --> pdb=" O VAL D 826 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL D 832 " --> pdb=" O ALA D 828 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU D 833 " --> pdb=" O ALA D 829 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER D 846 " --> pdb=" O PHE D 842 " (cutoff:3.500A) Processing helix chain 'D' and resid 856 through 870 removed outlier: 3.579A pdb=" N ALA D 860 " --> pdb=" O SER D 856 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL D 862 " --> pdb=" O CYS D 858 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU D 863 " --> pdb=" O SER D 859 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS D 870 " --> pdb=" O ARG D 866 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 removed outlier: 5.890A pdb=" N LEU A 36 " --> pdb=" O THR A 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 43 removed outlier: 6.377A pdb=" N GLY A 40 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE A 83 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N PHE A 42 " --> pdb=" O ILE A 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 131 removed outlier: 3.540A pdb=" N VAL A 147 " --> pdb=" O HIS A 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 175 through 176 Processing sheet with id=AA5, first strand: chain 'A' and resid 225 through 226 removed outlier: 6.398A pdb=" N VAL A 226 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N MET A 276 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU A 389 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N THR A 404 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL A 391 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 369 through 370 removed outlier: 3.540A pdb=" N GLY A 373 " --> pdb=" O GLY A 370 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 434 through 435 Processing sheet with id=AA8, first strand: chain 'A' and resid 735 through 738 Processing sheet with id=AA9, first strand: chain 'A' and resid 684 through 685 removed outlier: 5.934A pdb=" N ALA A 684 " --> pdb=" O VAL A 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 40 through 42 Processing sheet with id=AB2, first strand: chain 'B' and resid 130 through 131 removed outlier: 8.509A pdb=" N SER B 148 " --> pdb=" O ARG B 384 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 175 through 176 Processing sheet with id=AB4, first strand: chain 'B' and resid 225 through 226 removed outlier: 6.556A pdb=" N VAL B 226 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 368 through 370 removed outlier: 3.549A pdb=" N TRP B 368 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY B 373 " --> pdb=" O GLY B 370 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 389 through 390 Processing sheet with id=AB7, first strand: chain 'B' and resid 393 through 395 Processing sheet with id=AB8, first strand: chain 'B' and resid 434 through 436 removed outlier: 5.777A pdb=" N VAL B 435 " --> pdb=" O ARG B 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 527 through 529 Processing sheet with id=AC1, first strand: chain 'B' and resid 535 through 536 Processing sheet with id=AC2, first strand: chain 'B' and resid 681 through 683 removed outlier: 6.713A pdb=" N GLU B 681 " --> pdb=" O ALA B 734 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N LEU B 736 " --> pdb=" O GLU B 681 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N GLY B 683 " --> pdb=" O LEU B 736 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N GLU B 738 " --> pdb=" O GLY B 683 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N TYR B 733 " --> pdb=" O ARG B 543 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ARG B 543 " --> pdb=" O TYR B 733 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE B 540 " --> pdb=" O ILE B 755 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 35 through 37 removed outlier: 5.891A pdb=" N LEU C 36 " --> pdb=" O THR C 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 40 through 43 removed outlier: 6.377A pdb=" N GLY C 40 " --> pdb=" O GLN C 81 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE C 83 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N PHE C 42 " --> pdb=" O ILE C 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 129 through 131 removed outlier: 3.541A pdb=" N VAL C 147 " --> pdb=" O HIS C 129 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 175 through 176 Processing sheet with id=AC7, first strand: chain 'C' and resid 225 through 226 removed outlier: 6.399A pdb=" N VAL C 226 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N MET C 276 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU C 389 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N THR C 404 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL C 391 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 369 through 370 removed outlier: 3.539A pdb=" N GLY C 373 " --> pdb=" O GLY C 370 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 434 through 435 Processing sheet with id=AD1, first strand: chain 'C' and resid 735 through 738 Processing sheet with id=AD2, first strand: chain 'C' and resid 684 through 685 removed outlier: 5.933A pdb=" N ALA C 684 " --> pdb=" O VAL C 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 40 through 42 Processing sheet with id=AD4, first strand: chain 'D' and resid 130 through 131 removed outlier: 8.509A pdb=" N SER D 148 " --> pdb=" O ARG D 384 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 175 through 176 Processing sheet with id=AD6, first strand: chain 'D' and resid 225 through 226 removed outlier: 6.556A pdb=" N VAL D 226 " --> pdb=" O ILE D 255 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 368 through 370 removed outlier: 3.549A pdb=" N TRP D 368 " --> pdb=" O ILE D 375 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY D 373 " --> pdb=" O GLY D 370 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 389 through 390 Processing sheet with id=AD9, first strand: chain 'D' and resid 393 through 395 Processing sheet with id=AE1, first strand: chain 'D' and resid 434 through 436 removed outlier: 5.778A pdb=" N VAL D 435 " --> pdb=" O ARG D 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'D' and resid 527 through 529 Processing sheet with id=AE3, first strand: chain 'D' and resid 535 through 536 Processing sheet with id=AE4, first strand: chain 'D' and resid 681 through 683 removed outlier: 6.713A pdb=" N GLU D 681 " --> pdb=" O ALA D 734 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N LEU D 736 " --> pdb=" O GLU D 681 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N GLY D 683 " --> pdb=" O LEU D 736 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N GLU D 738 " --> pdb=" O GLY D 683 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N TYR D 733 " --> pdb=" O ARG D 543 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ARG D 543 " --> pdb=" O TYR D 733 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE D 540 " --> pdb=" O ILE D 755 " (cutoff:3.500A) 923 hydrogen bonds defined for protein. 2705 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: 5.54 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4467 1.31 - 1.44: 7818 1.44 - 1.57: 16349 1.57 - 1.70: 42 1.70 - 1.83: 276 Bond restraints: 28952 Sorted by residual: bond pdb=" C ASN C 557 " pdb=" N PRO C 558 " ideal model delta sigma weight residual 1.337 1.391 -0.054 9.80e-03 1.04e+04 3.09e+01 bond pdb=" C ASN A 557 " pdb=" N PRO A 558 " ideal model delta sigma weight residual 1.337 1.390 -0.054 9.80e-03 1.04e+04 3.00e+01 bond pdb=" C1 NAG A1006 " pdb=" O5 NAG A1006 " ideal model delta sigma weight residual 1.406 1.515 -0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C1 NAG C1006 " pdb=" O5 NAG C1006 " ideal model delta sigma weight residual 1.406 1.513 -0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C1 NAG D1010 " pdb=" O5 NAG D1010 " ideal model delta sigma weight residual 1.406 1.512 -0.106 2.00e-02 2.50e+03 2.79e+01 ... (remaining 28947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 37337 3.09 - 6.19: 1379 6.19 - 9.28: 240 9.28 - 12.37: 75 12.37 - 15.47: 21 Bond angle restraints: 39052 Sorted by residual: angle pdb=" C PRO D 597 " pdb=" N ASP D 598 " pdb=" CA ASP D 598 " ideal model delta sigma weight residual 121.54 136.62 -15.08 1.91e+00 2.74e-01 6.23e+01 angle pdb=" C PRO B 597 " pdb=" N ASP B 598 " pdb=" CA ASP B 598 " ideal model delta sigma weight residual 121.54 136.56 -15.02 1.91e+00 2.74e-01 6.19e+01 angle pdb=" C ILE C 424 " pdb=" N THR C 425 " pdb=" CA THR C 425 " ideal model delta sigma weight residual 121.54 132.16 -10.62 1.91e+00 2.74e-01 3.09e+01 angle pdb=" C ILE A 424 " pdb=" N THR A 425 " pdb=" CA THR A 425 " ideal model delta sigma weight residual 121.54 132.16 -10.62 1.91e+00 2.74e-01 3.09e+01 angle pdb=" N THR B 678 " pdb=" CA THR B 678 " pdb=" C THR B 678 " ideal model delta sigma weight residual 114.56 107.79 6.77 1.27e+00 6.20e-01 2.84e+01 ... (remaining 39047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.21: 17487 34.21 - 68.42: 532 68.42 - 102.63: 164 102.63 - 136.84: 76 136.84 - 171.06: 5 Dihedral angle restraints: 18264 sinusoidal: 8468 harmonic: 9796 Sorted by residual: dihedral pdb=" CA SER D 599 " pdb=" C SER D 599 " pdb=" N ASP D 600 " pdb=" CA ASP D 600 " ideal model delta harmonic sigma weight residual 180.00 115.32 64.68 0 5.00e+00 4.00e-02 1.67e+02 dihedral pdb=" CA SER B 599 " pdb=" C SER B 599 " pdb=" N ASP B 600 " pdb=" CA ASP B 600 " ideal model delta harmonic sigma weight residual 180.00 115.35 64.65 0 5.00e+00 4.00e-02 1.67e+02 dihedral pdb=" CA ASP D 598 " pdb=" C ASP D 598 " pdb=" N SER D 599 " pdb=" CA SER D 599 " ideal model delta harmonic sigma weight residual 180.00 121.93 58.07 0 5.00e+00 4.00e-02 1.35e+02 ... (remaining 18261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 4185 0.124 - 0.248: 185 0.248 - 0.371: 28 0.371 - 0.495: 7 0.495 - 0.619: 3 Chirality restraints: 4408 Sorted by residual: chirality pdb=" C1 NAG D1008 " pdb=" ND2 ASN D 73 " pdb=" C2 NAG D1008 " pdb=" O5 NAG D1008 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.58e+00 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN D 378 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 8.92e+00 chirality pdb=" C1 NAG B1006 " pdb=" ND2 ASN B 73 " pdb=" C2 NAG B1006 " pdb=" O5 NAG B1006 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 8.85e+00 ... (remaining 4405 not shown) Planarity restraints: 4832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 227 " -0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C ILE B 227 " 0.058 2.00e-02 2.50e+03 pdb=" O ILE B 227 " -0.022 2.00e-02 2.50e+03 pdb=" N PHE B 228 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 227 " 0.016 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C ILE D 227 " -0.057 2.00e-02 2.50e+03 pdb=" O ILE D 227 " 0.021 2.00e-02 2.50e+03 pdb=" N PHE D 228 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN D 596 " -0.053 5.00e-02 4.00e+02 8.21e-02 1.08e+01 pdb=" N PRO D 597 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO D 597 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO D 597 " -0.045 5.00e-02 4.00e+02 ... (remaining 4829 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 7262 2.79 - 3.32: 24892 3.32 - 3.85: 45071 3.85 - 4.37: 54002 4.37 - 4.90: 90619 Nonbonded interactions: 221846 Sorted by model distance: nonbonded pdb=" OG SER A 585 " pdb=" OE1 GLU B 841 " model vdw 2.269 3.040 nonbonded pdb=" OG SER A 560 " pdb=" OD1 ASP A 562 " model vdw 2.271 3.040 nonbonded pdb=" OG SER C 560 " pdb=" OD1 ASP C 562 " model vdw 2.272 3.040 nonbonded pdb=" OG SER B 560 " pdb=" OD1 ASP B 562 " model vdw 2.283 3.040 nonbonded pdb=" OG SER D 560 " pdb=" OD1 ASP D 562 " model vdw 2.283 3.040 ... (remaining 221841 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' and (resid 33 through 470 or resid 472 through 874 or resid 1003 thro \ ugh 1004 or resid 1007 through 1008)) selection = (chain 'B' and (resid 33 through 470 or resid 472 through 874 or resid 1003 thro \ ugh 1004 or resid 1007 through 1008)) selection = (chain 'C' and (resid 33 through 470 or resid 472 through 874 or resid 1003 thro \ ugh 1004 or resid 1007 through 1008)) selection = (chain 'D' and (resid 33 through 470 or resid 472 through 874 or resid 1003 thro \ ugh 1004 or resid 1007 through 1008)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'H' selection = chain 'L' } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.860 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: 0.040 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 34.370 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3380 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 : 0.009 0.109 29012 Z= 0.451 Angle : 1.509 18.837 39224 Z= 0.784 Chirality : 0.066 0.619 4408 Planarity : 0.008 0.082 4804 Dihedral : 19.719 171.055 11936 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.60 % Allowed : 12.05 % Favored : 87.35 % Rotamer: Outliers : 0.27 % Allowed : 5.52 % Favored : 94.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.62 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.01 (0.10), residues: 3364 helix: -4.26 (0.06), residues: 1416 sheet: -3.95 (0.21), residues: 426 loop : -3.61 (0.13), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 468 TYR 0.035 0.003 TYR C 566 PHE 0.050 0.003 PHE B 735 TRP 0.042 0.004 TRP D 134 HIS 0.022 0.002 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00945 (28952) covalent geometry : angle 1.48228 (39052) SS BOND : bond 0.00308 ( 8) SS BOND : angle 1.86831 ( 16) hydrogen bonds : bond 0.29765 ( 923) hydrogen bonds : angle 9.78139 ( 2705) link_ALPHA1-3 : bond 0.01285 ( 4) link_ALPHA1-3 : angle 7.71676 ( 12) link_ALPHA1-6 : bond 0.00658 ( 4) link_ALPHA1-6 : angle 1.79848 ( 12) link_BETA1-3 : bond 0.00547 ( 2) link_BETA1-3 : angle 4.82496 ( 6) link_BETA1-4 : bond 0.01178 ( 14) link_BETA1-4 : angle 3.46369 ( 42) link_NAG-ASN : bond 0.01035 ( 28) link_NAG-ASN : angle 4.94143 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 605 time to evaluate : 1.010 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 399 LEU cc_start: 0.6820 (mm) cc_final: 0.6445 (tp) REVERT: B 593 HIS cc_start: 0.6348 (m-70) cc_final: 0.6069 (m170) REVERT: C 161 LEU cc_start: 0.8061 (tp) cc_final: 0.7763 (tp) REVERT: C 247 MET cc_start: 0.5429 (mtp) cc_final: 0.5220 (mtp) REVERT: C 385 THR cc_start: 0.6563 (p) cc_final: 0.5366 (p) REVERT: C 509 LYS cc_start: 0.6760 (ttmp) cc_final: 0.6505 (tptp) REVERT: C 565 MET cc_start: 0.0605 (mmt) cc_final: 0.0336 (tmm) outliers start: 4 outliers final: 0 residues processed: 609 average time/residue: 0.1930 time to fit residues: 185.8891 Evaluate side-chains 340 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.0470 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 5.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 81 GLN ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 ASN A 165 GLN ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 ASN A 495 ASN A 499 ASN A 591 ASN A 596 ASN A 622 GLN A 749 ASN B 34 HIS B 136 HIS B 241 GLN ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 GLN B 348 ASN B 456 ASN B 557 ASN C 34 HIS C 81 GLN ** C 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN C 348 ASN C 495 ASN C 499 ASN C 591 ASN C 593 HIS C 596 ASN C 604 ASN C 622 GLN C 721 ASN C 749 ASN D 84 ASN D 141 ASN D 186 GLN D 348 ASN D 367 HIS D 456 ASN D 557 ASN D 604 ASN D 621 GLN D 721 ASN D 802 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.209761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.173910 restraints weight = 91195.062| |-----------------------------------------------------------------------------| r_work (start): 0.4177 rms_B_bonded: 4.38 r_work: 0.4028 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4013 r_free = 0.4013 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4010 r_free = 0.4010 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.4010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4808 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 29012 Z= 0.210 Angle : 1.018 16.518 39224 Z= 0.486 Chirality : 0.056 0.568 4408 Planarity : 0.007 0.073 4804 Dihedral : 20.965 156.338 5520 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.65 % Favored : 88.96 % Rotamer: Outliers : 1.77 % Allowed : 12.30 % Favored : 85.93 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.46 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.42 (0.12), residues: 3364 helix: -2.41 (0.10), residues: 1430 sheet: -3.42 (0.24), residues: 368 loop : -3.29 (0.14), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 358 TYR 0.042 0.003 TYR A 702 PHE 0.035 0.003 PHE B 735 TRP 0.036 0.003 TRP D 368 HIS 0.010 0.002 HIS D 328 Details of bonding type rmsd covalent geometry : bond 0.00455 (28952) covalent geometry : angle 0.99016 (39052) SS BOND : bond 0.01408 ( 8) SS BOND : angle 2.63497 ( 16) hydrogen bonds : bond 0.04995 ( 923) hydrogen bonds : angle 5.36119 ( 2705) link_ALPHA1-3 : bond 0.01483 ( 4) link_ALPHA1-3 : angle 7.68795 ( 12) link_ALPHA1-6 : bond 0.01106 ( 4) link_ALPHA1-6 : angle 2.76623 ( 12) link_BETA1-3 : bond 0.01070 ( 2) link_BETA1-3 : angle 4.92237 ( 6) link_BETA1-4 : bond 0.00964 ( 14) link_BETA1-4 : angle 2.73273 ( 42) link_NAG-ASN : bond 0.00810 ( 28) link_NAG-ASN : angle 3.41808 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 460 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7224 (mp10) REVERT: A 664 MET cc_start: 0.4967 (mpp) cc_final: 0.4134 (mpp) REVERT: A 717 LEU cc_start: 0.5542 (mt) cc_final: 0.5166 (mt) REVERT: B 641 TRP cc_start: 0.5865 (m-10) cc_final: 0.5586 (m-10) REVERT: B 747 GLN cc_start: 0.7005 (mm-40) cc_final: 0.5801 (pp30) REVERT: B 858 CYS cc_start: 0.4675 (m) cc_final: 0.4081 (p) REVERT: C 138 VAL cc_start: 0.8286 (t) cc_final: 0.8052 (m) REVERT: C 143 ASP cc_start: 0.5750 (t0) cc_final: 0.5516 (t0) REVERT: C 413 MET cc_start: 0.4797 (pmm) cc_final: 0.4491 (ptt) REVERT: C 466 LEU cc_start: 0.5691 (tp) cc_final: 0.5300 (tp) REVERT: C 509 LYS cc_start: 0.7162 (ttmp) cc_final: 0.6940 (tptp) REVERT: C 565 MET cc_start: 0.1822 (mmt) cc_final: 0.1418 (tmm) REVERT: C 770 MET cc_start: 0.5450 (tpt) cc_final: 0.4882 (tpt) REVERT: C 793 MET cc_start: 0.6200 (mmp) cc_final: 0.5676 (mtt) REVERT: C 861 MET cc_start: 0.5641 (tmm) cc_final: 0.4292 (mtm) REVERT: D 38 PHE cc_start: 0.6758 (OUTLIER) cc_final: 0.6315 (t80) REVERT: D 107 PHE cc_start: 0.6335 (m-80) cc_final: 0.5629 (m-80) REVERT: D 132 THR cc_start: 0.7636 (t) cc_final: 0.7289 (t) REVERT: D 695 LYS cc_start: 0.7458 (ttmt) cc_final: 0.6982 (tttm) REVERT: D 793 MET cc_start: 0.7574 (mmm) cc_final: 0.6882 (mmt) outliers start: 48 outliers final: 22 residues processed: 491 average time/residue: 0.1736 time to fit residues: 140.2985 Evaluate side-chains 363 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 339 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 456 ASN Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 666 SER Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain D residue 38 PHE Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 584 PHE Chi-restraints excluded: chain D residue 737 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 15 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 261 optimal weight: 0.9980 chunk 277 optimal weight: 0.9980 chunk 190 optimal weight: 0.7980 chunk 199 optimal weight: 0.0060 chunk 243 optimal weight: 0.8980 chunk 204 optimal weight: 0.9990 chunk 302 optimal weight: 0.9980 chunk 213 optimal weight: 3.9990 chunk 183 optimal weight: 0.5980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 GLN B 123 ASN ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 GLN B 622 GLN C 129 HIS C 721 ASN D 622 GLN D 721 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.215836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.180503 restraints weight = 119060.405| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 4.55 r_work: 0.4033 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4021 r_free = 0.4021 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4021 r_free = 0.4021 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.4021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5364 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 29012 Z= 0.180 Angle : 0.924 19.261 39224 Z= 0.433 Chirality : 0.051 0.492 4408 Planarity : 0.006 0.080 4804 Dihedral : 18.652 139.921 5520 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.65 % Favored : 89.05 % Rotamer: Outliers : 1.87 % Allowed : 15.57 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.42 (0.13), residues: 3364 helix: -1.20 (0.12), residues: 1436 sheet: -3.11 (0.26), residues: 326 loop : -3.14 (0.14), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 66 TYR 0.022 0.002 TYR A 251 PHE 0.027 0.002 PHE B 59 TRP 0.027 0.002 TRP B 169 HIS 0.013 0.001 HIS B 593 Details of bonding type rmsd covalent geometry : bond 0.00388 (28952) covalent geometry : angle 0.89081 (39052) SS BOND : bond 0.00252 ( 8) SS BOND : angle 2.23473 ( 16) hydrogen bonds : bond 0.04730 ( 923) hydrogen bonds : angle 4.83738 ( 2705) link_ALPHA1-3 : bond 0.01055 ( 4) link_ALPHA1-3 : angle 5.59831 ( 12) link_ALPHA1-6 : bond 0.01697 ( 4) link_ALPHA1-6 : angle 3.04554 ( 12) link_BETA1-3 : bond 0.01227 ( 2) link_BETA1-3 : angle 4.27970 ( 6) link_BETA1-4 : bond 0.01099 ( 14) link_BETA1-4 : angle 2.66068 ( 42) link_NAG-ASN : bond 0.01218 ( 28) link_NAG-ASN : angle 4.25028 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 397 time to evaluate : 1.017 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 399 LEU cc_start: 0.6960 (mm) cc_final: 0.6301 (tp) REVERT: A 705 MET cc_start: 0.4012 (mmm) cc_final: 0.3478 (mmm) REVERT: B 360 MET cc_start: 0.5603 (tmm) cc_final: 0.5004 (tmm) REVERT: B 413 MET cc_start: 0.6041 (mmm) cc_final: 0.5237 (mmm) REVERT: B 664 MET cc_start: 0.3322 (mpp) cc_final: 0.3029 (mtt) REVERT: B 858 CYS cc_start: 0.5400 (m) cc_final: 0.4770 (p) REVERT: C 106 ILE cc_start: 0.8135 (mm) cc_final: 0.7911 (mm) REVERT: C 107 PHE cc_start: 0.7407 (OUTLIER) cc_final: 0.6758 (t80) REVERT: C 143 ASP cc_start: 0.5489 (t0) cc_final: 0.5271 (t0) REVERT: C 167 PHE cc_start: 0.7532 (t80) cc_final: 0.7283 (m-10) REVERT: C 371 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7726 (mp) REVERT: C 413 MET cc_start: 0.4871 (pmm) cc_final: 0.4602 (ptt) REVERT: C 509 LYS cc_start: 0.7297 (ttmp) cc_final: 0.6968 (tptp) REVERT: C 565 MET cc_start: 0.2655 (mmt) cc_final: 0.2320 (tmm) REVERT: C 770 MET cc_start: 0.5514 (tpt) cc_final: 0.4881 (tpt) REVERT: C 793 MET cc_start: 0.6586 (mmp) cc_final: 0.6219 (mtt) REVERT: C 794 MET cc_start: 0.6582 (mpp) cc_final: 0.6215 (mpp) REVERT: D 132 THR cc_start: 0.7713 (t) cc_final: 0.7326 (t) REVERT: D 245 MET cc_start: 0.6588 (tpp) cc_final: 0.6286 (tpp) REVERT: D 340 MET cc_start: 0.5986 (tmm) cc_final: 0.5768 (tmm) REVERT: D 413 MET cc_start: 0.6085 (mmm) cc_final: 0.5234 (mmm) REVERT: D 793 MET cc_start: 0.7899 (mmm) cc_final: 0.7126 (mmt) outliers start: 51 outliers final: 27 residues processed: 428 average time/residue: 0.1674 time to fit residues: 120.2390 Evaluate side-chains 365 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 336 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 456 ASN Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 387 PHE Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 446 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 666 SER Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 296 TRP Chi-restraints excluded: chain D residue 721 ASN Chi-restraints excluded: chain D residue 737 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 323 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 271 optimal weight: 2.9990 chunk 318 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 111 optimal weight: 0.2980 chunk 156 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 GLN ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 GLN ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 721 ASN C 784 GLN D 253 HIS D 497 GLN D 557 ASN ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.212312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.175905 restraints weight = 109157.295| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 5.06 r_work: 0.4044 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4031 r_free = 0.4031 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4031 r_free = 0.4031 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.4031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.8020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 29012 Z= 0.279 Angle : 1.093 17.549 39224 Z= 0.523 Chirality : 0.063 1.296 4408 Planarity : 0.006 0.070 4804 Dihedral : 16.908 139.488 5520 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.02 % Favored : 87.77 % Rotamer: Outliers : 2.21 % Allowed : 16.66 % Favored : 81.13 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.46 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.24 (0.13), residues: 3364 helix: -0.97 (0.13), residues: 1428 sheet: -3.02 (0.26), residues: 364 loop : -3.09 (0.14), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 66 TYR 0.037 0.003 TYR A 176 PHE 0.045 0.003 PHE C 337 TRP 0.091 0.005 TRP C 353 HIS 0.031 0.002 HIS D 225 Details of bonding type rmsd covalent geometry : bond 0.00642 (28952) covalent geometry : angle 1.05941 (39052) SS BOND : bond 0.00728 ( 8) SS BOND : angle 2.11028 ( 16) hydrogen bonds : bond 0.04941 ( 923) hydrogen bonds : angle 5.20604 ( 2705) link_ALPHA1-3 : bond 0.02350 ( 4) link_ALPHA1-3 : angle 5.72957 ( 12) link_ALPHA1-6 : bond 0.01696 ( 4) link_ALPHA1-6 : angle 2.99250 ( 12) link_BETA1-3 : bond 0.00944 ( 2) link_BETA1-3 : angle 4.68875 ( 6) link_BETA1-4 : bond 0.00787 ( 14) link_BETA1-4 : angle 2.73669 ( 42) link_NAG-ASN : bond 0.01055 ( 28) link_NAG-ASN : angle 4.86980 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 442 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.6326 (tp) REVERT: A 316 MET cc_start: 0.4882 (OUTLIER) cc_final: 0.3448 (tpp) REVERT: B 143 ASP cc_start: 0.7104 (m-30) cc_final: 0.6733 (m-30) REVERT: B 793 MET cc_start: 0.7011 (mmp) cc_final: 0.6669 (mmm) REVERT: B 858 CYS cc_start: 0.5607 (m) cc_final: 0.5089 (p) REVERT: C 143 ASP cc_start: 0.5839 (t0) cc_final: 0.5607 (t0) REVERT: C 247 MET cc_start: 0.6153 (tpp) cc_final: 0.5473 (tpp) REVERT: C 509 LYS cc_start: 0.8210 (ttmp) cc_final: 0.7692 (tptp) REVERT: C 565 MET cc_start: 0.6541 (mmt) cc_final: 0.5800 (ttt) REVERT: C 627 MET cc_start: 0.6706 (pmm) cc_final: 0.4890 (mmt) REVERT: C 709 MET cc_start: 0.5706 (mmm) cc_final: 0.4612 (mtt) REVERT: C 858 CYS cc_start: 0.6020 (m) cc_final: 0.4894 (m) REVERT: C 861 MET cc_start: 0.5968 (tmm) cc_final: 0.4244 (mtp) REVERT: D 38 PHE cc_start: 0.6893 (OUTLIER) cc_final: 0.6576 (t80) REVERT: D 444 VAL cc_start: 0.7354 (OUTLIER) cc_final: 0.7021 (t) REVERT: D 721 ASN cc_start: 0.8512 (OUTLIER) cc_final: 0.8108 (t0) REVERT: D 793 MET cc_start: 0.8261 (mmm) cc_final: 0.7694 (mmt) outliers start: 61 outliers final: 24 residues processed: 482 average time/residue: 0.1738 time to fit residues: 138.0833 Evaluate side-chains 381 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 352 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 456 ASN Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 387 PHE Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 446 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 607 THR Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 745 VAL Chi-restraints excluded: chain D residue 38 PHE Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 721 ASN Chi-restraints excluded: chain D residue 826 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 43 optimal weight: 0.7980 chunk 82 optimal weight: 50.0000 chunk 78 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 194 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 27 optimal weight: 30.0000 chunk 95 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 GLN B 747 GLN B 792 HIS C 749 ASN D 721 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.216913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.181656 restraints weight = 122851.104| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 5.33 r_work: 0.3891 rms_B_bonded: 5.27 restraints_weight: 2.0000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3888 r_free = 0.3888 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3888 r_free = 0.3888 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.3888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.8771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 29012 Z= 0.178 Angle : 0.916 19.050 39224 Z= 0.427 Chirality : 0.055 0.987 4408 Planarity : 0.005 0.073 4804 Dihedral : 15.967 141.556 5520 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.89 % Favored : 88.90 % Rotamer: Outliers : 2.15 % Allowed : 19.11 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.43 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.14), residues: 3364 helix: -0.44 (0.13), residues: 1446 sheet: -2.84 (0.28), residues: 326 loop : -3.02 (0.14), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 66 TYR 0.024 0.002 TYR A 176 PHE 0.023 0.002 PHE D 584 TRP 0.061 0.003 TRP D 169 HIS 0.017 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00411 (28952) covalent geometry : angle 0.88597 (39052) SS BOND : bond 0.00198 ( 8) SS BOND : angle 1.87458 ( 16) hydrogen bonds : bond 0.04125 ( 923) hydrogen bonds : angle 4.82565 ( 2705) link_ALPHA1-3 : bond 0.01989 ( 4) link_ALPHA1-3 : angle 3.54120 ( 12) link_ALPHA1-6 : bond 0.01552 ( 4) link_ALPHA1-6 : angle 2.85765 ( 12) link_BETA1-3 : bond 0.01235 ( 2) link_BETA1-3 : angle 4.48540 ( 6) link_BETA1-4 : bond 0.00953 ( 14) link_BETA1-4 : angle 2.45446 ( 42) link_NAG-ASN : bond 0.00983 ( 28) link_NAG-ASN : angle 4.29233 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 390 time to evaluate : 1.179 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: A 316 MET cc_start: 0.5282 (tpp) cc_final: 0.3509 (tpp) REVERT: A 793 MET cc_start: 0.7484 (ttp) cc_final: 0.7222 (ttm) REVERT: A 800 ARG cc_start: 0.6339 (pmt170) cc_final: 0.6120 (ptt-90) REVERT: B 143 ASP cc_start: 0.7218 (m-30) cc_final: 0.6917 (m-30) REVERT: B 182 LEU cc_start: 0.7838 (mt) cc_final: 0.7626 (mt) REVERT: B 248 MET cc_start: 0.7207 (tpp) cc_final: 0.6856 (mmm) REVERT: B 858 CYS cc_start: 0.5778 (m) cc_final: 0.5236 (p) REVERT: C 143 ASP cc_start: 0.5851 (t0) cc_final: 0.5621 (t0) REVERT: C 223 GLU cc_start: 0.6491 (mt-10) cc_final: 0.6260 (mt-10) REVERT: C 247 MET cc_start: 0.6482 (tpp) cc_final: 0.5897 (tpp) REVERT: C 274 VAL cc_start: 0.7049 (p) cc_final: 0.6307 (p) REVERT: C 509 LYS cc_start: 0.8237 (ttmp) cc_final: 0.7932 (tptp) REVERT: C 565 MET cc_start: 0.6849 (mmt) cc_final: 0.5884 (ttt) REVERT: C 627 MET cc_start: 0.7139 (pmm) cc_final: 0.5662 (mmt) REVERT: C 709 MET cc_start: 0.6364 (mmm) cc_final: 0.5422 (mtt) REVERT: C 867 MET cc_start: 0.5232 (mmt) cc_final: 0.5004 (mmt) REVERT: D 793 MET cc_start: 0.8349 (mmm) cc_final: 0.7875 (mmt) outliers start: 59 outliers final: 36 residues processed: 424 average time/residue: 0.1639 time to fit residues: 117.4261 Evaluate side-chains 384 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 348 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 446 PHE Chi-restraints excluded: chain A residue 456 ASN Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 387 PHE Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 446 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 607 THR Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain D residue 59 PHE Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 538 ILE Chi-restraints excluded: chain D residue 817 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 230 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 144 optimal weight: 1.9990 chunk 281 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 330 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 258 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 172 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 HIS ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 GLN ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 621 GLN C 819 ASN D 622 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.198333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.157781 restraints weight = 81377.620| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 4.82 r_work: 0.3875 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3864 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3864 r_free = 0.3864 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3864 r_free = 0.3864 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.3864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 1.0088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 29012 Z= 0.210 Angle : 0.926 23.931 39224 Z= 0.438 Chirality : 0.053 0.720 4408 Planarity : 0.005 0.070 4804 Dihedral : 15.332 140.466 5520 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.05 % Favored : 87.77 % Rotamer: Outliers : 1.91 % Allowed : 20.03 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.14), residues: 3364 helix: -0.28 (0.13), residues: 1452 sheet: -2.78 (0.27), residues: 350 loop : -2.93 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 713 TYR 0.035 0.002 TYR C 682 PHE 0.039 0.002 PHE B 735 TRP 0.056 0.003 TRP D 169 HIS 0.009 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00483 (28952) covalent geometry : angle 0.89358 (39052) SS BOND : bond 0.00647 ( 8) SS BOND : angle 2.71627 ( 16) hydrogen bonds : bond 0.04187 ( 923) hydrogen bonds : angle 4.76965 ( 2705) link_ALPHA1-3 : bond 0.00776 ( 4) link_ALPHA1-3 : angle 3.42470 ( 12) link_ALPHA1-6 : bond 0.01833 ( 4) link_ALPHA1-6 : angle 2.89823 ( 12) link_BETA1-3 : bond 0.01178 ( 2) link_BETA1-3 : angle 4.71998 ( 6) link_BETA1-4 : bond 0.00914 ( 14) link_BETA1-4 : angle 2.22058 ( 42) link_NAG-ASN : bond 0.01460 ( 28) link_NAG-ASN : angle 4.59143 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 399 time to evaluate : 1.075 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: A 316 MET cc_start: 0.5493 (tpp) cc_final: 0.3561 (tpp) REVERT: A 389 LEU cc_start: 0.8433 (mt) cc_final: 0.8101 (tp) REVERT: A 418 LYS cc_start: 0.2947 (OUTLIER) cc_final: 0.2616 (pmmt) REVERT: A 479 GLU cc_start: 0.7546 (tp30) cc_final: 0.6844 (tt0) REVERT: A 714 GLN cc_start: 0.8457 (tt0) cc_final: 0.8248 (tm-30) REVERT: A 728 VAL cc_start: 0.8869 (t) cc_final: 0.8587 (p) REVERT: A 793 MET cc_start: 0.7837 (ttp) cc_final: 0.7497 (ttm) REVERT: B 143 ASP cc_start: 0.7269 (m-30) cc_final: 0.6892 (m-30) REVERT: B 182 LEU cc_start: 0.8200 (mt) cc_final: 0.7958 (mt) REVERT: B 305 PRO cc_start: 0.7260 (Cg_exo) cc_final: 0.7017 (Cg_endo) REVERT: B 316 MET cc_start: 0.7604 (tpp) cc_final: 0.7379 (mpp) REVERT: B 360 MET cc_start: 0.6823 (tmm) cc_final: 0.6239 (tmm) REVERT: B 698 LYS cc_start: 0.8018 (mptt) cc_final: 0.7679 (pttp) REVERT: B 737 MET cc_start: 0.8028 (ptp) cc_final: 0.7745 (mtp) REVERT: B 743 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8206 (tt0) REVERT: B 777 LYS cc_start: 0.8890 (mtmm) cc_final: 0.8541 (mtpp) REVERT: B 858 CYS cc_start: 0.6151 (m) cc_final: 0.5686 (p) REVERT: C 114 SER cc_start: 0.7946 (m) cc_final: 0.7668 (p) REVERT: C 143 ASP cc_start: 0.6573 (t0) cc_final: 0.6317 (t0) REVERT: C 223 GLU cc_start: 0.6800 (mt-10) cc_final: 0.6430 (mt-10) REVERT: C 247 MET cc_start: 0.6563 (tpp) cc_final: 0.5952 (tpp) REVERT: C 274 VAL cc_start: 0.6884 (p) cc_final: 0.5977 (p) REVERT: C 434 ILE cc_start: 0.7847 (mm) cc_final: 0.7618 (mt) REVERT: C 487 LYS cc_start: 0.7823 (tptm) cc_final: 0.7038 (tttt) REVERT: C 523 ARG cc_start: 0.8196 (mtt180) cc_final: 0.7994 (mtt180) REVERT: C 565 MET cc_start: 0.7630 (mmt) cc_final: 0.7381 (mmt) REVERT: C 572 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.7991 (mp) REVERT: C 627 MET cc_start: 0.7616 (pmm) cc_final: 0.6842 (mmp) REVERT: C 705 MET cc_start: 0.7049 (mtt) cc_final: 0.6765 (mtt) REVERT: C 709 MET cc_start: 0.6319 (mmm) cc_final: 0.5722 (mtt) REVERT: C 800 ARG cc_start: 0.7108 (tpp-160) cc_final: 0.6249 (ptt90) REVERT: D 793 MET cc_start: 0.8563 (mmm) cc_final: 0.7953 (mmt) outliers start: 52 outliers final: 32 residues processed: 429 average time/residue: 0.1688 time to fit residues: 121.2323 Evaluate side-chains 375 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 341 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 418 LYS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 456 ASN Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 446 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 607 THR Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 538 ILE Chi-restraints excluded: chain D residue 817 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 99 optimal weight: 0.0980 chunk 279 optimal weight: 20.0000 chunk 322 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 238 optimal weight: 0.8980 chunk 207 optimal weight: 0.0670 chunk 136 optimal weight: 0.7980 chunk 92 optimal weight: 6.9990 chunk 232 optimal weight: 3.9990 chunk 302 optimal weight: 0.8980 chunk 87 optimal weight: 8.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 GLN ** A 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 GLN C 604 ASN C 622 GLN D 721 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.200098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.160037 restraints weight = 75663.944| |-----------------------------------------------------------------------------| r_work (start): 0.4095 rms_B_bonded: 4.25 r_work: 0.3897 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3895 r_free = 0.3895 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3895 r_free = 0.3895 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.3895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 1.0409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29012 Z= 0.146 Angle : 0.886 25.624 39224 Z= 0.412 Chirality : 0.052 0.730 4408 Planarity : 0.005 0.080 4804 Dihedral : 14.929 141.340 5520 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.95 % Favored : 88.90 % Rotamer: Outliers : 1.53 % Allowed : 20.95 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.14), residues: 3364 helix: 0.07 (0.14), residues: 1444 sheet: -2.63 (0.28), residues: 348 loop : -2.91 (0.14), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 748 TYR 0.024 0.002 TYR A 521 PHE 0.030 0.002 PHE B 228 TRP 0.067 0.002 TRP D 798 HIS 0.004 0.001 HIS C 593 Details of bonding type rmsd covalent geometry : bond 0.00322 (28952) covalent geometry : angle 0.84644 (39052) SS BOND : bond 0.00517 ( 8) SS BOND : angle 2.23117 ( 16) hydrogen bonds : bond 0.03725 ( 923) hydrogen bonds : angle 4.55398 ( 2705) link_ALPHA1-3 : bond 0.01212 ( 4) link_ALPHA1-3 : angle 3.42109 ( 12) link_ALPHA1-6 : bond 0.01688 ( 4) link_ALPHA1-6 : angle 2.53643 ( 12) link_BETA1-3 : bond 0.01160 ( 2) link_BETA1-3 : angle 4.81410 ( 6) link_BETA1-4 : bond 0.00928 ( 14) link_BETA1-4 : angle 1.95703 ( 42) link_NAG-ASN : bond 0.00867 ( 28) link_NAG-ASN : angle 5.12782 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 359 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.5465 (tpp) cc_final: 0.3966 (tpp) REVERT: A 418 LYS cc_start: 0.2975 (OUTLIER) cc_final: 0.2660 (pmmt) REVERT: A 479 GLU cc_start: 0.7437 (tp30) cc_final: 0.6869 (tt0) REVERT: A 587 TYR cc_start: 0.7874 (m-80) cc_final: 0.7481 (m-10) REVERT: A 728 VAL cc_start: 0.8838 (t) cc_final: 0.8554 (p) REVERT: A 793 MET cc_start: 0.7738 (ttp) cc_final: 0.7429 (ttm) REVERT: A 802 ASN cc_start: 0.8048 (t0) cc_final: 0.6977 (m110) REVERT: B 143 ASP cc_start: 0.7235 (m-30) cc_final: 0.6880 (m-30) REVERT: B 305 PRO cc_start: 0.7375 (Cg_exo) cc_final: 0.7111 (Cg_endo) REVERT: B 441 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7657 (tt0) REVERT: B 569 LEU cc_start: 0.7902 (mm) cc_final: 0.7618 (mt) REVERT: B 698 LYS cc_start: 0.8047 (mptt) cc_final: 0.7802 (pttp) REVERT: B 858 CYS cc_start: 0.6243 (m) cc_final: 0.5821 (p) REVERT: C 114 SER cc_start: 0.7857 (m) cc_final: 0.7604 (p) REVERT: C 143 ASP cc_start: 0.6602 (t0) cc_final: 0.6331 (t0) REVERT: C 247 MET cc_start: 0.6500 (tpp) cc_final: 0.5953 (tpp) REVERT: C 434 ILE cc_start: 0.7760 (mm) cc_final: 0.7517 (mt) REVERT: C 487 LYS cc_start: 0.7835 (tptm) cc_final: 0.7224 (tttm) REVERT: C 523 ARG cc_start: 0.8091 (mtt180) cc_final: 0.7837 (mtp85) REVERT: C 565 MET cc_start: 0.7508 (mmt) cc_final: 0.7288 (mmt) REVERT: C 572 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8053 (mp) REVERT: C 627 MET cc_start: 0.7654 (pmm) cc_final: 0.6946 (mmp) REVERT: C 709 MET cc_start: 0.6311 (mmm) cc_final: 0.5770 (mtt) REVERT: C 800 ARG cc_start: 0.7010 (tpp-160) cc_final: 0.6745 (ptt90) REVERT: D 793 MET cc_start: 0.8410 (mmm) cc_final: 0.7851 (mmt) outliers start: 41 outliers final: 27 residues processed: 384 average time/residue: 0.1639 time to fit residues: 106.6858 Evaluate side-chains 359 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 329 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 418 LYS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 456 ASN Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 622 GLN Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 446 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 607 THR Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 538 ILE Chi-restraints excluded: chain D residue 721 ASN Chi-restraints excluded: chain D residue 817 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 22 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 231 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 143 optimal weight: 7.9990 chunk 180 optimal weight: 1.9990 chunk 268 optimal weight: 0.9990 chunk 213 optimal weight: 2.9990 chunk 256 optimal weight: 6.9990 chunk 234 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 GLN ** A 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 622 GLN ** D 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.195404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.156506 restraints weight = 115251.582| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 6.24 r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4019 r_free = 0.4019 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4019 r_free = 0.4019 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.4019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 1.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.120 29012 Z= 0.230 Angle : 0.958 18.704 39224 Z= 0.455 Chirality : 0.054 0.574 4408 Planarity : 0.005 0.073 4804 Dihedral : 14.798 140.077 5520 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.41 % Favored : 87.41 % Rotamer: Outliers : 1.57 % Allowed : 20.88 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.14), residues: 3364 helix: -0.05 (0.14), residues: 1434 sheet: -2.68 (0.27), residues: 368 loop : -2.85 (0.14), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 748 TYR 0.044 0.002 TYR C 682 PHE 0.027 0.002 PHE D 228 TRP 0.055 0.003 TRP C 169 HIS 0.009 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00542 (28952) covalent geometry : angle 0.92808 (39052) SS BOND : bond 0.00389 ( 8) SS BOND : angle 2.23556 ( 16) hydrogen bonds : bond 0.04289 ( 923) hydrogen bonds : angle 4.71822 ( 2705) link_ALPHA1-3 : bond 0.01008 ( 4) link_ALPHA1-3 : angle 3.44763 ( 12) link_ALPHA1-6 : bond 0.01078 ( 4) link_ALPHA1-6 : angle 2.74094 ( 12) link_BETA1-3 : bond 0.01060 ( 2) link_BETA1-3 : angle 5.07174 ( 6) link_BETA1-4 : bond 0.00857 ( 14) link_BETA1-4 : angle 2.12757 ( 42) link_NAG-ASN : bond 0.00745 ( 28) link_NAG-ASN : angle 4.51411 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 358 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.5501 (tpp) cc_final: 0.4216 (tpp) REVERT: A 418 LYS cc_start: 0.2879 (OUTLIER) cc_final: 0.2387 (pmmt) REVERT: A 479 GLU cc_start: 0.7584 (tp30) cc_final: 0.7351 (tt0) REVERT: A 682 TYR cc_start: 0.7409 (OUTLIER) cc_final: 0.6786 (m-80) REVERT: A 802 ASN cc_start: 0.8159 (t0) cc_final: 0.7302 (m110) REVERT: B 276 MET cc_start: 0.7470 (mtt) cc_final: 0.7245 (mtt) REVERT: B 305 PRO cc_start: 0.7036 (Cg_exo) cc_final: 0.6786 (Cg_endo) REVERT: B 566 TYR cc_start: 0.8207 (m-10) cc_final: 0.7936 (m-10) REVERT: B 569 LEU cc_start: 0.8405 (mm) cc_final: 0.8173 (mt) REVERT: B 698 LYS cc_start: 0.8612 (mptt) cc_final: 0.8188 (pttp) REVERT: B 777 LYS cc_start: 0.8763 (mtmm) cc_final: 0.8486 (mtmm) REVERT: C 247 MET cc_start: 0.6046 (tpp) cc_final: 0.5712 (tpp) REVERT: C 487 LYS cc_start: 0.7925 (tptm) cc_final: 0.7633 (mmmm) REVERT: C 529 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.7831 (m-80) REVERT: C 565 MET cc_start: 0.7041 (mmt) cc_final: 0.6833 (mmt) REVERT: C 588 GLU cc_start: 0.7781 (tp30) cc_final: 0.7141 (tp30) REVERT: C 800 ARG cc_start: 0.7715 (tpp-160) cc_final: 0.7066 (ptt-90) REVERT: D 511 ASP cc_start: 0.6097 (m-30) cc_final: 0.5855 (m-30) REVERT: D 793 MET cc_start: 0.8271 (mmm) cc_final: 0.7707 (mmt) outliers start: 42 outliers final: 26 residues processed: 385 average time/residue: 0.1713 time to fit residues: 109.8158 Evaluate side-chains 344 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 315 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 418 LYS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 682 TYR Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 145 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 529 PHE Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 607 THR Chi-restraints excluded: chain C residue 664 MET Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 538 ILE Chi-restraints excluded: chain D residue 817 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 296 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 291 optimal weight: 20.0000 chunk 15 optimal weight: 0.9980 chunk 66 optimal weight: 0.0060 chunk 190 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 239 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 234 optimal weight: 0.8980 chunk 274 optimal weight: 0.4980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 622 GLN ** D 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 721 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.193212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.152506 restraints weight = 92554.050| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 5.41 r_work: 0.3763 rms_B_bonded: 5.29 restraints_weight: 2.0000 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3767 r_free = 0.3767 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3767 r_free = 0.3767 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.3767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 1.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29012 Z= 0.147 Angle : 0.868 14.831 39224 Z= 0.408 Chirality : 0.050 0.573 4408 Planarity : 0.005 0.072 4804 Dihedral : 14.351 141.329 5520 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.80 % Favored : 89.14 % Rotamer: Outliers : 1.12 % Allowed : 22.00 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.14), residues: 3364 helix: 0.25 (0.14), residues: 1446 sheet: -2.56 (0.28), residues: 340 loop : -2.78 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 748 TYR 0.028 0.002 TYR A 521 PHE 0.028 0.002 PHE D 606 TRP 0.096 0.002 TRP C 169 HIS 0.011 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00330 (28952) covalent geometry : angle 0.83823 (39052) SS BOND : bond 0.00361 ( 8) SS BOND : angle 1.99049 ( 16) hydrogen bonds : bond 0.03650 ( 923) hydrogen bonds : angle 4.50109 ( 2705) link_ALPHA1-3 : bond 0.00967 ( 4) link_ALPHA1-3 : angle 3.28866 ( 12) link_ALPHA1-6 : bond 0.01510 ( 4) link_ALPHA1-6 : angle 2.34295 ( 12) link_BETA1-3 : bond 0.01011 ( 2) link_BETA1-3 : angle 5.36383 ( 6) link_BETA1-4 : bond 0.00821 ( 14) link_BETA1-4 : angle 1.90109 ( 42) link_NAG-ASN : bond 0.00722 ( 28) link_NAG-ASN : angle 4.23103 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 332 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.5861 (tpp) cc_final: 0.5204 (tpp) REVERT: A 418 LYS cc_start: 0.2905 (OUTLIER) cc_final: 0.2553 (pttm) REVERT: A 479 GLU cc_start: 0.7683 (tp30) cc_final: 0.7388 (tt0) REVERT: A 682 TYR cc_start: 0.7607 (OUTLIER) cc_final: 0.7287 (m-10) REVERT: A 764 TYR cc_start: 0.8397 (m-10) cc_final: 0.8143 (m-10) REVERT: B 305 PRO cc_start: 0.7566 (Cg_exo) cc_final: 0.7342 (Cg_endo) REVERT: B 360 MET cc_start: 0.7502 (ttm) cc_final: 0.7059 (ttm) REVERT: B 566 TYR cc_start: 0.8599 (m-10) cc_final: 0.8334 (m-10) REVERT: B 605 ASN cc_start: 0.8814 (t0) cc_final: 0.8381 (t0) REVERT: B 698 LYS cc_start: 0.8595 (mptt) cc_final: 0.8262 (pttp) REVERT: B 777 LYS cc_start: 0.9040 (mtmm) cc_final: 0.8798 (mtmm) REVERT: C 247 MET cc_start: 0.6940 (tpp) cc_final: 0.6314 (tpp) REVERT: C 487 LYS cc_start: 0.8457 (tptm) cc_final: 0.8206 (mmmm) REVERT: C 565 MET cc_start: 0.7954 (mmt) cc_final: 0.7739 (mmt) REVERT: C 588 GLU cc_start: 0.7383 (tp30) cc_final: 0.6914 (tp30) REVERT: C 800 ARG cc_start: 0.7580 (tpp-160) cc_final: 0.7067 (ptt-90) REVERT: D 793 MET cc_start: 0.8668 (mmm) cc_final: 0.8099 (mmt) outliers start: 29 outliers final: 22 residues processed: 353 average time/residue: 0.1644 time to fit residues: 98.2819 Evaluate side-chains 336 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 312 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 418 LYS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 682 TYR Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 145 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 607 THR Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 468 ARG Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 538 ILE Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 721 ASN Chi-restraints excluded: chain D residue 817 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 103 optimal weight: 2.9990 chunk 273 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 248 optimal weight: 6.9990 chunk 334 optimal weight: 9.9990 chunk 123 optimal weight: 0.0020 chunk 294 optimal weight: 0.0050 chunk 312 optimal weight: 0.9980 chunk 177 optimal weight: 4.9990 chunk 131 optimal weight: 0.3980 chunk 119 optimal weight: 0.5980 overall best weight: 0.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 GLN C 622 GLN ** D 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 721 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.192147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.152498 restraints weight = 79459.702| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 4.57 r_work: 0.3797 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3801 r_free = 0.3801 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3801 r_free = 0.3801 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.3801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 1.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 29012 Z= 0.184 Angle : 0.965 59.199 39224 Z= 0.486 Chirality : 0.051 0.572 4408 Planarity : 0.005 0.072 4804 Dihedral : 14.349 141.340 5520 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.95 % Favored : 88.99 % Rotamer: Outliers : 1.53 % Allowed : 21.56 % Favored : 76.91 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.14), residues: 3364 helix: 0.27 (0.14), residues: 1446 sheet: -2.55 (0.28), residues: 340 loop : -2.77 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 358 TYR 0.040 0.002 TYR C 764 PHE 0.029 0.002 PHE C 228 TRP 0.153 0.003 TRP C 169 HIS 0.065 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00411 (28952) covalent geometry : angle 0.93918 (39052) SS BOND : bond 0.00355 ( 8) SS BOND : angle 1.97325 ( 16) hydrogen bonds : bond 0.03664 ( 923) hydrogen bonds : angle 4.50669 ( 2705) link_ALPHA1-3 : bond 0.00969 ( 4) link_ALPHA1-3 : angle 3.28061 ( 12) link_ALPHA1-6 : bond 0.01269 ( 4) link_ALPHA1-6 : angle 2.26400 ( 12) link_BETA1-3 : bond 0.01015 ( 2) link_BETA1-3 : angle 5.36275 ( 6) link_BETA1-4 : bond 0.00752 ( 14) link_BETA1-4 : angle 1.92279 ( 42) link_NAG-ASN : bond 0.00715 ( 28) link_NAG-ASN : angle 4.23703 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 312 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.5775 (tpp) cc_final: 0.5178 (tpp) REVERT: A 418 LYS cc_start: 0.2911 (OUTLIER) cc_final: 0.2527 (pttm) REVERT: A 479 GLU cc_start: 0.7623 (tp30) cc_final: 0.7360 (tt0) REVERT: A 682 TYR cc_start: 0.7672 (OUTLIER) cc_final: 0.7303 (m-10) REVERT: B 305 PRO cc_start: 0.7475 (Cg_exo) cc_final: 0.7259 (Cg_endo) REVERT: B 360 MET cc_start: 0.7464 (ttm) cc_final: 0.7027 (ttm) REVERT: B 566 TYR cc_start: 0.8578 (m-10) cc_final: 0.8301 (m-10) REVERT: B 605 ASN cc_start: 0.8819 (t0) cc_final: 0.8407 (t0) REVERT: B 698 LYS cc_start: 0.8606 (mptt) cc_final: 0.8277 (pttp) REVERT: B 777 LYS cc_start: 0.9021 (mtmm) cc_final: 0.8780 (mtmm) REVERT: C 247 MET cc_start: 0.6766 (tpp) cc_final: 0.6203 (tpp) REVERT: C 487 LYS cc_start: 0.8393 (tptm) cc_final: 0.8173 (mmmm) REVERT: C 565 MET cc_start: 0.7867 (mmt) cc_final: 0.7652 (mmt) REVERT: C 588 GLU cc_start: 0.7311 (tp30) cc_final: 0.6837 (tp30) REVERT: C 764 TYR cc_start: 0.8434 (m-10) cc_final: 0.8160 (m-10) REVERT: C 800 ARG cc_start: 0.7468 (tpp-160) cc_final: 0.7033 (ptt-90) REVERT: D 793 MET cc_start: 0.8617 (mmm) cc_final: 0.8038 (mmt) outliers start: 41 outliers final: 36 residues processed: 335 average time/residue: 0.1601 time to fit residues: 91.7095 Evaluate side-chains 346 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 308 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 418 LYS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 682 TYR Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 145 PHE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 607 THR Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 468 ARG Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 538 ILE Chi-restraints excluded: chain D residue 584 PHE Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 721 ASN Chi-restraints excluded: chain D residue 817 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 245 optimal weight: 30.0000 chunk 178 optimal weight: 6.9990 chunk 244 optimal weight: 0.8980 chunk 235 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 chunk 79 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 227 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 300 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 622 GLN ** D 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 721 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.192191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.151870 restraints weight = 83460.147| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 5.09 r_work: 0.3787 rms_B_bonded: 5.05 restraints_weight: 2.0000 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3787 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3787 r_free = 0.3787 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3787 r_free = 0.3787 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.3787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 1.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 29012 Z= 0.184 Angle : 0.961 55.324 39224 Z= 0.486 Chirality : 0.051 0.572 4408 Planarity : 0.005 0.072 4804 Dihedral : 14.349 141.340 5520 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.95 % Favored : 88.99 % Rotamer: Outliers : 1.46 % Allowed : 21.66 % Favored : 76.87 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.14), residues: 3364 helix: 0.27 (0.14), residues: 1446 sheet: -2.55 (0.28), residues: 340 loop : -2.77 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 358 TYR 0.040 0.002 TYR C 764 PHE 0.029 0.002 PHE C 228 TRP 0.153 0.003 TRP C 169 HIS 0.065 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00411 (28952) covalent geometry : angle 0.93542 (39052) SS BOND : bond 0.00355 ( 8) SS BOND : angle 1.97325 ( 16) hydrogen bonds : bond 0.03664 ( 923) hydrogen bonds : angle 4.50669 ( 2705) link_ALPHA1-3 : bond 0.00969 ( 4) link_ALPHA1-3 : angle 3.28061 ( 12) link_ALPHA1-6 : bond 0.01269 ( 4) link_ALPHA1-6 : angle 2.26401 ( 12) link_BETA1-3 : bond 0.01015 ( 2) link_BETA1-3 : angle 5.36275 ( 6) link_BETA1-4 : bond 0.00752 ( 14) link_BETA1-4 : angle 1.92279 ( 42) link_NAG-ASN : bond 0.00715 ( 28) link_NAG-ASN : angle 4.23703 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8133.93 seconds wall clock time: 140 minutes 18.29 seconds (8418.29 seconds total)