Starting phenix.real_space_refine on Sun Jul 5 09:40:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fwq_29515/07_2026/8fwq_29515.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fwq_29515/07_2026/8fwq_29515.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fwq_29515/07_2026/8fwq_29515.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fwq_29515/07_2026/8fwq_29515.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8fwq_29515/07_2026/8fwq_29515.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fwq_29515/07_2026/8fwq_29515.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fwq_29515/07_2026/8fwq_29515.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fwq_29515/07_2026/8fwq_29515.map" } resolution = 3.96 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= 0.003 sd= 0.043 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 S 148 5.16 5 Na 1 4.78 5 C 17140 2.51 5 N 4366 2.21 5 O 5146 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 50 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26805 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 6477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6477 Classifications: {'peptide': 818} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 784} Chain: "B" Number of atoms: 6477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6477 Classifications: {'peptide': 818} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 784} Chain: "C" Number of atoms: 6477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6477 Classifications: {'peptide': 818} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 784} Chain: "D" Number of atoms: 6477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6477 Classifications: {'peptide': 818} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 784} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "I" 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 chiralities: 4 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 chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "N" 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 chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "P" 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 chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "R" 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 chiralities: 4 Chain: "S" 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 chiralities: 2 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "U" 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 chiralities: 2 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 73 Unusual residues: {' NA': 1, '2J9': 1, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 58 Unusual residues: {'2J9': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 72 Unusual residues: {'2J9': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 58 Unusual residues: {'2J9': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.14, per 1000 atoms: 0.19 Number of scatterers: 26805 At special positions: 0 Unit cell: (97.125, 160.025, 201.65, 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 148 16.00 Na 1 11.00 F 4 9.00 O 5146 8.00 N 4366 7.00 C 17140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.04 Simple disulfide: pdb=" SG CYS A 595 " - pdb=" SG CYS B 595 " distance=2.11 Simple disulfide: pdb=" SG CYS A 750 " - pdb=" SG CYS A 804 " distance=2.00 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=2.04 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.04 Simple disulfide: pdb=" SG CYS C 595 " - pdb=" SG CYS D 595 " distance=1.95 Simple disulfide: pdb=" SG CYS C 750 " - pdb=" SG CYS C 804 " distance=2.00 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=2.04 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 BETA1-3 " NAG F 2 " - " BMA F 3 " " BMA I 3 " - " BMA I 4 " " NAG O 2 " - " BMA O 3 " " BMA R 3 " - " BMA R 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " 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 M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " NAG-ASN " NAG A1001 " - " ASN A 275 " " NAG A1002 " - " ASN A 546 " " NAG A1003 " - " ASN A 423 " " NAG A1004 " - " ASN A 412 " " NAG B1001 " - " ASN B 275 " " NAG B1002 " - " ASN B 423 " " NAG B1003 " - " ASN B 412 " " NAG C1002 " - " ASN C 275 " " NAG C1003 " - " ASN C 546 " " NAG C1004 " - " ASN C 423 " " NAG C1005 " - " ASN C 412 " " NAG D1002 " - " ASN D 275 " " NAG D1003 " - " ASN D 423 " " NAG D1004 " - " ASN D 412 " " NAG E 1 " - " ASN A 751 " " NAG F 1 " - " ASN A 378 " " NAG G 1 " - " ASN A 430 " " NAG H 1 " - " ASN A 67 " " NAG I 1 " - " ASN B 546 " " NAG J 1 " - " ASN B 751 " " NAG K 1 " - " ASN B 378 " " NAG L 1 " - " ASN B 430 " " NAG M 1 " - " ASN B 67 " " NAG N 1 " - " ASN C 751 " " NAG O 1 " - " ASN C 378 " " NAG P 1 " - " ASN C 430 " " NAG Q 1 " - " ASN C 67 " " NAG R 1 " - " ASN D 546 " " NAG S 1 " - " ASN D 751 " " NAG T 1 " - " ASN D 378 " " NAG U 1 " - " ASN D 430 " " NAG V 1 " - " ASN D 67 " Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 919.8 milliseconds 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6096 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 38 sheets defined 46.1% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 51 through 65 Processing helix chain 'A' and resid 87 through 102 Processing helix chain 'A' and resid 111 through 125 removed outlier: 4.286A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 167 removed outlier: 4.051A pdb=" N ARG A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 185 through 190 removed outlier: 3.532A pdb=" N LYS A 190 " --> pdb=" O GLN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 194 Processing helix chain 'A' and resid 211 through 221 Processing helix chain 'A' and resid 231 through 244 removed outlier: 3.627A pdb=" N GLY A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 238 " --> pdb=" O MET A 234 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLN A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 264 Processing helix chain 'A' and resid 266 through 270 removed outlier: 3.659A pdb=" N ARG A 270 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 301 removed outlier: 3.923A pdb=" N MET A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU A 299 " --> pdb=" O LYS A 295 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 336 removed outlier: 3.888A pdb=" N VAL A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N HIS A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 333 " --> pdb=" O VAL A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 365 removed outlier: 3.759A pdb=" N MET A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 475 removed outlier: 3.775A pdb=" N ILE A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.768A pdb=" N GLU A 504 " --> pdb=" O GLY A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.700A pdb=" N LYS A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 585 removed outlier: 3.512A pdb=" N LEU A 568 " --> pdb=" O TRP A 564 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N CYS A 576 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 580 " --> pdb=" O CYS A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 Processing helix chain 'A' and resid 630 through 662 removed outlier: 3.557A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A 646 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 677 removed outlier: 3.888A pdb=" N GLN A 677 " --> pdb=" O ASP A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 697 Processing helix chain 'A' and resid 699 through 712 removed outlier: 4.103A pdb=" N LYS A 704 " --> pdb=" O SER A 700 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET A 705 " --> pdb=" O THR A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 731 removed outlier: 3.604A pdb=" N GLN A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG A 727 " --> pdb=" O GLU A 723 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL A 728 " --> pdb=" O GLY A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 748 removed outlier: 4.195A pdb=" N VAL A 745 " --> pdb=" O THR A 741 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN A 747 " --> pdb=" O GLU A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 788 removed outlier: 3.883A pdb=" N LYS A 777 " --> pdb=" O PRO A 773 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 779 " --> pdb=" O ARG A 775 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU A 787 " --> pdb=" O LEU A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 799 removed outlier: 3.815A pdb=" N MET A 793 " --> pdb=" O GLY A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 850 removed outlier: 3.646A pdb=" N LEU A 827 " --> pdb=" O ILE A 823 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 67 Processing helix chain 'B' and resid 87 through 102 Processing helix chain 'B' and resid 111 through 125 removed outlier: 3.689A pdb=" N ASN B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 167 removed outlier: 4.021A pdb=" N ARG B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 185 removed outlier: 4.198A pdb=" N ILE B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) 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 221 removed outlier: 3.543A pdb=" N GLU B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 244 removed outlier: 3.708A pdb=" N GLY B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 266 through 270 removed outlier: 3.596A pdb=" N ARG B 270 " --> pdb=" O GLU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 301 removed outlier: 3.555A pdb=" N SER B 297 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N MET B 298 " --> pdb=" O GLU B 294 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 336 removed outlier: 3.599A pdb=" N VAL B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N HIS B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 364 removed outlier: 3.698A pdb=" N MET B 360 " --> pdb=" O GLY B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 417 removed outlier: 3.597A pdb=" N SER B 416 " --> pdb=" O MET B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 474 removed outlier: 3.500A pdb=" N ASP B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU B 469 " --> pdb=" O ASP B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 507 Processing helix chain 'B' and resid 520 through 525 removed outlier: 3.587A pdb=" N LYS B 525 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 557 Processing helix chain 'B' and resid 560 through 585 removed outlier: 3.734A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG B 583 " --> pdb=" O PHE B 579 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 589 Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.736A pdb=" N PHE B 612 " --> pdb=" O LEU B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 659 removed outlier: 3.666A pdb=" N ILE B 646 " --> pdb=" O PHE B 642 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 675 removed outlier: 3.538A pdb=" N LEU B 674 " --> pdb=" O SER B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 696 Processing helix chain 'B' and resid 699 through 711 removed outlier: 3.610A pdb=" N MET B 709 " --> pdb=" O MET B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 731 removed outlier: 3.580A pdb=" N GLN B 726 " --> pdb=" O GLU B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 748 removed outlier: 3.570A pdb=" N GLU B 743 " --> pdb=" O SER B 739 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE B 744 " --> pdb=" O THR B 740 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN B 747 " --> pdb=" O GLU B 743 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG B 748 " --> pdb=" O PHE B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 788 removed outlier: 3.727A pdb=" N LYS B 777 " --> pdb=" O PRO B 773 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 785 " --> pdb=" O ALA B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 799 removed outlier: 3.791A pdb=" N LYS B 795 " --> pdb=" O LEU B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 850 removed outlier: 4.062A pdb=" N ILE B 825 " --> pdb=" O GLY B 821 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 833 " --> pdb=" O ALA B 829 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 835 " --> pdb=" O LEU B 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 65 Processing helix chain 'C' and resid 87 through 102 Processing helix chain 'C' and resid 111 through 125 removed outlier: 4.286A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 118 " --> pdb=" O SER C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 167 removed outlier: 4.051A pdb=" N ARG C 158 " --> pdb=" O SER C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 185 through 190 removed outlier: 3.532A pdb=" N LYS C 190 " --> pdb=" O GLN C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 194 Processing helix chain 'C' and resid 211 through 221 Processing helix chain 'C' and resid 231 through 244 removed outlier: 3.627A pdb=" N GLY C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE C 238 " --> pdb=" O MET C 234 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS C 240 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLN C 241 " --> pdb=" O GLY C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 264 Processing helix chain 'C' and resid 266 through 270 removed outlier: 3.660A pdb=" N ARG C 270 " --> pdb=" O GLU C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 301 removed outlier: 3.923A pdb=" N MET C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU C 299 " --> pdb=" O LYS C 295 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 336 removed outlier: 3.888A pdb=" N VAL C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N HIS C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA C 333 " --> pdb=" O VAL C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 365 removed outlier: 3.760A pdb=" N MET C 360 " --> pdb=" O GLY C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 475 removed outlier: 3.775A pdb=" N ILE C 473 " --> pdb=" O GLU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.767A pdb=" N GLU C 504 " --> pdb=" O GLY C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.700A pdb=" N LYS C 525 " --> pdb=" O TYR C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 585 removed outlier: 3.512A pdb=" N LEU C 568 " --> pdb=" O TRP C 564 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N CYS C 576 " --> pdb=" O LEU C 572 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL C 580 " --> pdb=" O CYS C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 Processing helix chain 'C' and resid 630 through 662 removed outlier: 3.557A pdb=" N VAL C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE C 646 " --> pdb=" O PHE C 642 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA C 653 " --> pdb=" O SER C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 677 removed outlier: 3.888A pdb=" N GLN C 677 " --> pdb=" O ASP C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 697 Processing helix chain 'C' and resid 699 through 712 removed outlier: 4.103A pdb=" N LYS C 704 " --> pdb=" O SER C 700 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET C 705 " --> pdb=" O THR C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 731 removed outlier: 3.604A pdb=" N GLN C 726 " --> pdb=" O GLU C 722 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG C 727 " --> pdb=" O GLU C 723 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL C 728 " --> pdb=" O GLY C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 748 removed outlier: 4.197A pdb=" N VAL C 745 " --> pdb=" O THR C 741 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN C 747 " --> pdb=" O GLU C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 788 removed outlier: 3.883A pdb=" N LYS C 777 " --> pdb=" O PRO C 773 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR C 779 " --> pdb=" O ARG C 775 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU C 787 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 799 removed outlier: 3.815A pdb=" N MET C 793 " --> pdb=" O GLY C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 850 removed outlier: 3.647A pdb=" N LEU C 827 " --> pdb=" O ILE C 823 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU C 833 " --> pdb=" O ALA C 829 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 67 Processing helix chain 'D' and resid 87 through 102 Processing helix chain 'D' and resid 111 through 125 removed outlier: 3.690A pdb=" N ASN D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 167 removed outlier: 4.021A pdb=" N ARG D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 185 removed outlier: 4.197A pdb=" N ILE D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) 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 221 removed outlier: 3.543A pdb=" N GLU D 217 " --> pdb=" O PRO D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 244 removed outlier: 3.709A pdb=" N GLY D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLN D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 266 through 270 removed outlier: 3.595A pdb=" N ARG D 270 " --> pdb=" O GLU D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 301 removed outlier: 3.555A pdb=" N SER D 297 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N MET D 298 " --> pdb=" O GLU D 294 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU D 299 " --> pdb=" O LYS D 295 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 336 removed outlier: 3.599A pdb=" N VAL D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 364 removed outlier: 3.698A pdb=" N MET D 360 " --> pdb=" O GLY D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 417 removed outlier: 3.597A pdb=" N SER D 416 " --> pdb=" O MET D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 474 removed outlier: 3.501A pdb=" N ASP D 465 " --> pdb=" O GLY D 461 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU D 469 " --> pdb=" O ASP D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 507 Processing helix chain 'D' and resid 520 through 525 removed outlier: 3.587A pdb=" N LYS D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 557 Processing helix chain 'D' and resid 560 through 585 removed outlier: 3.733A pdb=" N LEU D 568 " --> pdb=" O TRP D 564 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG D 583 " --> pdb=" O PHE D 579 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE D 584 " --> pdb=" O VAL D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 589 Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.735A pdb=" N PHE D 612 " --> pdb=" O LEU D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 659 removed outlier: 3.666A pdb=" N ILE D 646 " --> pdb=" O PHE D 642 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 675 removed outlier: 3.539A pdb=" N LEU D 674 " --> pdb=" O SER D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 696 Processing helix chain 'D' and resid 699 through 711 removed outlier: 3.610A pdb=" N MET D 709 " --> pdb=" O MET D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 731 removed outlier: 3.580A pdb=" N GLN D 726 " --> pdb=" O GLU D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 748 removed outlier: 3.570A pdb=" N GLU D 743 " --> pdb=" O SER D 739 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE D 744 " --> pdb=" O THR D 740 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN D 747 " --> pdb=" O GLU D 743 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG D 748 " --> pdb=" O PHE D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 773 through 788 removed outlier: 3.727A pdb=" N LYS D 777 " --> pdb=" O PRO D 773 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU D 785 " --> pdb=" O ALA D 781 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 799 removed outlier: 3.792A pdb=" N LYS D 795 " --> pdb=" O LEU D 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 850 removed outlier: 4.062A pdb=" N ILE D 825 " --> pdb=" O GLY D 821 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D 833 " --> pdb=" O ALA D 829 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 835 " --> pdb=" O LEU D 831 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 43 removed outlier: 6.194A pdb=" N HIS A 34 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR A 77 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LEU A 36 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ASP A 79 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N PHE A 38 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N GLN A 81 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLY A 40 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ILE A 83 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N PHE A 42 " --> pdb=" O ILE A 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 131 Processing sheet with id=AA3, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.074A pdb=" N VAL A 174 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL A 226 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR A 254 " --> pdb=" O THR A 277 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 368 through 370 removed outlier: 3.937A pdb=" N TRP A 368 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY A 373 " --> pdb=" O GLY A 370 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 389 through 394 removed outlier: 6.442A pdb=" N LEU A 389 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N THR A 404 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL A 391 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 432 through 435 removed outlier: 6.241A pdb=" N LEU A 433 " --> pdb=" O GLU A 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AA8, first strand: chain 'A' and resid 528 through 529 Processing sheet with id=AA9, first strand: chain 'A' and resid 534 through 536 removed outlier: 3.934A pdb=" N MET A 534 " --> pdb=" O TYR A 764 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 681 through 684 removed outlier: 7.504A pdb=" N GLU A 681 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU A 736 " --> pdb=" O GLU A 681 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY A 683 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N GLU A 738 " --> pdb=" O GLY A 683 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N TYR A 733 " --> pdb=" O ARG A 543 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ARG A 543 " --> pdb=" O TYR A 733 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 735 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE A 540 " --> pdb=" O ILE A 755 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 755 " --> pdb=" O ILE A 540 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 34 through 43 removed outlier: 6.103A pdb=" N HIS B 34 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR B 77 " --> pdb=" O HIS B 34 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LEU B 36 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ASP B 79 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N PHE B 38 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N GLN B 81 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLY B 40 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE B 83 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N PHE B 42 " --> pdb=" O ILE B 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 129 through 131 Processing sheet with id=AB4, first strand: chain 'B' and resid 200 through 203 removed outlier: 6.029A pdb=" N VAL B 174 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N PHE B 279 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N MET B 276 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 394 " --> pdb=" O MET B 276 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU B 389 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N THR B 404 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL B 391 " --> pdb=" O ILE B 402 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 369 through 370 removed outlier: 3.801A pdb=" N GLY B 373 " --> pdb=" O GLY B 370 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 435 through 437 removed outlier: 5.558A pdb=" N VAL B 435 " --> pdb=" O ARG B 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AB8, first strand: chain 'B' and resid 528 through 529 Processing sheet with id=AB9, first strand: chain 'B' and resid 534 through 536 removed outlier: 3.996A pdb=" N MET B 534 " --> pdb=" O TYR B 764 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 735 through 738 removed outlier: 4.139A pdb=" N ILE B 540 " --> pdb=" O ILE B 755 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 34 through 43 removed outlier: 6.194A pdb=" N HIS C 34 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR C 77 " --> pdb=" O HIS C 34 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LEU C 36 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ASP C 79 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N PHE C 38 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N GLN C 81 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLY C 40 " --> pdb=" O GLN C 81 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ILE C 83 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE C 42 " --> pdb=" O ILE C 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 129 through 131 Processing sheet with id=AC4, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.075A pdb=" N VAL C 174 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL C 226 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR C 254 " --> pdb=" O THR C 277 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 368 through 370 removed outlier: 3.937A pdb=" N TRP C 368 " --> pdb=" O ILE C 375 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY C 373 " --> pdb=" O GLY C 370 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 389 through 394 removed outlier: 6.442A pdb=" N LEU C 389 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N THR C 404 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL C 391 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 432 through 435 removed outlier: 6.242A pdb=" N LEU C 433 " --> pdb=" O GLU C 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 445 through 446 Processing sheet with id=AC9, first strand: chain 'C' and resid 528 through 529 Processing sheet with id=AD1, first strand: chain 'C' and resid 534 through 536 removed outlier: 3.935A pdb=" N MET C 534 " --> pdb=" O TYR C 764 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 681 through 684 removed outlier: 7.504A pdb=" N GLU C 681 " --> pdb=" O ALA C 734 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU C 736 " --> pdb=" O GLU C 681 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLY C 683 " --> pdb=" O LEU C 736 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N GLU C 738 " --> pdb=" O GLY C 683 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N TYR C 733 " --> pdb=" O ARG C 543 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ARG C 543 " --> pdb=" O TYR C 733 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE C 735 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE C 540 " --> pdb=" O ILE C 755 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE C 755 " --> pdb=" O ILE C 540 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 34 through 43 removed outlier: 6.104A pdb=" N HIS D 34 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THR D 77 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N LEU D 36 " --> pdb=" O THR D 77 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ASP D 79 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N PHE D 38 " --> pdb=" O ASP D 79 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N GLN D 81 " --> pdb=" O PHE D 38 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLY D 40 " --> pdb=" O GLN D 81 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE D 83 " --> pdb=" O GLY D 40 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N PHE D 42 " --> pdb=" O ILE D 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 129 through 131 Processing sheet with id=AD5, first strand: chain 'D' and resid 200 through 203 removed outlier: 6.029A pdb=" N VAL D 174 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N PHE D 279 " --> pdb=" O PHE D 256 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N MET D 276 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 394 " --> pdb=" O MET D 276 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU D 389 " --> pdb=" O THR D 404 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N THR D 404 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL D 391 " --> pdb=" O ILE D 402 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 369 through 370 removed outlier: 3.800A pdb=" N GLY D 373 " --> pdb=" O GLY D 370 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 435 through 437 removed outlier: 5.558A pdb=" N VAL D 435 " --> pdb=" O ARG D 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AD9, first strand: chain 'D' and resid 528 through 529 Processing sheet with id=AE1, first strand: chain 'D' and resid 534 through 536 removed outlier: 3.995A pdb=" N MET D 534 " --> pdb=" O TYR D 764 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 735 through 738 removed outlier: 4.138A pdb=" N ILE D 540 " --> pdb=" O ILE D 755 " (cutoff:3.500A) 1024 hydrogen bonds defined for protein. 2934 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: 4.61 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7479 1.33 - 1.46: 6257 1.46 - 1.58: 13400 1.58 - 1.70: 20 1.70 - 1.82: 252 Bond restraints: 27408 Sorted by residual: bond pdb=" OAA 2J9 C1001 " pdb=" SAP 2J9 C1001 " ideal model delta sigma weight residual 1.452 1.655 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" OAA 2J9 B1004 " pdb=" SAP 2J9 B1004 " ideal model delta sigma weight residual 1.452 1.654 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" OAA 2J9 A1005 " pdb=" SAP 2J9 A1005 " ideal model delta sigma weight residual 1.452 1.654 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" OAA 2J9 D1001 " pdb=" SAP 2J9 D1001 " ideal model delta sigma weight residual 1.452 1.654 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" OAB 2J9 D1001 " pdb=" SAP 2J9 D1001 " ideal model delta sigma weight residual 1.452 1.649 -0.197 2.00e-02 2.50e+03 9.69e+01 ... (remaining 27403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.61: 37026 6.61 - 13.22: 112 13.22 - 19.83: 0 19.83 - 26.44: 0 26.44 - 33.05: 8 Bond angle restraints: 37146 Sorted by residual: angle pdb=" CAH 2J9 C1001 " pdb=" CAN 2J9 C1001 " pdb=" NAO 2J9 C1001 " ideal model delta sigma weight residual 117.67 150.72 -33.05 3.00e+00 1.11e-01 1.21e+02 angle pdb=" CAH 2J9 A1005 " pdb=" CAN 2J9 A1005 " pdb=" NAO 2J9 A1005 " ideal model delta sigma weight residual 117.67 150.22 -32.55 3.00e+00 1.11e-01 1.18e+02 angle pdb=" CAH 2J9 B1004 " pdb=" CAN 2J9 B1004 " pdb=" NAO 2J9 B1004 " ideal model delta sigma weight residual 117.67 149.90 -32.23 3.00e+00 1.11e-01 1.15e+02 angle pdb=" CAH 2J9 D1001 " pdb=" CAN 2J9 D1001 " pdb=" NAO 2J9 D1001 " ideal model delta sigma weight residual 117.67 149.83 -32.16 3.00e+00 1.11e-01 1.15e+02 angle pdb=" CAG 2J9 D1001 " pdb=" CAN 2J9 D1001 " pdb=" NAO 2J9 D1001 " ideal model delta sigma weight residual 118.82 150.21 -31.39 3.00e+00 1.11e-01 1.09e+02 ... (remaining 37141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 15102 17.94 - 35.88: 612 35.88 - 53.82: 114 53.82 - 71.76: 18 71.76 - 89.70: 12 Dihedral angle restraints: 15858 sinusoidal: 6374 harmonic: 9484 Sorted by residual: dihedral pdb=" CA TYR B 478 " pdb=" C TYR B 478 " pdb=" N GLU B 479 " pdb=" CA GLU B 479 " ideal model delta harmonic sigma weight residual -180.00 -129.67 -50.33 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CA TYR D 478 " pdb=" C TYR D 478 " pdb=" N GLU D 479 " pdb=" CA GLU D 479 " ideal model delta harmonic sigma weight residual -180.00 -129.68 -50.32 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CA ALA B 422 " pdb=" C ALA B 422 " pdb=" N ASN B 423 " pdb=" CA ASN B 423 " ideal model delta harmonic sigma weight residual -180.00 -140.25 -39.75 0 5.00e+00 4.00e-02 6.32e+01 ... (remaining 15855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.463: 4299 0.463 - 0.926: 9 0.926 - 1.389: 1 1.389 - 1.852: 1 1.852 - 2.315: 4 Chirality restraints: 4314 Sorted by residual: chirality pdb=" CAN 2J9 C1001 " pdb=" CAG 2J9 C1001 " pdb=" CAH 2J9 C1001 " pdb=" NAO 2J9 C1001 " both_signs ideal model delta sigma weight residual True 2.32 0.00 2.32 2.00e-01 2.50e+01 1.34e+02 chirality pdb=" CAN 2J9 D1001 " pdb=" CAG 2J9 D1001 " pdb=" CAH 2J9 D1001 " pdb=" NAO 2J9 D1001 " both_signs ideal model delta sigma weight residual True 2.32 0.01 2.31 2.00e-01 2.50e+01 1.34e+02 chirality pdb=" CAN 2J9 B1004 " pdb=" CAG 2J9 B1004 " pdb=" CAH 2J9 B1004 " pdb=" NAO 2J9 B1004 " both_signs ideal model delta sigma weight residual True 2.32 -0.01 2.31 2.00e-01 2.50e+01 1.33e+02 ... (remaining 4311 not shown) Planarity restraints: 4650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 300 " -0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C ARG B 300 " 0.061 2.00e-02 2.50e+03 pdb=" O ARG B 300 " -0.023 2.00e-02 2.50e+03 pdb=" N LEU B 301 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 300 " -0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C ARG D 300 " 0.061 2.00e-02 2.50e+03 pdb=" O ARG D 300 " -0.023 2.00e-02 2.50e+03 pdb=" N LEU D 301 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 300 " -0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C ARG C 300 " 0.058 2.00e-02 2.50e+03 pdb=" O ARG C 300 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU C 301 " -0.020 2.00e-02 2.50e+03 ... (remaining 4647 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 4083 2.75 - 3.29: 25533 3.29 - 3.83: 44328 3.83 - 4.36: 52231 4.36 - 4.90: 87495 Nonbonded interactions: 213670 Sorted by model distance: nonbonded pdb=" OG SER C 554 " pdb=" O ASN C 819 " model vdw 2.216 3.040 nonbonded pdb=" OG SER A 554 " pdb=" O ASN A 819 " model vdw 2.216 3.040 nonbonded pdb=" O SER A 632 " pdb=" OG SER B 834 " model vdw 2.245 3.040 nonbonded pdb=" OG SER B 585 " pdb=" OE1 GLU C 841 " model vdw 2.256 3.040 nonbonded pdb=" O SER C 100 " pdb=" OG SER C 344 " model vdw 2.256 3.040 ... (remaining 213665 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 850 or resid 1002 through 1003)) selection = (chain 'B' and (resid 33 through 850 or resid 1002 through 1003)) selection = (chain 'C' and (resid 33 through 850 or resid 1002 through 1003)) selection = (chain 'D' and (resid 33 through 850 or resid 1002 through 1003)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'S' selection = chain 'U' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'T' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.610 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: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 21.680 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 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 : 0.010 0.203 27480 Z= 0.464 Angle : 1.332 33.045 37352 Z= 0.632 Chirality : 0.101 2.315 4314 Planarity : 0.007 0.070 4618 Dihedral : 10.867 89.703 9732 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.67 % Allowed : 7.87 % Favored : 91.45 % Rotamer: Outliers : 0.28 % Allowed : 3.94 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.64 % 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: -4.98 (0.11), residues: 3264 helix: -3.56 (0.08), residues: 1332 sheet: -2.94 (0.22), residues: 426 loop : -3.06 (0.14), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 184 TYR 0.023 0.003 TYR D 702 PHE 0.022 0.003 PHE B 446 TRP 0.033 0.004 TRP C 134 HIS 0.013 0.003 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00948 / 0.46 (27408) covalent geometry : angle 1.21249 / 0.61 (37146) SS BOND : bond 0.03958 / 1.77 ( 10) SS BOND : angle 1.64473 / 1.01 ( 20) hydrogen bonds : bond 0.28287 / 18.59 ( 1024) hydrogen bonds : angle 9.46198 / 6.55 ( 2934) link_BETA1-3 : bond 0.01152 / 0.56 ( 4) link_BETA1-3 : angle 4.23343 / 2.44 ( 12) link_BETA1-4 : bond 0.02876 / 2.25 ( 26) link_BETA1-4 : angle 8.81418 / 6.58 ( 78) link_NAG-ASN : bond 0.01642 / 1.26 ( 32) link_NAG-ASN : angle 7.46095 / 5.57 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 560 time to evaluate : 0.934 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.7044 (mtm) cc_final: 0.6771 (mtt) REVERT: A 57 PHE cc_start: 0.8817 (t80) cc_final: 0.8216 (t80) REVERT: A 155 SER cc_start: 0.9226 (m) cc_final: 0.8773 (p) REVERT: A 156 LEU cc_start: 0.9327 (mt) cc_final: 0.9003 (mt) REVERT: A 172 VAL cc_start: 0.9459 (t) cc_final: 0.9127 (m) REVERT: A 571 CYS cc_start: 0.9092 (m) cc_final: 0.8804 (t) REVERT: A 650 SER cc_start: 0.9122 (m) cc_final: 0.8805 (t) REVERT: B 627 MET cc_start: 0.8609 (mmt) cc_final: 0.8269 (mmm) REVERT: B 633 THR cc_start: 0.8738 (p) cc_final: 0.8252 (t) REVERT: B 811 GLU cc_start: 0.8593 (pt0) cc_final: 0.8309 (pm20) REVERT: C 50 MET cc_start: 0.7134 (mtm) cc_final: 0.6850 (mtt) REVERT: C 57 PHE cc_start: 0.8849 (t80) cc_final: 0.8200 (t80) REVERT: C 155 SER cc_start: 0.9252 (m) cc_final: 0.8767 (p) REVERT: C 156 LEU cc_start: 0.9401 (mt) cc_final: 0.9058 (mt) REVERT: C 172 VAL cc_start: 0.9511 (t) cc_final: 0.9178 (m) REVERT: C 247 MET cc_start: 0.7991 (mtp) cc_final: 0.7051 (mtm) REVERT: C 514 VAL cc_start: 0.8782 (t) cc_final: 0.8468 (p) REVERT: C 571 CYS cc_start: 0.8959 (m) cc_final: 0.8617 (t) REVERT: C 650 SER cc_start: 0.9137 (m) cc_final: 0.8830 (t) REVERT: C 691 MET cc_start: 0.8817 (ptm) cc_final: 0.8572 (ptt) REVERT: C 786 GLN cc_start: 0.8716 (tp40) cc_final: 0.8491 (tt0) REVERT: D 229 ASP cc_start: 0.8375 (t70) cc_final: 0.8147 (t70) REVERT: D 478 TYR cc_start: 0.7762 (p90) cc_final: 0.6713 (p90) REVERT: D 627 MET cc_start: 0.8650 (mmt) cc_final: 0.8013 (mmt) REVERT: D 633 THR cc_start: 0.8794 (p) cc_final: 0.8458 (t) REVERT: D 694 PHE cc_start: 0.8548 (m-80) cc_final: 0.8081 (m-10) REVERT: D 705 MET cc_start: 0.8796 (mtp) cc_final: 0.8334 (mtp) REVERT: D 709 MET cc_start: 0.8967 (mtp) cc_final: 0.8662 (ptp) REVERT: D 750 CYS cc_start: 0.7693 (m) cc_final: 0.7492 (t) REVERT: D 811 GLU cc_start: 0.8553 (pt0) cc_final: 0.8218 (pm20) outliers start: 8 outliers final: 0 residues processed: 566 average time/residue: 0.1741 time to fit residues: 157.1374 Evaluate side-chains 289 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 7.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 ASN A 165 GLN ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 GLN A 350 HIS A 456 ASN A 497 GLN A 591 ASN A 596 ASN A 604 ASN A 610 ASN ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN B 350 HIS B 456 ASN B 495 ASN B 604 ASN B 621 GLN B 802 ASN B 819 ASN C 136 HIS C 141 ASN C 165 GLN ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 GLN C 350 HIS C 456 ASN C 497 GLN C 591 ASN C 593 HIS C 596 ASN C 604 ASN C 610 ASN ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 ASN D 350 HIS D 456 ASN D 495 ASN D 604 ASN ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 802 ASN D 819 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.085303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.066289 restraints weight = 125684.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.066791 restraints weight = 74322.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.067582 restraints weight = 60546.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.068043 restraints weight = 48837.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.068346 restraints weight = 46255.980| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27480 Z= 0.179 Angle : 0.901 21.008 37352 Z= 0.422 Chirality : 0.055 0.606 4314 Planarity : 0.006 0.053 4618 Dihedral : 6.970 139.825 3556 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.57 % Favored : 92.10 % Rotamer: Outliers : 1.97 % Allowed : 10.14 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -3.36 (0.13), residues: 3264 helix: -1.40 (0.12), residues: 1442 sheet: -2.57 (0.22), residues: 430 loop : -2.97 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 713 TYR 0.025 0.001 TYR B 478 PHE 0.021 0.002 PHE C 584 TRP 0.031 0.002 TRP B 706 HIS 0.005 0.001 HIS C 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 (27408) covalent geometry : angle 0.81201 / 0.40 (37146) SS BOND : bond 0.00477 / 0.27 ( 10) SS BOND : angle 1.13771 / 0.80 ( 20) hydrogen bonds : bond 0.05860 / 3.82 ( 1024) hydrogen bonds : angle 5.36716 / 3.69 ( 2934) link_BETA1-3 : bond 0.00916 / 0.44 ( 4) link_BETA1-3 : angle 3.57339 / 1.99 ( 12) link_BETA1-4 : bond 0.02038 / 1.65 ( 26) link_BETA1-4 : angle 6.05592 / 4.51 ( 78) link_NAG-ASN : bond 0.00942 / 0.69 ( 32) link_NAG-ASN : angle 5.42266 / 4.11 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 341 time to evaluate : 1.038 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 53 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.6321 (mm-30) REVERT: A 57 PHE cc_start: 0.8776 (t80) cc_final: 0.8302 (t80) REVERT: A 155 SER cc_start: 0.9501 (m) cc_final: 0.9276 (p) REVERT: A 156 LEU cc_start: 0.9358 (mt) cc_final: 0.9116 (mt) REVERT: A 450 ASP cc_start: 0.7165 (p0) cc_final: 0.6856 (t70) REVERT: A 501 MET cc_start: 0.8723 (ttm) cc_final: 0.8285 (mmm) REVERT: A 534 MET cc_start: 0.8594 (tpp) cc_final: 0.8079 (ttm) REVERT: A 565 MET cc_start: 0.8611 (mmt) cc_final: 0.7824 (mpp) REVERT: A 571 CYS cc_start: 0.9148 (m) cc_final: 0.8922 (t) REVERT: A 621 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8441 (tp40) REVERT: A 649 SER cc_start: 0.9261 (m) cc_final: 0.8823 (t) REVERT: A 650 SER cc_start: 0.9108 (m) cc_final: 0.8907 (t) REVERT: A 704 LYS cc_start: 0.9431 (mmmt) cc_final: 0.9189 (tptm) REVERT: B 223 GLU cc_start: 0.7314 (mt-10) cc_final: 0.6505 (mt-10) REVERT: B 234 MET cc_start: 0.8461 (mmp) cc_final: 0.8037 (ttm) REVERT: B 247 MET cc_start: 0.7622 (mtt) cc_final: 0.7030 (mmt) REVERT: B 248 MET cc_start: 0.8144 (mmm) cc_final: 0.7880 (mmm) REVERT: B 536 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8321 (pt) REVERT: B 633 THR cc_start: 0.8687 (p) cc_final: 0.8418 (t) REVERT: B 665 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7235 (tm-30) REVERT: C 53 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.6079 (mm-30) REVERT: C 57 PHE cc_start: 0.8767 (t80) cc_final: 0.8270 (t80) REVERT: C 501 MET cc_start: 0.8627 (ttm) cc_final: 0.8160 (mmm) REVERT: C 565 MET cc_start: 0.8612 (mmt) cc_final: 0.7839 (mpp) REVERT: C 571 CYS cc_start: 0.9208 (m) cc_final: 0.8831 (t) REVERT: C 572 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9159 (mm) REVERT: C 650 SER cc_start: 0.9121 (m) cc_final: 0.8909 (t) REVERT: C 704 LYS cc_start: 0.9429 (mmmt) cc_final: 0.9159 (tptm) REVERT: C 709 MET cc_start: 0.8960 (mtm) cc_final: 0.8723 (ptp) REVERT: C 740 THR cc_start: 0.9276 (p) cc_final: 0.8938 (t) REVERT: C 741 THR cc_start: 0.8901 (p) cc_final: 0.8553 (t) REVERT: C 786 GLN cc_start: 0.8608 (tp40) cc_final: 0.8090 (tt0) REVERT: D 152 ASP cc_start: 0.7984 (t0) cc_final: 0.7621 (t0) REVERT: D 223 GLU cc_start: 0.7240 (mt-10) cc_final: 0.6602 (mt-10) REVERT: D 234 MET cc_start: 0.8378 (mmp) cc_final: 0.8060 (ttm) REVERT: D 247 MET cc_start: 0.7448 (mtm) cc_final: 0.6782 (mtt) REVERT: D 248 MET cc_start: 0.8079 (mmm) cc_final: 0.7748 (mmm) REVERT: D 322 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9271 (mm) REVERT: D 536 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8424 (pt) REVERT: D 633 THR cc_start: 0.8843 (p) cc_final: 0.8482 (t) REVERT: D 665 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7434 (pp20) REVERT: D 691 MET cc_start: 0.8823 (tmm) cc_final: 0.8606 (tmm) REVERT: D 705 MET cc_start: 0.8836 (mtp) cc_final: 0.8619 (mtp) outliers start: 56 outliers final: 25 residues processed: 379 average time/residue: 0.1614 time to fit residues: 101.8057 Evaluate side-chains 286 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 255 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 672 ASP Chi-restraints excluded: chain D residue 793 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 125 optimal weight: 10.0000 chunk 221 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 321 optimal weight: 10.0000 chunk 311 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 119 optimal weight: 40.0000 chunk 17 optimal weight: 0.9990 chunk 278 optimal weight: 8.9990 overall best weight: 5.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 HIS A 593 HIS A 621 GLN A 622 GLN ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 508 HIS ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 HIS ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.080687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.061792 restraints weight = 130029.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.062625 restraints weight = 77949.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.063106 restraints weight = 62672.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.063315 restraints weight = 50302.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.063417 restraints weight = 49300.962| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 27480 Z= 0.341 Angle : 1.003 21.822 37352 Z= 0.477 Chirality : 0.057 0.577 4314 Planarity : 0.006 0.094 4618 Dihedral : 7.145 140.242 3556 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.13 % Favored : 90.53 % Rotamer: Outliers : 3.80 % Allowed : 11.16 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -2.62 (0.14), residues: 3264 helix: -0.57 (0.13), residues: 1448 sheet: -2.32 (0.25), residues: 418 loop : -2.81 (0.15), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 384 TYR 0.042 0.003 TYR D 478 PHE 0.022 0.003 PHE B 708 TRP 0.031 0.003 TRP C 706 HIS 0.015 0.002 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00728 / 0.34 (27408) covalent geometry : angle 0.92888 / 0.46 (37146) SS BOND : bond 0.00692 / 0.39 ( 10) SS BOND : angle 1.42107 / 1.00 ( 20) hydrogen bonds : bond 0.04996 / 3.32 ( 1024) hydrogen bonds : angle 5.29757 / 3.61 ( 2934) link_BETA1-3 : bond 0.00955 / 0.46 ( 4) link_BETA1-3 : angle 3.47428 / 1.94 ( 12) link_BETA1-4 : bond 0.01797 / 1.47 ( 26) link_BETA1-4 : angle 5.82899 / 4.30 ( 78) link_NAG-ASN : bond 0.00742 / 0.54 ( 32) link_NAG-ASN : angle 5.30160 / 4.01 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 247 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.8834 (t80) cc_final: 0.8432 (t80) REVERT: A 156 LEU cc_start: 0.9358 (mt) cc_final: 0.9127 (mt) REVERT: A 245 MET cc_start: 0.7643 (ttm) cc_final: 0.7394 (ttt) REVERT: A 450 ASP cc_start: 0.7104 (p0) cc_final: 0.6789 (t70) REVERT: A 565 MET cc_start: 0.8692 (mmt) cc_final: 0.7942 (mpp) REVERT: A 571 CYS cc_start: 0.9124 (m) cc_final: 0.8871 (t) REVERT: A 705 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8345 (mmm) REVERT: A 738 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8808 (pm20) REVERT: A 770 MET cc_start: 0.8178 (mmt) cc_final: 0.7960 (mmt) REVERT: B 90 GLU cc_start: 0.8583 (tt0) cc_final: 0.8109 (tt0) REVERT: B 130 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8786 (tp) REVERT: B 223 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6838 (mt-10) REVERT: B 248 MET cc_start: 0.8364 (mmm) cc_final: 0.8100 (mmm) REVERT: B 501 MET cc_start: 0.8948 (mmm) cc_final: 0.8247 (mmm) REVERT: B 536 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8387 (pp) REVERT: B 565 MET cc_start: 0.8216 (mmt) cc_final: 0.7992 (mmp) REVERT: B 633 THR cc_start: 0.8753 (p) cc_final: 0.8424 (t) REVERT: C 57 PHE cc_start: 0.8814 (t80) cc_final: 0.8401 (t80) REVERT: C 347 CYS cc_start: 0.6089 (OUTLIER) cc_final: 0.5652 (p) REVERT: C 565 MET cc_start: 0.8710 (mmt) cc_final: 0.7971 (mpp) REVERT: C 571 CYS cc_start: 0.9192 (m) cc_final: 0.8830 (t) REVERT: C 621 GLN cc_start: 0.9002 (tp40) cc_final: 0.8704 (tp40) REVERT: C 705 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.8331 (mmm) REVERT: C 709 MET cc_start: 0.9006 (mtm) cc_final: 0.8691 (ptp) REVERT: C 770 MET cc_start: 0.8257 (mmt) cc_final: 0.8048 (mmt) REVERT: C 786 GLN cc_start: 0.8575 (tp40) cc_final: 0.8023 (tt0) REVERT: D 50 MET cc_start: 0.4739 (mtm) cc_final: 0.4521 (mtm) REVERT: D 218 MET cc_start: 0.8579 (tpp) cc_final: 0.8350 (tpp) REVERT: D 247 MET cc_start: 0.7790 (mtm) cc_final: 0.7277 (ttm) REVERT: D 248 MET cc_start: 0.8158 (mmm) cc_final: 0.7879 (mmm) REVERT: D 501 MET cc_start: 0.8977 (mmm) cc_final: 0.8200 (mmm) REVERT: D 536 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8453 (pp) REVERT: D 627 MET cc_start: 0.8843 (mmm) cc_final: 0.8217 (mtt) REVERT: D 633 THR cc_start: 0.8866 (p) cc_final: 0.8448 (t) REVERT: D 665 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7429 (tm-30) REVERT: D 705 MET cc_start: 0.9029 (mtp) cc_final: 0.8700 (mtp) REVERT: D 738 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8095 (mm-30) outliers start: 108 outliers final: 57 residues processed: 334 average time/residue: 0.1472 time to fit residues: 83.6636 Evaluate side-chains 272 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 208 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 738 GLU Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 750 CYS Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 820 ILE Chi-restraints excluded: chain C residue 834 SER Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 672 ASP Chi-restraints excluded: chain D residue 750 CYS Chi-restraints excluded: chain D residue 793 MET Chi-restraints excluded: chain D residue 817 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 170 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 186 optimal weight: 8.9990 chunk 236 optimal weight: 0.8980 chunk 209 optimal weight: 1.9990 chunk 169 optimal weight: 8.9990 chunk 259 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 GLN ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.082643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.063745 restraints weight = 128185.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.064480 restraints weight = 78297.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.065098 restraints weight = 61387.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.065511 restraints weight = 50033.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.065751 restraints weight = 47555.550| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27480 Z= 0.174 Angle : 0.841 20.887 37352 Z= 0.385 Chirality : 0.052 0.519 4314 Planarity : 0.005 0.060 4618 Dihedral : 6.673 140.282 3556 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.87 % Favored : 91.88 % Rotamer: Outliers : 3.31 % Allowed : 12.22 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: 3264 helix: -0.00 (0.13), residues: 1460 sheet: -2.23 (0.24), residues: 426 loop : -2.66 (0.15), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 58 TYR 0.017 0.001 TYR A 733 PHE 0.017 0.002 PHE D 228 TRP 0.018 0.002 TRP B 706 HIS 0.006 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (27408) covalent geometry : angle 0.75703 / 0.37 (37146) SS BOND : bond 0.00715 / 0.44 ( 10) SS BOND : angle 2.78256 / 2.01 ( 20) hydrogen bonds : bond 0.04119 / 2.75 ( 1024) hydrogen bonds : angle 4.75193 / 3.22 ( 2934) link_BETA1-3 : bond 0.00945 / 0.46 ( 4) link_BETA1-3 : angle 3.20000 / 1.79 ( 12) link_BETA1-4 : bond 0.01926 / 1.51 ( 26) link_BETA1-4 : angle 5.53250 / 4.12 ( 78) link_NAG-ASN : bond 0.00825 / 0.60 ( 32) link_NAG-ASN : angle 5.08628 / 3.83 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 258 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.8848 (t80) cc_final: 0.8391 (t80) REVERT: A 245 MET cc_start: 0.7639 (ttm) cc_final: 0.7263 (ttp) REVERT: A 450 ASP cc_start: 0.7032 (p0) cc_final: 0.6822 (t70) REVERT: A 534 MET cc_start: 0.8543 (tpp) cc_final: 0.8136 (ttm) REVERT: A 565 MET cc_start: 0.8659 (mmt) cc_final: 0.7959 (mpp) REVERT: A 649 SER cc_start: 0.9330 (m) cc_final: 0.8840 (t) REVERT: A 691 MET cc_start: 0.8586 (ptp) cc_final: 0.8217 (ptp) REVERT: A 752 LEU cc_start: 0.9093 (mt) cc_final: 0.8893 (mt) REVERT: B 90 GLU cc_start: 0.8576 (tt0) cc_final: 0.8134 (tt0) REVERT: B 223 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6347 (mt-10) REVERT: B 234 MET cc_start: 0.8314 (mmp) cc_final: 0.8101 (tpt) REVERT: B 248 MET cc_start: 0.8286 (mmm) cc_final: 0.8063 (mmm) REVERT: B 536 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8654 (pt) REVERT: B 565 MET cc_start: 0.8108 (mmt) cc_final: 0.7876 (mmp) REVERT: B 633 THR cc_start: 0.8671 (p) cc_final: 0.8366 (t) REVERT: B 665 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7422 (pp20) REVERT: B 738 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8084 (mm-30) REVERT: C 57 PHE cc_start: 0.8824 (t80) cc_final: 0.8356 (t80) REVERT: C 347 CYS cc_start: 0.6175 (OUTLIER) cc_final: 0.5785 (p) REVERT: C 450 ASP cc_start: 0.6949 (p0) cc_final: 0.6730 (t70) REVERT: C 501 MET cc_start: 0.8973 (mmm) cc_final: 0.8767 (mmm) REVERT: C 534 MET cc_start: 0.8475 (tpp) cc_final: 0.8071 (ttm) REVERT: C 565 MET cc_start: 0.8693 (mmt) cc_final: 0.7908 (mpp) REVERT: C 571 CYS cc_start: 0.9145 (m) cc_final: 0.8904 (t) REVERT: C 621 GLN cc_start: 0.8996 (tp40) cc_final: 0.8555 (tp40) REVERT: C 645 LEU cc_start: 0.8743 (tp) cc_final: 0.8502 (tt) REVERT: C 649 SER cc_start: 0.9252 (m) cc_final: 0.8871 (t) REVERT: C 709 MET cc_start: 0.8933 (mtm) cc_final: 0.8718 (ptp) REVERT: C 740 THR cc_start: 0.9300 (p) cc_final: 0.8928 (t) REVERT: C 786 GLN cc_start: 0.8456 (tp40) cc_final: 0.8167 (tm-30) REVERT: D 90 GLU cc_start: 0.8620 (tt0) cc_final: 0.8139 (tt0) REVERT: D 248 MET cc_start: 0.8248 (mmm) cc_final: 0.8004 (mmm) REVERT: D 322 LEU cc_start: 0.9502 (mm) cc_final: 0.9088 (tp) REVERT: D 323 MET cc_start: 0.9023 (tpp) cc_final: 0.8533 (ttm) REVERT: D 536 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8201 (pp) REVERT: D 627 MET cc_start: 0.8668 (mmm) cc_final: 0.8191 (mtt) REVERT: D 633 THR cc_start: 0.8852 (p) cc_final: 0.8455 (t) REVERT: D 665 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7417 (tm-30) REVERT: D 673 ASP cc_start: 0.8825 (t0) cc_final: 0.8579 (t0) REVERT: D 705 MET cc_start: 0.8997 (mtp) cc_final: 0.8644 (mtp) REVERT: D 738 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7979 (mm-30) outliers start: 94 outliers final: 52 residues processed: 332 average time/residue: 0.1436 time to fit residues: 81.5073 Evaluate side-chains 283 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 228 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 650 SER Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 820 ILE Chi-restraints excluded: chain C residue 834 SER Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 672 ASP Chi-restraints excluded: chain D residue 793 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 253 optimal weight: 0.0020 chunk 260 optimal weight: 0.7980 chunk 64 optimal weight: 0.4980 chunk 149 optimal weight: 8.9990 chunk 183 optimal weight: 5.9990 chunk 294 optimal weight: 1.9990 chunk 266 optimal weight: 6.9990 chunk 279 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 318 optimal weight: 0.9990 chunk 290 optimal weight: 6.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 ASN A 288 GLN B 123 ASN ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 ASN ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.084022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.065325 restraints weight = 125848.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.067830 restraints weight = 74253.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.067723 restraints weight = 56317.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.067808 restraints weight = 44351.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.068044 restraints weight = 42089.590| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27480 Z= 0.136 Angle : 0.814 20.861 37352 Z= 0.365 Chirality : 0.051 0.490 4314 Planarity : 0.004 0.058 4618 Dihedral : 6.304 140.399 3556 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.44 % Favored : 92.43 % Rotamer: Outliers : 2.89 % Allowed : 12.89 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.72 (0.14), residues: 3264 helix: 0.35 (0.14), residues: 1460 sheet: -1.94 (0.25), residues: 436 loop : -2.56 (0.15), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 634 TYR 0.016 0.001 TYR A 733 PHE 0.015 0.001 PHE B 579 TRP 0.019 0.001 TRP B 706 HIS 0.006 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (27408) covalent geometry : angle 0.73033 / 0.34 (37146) SS BOND : bond 0.00280 / 0.15 ( 10) SS BOND : angle 2.30934 / 1.63 ( 20) hydrogen bonds : bond 0.03770 / 2.52 ( 1024) hydrogen bonds : angle 4.45198 / 3.00 ( 2934) link_BETA1-3 : bond 0.00927 / 0.45 ( 4) link_BETA1-3 : angle 2.96872 / 1.66 ( 12) link_BETA1-4 : bond 0.01844 / 1.43 ( 26) link_BETA1-4 : angle 5.41238 / 4.06 ( 78) link_NAG-ASN : bond 0.00956 / 0.69 ( 32) link_NAG-ASN : angle 5.01456 / 3.78 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 267 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7061 (mm-30) REVERT: A 57 PHE cc_start: 0.8793 (t80) cc_final: 0.8264 (t80) REVERT: A 247 MET cc_start: 0.7812 (mmm) cc_final: 0.7372 (tpp) REVERT: A 347 CYS cc_start: 0.6241 (OUTLIER) cc_final: 0.5785 (p) REVERT: A 534 MET cc_start: 0.8598 (tpp) cc_final: 0.8162 (ttm) REVERT: A 565 MET cc_start: 0.8651 (mmt) cc_final: 0.7884 (mpp) REVERT: A 645 LEU cc_start: 0.8536 (tp) cc_final: 0.8248 (tt) REVERT: A 649 SER cc_start: 0.9186 (m) cc_final: 0.8820 (t) REVERT: A 738 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8750 (pm20) REVERT: A 740 THR cc_start: 0.9346 (p) cc_final: 0.8998 (t) REVERT: A 752 LEU cc_start: 0.9013 (mt) cc_final: 0.8779 (mt) REVERT: A 786 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8383 (tt0) REVERT: B 90 GLU cc_start: 0.8541 (tt0) cc_final: 0.8097 (tt0) REVERT: B 130 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8726 (tp) REVERT: B 218 MET cc_start: 0.8129 (tpp) cc_final: 0.7773 (tpp) REVERT: B 223 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6300 (mt-10) REVERT: B 228 PHE cc_start: 0.9215 (OUTLIER) cc_final: 0.8895 (m-10) REVERT: B 248 MET cc_start: 0.8265 (mmm) cc_final: 0.7991 (mmm) REVERT: B 323 MET cc_start: 0.8931 (tpp) cc_final: 0.8483 (ttm) REVERT: B 536 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8488 (pt) REVERT: B 565 MET cc_start: 0.8043 (mmt) cc_final: 0.7808 (mmp) REVERT: B 633 THR cc_start: 0.8627 (p) cc_final: 0.8297 (t) REVERT: B 665 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7338 (pp20) REVERT: C 57 PHE cc_start: 0.8777 (t80) cc_final: 0.8281 (t80) REVERT: C 534 MET cc_start: 0.8538 (tpp) cc_final: 0.8127 (ttm) REVERT: C 565 MET cc_start: 0.8604 (mmt) cc_final: 0.7826 (mpp) REVERT: C 649 SER cc_start: 0.9255 (m) cc_final: 0.8999 (t) REVERT: C 740 THR cc_start: 0.9355 (p) cc_final: 0.8977 (t) REVERT: C 786 GLN cc_start: 0.8352 (tp40) cc_final: 0.8099 (tm-30) REVERT: D 90 GLU cc_start: 0.8560 (tt0) cc_final: 0.8116 (tt0) REVERT: D 228 PHE cc_start: 0.9258 (OUTLIER) cc_final: 0.9017 (m-10) REVERT: D 248 MET cc_start: 0.8215 (mmm) cc_final: 0.7804 (mmm) REVERT: D 322 LEU cc_start: 0.9430 (mm) cc_final: 0.9030 (tp) REVERT: D 323 MET cc_start: 0.8994 (tpp) cc_final: 0.8479 (ttm) REVERT: D 536 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8000 (pp) REVERT: D 627 MET cc_start: 0.8626 (mmm) cc_final: 0.8221 (mtt) REVERT: D 633 THR cc_start: 0.8805 (p) cc_final: 0.8405 (t) REVERT: D 665 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7447 (pp20) REVERT: D 673 ASP cc_start: 0.8740 (t0) cc_final: 0.8495 (t0) REVERT: D 705 MET cc_start: 0.8915 (mtp) cc_final: 0.8576 (mtp) REVERT: D 738 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7853 (mm-30) outliers start: 82 outliers final: 46 residues processed: 325 average time/residue: 0.1518 time to fit residues: 84.6626 Evaluate side-chains 290 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 235 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 738 GLU Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 786 GLN Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 799 TRP Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 650 SER Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 672 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 306 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 305 optimal weight: 1.9990 chunk 319 optimal weight: 1.9990 chunk 296 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 205 optimal weight: 7.9990 chunk 266 optimal weight: 1.9990 chunk 238 optimal weight: 4.9990 chunk 309 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 677 GLN ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 GLN ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 GLN ** 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 = 0.3859 r_free = 0.3859 target = 0.083298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.064285 restraints weight = 127595.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.064746 restraints weight = 81899.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.065465 restraints weight = 63804.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.065895 restraints weight = 52121.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.066194 restraints weight = 48904.280| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27480 Z= 0.154 Angle : 0.814 20.600 37352 Z= 0.367 Chirality : 0.051 0.490 4314 Planarity : 0.004 0.058 4618 Dihedral : 6.209 140.523 3556 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.69 % Favored : 92.19 % Rotamer: Outliers : 3.03 % Allowed : 13.59 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.45 (0.15), residues: 3264 helix: 0.59 (0.14), residues: 1452 sheet: -1.98 (0.24), residues: 462 loop : -2.33 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 583 TYR 0.016 0.001 TYR A 733 PHE 0.018 0.001 PHE D 694 TRP 0.016 0.001 TRP B 706 HIS 0.006 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (27408) covalent geometry : angle 0.73697 / 0.35 (37146) SS BOND : bond 0.00527 / 0.32 ( 10) SS BOND : angle 1.95596 / 1.42 ( 20) hydrogen bonds : bond 0.03708 / 2.47 ( 1024) hydrogen bonds : angle 4.39165 / 2.97 ( 2934) link_BETA1-3 : bond 0.00868 / 0.42 ( 4) link_BETA1-3 : angle 2.86341 / 1.60 ( 12) link_BETA1-4 : bond 0.01804 / 1.40 ( 26) link_BETA1-4 : angle 5.28865 / 3.97 ( 78) link_NAG-ASN : bond 0.00836 / 0.61 ( 32) link_NAG-ASN : angle 4.79212 / 3.63 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 240 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9002 (mm) REVERT: A 57 PHE cc_start: 0.8820 (t80) cc_final: 0.8371 (t80) REVERT: A 347 CYS cc_start: 0.6345 (OUTLIER) cc_final: 0.5964 (p) REVERT: A 501 MET cc_start: 0.8613 (mmm) cc_final: 0.8216 (tpt) REVERT: A 565 MET cc_start: 0.8695 (mmt) cc_final: 0.7953 (mpp) REVERT: A 649 SER cc_start: 0.9158 (m) cc_final: 0.8835 (t) REVERT: A 691 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8149 (ptp) REVERT: A 737 MET cc_start: 0.7903 (ptp) cc_final: 0.7549 (ttp) REVERT: A 738 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8764 (pm20) REVERT: A 740 THR cc_start: 0.9434 (p) cc_final: 0.9174 (t) REVERT: A 752 LEU cc_start: 0.9043 (mt) cc_final: 0.8836 (mt) REVERT: A 786 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8395 (tt0) REVERT: B 90 GLU cc_start: 0.8601 (tt0) cc_final: 0.8133 (tt0) REVERT: B 130 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8731 (tp) REVERT: B 218 MET cc_start: 0.8134 (tpp) cc_final: 0.7774 (tpp) REVERT: B 223 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6352 (mt-10) REVERT: B 228 PHE cc_start: 0.9237 (OUTLIER) cc_final: 0.8928 (m-10) REVERT: B 360 MET cc_start: 0.8059 (mmm) cc_final: 0.7855 (mmm) REVERT: B 536 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8619 (pt) REVERT: B 565 MET cc_start: 0.8058 (mmt) cc_final: 0.7823 (mmp) REVERT: B 633 THR cc_start: 0.8690 (p) cc_final: 0.8347 (t) REVERT: B 665 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7235 (pp20) REVERT: B 770 MET cc_start: 0.8832 (tpt) cc_final: 0.8568 (mmt) REVERT: C 55 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9185 (mm) REVERT: C 57 PHE cc_start: 0.8829 (t80) cc_final: 0.8372 (t80) REVERT: C 245 MET cc_start: 0.8352 (ppp) cc_final: 0.7680 (ppp) REVERT: C 277 THR cc_start: 0.9074 (OUTLIER) cc_final: 0.8749 (p) REVERT: C 347 CYS cc_start: 0.5932 (OUTLIER) cc_final: 0.5478 (p) REVERT: C 565 MET cc_start: 0.8632 (mmt) cc_final: 0.8040 (mpp) REVERT: C 621 GLN cc_start: 0.8959 (tp40) cc_final: 0.8559 (tp40) REVERT: C 649 SER cc_start: 0.9296 (m) cc_final: 0.8964 (t) REVERT: C 709 MET cc_start: 0.9039 (mtm) cc_final: 0.8567 (mtt) REVERT: C 740 THR cc_start: 0.9409 (p) cc_final: 0.9137 (t) REVERT: D 90 GLU cc_start: 0.8602 (tt0) cc_final: 0.8138 (tt0) REVERT: D 152 ASP cc_start: 0.7613 (t0) cc_final: 0.7268 (t0) REVERT: D 228 PHE cc_start: 0.9279 (OUTLIER) cc_final: 0.8980 (m-10) REVERT: D 248 MET cc_start: 0.8170 (mmm) cc_final: 0.7817 (mmm) REVERT: D 322 LEU cc_start: 0.9461 (mm) cc_final: 0.9050 (tp) REVERT: D 323 MET cc_start: 0.9069 (tpp) cc_final: 0.8473 (ttm) REVERT: D 536 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8585 (pt) REVERT: D 627 MET cc_start: 0.8656 (mmm) cc_final: 0.8246 (mtt) REVERT: D 633 THR cc_start: 0.8790 (p) cc_final: 0.8385 (t) REVERT: D 665 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7451 (pp20) REVERT: D 673 ASP cc_start: 0.8803 (t0) cc_final: 0.8534 (t0) REVERT: D 705 MET cc_start: 0.8961 (mtp) cc_final: 0.8637 (mtp) outliers start: 86 outliers final: 55 residues processed: 310 average time/residue: 0.1440 time to fit residues: 75.7943 Evaluate side-chains 289 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 221 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 738 GLU Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 786 GLN Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 799 TRP Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 650 SER Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 820 ILE Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 672 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 97 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 203 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 282 optimal weight: 10.0000 chunk 265 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 232 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS B 754 GLN ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 123 ASN ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 754 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.081670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.062773 restraints weight = 129550.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.063315 restraints weight = 80838.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.063938 restraints weight = 65223.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.064362 restraints weight = 52875.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.064627 restraints weight = 50102.494| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27480 Z= 0.197 Angle : 0.847 20.372 37352 Z= 0.387 Chirality : 0.051 0.483 4314 Planarity : 0.004 0.064 4618 Dihedral : 6.337 140.645 3556 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.36 % Favored : 91.45 % Rotamer: Outliers : 3.42 % Allowed : 14.05 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.31 (0.15), residues: 3264 helix: 0.69 (0.14), residues: 1444 sheet: -1.84 (0.25), residues: 446 loop : -2.25 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 220 TYR 0.015 0.001 TYR A 733 PHE 0.027 0.002 PHE D 337 TRP 0.015 0.002 TRP B 706 HIS 0.006 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.20 (27408) covalent geometry : angle 0.77635 / 0.37 (37146) SS BOND : bond 0.00359 / 0.18 ( 10) SS BOND : angle 1.75081 / 1.27 ( 20) hydrogen bonds : bond 0.03743 / 2.52 ( 1024) hydrogen bonds : angle 4.51381 / 3.05 ( 2934) link_BETA1-3 : bond 0.00786 / 0.38 ( 4) link_BETA1-3 : angle 2.77516 / 1.55 ( 12) link_BETA1-4 : bond 0.01785 / 1.35 ( 26) link_BETA1-4 : angle 5.17395 / 3.88 ( 78) link_NAG-ASN : bond 0.00738 / 0.54 ( 32) link_NAG-ASN : angle 4.74485 / 3.59 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 232 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.8865 (t80) cc_final: 0.8462 (t80) REVERT: A 234 MET cc_start: 0.8691 (mpp) cc_final: 0.8379 (mpp) REVERT: A 277 THR cc_start: 0.9054 (OUTLIER) cc_final: 0.8656 (p) REVERT: A 347 CYS cc_start: 0.6157 (OUTLIER) cc_final: 0.5791 (p) REVERT: A 501 MET cc_start: 0.8554 (mmm) cc_final: 0.8121 (tpt) REVERT: A 534 MET cc_start: 0.8273 (tpp) cc_final: 0.8029 (ttm) REVERT: A 565 MET cc_start: 0.8639 (mmt) cc_final: 0.8071 (mpp) REVERT: A 649 SER cc_start: 0.9309 (m) cc_final: 0.8861 (t) REVERT: A 676 LYS cc_start: 0.9137 (tppt) cc_final: 0.8801 (tptt) REVERT: A 691 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.8210 (ptp) REVERT: A 738 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8726 (pm20) REVERT: A 740 THR cc_start: 0.9441 (p) cc_final: 0.9061 (t) REVERT: A 752 LEU cc_start: 0.9040 (mt) cc_final: 0.8796 (mt) REVERT: A 786 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8414 (tt0) REVERT: B 50 MET cc_start: 0.3189 (ttp) cc_final: 0.2789 (tmm) REVERT: B 90 GLU cc_start: 0.8594 (tt0) cc_final: 0.8149 (tt0) REVERT: B 130 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8800 (tp) REVERT: B 218 MET cc_start: 0.8191 (tpp) cc_final: 0.7933 (tpp) REVERT: B 223 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6342 (mt-10) REVERT: B 228 PHE cc_start: 0.9257 (OUTLIER) cc_final: 0.8953 (m-10) REVERT: B 247 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.7072 (mmt) REVERT: B 360 MET cc_start: 0.8175 (mmm) cc_final: 0.7915 (mmm) REVERT: B 536 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8668 (pt) REVERT: B 565 MET cc_start: 0.8051 (mmt) cc_final: 0.7825 (mmp) REVERT: B 629 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8817 (ptmt) REVERT: B 633 THR cc_start: 0.8777 (p) cc_final: 0.8447 (t) REVERT: B 665 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7284 (pp20) REVERT: C 57 PHE cc_start: 0.8842 (t80) cc_final: 0.8424 (t80) REVERT: C 245 MET cc_start: 0.8313 (ppp) cc_final: 0.7628 (ppp) REVERT: C 247 MET cc_start: 0.8926 (mmp) cc_final: 0.8284 (tpp) REVERT: C 347 CYS cc_start: 0.5979 (OUTLIER) cc_final: 0.5538 (p) REVERT: C 501 MET cc_start: 0.8564 (mmm) cc_final: 0.8183 (tpt) REVERT: C 565 MET cc_start: 0.8662 (mmt) cc_final: 0.8091 (mpp) REVERT: C 647 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8969 (tp) REVERT: C 649 SER cc_start: 0.9292 (m) cc_final: 0.8927 (t) REVERT: C 740 THR cc_start: 0.9440 (p) cc_final: 0.9116 (t) REVERT: C 752 LEU cc_start: 0.9069 (mt) cc_final: 0.8802 (mt) REVERT: D 90 GLU cc_start: 0.8643 (tt0) cc_final: 0.8175 (tt0) REVERT: D 152 ASP cc_start: 0.7763 (t0) cc_final: 0.7449 (t0) REVERT: D 228 PHE cc_start: 0.9285 (OUTLIER) cc_final: 0.8954 (m-10) REVERT: D 247 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.6896 (mmt) REVERT: D 248 MET cc_start: 0.8220 (mmm) cc_final: 0.7956 (mmm) REVERT: D 322 LEU cc_start: 0.9493 (mm) cc_final: 0.9101 (tp) REVERT: D 323 MET cc_start: 0.9118 (tpp) cc_final: 0.8779 (ttm) REVERT: D 360 MET cc_start: 0.7910 (mmm) cc_final: 0.7675 (mmm) REVERT: D 476 PHE cc_start: 0.7894 (p90) cc_final: 0.7690 (p90) REVERT: D 501 MET cc_start: 0.8592 (mmm) cc_final: 0.7953 (mmm) REVERT: D 536 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8302 (pp) REVERT: D 633 THR cc_start: 0.8864 (p) cc_final: 0.8440 (t) REVERT: D 665 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7460 (tm-30) REVERT: D 673 ASP cc_start: 0.8782 (t0) cc_final: 0.8523 (t0) REVERT: D 705 MET cc_start: 0.8930 (mtp) cc_final: 0.8626 (mtp) REVERT: D 737 MET cc_start: 0.7102 (tmm) cc_final: 0.6867 (tmm) REVERT: D 738 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7846 (mm-30) outliers start: 97 outliers final: 57 residues processed: 308 average time/residue: 0.1570 time to fit residues: 81.4120 Evaluate side-chains 287 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 215 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 738 GLU Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 786 GLN Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 629 LYS Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 650 SER Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 820 ILE Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 672 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 171 optimal weight: 0.9980 chunk 109 optimal weight: 0.4980 chunk 36 optimal weight: 5.9990 chunk 249 optimal weight: 0.4980 chunk 300 optimal weight: 7.9990 chunk 15 optimal weight: 0.5980 chunk 108 optimal weight: 0.4980 chunk 247 optimal weight: 7.9990 chunk 167 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 269 optimal weight: 7.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.083770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.065178 restraints weight = 126815.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.067317 restraints weight = 76496.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.067357 restraints weight = 58677.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.067312 restraints weight = 49141.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.067490 restraints weight = 45563.625| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27480 Z= 0.126 Angle : 0.814 20.284 37352 Z= 0.361 Chirality : 0.050 0.477 4314 Planarity : 0.004 0.060 4618 Dihedral : 6.109 140.330 3556 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.23 % Favored : 92.68 % Rotamer: Outliers : 2.15 % Allowed : 15.74 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.09 (0.15), residues: 3264 helix: 0.86 (0.14), residues: 1446 sheet: -1.72 (0.25), residues: 442 loop : -2.14 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 220 TYR 0.017 0.001 TYR A 733 PHE 0.024 0.001 PHE C 279 TRP 0.019 0.001 TRP C 706 HIS 0.006 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (27408) covalent geometry : angle 0.74304 / 0.34 (37146) SS BOND : bond 0.00242 / 0.14 ( 10) SS BOND : angle 1.68310 / 1.22 ( 20) hydrogen bonds : bond 0.03447 / 2.32 ( 1024) hydrogen bonds : angle 4.28763 / 2.89 ( 2934) link_BETA1-3 : bond 0.00911 / 0.44 ( 4) link_BETA1-3 : angle 2.64312 / 1.47 ( 12) link_BETA1-4 : bond 0.01784 / 1.37 ( 26) link_BETA1-4 : angle 5.10694 / 3.85 ( 78) link_NAG-ASN : bond 0.00881 / 0.64 ( 32) link_NAG-ASN : angle 4.64313 / 3.52 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 243 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.8851 (t80) cc_final: 0.8406 (t80) REVERT: A 234 MET cc_start: 0.8678 (mpp) cc_final: 0.8319 (mpp) REVERT: A 277 THR cc_start: 0.8992 (OUTLIER) cc_final: 0.8590 (p) REVERT: A 347 CYS cc_start: 0.6167 (OUTLIER) cc_final: 0.5756 (p) REVERT: A 501 MET cc_start: 0.8550 (mmm) cc_final: 0.8168 (tpt) REVERT: A 534 MET cc_start: 0.8394 (tpp) cc_final: 0.8079 (ttm) REVERT: A 565 MET cc_start: 0.8618 (mmt) cc_final: 0.8043 (mpp) REVERT: A 649 SER cc_start: 0.9168 (m) cc_final: 0.8934 (t) REVERT: A 676 LYS cc_start: 0.9223 (tppt) cc_final: 0.8804 (tptt) REVERT: A 737 MET cc_start: 0.7644 (ptp) cc_final: 0.7337 (ttp) REVERT: A 738 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8658 (pm20) REVERT: A 740 THR cc_start: 0.9396 (p) cc_final: 0.8985 (t) REVERT: A 752 LEU cc_start: 0.9027 (mt) cc_final: 0.8815 (mt) REVERT: B 50 MET cc_start: 0.2989 (ttp) cc_final: 0.2599 (tmm) REVERT: B 90 GLU cc_start: 0.8556 (tt0) cc_final: 0.8128 (tt0) REVERT: B 218 MET cc_start: 0.8090 (tpp) cc_final: 0.7877 (tpp) REVERT: B 223 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6308 (mt-10) REVERT: B 228 PHE cc_start: 0.9238 (OUTLIER) cc_final: 0.8837 (m-10) REVERT: B 247 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7204 (mmt) REVERT: B 323 MET cc_start: 0.8975 (tpp) cc_final: 0.8562 (ttt) REVERT: B 360 MET cc_start: 0.8058 (mmm) cc_final: 0.7778 (mmm) REVERT: B 501 MET cc_start: 0.8590 (mmm) cc_final: 0.7665 (mmm) REVERT: B 536 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8498 (pt) REVERT: B 629 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8771 (ptmt) REVERT: B 633 THR cc_start: 0.8660 (p) cc_final: 0.8329 (t) REVERT: B 665 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7139 (pp20) REVERT: B 770 MET cc_start: 0.8762 (tpt) cc_final: 0.8554 (mmt) REVERT: C 57 PHE cc_start: 0.8810 (t80) cc_final: 0.8354 (t80) REVERT: C 245 MET cc_start: 0.8243 (ppp) cc_final: 0.7657 (ppp) REVERT: C 277 THR cc_start: 0.9002 (OUTLIER) cc_final: 0.8606 (p) REVERT: C 347 CYS cc_start: 0.6153 (OUTLIER) cc_final: 0.5694 (p) REVERT: C 501 MET cc_start: 0.8540 (mmm) cc_final: 0.8118 (tpt) REVERT: C 565 MET cc_start: 0.8631 (mmt) cc_final: 0.8000 (mpp) REVERT: C 649 SER cc_start: 0.9250 (m) cc_final: 0.8983 (t) REVERT: C 709 MET cc_start: 0.8885 (mtm) cc_final: 0.8445 (mtt) REVERT: D 90 GLU cc_start: 0.8578 (tt0) cc_final: 0.8142 (tt0) REVERT: D 152 ASP cc_start: 0.7640 (t0) cc_final: 0.7313 (t0) REVERT: D 223 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6882 (mt-10) REVERT: D 228 PHE cc_start: 0.9247 (OUTLIER) cc_final: 0.8833 (m-10) REVERT: D 247 MET cc_start: 0.7453 (OUTLIER) cc_final: 0.7030 (mmt) REVERT: D 248 MET cc_start: 0.8143 (mmm) cc_final: 0.7843 (mmm) REVERT: D 322 LEU cc_start: 0.9422 (mm) cc_final: 0.9034 (tp) REVERT: D 323 MET cc_start: 0.9002 (tpp) cc_final: 0.8692 (ttm) REVERT: D 360 MET cc_start: 0.7790 (mmm) cc_final: 0.7574 (mmm) REVERT: D 536 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.7845 (pp) REVERT: D 627 MET cc_start: 0.8719 (mmm) cc_final: 0.8197 (ttm) REVERT: D 633 THR cc_start: 0.8792 (p) cc_final: 0.8365 (t) REVERT: D 665 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7341 (pp20) REVERT: D 673 ASP cc_start: 0.8738 (t0) cc_final: 0.8456 (t0) REVERT: D 705 MET cc_start: 0.8849 (mtp) cc_final: 0.8208 (mtp) REVERT: D 738 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7801 (mm-30) outliers start: 61 outliers final: 40 residues processed: 292 average time/residue: 0.1462 time to fit residues: 73.1702 Evaluate side-chains 275 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 223 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 738 GLU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 629 LYS Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 650 SER Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 672 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 16 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 56 optimal weight: 0.6980 chunk 93 optimal weight: 9.9990 chunk 300 optimal weight: 10.0000 chunk 277 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 146 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.083667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.064827 restraints weight = 127966.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.065197 restraints weight = 83292.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.065843 restraints weight = 65891.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.066400 restraints weight = 53144.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.066591 restraints weight = 49326.017| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27480 Z= 0.138 Angle : 0.817 19.970 37352 Z= 0.364 Chirality : 0.050 0.473 4314 Planarity : 0.004 0.062 4618 Dihedral : 6.042 140.360 3556 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.51 % Favored : 92.40 % Rotamer: Outliers : 2.04 % Allowed : 16.37 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.00 (0.15), residues: 3264 helix: 0.98 (0.14), residues: 1432 sheet: -1.66 (0.25), residues: 444 loop : -2.10 (0.16), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 220 TYR 0.019 0.001 TYR A 733 PHE 0.021 0.001 PHE B 579 TRP 0.055 0.002 TRP B 613 HIS 0.006 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (27408) covalent geometry : angle 0.74834 / 0.35 (37146) SS BOND : bond 0.00400 / 0.21 ( 10) SS BOND : angle 1.77000 / 1.33 ( 20) hydrogen bonds : bond 0.03412 / 2.30 ( 1024) hydrogen bonds : angle 4.27422 / 2.88 ( 2934) link_BETA1-3 : bond 0.00853 / 0.41 ( 4) link_BETA1-3 : angle 2.55091 / 1.42 ( 12) link_BETA1-4 : bond 0.01753 / 1.34 ( 26) link_BETA1-4 : angle 5.07286 / 3.82 ( 78) link_NAG-ASN : bond 0.00828 / 0.61 ( 32) link_NAG-ASN : angle 4.52689 / 3.44 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 232 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.8863 (t80) cc_final: 0.8411 (t80) REVERT: A 218 MET cc_start: 0.8723 (ttp) cc_final: 0.8497 (ttt) REVERT: A 234 MET cc_start: 0.8690 (mpp) cc_final: 0.8303 (mpp) REVERT: A 245 MET cc_start: 0.8302 (ppp) cc_final: 0.7711 (ppp) REVERT: A 347 CYS cc_start: 0.6144 (OUTLIER) cc_final: 0.5851 (p) REVERT: A 501 MET cc_start: 0.8527 (mmm) cc_final: 0.7943 (tpt) REVERT: A 534 MET cc_start: 0.8510 (tpp) cc_final: 0.7963 (ttm) REVERT: A 565 MET cc_start: 0.8651 (mmt) cc_final: 0.8042 (mpp) REVERT: A 649 SER cc_start: 0.9130 (m) cc_final: 0.8832 (t) REVERT: A 676 LYS cc_start: 0.9246 (tppt) cc_final: 0.8849 (tptt) REVERT: A 738 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8699 (pm20) REVERT: A 740 THR cc_start: 0.9394 (p) cc_final: 0.8995 (t) REVERT: A 752 LEU cc_start: 0.9026 (mt) cc_final: 0.8795 (mt) REVERT: B 50 MET cc_start: 0.3172 (ttp) cc_final: 0.2769 (tmm) REVERT: B 90 GLU cc_start: 0.8572 (tt0) cc_final: 0.8135 (tt0) REVERT: B 152 ASP cc_start: 0.7767 (t0) cc_final: 0.7535 (t0) REVERT: B 218 MET cc_start: 0.8042 (tpp) cc_final: 0.7780 (tpp) REVERT: B 223 GLU cc_start: 0.7065 (mt-10) cc_final: 0.6308 (mt-10) REVERT: B 228 PHE cc_start: 0.9248 (OUTLIER) cc_final: 0.8923 (m-10) REVERT: B 247 MET cc_start: 0.7362 (mtt) cc_final: 0.7063 (mmt) REVERT: B 323 MET cc_start: 0.9020 (tpp) cc_final: 0.8574 (ttt) REVERT: B 360 MET cc_start: 0.8047 (mmm) cc_final: 0.7754 (mmm) REVERT: B 501 MET cc_start: 0.8662 (mmm) cc_final: 0.7814 (mmm) REVERT: B 536 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8557 (pt) REVERT: B 629 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8793 (ptmt) REVERT: B 633 THR cc_start: 0.8702 (p) cc_final: 0.8362 (t) REVERT: B 665 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7126 (pp20) REVERT: B 737 MET cc_start: 0.7587 (tmm) cc_final: 0.7352 (tmm) REVERT: B 770 MET cc_start: 0.8820 (tpt) cc_final: 0.8572 (mmt) REVERT: C 57 PHE cc_start: 0.8816 (t80) cc_final: 0.8397 (t80) REVERT: C 245 MET cc_start: 0.8182 (ppp) cc_final: 0.7662 (ppp) REVERT: C 347 CYS cc_start: 0.5918 (OUTLIER) cc_final: 0.5429 (p) REVERT: C 501 MET cc_start: 0.8525 (mmm) cc_final: 0.8134 (tpt) REVERT: C 565 MET cc_start: 0.8572 (mmt) cc_final: 0.7970 (mpp) REVERT: C 649 SER cc_start: 0.9242 (m) cc_final: 0.8984 (t) REVERT: C 709 MET cc_start: 0.8981 (mtm) cc_final: 0.8562 (mtt) REVERT: D 90 GLU cc_start: 0.8589 (tt0) cc_final: 0.8151 (tt0) REVERT: D 152 ASP cc_start: 0.7654 (t0) cc_final: 0.7381 (t0) REVERT: D 228 PHE cc_start: 0.9240 (OUTLIER) cc_final: 0.8874 (m-10) REVERT: D 247 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.6986 (mmt) REVERT: D 248 MET cc_start: 0.8047 (mmm) cc_final: 0.7781 (mmm) REVERT: D 322 LEU cc_start: 0.9388 (mm) cc_final: 0.8932 (tp) REVERT: D 323 MET cc_start: 0.9057 (tpp) cc_final: 0.8569 (ttm) REVERT: D 360 MET cc_start: 0.7828 (mmm) cc_final: 0.7618 (mmm) REVERT: D 536 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8043 (pp) REVERT: D 633 THR cc_start: 0.8810 (p) cc_final: 0.8369 (t) REVERT: D 665 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7409 (pp20) REVERT: D 738 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7815 (mm-30) outliers start: 58 outliers final: 43 residues processed: 279 average time/residue: 0.1516 time to fit residues: 71.3911 Evaluate side-chains 272 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 220 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 738 GLU Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 629 LYS Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 650 SER Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 645 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 239 optimal weight: 30.0000 chunk 167 optimal weight: 8.9990 chunk 293 optimal weight: 9.9990 chunk 140 optimal weight: 2.9990 chunk 214 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 274 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 292 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 237 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 HIS C 111 HIS ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 HIS ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.081952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.063150 restraints weight = 129196.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.063616 restraints weight = 80289.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.064222 restraints weight = 65201.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.064648 restraints weight = 52520.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.064976 restraints weight = 49426.208| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27480 Z= 0.192 Angle : 0.845 19.835 37352 Z= 0.384 Chirality : 0.051 0.472 4314 Planarity : 0.004 0.066 4618 Dihedral : 6.208 140.554 3556 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.03 % Favored : 91.85 % Rotamer: Outliers : 2.29 % Allowed : 16.23 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.01 (0.15), residues: 3264 helix: 0.91 (0.14), residues: 1442 sheet: -1.51 (0.26), residues: 422 loop : -2.14 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 634 TYR 0.017 0.001 TYR A 733 PHE 0.021 0.002 PHE C 279 TRP 0.088 0.002 TRP D 613 HIS 0.006 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 (27408) covalent geometry : angle 0.78032 / 0.37 (37146) SS BOND : bond 0.00266 / 0.14 ( 10) SS BOND : angle 1.65470 / 1.26 ( 20) hydrogen bonds : bond 0.03602 / 2.41 ( 1024) hydrogen bonds : angle 4.42396 / 2.98 ( 2934) link_BETA1-3 : bond 0.00733 / 0.35 ( 4) link_BETA1-3 : angle 2.52349 / 1.41 ( 12) link_BETA1-4 : bond 0.01696 / 1.29 ( 26) link_BETA1-4 : angle 5.03955 / 3.79 ( 78) link_NAG-ASN : bond 0.00716 / 0.52 ( 32) link_NAG-ASN : angle 4.52451 / 3.44 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 217 time to evaluate : 1.016 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 57 PHE cc_start: 0.8911 (t80) cc_final: 0.8557 (t80) REVERT: A 234 MET cc_start: 0.8774 (mpp) cc_final: 0.8346 (mpp) REVERT: A 245 MET cc_start: 0.8325 (ppp) cc_final: 0.7695 (ppp) REVERT: A 347 CYS cc_start: 0.6216 (OUTLIER) cc_final: 0.5943 (p) REVERT: A 501 MET cc_start: 0.8451 (mmm) cc_final: 0.7860 (tpt) REVERT: A 534 MET cc_start: 0.8512 (tpp) cc_final: 0.8050 (ttm) REVERT: A 565 MET cc_start: 0.8646 (mmt) cc_final: 0.8094 (mpp) REVERT: A 649 SER cc_start: 0.9263 (m) cc_final: 0.8809 (t) REVERT: A 676 LYS cc_start: 0.9295 (tppt) cc_final: 0.8777 (tptp) REVERT: A 738 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8689 (pm20) REVERT: A 740 THR cc_start: 0.9402 (p) cc_final: 0.9014 (t) REVERT: A 752 LEU cc_start: 0.9066 (mt) cc_final: 0.8791 (mt) REVERT: B 50 MET cc_start: 0.2984 (ttp) cc_final: 0.2752 (tmm) REVERT: B 90 GLU cc_start: 0.8616 (tt0) cc_final: 0.8193 (tt0) REVERT: B 218 MET cc_start: 0.8099 (tpp) cc_final: 0.7798 (tpp) REVERT: B 223 GLU cc_start: 0.7095 (mt-10) cc_final: 0.6283 (mt-10) REVERT: B 228 PHE cc_start: 0.9271 (OUTLIER) cc_final: 0.8993 (m-10) REVERT: B 247 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.7064 (mmt) REVERT: B 323 MET cc_start: 0.9062 (tpp) cc_final: 0.8638 (ttt) REVERT: B 340 MET cc_start: 0.8196 (mmm) cc_final: 0.7635 (mmm) REVERT: B 360 MET cc_start: 0.8105 (mmm) cc_final: 0.7805 (mmm) REVERT: B 536 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8623 (pt) REVERT: B 565 MET cc_start: 0.7996 (mmt) cc_final: 0.7774 (mmp) REVERT: B 629 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8829 (ptmt) REVERT: B 633 THR cc_start: 0.8753 (p) cc_final: 0.8418 (t) REVERT: B 665 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7163 (pp20) REVERT: B 770 MET cc_start: 0.8838 (tpt) cc_final: 0.8571 (mmt) REVERT: C 57 PHE cc_start: 0.8885 (t80) cc_final: 0.8481 (t80) REVERT: C 245 MET cc_start: 0.8334 (ppp) cc_final: 0.7839 (ppp) REVERT: C 340 MET cc_start: 0.8662 (tmm) cc_final: 0.8381 (tmm) REVERT: C 347 CYS cc_start: 0.5848 (OUTLIER) cc_final: 0.5407 (p) REVERT: C 501 MET cc_start: 0.8519 (mmm) cc_final: 0.8092 (tpt) REVERT: C 565 MET cc_start: 0.8634 (mmt) cc_final: 0.8044 (mpp) REVERT: C 647 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8977 (tp) REVERT: C 649 SER cc_start: 0.9246 (m) cc_final: 0.8915 (t) REVERT: C 687 ASP cc_start: 0.8774 (m-30) cc_final: 0.8457 (m-30) REVERT: D 90 GLU cc_start: 0.8661 (tt0) cc_final: 0.8198 (tt0) REVERT: D 152 ASP cc_start: 0.7714 (t0) cc_final: 0.7441 (t0) REVERT: D 228 PHE cc_start: 0.9266 (OUTLIER) cc_final: 0.8950 (m-10) REVERT: D 247 MET cc_start: 0.7282 (OUTLIER) cc_final: 0.6884 (mmt) REVERT: D 248 MET cc_start: 0.8121 (mmm) cc_final: 0.7875 (mmm) REVERT: D 322 LEU cc_start: 0.9450 (mm) cc_final: 0.9169 (mm) REVERT: D 323 MET cc_start: 0.9150 (tpp) cc_final: 0.8771 (tpp) REVERT: D 360 MET cc_start: 0.7894 (mmm) cc_final: 0.7661 (mmm) REVERT: D 536 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8110 (pp) REVERT: D 627 MET cc_start: 0.8782 (mmm) cc_final: 0.8219 (ttt) REVERT: D 633 THR cc_start: 0.8887 (p) cc_final: 0.8457 (t) REVERT: D 665 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7409 (pp20) REVERT: D 705 MET cc_start: 0.9005 (mtp) cc_final: 0.8784 (mtm) REVERT: D 738 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7809 (mm-30) outliers start: 65 outliers final: 50 residues processed: 263 average time/residue: 0.1452 time to fit residues: 65.7160 Evaluate side-chains 274 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 213 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 738 GLU Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 629 LYS Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 650 SER Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 820 ILE Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 645 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 3 optimal weight: 5.9990 chunk 254 optimal weight: 0.8980 chunk 162 optimal weight: 20.0000 chunk 177 optimal weight: 0.6980 chunk 114 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 184 optimal weight: 0.9980 chunk 126 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.083680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.065209 restraints weight = 126025.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.067230 restraints weight = 76229.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.067303 restraints weight = 59423.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.067362 restraints weight = 47045.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.067659 restraints weight = 44437.599| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.5386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 27480 Z= 0.129 Angle : 0.814 19.814 37352 Z= 0.361 Chirality : 0.050 0.473 4314 Planarity : 0.004 0.062 4618 Dihedral : 6.033 140.110 3556 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.20 % Favored : 92.74 % Rotamer: Outliers : 2.01 % Allowed : 16.55 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.87 (0.15), residues: 3264 helix: 1.07 (0.14), residues: 1430 sheet: -1.36 (0.26), residues: 420 loop : -2.12 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 634 TYR 0.019 0.001 TYR A 733 PHE 0.016 0.001 PHE C 279 TRP 0.111 0.002 TRP D 613 HIS 0.007 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (27408) covalent geometry : angle 0.74728 / 0.35 (37146) SS BOND : bond 0.00233 / 0.13 ( 10) SS BOND : angle 1.60255 / 1.21 ( 20) hydrogen bonds : bond 0.03397 / 2.28 ( 1024) hydrogen bonds : angle 4.24090 / 2.85 ( 2934) link_BETA1-3 : bond 0.00913 / 0.44 ( 4) link_BETA1-3 : angle 2.44183 / 1.36 ( 12) link_BETA1-4 : bond 0.01774 / 1.34 ( 26) link_BETA1-4 : angle 5.01246 / 3.77 ( 78) link_NAG-ASN : bond 0.00867 / 0.64 ( 32) link_NAG-ASN : angle 4.45127 / 3.38 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4191.61 seconds wall clock time: 73 minutes 42.86 seconds (4422.86 seconds total)