Starting phenix.real_space_refine on Mon Aug 25 09:44:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fwq_29515/08_2025/8fwq_29515.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fwq_29515/08_2025/8fwq_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8fwq_29515/08_2025/8fwq_29515.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fwq_29515/08_2025/8fwq_29515.map" model { file = "/net/cci-nas-00/data/ceres_data/8fwq_29515/08_2025/8fwq_29515.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fwq_29515/08_2025/8fwq_29515.cif" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 12 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 dihedrals: 9 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 dihedrals: 12 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.53, per 1000 atoms: 0.28 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: 5.97 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.82 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: 4.73 Time building geometry restraints manager: 3.46 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 - 22.84: 16131 22.84 - 45.69: 597 45.69 - 68.53: 184 68.53 - 91.38: 78 91.38 - 114.22: 146 Dihedral angle restraints: 17136 sinusoidal: 7652 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 17133 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: 5.650 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: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.580 Find NCS groups from input model: 0.670 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: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 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 : 18.586 114.222 11010 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 aren 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 covalent geometry : bond 0.00948 (27408) covalent geometry : angle 1.21249 (37146) SS BOND : bond 0.03958 ( 10) SS BOND : angle 1.64473 ( 20) hydrogen bonds : bond 0.28287 ( 1024) hydrogen bonds : angle 9.46198 ( 2934) link_BETA1-3 : bond 0.01152 ( 4) link_BETA1-3 : angle 4.23343 ( 12) link_BETA1-4 : bond 0.02876 ( 26) link_BETA1-4 : angle 8.81418 ( 78) link_NAG-ASN : bond 0.01642 ( 32) link_NAG-ASN : angle 7.46095 ( 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 : 0.994 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: 0.8772 (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: 0.8308 (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: 0.8651 (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: 0.1552 time to fit residues: 139.1209 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 : 0.920 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 141 ASN A 165 GLN A 286 ASN 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 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: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.085190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.066211 restraints weight = 124929.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.067087 restraints weight = 71801.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.067846 restraints weight = 59402.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.068039 restraints weight = 47515.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.068581 restraints weight = 44913.384| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 27480 Z= 0.181 Angle : 0.940 20.959 37352 Z= 0.431 Chirality : 0.055 0.638 4314 Planarity : 0.006 0.053 4618 Dihedral : 19.081 140.707 4834 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.57 % Favored : 92.10 % Rotamer: Outliers : 2.01 % Allowed : 9.93 % Favored : 88.06 % 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 aren not related in a simple way. whole: -3.38 (0.13), residues: 3264 helix: -1.43 (0.11), residues: 1440 sheet: -2.54 (0.23), residues: 430 loop : -2.97 (0.15), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 68 TYR 0.026 0.001 TYR B 478 PHE 0.023 0.002 PHE C 584 TRP 0.035 0.002 TRP B 706 HIS 0.005 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00381 (27408) covalent geometry : angle 0.84779 (37146) SS BOND : bond 0.01559 ( 10) SS BOND : angle 1.09434 ( 20) hydrogen bonds : bond 0.05586 ( 1024) hydrogen bonds : angle 5.32581 ( 2934) link_BETA1-3 : bond 0.00983 ( 4) link_BETA1-3 : angle 4.43727 ( 12) link_BETA1-4 : bond 0.02206 ( 26) link_BETA1-4 : angle 6.32027 ( 78) link_NAG-ASN : bond 0.00956 ( 32) link_NAG-ASN : angle 5.54722 ( 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 402 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 345 time to evaluate : 0.947 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: 0.7939 (OUTLIER) cc_final: 0.6341 (mm-30) REVERT: A 57 PHE cc_start: 0.8810 (t80) cc_final: 0.8320 (t80) REVERT: A 155 SER cc_start: 0.9501 (m) cc_final: 0.9279 (p) REVERT: A 156 LEU cc_start: 0.9341 (mt) cc_final: 0.9102 (mt) REVERT: A 245 MET cc_start: 0.7783 (ttm) cc_final: 0.7323 (ttm) REVERT: A 450 ASP cc_start: 0.7110 (p0) cc_final: 0.6828 (t70) REVERT: A 534 MET cc_start: 0.8579 (tpp) cc_final: 0.8065 (ttm) REVERT: A 565 MET cc_start: 0.8592 (mmt) cc_final: 0.7800 (mpp) REVERT: A 571 CYS cc_start: 0.9204 (m) cc_final: 0.8931 (t) REVERT: A 621 GLN cc_start: 0.8780 (mm-40) cc_final: 0.8465 (tp40) REVERT: A 649 SER cc_start: 0.9246 (m) cc_final: 0.8825 (t) REVERT: A 650 SER cc_start: 0.9102 (m) cc_final: 0.8898 (t) REVERT: A 704 LYS cc_start: 0.9426 (mmmt) cc_final: 0.9195 (tptm) REVERT: B 223 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6467 (mt-10) REVERT: B 234 MET cc_start: 0.8442 (mmp) cc_final: 0.8136 (mmp) REVERT: B 247 MET cc_start: 0.7461 (mtt) cc_final: 0.7044 (mmt) REVERT: B 248 MET cc_start: 0.8113 (mmm) cc_final: 0.7861 (mmm) REVERT: B 536 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8326 (pt) REVERT: B 633 THR cc_start: 0.8693 (p) cc_final: 0.8423 (t) REVERT: B 665 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7243 (tm-30) REVERT: C 53 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.6121 (mm-30) REVERT: C 57 PHE cc_start: 0.8780 (t80) cc_final: 0.8291 (t80) REVERT: C 245 MET cc_start: 0.7891 (ttm) cc_final: 0.7659 (ttt) REVERT: C 565 MET cc_start: 0.8610 (mmt) cc_final: 0.7829 (mpp) REVERT: C 571 CYS cc_start: 0.9218 (m) cc_final: 0.8838 (t) REVERT: C 572 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9161 (mm) REVERT: C 649 SER cc_start: 0.9274 (m) cc_final: 0.8838 (t) REVERT: C 650 SER cc_start: 0.9120 (m) cc_final: 0.8899 (t) REVERT: C 704 LYS cc_start: 0.9409 (mmmt) cc_final: 0.9158 (tptm) REVERT: C 740 THR cc_start: 0.9288 (p) cc_final: 0.8950 (t) REVERT: C 741 THR cc_start: 0.8910 (p) cc_final: 0.8577 (t) REVERT: C 786 GLN cc_start: 0.8534 (tp40) cc_final: 0.8075 (tt0) REVERT: D 152 ASP cc_start: 0.7945 (t0) cc_final: 0.7591 (t0) REVERT: D 223 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6586 (mt-10) REVERT: D 234 MET cc_start: 0.8322 (mmp) cc_final: 0.8106 (ttm) REVERT: D 247 MET cc_start: 0.7460 (mtm) cc_final: 0.6873 (mtt) REVERT: D 248 MET cc_start: 0.8105 (mmm) cc_final: 0.7785 (mmm) REVERT: D 322 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9260 (mm) REVERT: D 329 VAL cc_start: 0.8410 (t) cc_final: 0.8209 (p) REVERT: D 536 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8399 (pt) REVERT: D 633 THR cc_start: 0.8849 (p) cc_final: 0.8498 (t) REVERT: D 665 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7451 (pp20) REVERT: D 705 MET cc_start: 0.8765 (mtp) cc_final: 0.8371 (mtp) outliers start: 57 outliers final: 21 residues processed: 384 average time/residue: 0.1513 time to fit residues: 96.3797 Evaluate side-chains 283 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 256 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 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 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 125 optimal weight: 3.9990 chunk 221 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 chunk 321 optimal weight: 8.9990 chunk 311 optimal weight: 20.0000 chunk 131 optimal weight: 0.9990 chunk 82 optimal weight: 0.1980 chunk 116 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 278 optimal weight: 9.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 HIS A 593 HIS ** A 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 508 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.083628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.064665 restraints weight = 128249.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.065041 restraints weight = 81550.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.065760 restraints weight = 64615.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.066159 restraints weight = 52941.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.066500 restraints weight = 49262.506| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27480 Z= 0.198 Angle : 0.918 22.135 37352 Z= 0.413 Chirality : 0.053 0.582 4314 Planarity : 0.005 0.096 4618 Dihedral : 15.972 140.608 4834 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.75 % Favored : 91.97 % Rotamer: Outliers : 3.24 % Allowed : 10.92 % Favored : 85.85 % 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 aren not related in a simple way. whole: -2.49 (0.14), residues: 3264 helix: -0.41 (0.13), residues: 1462 sheet: -2.36 (0.23), residues: 460 loop : -2.78 (0.15), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 384 TYR 0.044 0.002 TYR D 478 PHE 0.019 0.002 PHE C 693 TRP 0.025 0.002 TRP B 706 HIS 0.008 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00418 (27408) covalent geometry : angle 0.82586 (37146) SS BOND : bond 0.00856 ( 10) SS BOND : angle 1.30264 ( 20) hydrogen bonds : bond 0.04601 ( 1024) hydrogen bonds : angle 4.83904 ( 2934) link_BETA1-3 : bond 0.00939 ( 4) link_BETA1-3 : angle 4.49448 ( 12) link_BETA1-4 : bond 0.02114 ( 26) link_BETA1-4 : angle 6.21850 ( 78) link_NAG-ASN : bond 0.00929 ( 32) link_NAG-ASN : angle 5.45194 ( 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 365 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 273 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.8772 (t80) cc_final: 0.8304 (t80) REVERT: A 156 LEU cc_start: 0.9373 (mt) cc_final: 0.9153 (mt) REVERT: A 219 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.7997 (ptpp) REVERT: A 247 MET cc_start: 0.8252 (mmm) cc_final: 0.7826 (mmm) REVERT: A 450 ASP cc_start: 0.7128 (p0) cc_final: 0.6890 (t70) REVERT: A 565 MET cc_start: 0.8700 (mmt) cc_final: 0.7884 (mpp) REVERT: A 571 CYS cc_start: 0.9200 (m) cc_final: 0.8932 (t) REVERT: A 621 GLN cc_start: 0.8923 (mm-40) cc_final: 0.8713 (tp40) REVERT: A 649 SER cc_start: 0.9318 (m) cc_final: 0.8801 (t) REVERT: A 650 SER cc_start: 0.9106 (m) cc_final: 0.8832 (t) REVERT: A 705 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8395 (mmm) REVERT: B 90 GLU cc_start: 0.8442 (tt0) cc_final: 0.7933 (tt0) REVERT: B 130 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8725 (tp) REVERT: B 223 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6257 (mt-10) REVERT: B 247 MET cc_start: 0.7621 (mtt) cc_final: 0.7081 (mmt) REVERT: B 323 MET cc_start: 0.9041 (tpp) cc_final: 0.8429 (ttm) REVERT: B 536 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8575 (pt) REVERT: B 538 ILE cc_start: 0.9525 (mt) cc_final: 0.9184 (mt) REVERT: B 565 MET cc_start: 0.8128 (mmt) cc_final: 0.7888 (mmp) REVERT: B 627 MET cc_start: 0.8491 (mmm) cc_final: 0.8232 (mtt) REVERT: B 633 THR cc_start: 0.8690 (p) cc_final: 0.8394 (t) REVERT: B 665 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7316 (tm-30) REVERT: B 793 MET cc_start: 0.9232 (tpt) cc_final: 0.9029 (tpt) REVERT: C 57 PHE cc_start: 0.8759 (t80) cc_final: 0.8272 (t80) REVERT: C 450 ASP cc_start: 0.6899 (p0) cc_final: 0.6624 (t70) REVERT: C 565 MET cc_start: 0.8694 (mmt) cc_final: 0.7951 (mpp) REVERT: C 571 CYS cc_start: 0.9239 (m) cc_final: 0.8891 (t) REVERT: C 649 SER cc_start: 0.9282 (m) cc_final: 0.8834 (t) REVERT: C 650 SER cc_start: 0.9145 (m) cc_final: 0.8890 (t) REVERT: C 705 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8455 (mmm) REVERT: C 740 THR cc_start: 0.9308 (p) cc_final: 0.8977 (t) REVERT: C 786 GLN cc_start: 0.8507 (tp40) cc_final: 0.8086 (tm-30) REVERT: D 90 GLU cc_start: 0.8567 (tt0) cc_final: 0.8115 (tt0) REVERT: D 152 ASP cc_start: 0.7905 (t0) cc_final: 0.7457 (t0) REVERT: D 218 MET cc_start: 0.8540 (tpp) cc_final: 0.8261 (tpp) REVERT: D 247 MET cc_start: 0.7334 (mtm) cc_final: 0.6749 (mtt) REVERT: D 248 MET cc_start: 0.8127 (mmm) cc_final: 0.7897 (mmm) REVERT: D 322 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9215 (mm) REVERT: D 501 MET cc_start: 0.8928 (mmm) cc_final: 0.8659 (mmm) REVERT: D 536 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8715 (pt) REVERT: D 565 MET cc_start: 0.8074 (mmt) cc_final: 0.7849 (mmp) REVERT: D 627 MET cc_start: 0.8956 (mmm) cc_final: 0.8212 (mtt) REVERT: D 633 THR cc_start: 0.8846 (p) cc_final: 0.8435 (t) REVERT: D 665 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7374 (pp20) REVERT: D 705 MET cc_start: 0.9048 (mtp) cc_final: 0.8625 (mtp) REVERT: D 794 MET cc_start: 0.9415 (mtt) cc_final: 0.9142 (mtp) outliers start: 92 outliers final: 41 residues processed: 335 average time/residue: 0.1370 time to fit residues: 78.1763 Evaluate side-chains 289 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 241 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 264 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 652 THR Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 274 VAL 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 569 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 672 ASP 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 444 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 648 ILE Chi-restraints excluded: chain C residue 652 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 319 ASP Chi-restraints excluded: chain D residue 322 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 170 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 182 optimal weight: 5.9990 chunk 186 optimal weight: 0.9980 chunk 236 optimal weight: 0.9980 chunk 209 optimal weight: 7.9990 chunk 169 optimal weight: 0.2980 chunk 259 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 HIS ** 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 = 0.3897 r_free = 0.3897 target = 0.085189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.066483 restraints weight = 125496.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.067562 restraints weight = 76241.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.068147 restraints weight = 59290.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.068580 restraints weight = 47550.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.068925 restraints weight = 44559.154| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27480 Z= 0.139 Angle : 0.865 21.105 37352 Z= 0.381 Chirality : 0.051 0.504 4314 Planarity : 0.004 0.053 4618 Dihedral : 13.707 140.273 4834 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.80 % Favored : 92.89 % Rotamer: Outliers : 2.50 % Allowed : 12.01 % Favored : 85.49 % 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 aren not related in a simple way. whole: -1.88 (0.14), residues: 3264 helix: 0.17 (0.13), residues: 1456 sheet: -1.99 (0.24), residues: 444 loop : -2.58 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 583 TYR 0.042 0.001 TYR B 478 PHE 0.014 0.001 PHE D 708 TRP 0.030 0.001 TRP C 169 HIS 0.006 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00293 (27408) covalent geometry : angle 0.76807 (37146) SS BOND : bond 0.00348 ( 10) SS BOND : angle 0.96269 ( 20) hydrogen bonds : bond 0.03949 ( 1024) hydrogen bonds : angle 4.46825 ( 2934) link_BETA1-3 : bond 0.01230 ( 4) link_BETA1-3 : angle 3.98561 ( 12) link_BETA1-4 : bond 0.02058 ( 26) link_BETA1-4 : angle 6.15222 ( 78) link_NAG-ASN : bond 0.00927 ( 32) link_NAG-ASN : angle 5.44444 ( 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 360 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 289 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.8739 (t80) cc_final: 0.8244 (t80) REVERT: A 99 LEU cc_start: 0.8299 (mm) cc_final: 0.7914 (pp) REVERT: A 229 ASP cc_start: 0.8088 (t0) cc_final: 0.7777 (t0) REVERT: A 245 MET cc_start: 0.7478 (ttm) cc_final: 0.7248 (ttp) REVERT: A 534 MET cc_start: 0.8536 (tpp) cc_final: 0.8150 (ttm) REVERT: A 565 MET cc_start: 0.8632 (mmt) cc_final: 0.7901 (mpp) REVERT: A 649 SER cc_start: 0.9218 (m) cc_final: 0.8862 (t) REVERT: A 650 SER cc_start: 0.9031 (m) cc_final: 0.8766 (t) REVERT: A 740 THR cc_start: 0.9300 (p) cc_final: 0.8924 (t) REVERT: B 90 GLU cc_start: 0.8437 (tt0) cc_final: 0.7975 (tt0) REVERT: B 130 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8681 (tp) REVERT: B 223 GLU cc_start: 0.6995 (mt-10) cc_final: 0.6747 (mt-10) REVERT: B 228 PHE cc_start: 0.9167 (OUTLIER) cc_final: 0.8947 (m-10) REVERT: B 247 MET cc_start: 0.7301 (mtt) cc_final: 0.6854 (mmt) REVERT: B 323 MET cc_start: 0.9003 (tpp) cc_final: 0.8702 (tpp) REVERT: B 536 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8452 (pt) REVERT: B 538 ILE cc_start: 0.9506 (mt) cc_final: 0.9143 (mt) REVERT: B 565 MET cc_start: 0.8086 (mmt) cc_final: 0.7851 (mmp) REVERT: B 633 THR cc_start: 0.8616 (p) cc_final: 0.8334 (t) REVERT: B 665 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7284 (tm-30) REVERT: B 705 MET cc_start: 0.9073 (mtp) cc_final: 0.8814 (ptp) REVERT: B 770 MET cc_start: 0.8772 (tpt) cc_final: 0.8509 (mmt) REVERT: C 57 PHE cc_start: 0.8751 (t80) cc_final: 0.8229 (t80) REVERT: C 147 VAL cc_start: 0.7865 (OUTLIER) cc_final: 0.7631 (m) REVERT: C 347 CYS cc_start: 0.5952 (OUTLIER) cc_final: 0.5424 (p) REVERT: C 450 ASP cc_start: 0.6886 (p0) cc_final: 0.6626 (t70) REVERT: C 534 MET cc_start: 0.8476 (tpp) cc_final: 0.8089 (ttm) REVERT: C 565 MET cc_start: 0.8648 (mmt) cc_final: 0.7830 (mpp) REVERT: C 571 CYS cc_start: 0.9152 (m) cc_final: 0.8866 (t) REVERT: C 649 SER cc_start: 0.9228 (m) cc_final: 0.8908 (t) REVERT: C 650 SER cc_start: 0.9151 (m) cc_final: 0.8852 (t) REVERT: C 740 THR cc_start: 0.9282 (p) cc_final: 0.8924 (t) REVERT: C 786 GLN cc_start: 0.8354 (tp40) cc_final: 0.8088 (tm-30) REVERT: D 50 MET cc_start: 0.4686 (OUTLIER) cc_final: 0.4389 (mtp) REVERT: D 90 GLU cc_start: 0.8533 (tt0) cc_final: 0.8086 (tt0) REVERT: D 152 ASP cc_start: 0.7774 (t0) cc_final: 0.7489 (t0) REVERT: D 223 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6063 (mt-10) REVERT: D 228 PHE cc_start: 0.9213 (OUTLIER) cc_final: 0.8980 (m-10) REVERT: D 248 MET cc_start: 0.8169 (mmm) cc_final: 0.7933 (mmm) REVERT: D 322 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9137 (mm) REVERT: D 323 MET cc_start: 0.8956 (tpp) cc_final: 0.8329 (ttm) REVERT: D 501 MET cc_start: 0.9019 (mmm) cc_final: 0.8351 (mmm) REVERT: D 536 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8469 (pt) REVERT: D 538 ILE cc_start: 0.9509 (mt) cc_final: 0.9158 (mt) REVERT: D 619 LEU cc_start: 0.8550 (tt) cc_final: 0.8337 (tp) REVERT: D 627 MET cc_start: 0.8890 (mmm) cc_final: 0.8201 (mtt) REVERT: D 633 THR cc_start: 0.8743 (p) cc_final: 0.8371 (t) REVERT: D 673 ASP cc_start: 0.8789 (t0) cc_final: 0.8512 (t0) REVERT: D 705 MET cc_start: 0.9023 (mtp) cc_final: 0.8570 (mtp) outliers start: 71 outliers final: 38 residues processed: 341 average time/residue: 0.1537 time to fit residues: 88.8879 Evaluate side-chains 297 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 250 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 155 SER Chi-restraints excluded: chain A residue 218 MET 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 678 THR Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 804 CYS 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 228 PHE 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 635 ILE Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 147 VAL 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 345 LEU Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 50 MET 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 322 LEU Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 635 ILE 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: 0.9990 chunk 260 optimal weight: 0.9980 chunk 64 optimal weight: 0.3980 chunk 149 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 294 optimal weight: 9.9990 chunk 266 optimal weight: 0.9990 chunk 279 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 318 optimal weight: 1.9990 chunk 290 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 HIS ** 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 = 0.3895 r_free = 0.3895 target = 0.085140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.066443 restraints weight = 126503.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.066968 restraints weight = 79411.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.067788 restraints weight = 62186.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.068259 restraints weight = 50470.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.068590 restraints weight = 47115.227| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27480 Z= 0.134 Angle : 0.837 20.935 37352 Z= 0.370 Chirality : 0.050 0.494 4314 Planarity : 0.004 0.066 4618 Dihedral : 12.399 140.674 4834 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.95 % Favored : 92.83 % Rotamer: Outliers : 2.57 % Allowed : 12.96 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.15), residues: 3264 helix: 0.47 (0.14), residues: 1452 sheet: -2.09 (0.24), residues: 448 loop : -2.38 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 220 TYR 0.037 0.001 TYR B 478 PHE 0.013 0.001 PHE C 708 TRP 0.031 0.001 TRP C 169 HIS 0.004 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00282 (27408) covalent geometry : angle 0.74323 (37146) SS BOND : bond 0.00528 ( 10) SS BOND : angle 1.81324 ( 20) hydrogen bonds : bond 0.03697 ( 1024) hydrogen bonds : angle 4.33562 ( 2934) link_BETA1-3 : bond 0.01187 ( 4) link_BETA1-3 : angle 3.60031 ( 12) link_BETA1-4 : bond 0.02013 ( 26) link_BETA1-4 : angle 6.05052 ( 78) link_NAG-ASN : bond 0.00968 ( 32) link_NAG-ASN : angle 5.19430 ( 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 339 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 266 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.8751 (t80) cc_final: 0.8225 (t80) REVERT: A 234 MET cc_start: 0.8627 (mpp) cc_final: 0.8222 (mpp) REVERT: A 316 MET cc_start: 0.7955 (pmm) cc_final: 0.7735 (pmm) REVERT: A 534 MET cc_start: 0.8628 (tpp) cc_final: 0.8157 (ttm) REVERT: A 565 MET cc_start: 0.8643 (mmt) cc_final: 0.7922 (mpp) REVERT: A 649 SER cc_start: 0.9220 (m) cc_final: 0.8908 (t) REVERT: A 650 SER cc_start: 0.9019 (m) cc_final: 0.8748 (t) REVERT: A 740 THR cc_start: 0.9303 (p) cc_final: 0.8932 (t) REVERT: B 90 GLU cc_start: 0.8439 (tt0) cc_final: 0.8004 (tt0) REVERT: B 130 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8594 (tp) REVERT: B 228 PHE cc_start: 0.9216 (OUTLIER) cc_final: 0.8909 (m-10) REVERT: B 247 MET cc_start: 0.7330 (mtt) cc_final: 0.6824 (mmt) REVERT: B 322 LEU cc_start: 0.9510 (mm) cc_final: 0.9175 (tp) REVERT: B 360 MET cc_start: 0.8012 (mmm) cc_final: 0.7764 (mmm) REVERT: B 536 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8492 (pt) REVERT: B 538 ILE cc_start: 0.9502 (mt) cc_final: 0.9129 (mt) REVERT: B 565 MET cc_start: 0.8056 (mmt) cc_final: 0.7811 (mmp) REVERT: B 627 MET cc_start: 0.8412 (mpp) cc_final: 0.8114 (mpp) REVERT: B 633 THR cc_start: 0.8586 (p) cc_final: 0.8281 (t) REVERT: B 665 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7262 (pp20) REVERT: B 770 MET cc_start: 0.8731 (tpt) cc_final: 0.8425 (mmt) REVERT: C 57 PHE cc_start: 0.8773 (t80) cc_final: 0.8289 (t80) REVERT: C 147 VAL cc_start: 0.7928 (OUTLIER) cc_final: 0.7693 (m) REVERT: C 245 MET cc_start: 0.7882 (ppp) cc_final: 0.7471 (ppp) REVERT: C 347 CYS cc_start: 0.5979 (OUTLIER) cc_final: 0.5491 (p) REVERT: C 565 MET cc_start: 0.8619 (mmt) cc_final: 0.7852 (mpp) REVERT: C 649 SER cc_start: 0.9256 (m) cc_final: 0.8922 (t) REVERT: C 650 SER cc_start: 0.9202 (m) cc_final: 0.8887 (t) REVERT: C 738 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8709 (pm20) REVERT: C 740 THR cc_start: 0.9291 (p) cc_final: 0.8998 (t) REVERT: C 786 GLN cc_start: 0.8346 (tp40) cc_final: 0.8100 (tm-30) REVERT: D 90 GLU cc_start: 0.8526 (tt0) cc_final: 0.8073 (tt0) REVERT: D 152 ASP cc_start: 0.7709 (t0) cc_final: 0.7456 (t0) REVERT: D 247 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6808 (mmt) REVERT: D 322 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9098 (mm) REVERT: D 323 MET cc_start: 0.8951 (tpp) cc_final: 0.8601 (ttm) REVERT: D 360 MET cc_start: 0.7845 (mmm) cc_final: 0.7595 (mmm) REVERT: D 536 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8551 (pt) REVERT: D 538 ILE cc_start: 0.9512 (mt) cc_final: 0.9163 (mt) REVERT: D 577 VAL cc_start: 0.8876 (t) cc_final: 0.8670 (p) REVERT: D 627 MET cc_start: 0.8898 (mmm) cc_final: 0.8270 (mtt) REVERT: D 633 THR cc_start: 0.8742 (p) cc_final: 0.8363 (t) REVERT: D 705 MET cc_start: 0.8970 (mtp) cc_final: 0.8579 (mtp) REVERT: D 737 MET cc_start: 0.7110 (tmm) cc_final: 0.6895 (tmm) outliers start: 73 outliers final: 42 residues processed: 318 average time/residue: 0.1481 time to fit residues: 79.1733 Evaluate side-chains 287 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 236 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 155 SER 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 540 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 340 MET 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 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 147 VAL Chi-restraints excluded: chain C residue 219 LYS 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 540 ILE Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 738 GLU Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 340 MET 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 793 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 306 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 305 optimal weight: 5.9990 chunk 319 optimal weight: 5.9990 chunk 296 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 266 optimal weight: 3.9990 chunk 238 optimal weight: 3.9990 chunk 309 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3830 r_free = 0.3830 target = 0.082011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.063037 restraints weight = 128352.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.064736 restraints weight = 77362.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.064986 restraints weight = 60022.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.064807 restraints weight = 51870.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.065031 restraints weight = 48853.857| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 27480 Z= 0.235 Angle : 0.887 20.788 37352 Z= 0.406 Chirality : 0.052 0.500 4314 Planarity : 0.005 0.068 4618 Dihedral : 11.860 141.137 4834 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.03 % Favored : 91.73 % Rotamer: Outliers : 3.20 % Allowed : 12.75 % Favored : 84.05 % 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 aren not related in a simple way. whole: -1.43 (0.15), residues: 3264 helix: 0.61 (0.14), residues: 1428 sheet: -1.88 (0.24), residues: 446 loop : -2.33 (0.16), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 775 TYR 0.035 0.002 TYR B 478 PHE 0.027 0.002 PHE A 224 TRP 0.049 0.002 TRP A 169 HIS 0.017 0.002 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00507 (27408) covalent geometry : angle 0.80470 (37146) SS BOND : bond 0.00497 ( 10) SS BOND : angle 1.35344 ( 20) hydrogen bonds : bond 0.03877 ( 1024) hydrogen bonds : angle 4.57296 ( 2934) link_BETA1-3 : bond 0.00950 ( 4) link_BETA1-3 : angle 3.20884 ( 12) link_BETA1-4 : bond 0.01755 ( 26) link_BETA1-4 : angle 5.98127 ( 78) link_NAG-ASN : bond 0.00748 ( 32) link_NAG-ASN : angle 4.99301 ( 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: 91 poor density : 235 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9161 (mm) REVERT: A 57 PHE cc_start: 0.8801 (t80) cc_final: 0.8359 (t80) REVERT: A 234 MET cc_start: 0.8771 (mpp) cc_final: 0.8221 (mpp) REVERT: A 347 CYS cc_start: 0.6150 (OUTLIER) cc_final: 0.5759 (p) REVERT: A 501 MET cc_start: 0.8561 (mmm) cc_final: 0.8139 (tpt) REVERT: A 565 MET cc_start: 0.8683 (mmt) cc_final: 0.7979 (mpp) REVERT: A 649 SER cc_start: 0.9288 (m) cc_final: 0.8829 (t) REVERT: A 650 SER cc_start: 0.9113 (m) cc_final: 0.8865 (t) REVERT: A 691 MET cc_start: 0.8395 (ptp) cc_final: 0.8066 (mpp) REVERT: A 740 THR cc_start: 0.9407 (p) cc_final: 0.9116 (t) REVERT: B 90 GLU cc_start: 0.8564 (tt0) cc_final: 0.8100 (tt0) REVERT: B 218 MET cc_start: 0.7880 (tpp) cc_final: 0.7668 (tpp) REVERT: B 228 PHE cc_start: 0.9243 (OUTLIER) cc_final: 0.8960 (m-10) REVERT: B 247 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.7083 (mmt) REVERT: B 322 LEU cc_start: 0.9536 (mm) cc_final: 0.9221 (tp) REVERT: B 323 MET cc_start: 0.9029 (tpp) cc_final: 0.8585 (ttm) REVERT: B 536 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8750 (pt) REVERT: B 538 ILE cc_start: 0.9536 (mt) cc_final: 0.9143 (mt) REVERT: B 565 MET cc_start: 0.8064 (mmt) cc_final: 0.7834 (mmp) REVERT: B 633 THR cc_start: 0.8694 (p) cc_final: 0.8380 (t) REVERT: B 665 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7340 (pp20) REVERT: B 737 MET cc_start: 0.7243 (tmm) cc_final: 0.7021 (tmm) REVERT: C 55 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9106 (mm) REVERT: C 57 PHE cc_start: 0.8831 (t80) cc_final: 0.8433 (t80) REVERT: C 347 CYS cc_start: 0.5949 (OUTLIER) cc_final: 0.5538 (p) REVERT: C 534 MET cc_start: 0.8380 (tpp) cc_final: 0.8022 (ttm) REVERT: C 565 MET cc_start: 0.8679 (mmt) cc_final: 0.8107 (mpp) REVERT: C 649 SER cc_start: 0.9268 (m) cc_final: 0.8856 (t) REVERT: C 740 THR cc_start: 0.9364 (p) cc_final: 0.9027 (t) REVERT: D 90 GLU cc_start: 0.8584 (tt0) cc_final: 0.8172 (tt0) REVERT: D 152 ASP cc_start: 0.7865 (t0) cc_final: 0.7480 (t0) REVERT: D 247 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.7057 (mmt) REVERT: D 248 MET cc_start: 0.8356 (mmm) cc_final: 0.8139 (mmm) REVERT: D 322 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9202 (mm) REVERT: D 360 MET cc_start: 0.7972 (mmm) cc_final: 0.7743 (mmm) REVERT: D 536 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8308 (pp) REVERT: D 538 ILE cc_start: 0.9537 (mt) cc_final: 0.9243 (mt) REVERT: D 565 MET cc_start: 0.7921 (mmt) cc_final: 0.7705 (mmp) REVERT: D 633 THR cc_start: 0.8841 (p) cc_final: 0.8443 (t) REVERT: D 665 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7436 (pp20) REVERT: D 705 MET cc_start: 0.8962 (mtp) cc_final: 0.8590 (mtp) REVERT: D 738 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7910 (mm-30) outliers start: 91 outliers final: 58 residues processed: 302 average time/residue: 0.1425 time to fit residues: 73.2043 Evaluate side-chains 280 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 212 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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 155 SER 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 505 LEU 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 652 THR Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 34 HIS 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 340 MET 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 478 TYR 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 672 ASP Chi-restraints excluded: chain B residue 680 ILE 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 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 652 THR Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 820 ILE Chi-restraints excluded: chain C residue 834 SER Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 340 MET 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 97 optimal weight: 3.9990 chunk 156 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 203 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 282 optimal weight: 0.2980 chunk 265 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 232 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 123 ASN ** 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 = 0.3826 r_free = 0.3826 target = 0.081885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.062941 restraints weight = 128553.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.063867 restraints weight = 78354.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.064371 restraints weight = 65558.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.064600 restraints weight = 51945.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.065040 restraints weight = 49500.295| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27480 Z= 0.201 Angle : 0.866 20.966 37352 Z= 0.392 Chirality : 0.051 0.488 4314 Planarity : 0.004 0.066 4618 Dihedral : 11.364 140.698 4834 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.84 % Favored : 91.91 % Rotamer: Outliers : 2.92 % Allowed : 13.70 % 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 aren not related in a simple way. whole: -1.31 (0.15), residues: 3264 helix: 0.73 (0.14), residues: 1432 sheet: -1.86 (0.25), residues: 446 loop : -2.28 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 775 TYR 0.035 0.002 TYR B 478 PHE 0.016 0.002 PHE B 584 TRP 0.047 0.002 TRP A 169 HIS 0.008 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00435 (27408) covalent geometry : angle 0.78533 (37146) SS BOND : bond 0.00462 ( 10) SS BOND : angle 1.59973 ( 20) hydrogen bonds : bond 0.03758 ( 1024) hydrogen bonds : angle 4.54272 ( 2934) link_BETA1-3 : bond 0.00911 ( 4) link_BETA1-3 : angle 2.87317 ( 12) link_BETA1-4 : bond 0.01712 ( 26) link_BETA1-4 : angle 5.79132 ( 78) link_NAG-ASN : bond 0.00778 ( 32) link_NAG-ASN : angle 4.95873 ( 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 314 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 231 time to evaluate : 0.775 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: 0.8839 (t80) cc_final: 0.8400 (t80) REVERT: A 234 MET cc_start: 0.8896 (mpp) cc_final: 0.8467 (mpp) REVERT: A 279 PHE cc_start: 0.8519 (m-80) cc_final: 0.8307 (m-10) REVERT: A 347 CYS cc_start: 0.5996 (OUTLIER) cc_final: 0.5628 (p) REVERT: A 501 MET cc_start: 0.8617 (mmm) cc_final: 0.8198 (tpt) REVERT: A 534 MET cc_start: 0.8311 (tpp) cc_final: 0.8031 (ttm) REVERT: A 565 MET cc_start: 0.8671 (mmt) cc_final: 0.7966 (mpp) REVERT: A 621 GLN cc_start: 0.8993 (tp40) cc_final: 0.8544 (tp40) REVERT: A 649 SER cc_start: 0.9337 (m) cc_final: 0.8896 (t) REVERT: A 650 SER cc_start: 0.9163 (m) cc_final: 0.8920 (t) REVERT: A 691 MET cc_start: 0.8357 (ptp) cc_final: 0.8109 (ptp) REVERT: A 738 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8553 (mp0) REVERT: A 740 THR cc_start: 0.9458 (p) cc_final: 0.9097 (t) REVERT: B 90 GLU cc_start: 0.8603 (tt0) cc_final: 0.8154 (tt0) REVERT: B 223 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6530 (mt-10) REVERT: B 228 PHE cc_start: 0.9282 (OUTLIER) cc_final: 0.8976 (m-10) REVERT: B 322 LEU cc_start: 0.9529 (mm) cc_final: 0.9204 (tp) REVERT: B 360 MET cc_start: 0.8044 (mmm) cc_final: 0.7819 (mmm) REVERT: B 536 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8718 (pt) REVERT: B 538 ILE cc_start: 0.9532 (mt) cc_final: 0.9103 (mt) REVERT: B 565 MET cc_start: 0.8076 (mmt) cc_final: 0.7849 (mmp) REVERT: B 633 THR cc_start: 0.8752 (p) cc_final: 0.8433 (t) REVERT: B 665 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7229 (pp20) REVERT: B 737 MET cc_start: 0.7204 (tmm) cc_final: 0.6880 (tmm) REVERT: C 57 PHE cc_start: 0.8839 (t80) cc_final: 0.8435 (t80) REVERT: C 245 MET cc_start: 0.8128 (ppp) cc_final: 0.7510 (ppp) REVERT: C 279 PHE cc_start: 0.8580 (m-80) cc_final: 0.8373 (m-10) REVERT: C 347 CYS cc_start: 0.5921 (OUTLIER) cc_final: 0.5547 (p) REVERT: C 501 MET cc_start: 0.8501 (mmm) cc_final: 0.8078 (tpt) REVERT: C 534 MET cc_start: 0.8480 (tpp) cc_final: 0.8040 (ttm) REVERT: C 565 MET cc_start: 0.8685 (mmt) cc_final: 0.8108 (mpp) REVERT: C 621 GLN cc_start: 0.9096 (tp40) cc_final: 0.8847 (tp40) REVERT: C 649 SER cc_start: 0.9281 (m) cc_final: 0.8921 (t) REVERT: C 709 MET cc_start: 0.8889 (mtm) cc_final: 0.8269 (mtt) REVERT: C 740 THR cc_start: 0.9444 (p) cc_final: 0.9087 (t) REVERT: D 90 GLU cc_start: 0.8637 (tt0) cc_final: 0.8181 (tt0) REVERT: D 152 ASP cc_start: 0.7924 (t0) cc_final: 0.7568 (t0) REVERT: D 228 PHE cc_start: 0.9292 (OUTLIER) cc_final: 0.8915 (m-10) REVERT: D 248 MET cc_start: 0.8251 (mmm) cc_final: 0.7960 (mmm) REVERT: D 322 LEU cc_start: 0.9437 (mm) cc_final: 0.9171 (mm) REVERT: D 536 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8296 (pp) REVERT: D 538 ILE cc_start: 0.9559 (mt) cc_final: 0.9204 (mt) REVERT: D 627 MET cc_start: 0.8820 (mmm) cc_final: 0.8274 (ttm) REVERT: D 633 THR cc_start: 0.8859 (p) cc_final: 0.8436 (t) REVERT: D 665 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7457 (pp20) REVERT: D 705 MET cc_start: 0.8964 (mtp) cc_final: 0.8580 (mtp) REVERT: D 738 GLU cc_start: 0.8266 (mm-30) cc_final: 0.8020 (mm-30) outliers start: 83 outliers final: 53 residues processed: 294 average time/residue: 0.1283 time to fit residues: 64.9355 Evaluate side-chains 281 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 221 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 155 SER 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 505 LEU Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 572 LEU 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 804 CYS Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 34 HIS 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 466 LEU Chi-restraints excluded: chain B residue 478 TYR 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 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 219 LYS 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 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 650 SER Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 718 VAL 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 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 635 ILE Chi-restraints excluded: chain D residue 645 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 171 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 249 optimal weight: 4.9990 chunk 300 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 108 optimal weight: 0.0470 chunk 247 optimal weight: 7.9990 chunk 167 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 269 optimal weight: 9.9990 overall best weight: 2.7284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 754 GLN ** 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 = 0.3825 r_free = 0.3825 target = 0.081894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.062930 restraints weight = 128439.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.063832 restraints weight = 78795.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.064458 restraints weight = 64482.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.064518 restraints weight = 51826.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.064954 restraints weight = 49429.658| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 27480 Z= 0.185 Angle : 0.864 20.826 37352 Z= 0.388 Chirality : 0.050 0.478 4314 Planarity : 0.004 0.068 4618 Dihedral : 11.003 140.630 4834 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.72 % Favored : 92.03 % Rotamer: Outliers : 2.68 % Allowed : 14.19 % Favored : 83.13 % 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 aren not related in a simple way. whole: -1.20 (0.15), residues: 3264 helix: 0.82 (0.14), residues: 1432 sheet: -1.83 (0.25), residues: 446 loop : -2.20 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 775 TYR 0.036 0.001 TYR B 478 PHE 0.015 0.002 PHE B 579 TRP 0.048 0.002 TRP C 169 HIS 0.006 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00405 (27408) covalent geometry : angle 0.78591 (37146) SS BOND : bond 0.00395 ( 10) SS BOND : angle 1.41576 ( 20) hydrogen bonds : bond 0.03647 ( 1024) hydrogen bonds : angle 4.49285 ( 2934) link_BETA1-3 : bond 0.00864 ( 4) link_BETA1-3 : angle 2.67379 ( 12) link_BETA1-4 : bond 0.01658 ( 26) link_BETA1-4 : angle 5.70483 ( 78) link_NAG-ASN : bond 0.00748 ( 32) link_NAG-ASN : angle 4.90138 ( 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 301 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 225 time to evaluate : 0.985 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: 0.8900 (t80) cc_final: 0.8443 (t80) REVERT: A 234 MET cc_start: 0.8966 (mpp) cc_final: 0.8542 (mpp) REVERT: A 245 MET cc_start: 0.8167 (ppp) cc_final: 0.7506 (ppp) REVERT: A 347 CYS cc_start: 0.6133 (OUTLIER) cc_final: 0.5787 (p) REVERT: A 501 MET cc_start: 0.8586 (mmm) cc_final: 0.7965 (tpt) REVERT: A 534 MET cc_start: 0.8438 (tpp) cc_final: 0.8020 (ttm) REVERT: A 565 MET cc_start: 0.8648 (mmt) cc_final: 0.8083 (mpp) REVERT: A 649 SER cc_start: 0.9277 (m) cc_final: 0.8861 (t) REVERT: A 650 SER cc_start: 0.9146 (m) cc_final: 0.8928 (t) REVERT: A 740 THR cc_start: 0.9441 (p) cc_final: 0.9075 (t) REVERT: B 50 MET cc_start: 0.3444 (tmm) cc_final: 0.2976 (tmm) REVERT: B 90 GLU cc_start: 0.8614 (tt0) cc_final: 0.8159 (tt0) REVERT: B 223 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6941 (mt-10) REVERT: B 228 PHE cc_start: 0.9293 (OUTLIER) cc_final: 0.8952 (m-10) REVERT: B 247 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.7076 (mmt) REVERT: B 322 LEU cc_start: 0.9517 (mm) cc_final: 0.9188 (tp) REVERT: B 323 MET cc_start: 0.8932 (tpp) cc_final: 0.8686 (ttt) REVERT: B 340 MET cc_start: 0.8510 (tpp) cc_final: 0.8145 (mmm) REVERT: B 501 MET cc_start: 0.8634 (mmm) cc_final: 0.7698 (mmm) REVERT: B 536 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8629 (pt) REVERT: B 538 ILE cc_start: 0.9530 (mt) cc_final: 0.9096 (mt) REVERT: B 565 MET cc_start: 0.8086 (mmt) cc_final: 0.7857 (mmp) REVERT: B 633 THR cc_start: 0.8733 (p) cc_final: 0.8455 (t) REVERT: B 665 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7183 (pp20) REVERT: B 770 MET cc_start: 0.8431 (mmt) cc_final: 0.8198 (mmt) REVERT: C 57 PHE cc_start: 0.8851 (t80) cc_final: 0.8457 (t80) REVERT: C 245 MET cc_start: 0.8167 (ppp) cc_final: 0.7530 (ppp) REVERT: C 347 CYS cc_start: 0.5875 (OUTLIER) cc_final: 0.5525 (p) REVERT: C 501 MET cc_start: 0.8476 (mmm) cc_final: 0.7990 (tpt) REVERT: C 534 MET cc_start: 0.8472 (tpp) cc_final: 0.8065 (ttm) REVERT: C 565 MET cc_start: 0.8706 (mmt) cc_final: 0.8122 (mpp) REVERT: C 621 GLN cc_start: 0.9128 (tp40) cc_final: 0.8882 (tp40) REVERT: C 649 SER cc_start: 0.9273 (m) cc_final: 0.8906 (t) REVERT: C 705 MET cc_start: 0.8813 (mmm) cc_final: 0.8587 (mmm) REVERT: C 709 MET cc_start: 0.8879 (mtm) cc_final: 0.8344 (mtt) REVERT: C 740 THR cc_start: 0.9424 (p) cc_final: 0.9068 (t) REVERT: D 90 GLU cc_start: 0.8638 (tt0) cc_final: 0.8181 (tt0) REVERT: D 152 ASP cc_start: 0.7889 (t0) cc_final: 0.7612 (t0) REVERT: D 228 PHE cc_start: 0.9292 (OUTLIER) cc_final: 0.8910 (m-10) REVERT: D 247 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.6926 (mmt) REVERT: D 248 MET cc_start: 0.8308 (mmm) cc_final: 0.8067 (mmm) REVERT: D 322 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9156 (mm) REVERT: D 536 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8195 (pp) REVERT: D 538 ILE cc_start: 0.9565 (mt) cc_final: 0.9205 (mt) REVERT: D 633 THR cc_start: 0.8856 (p) cc_final: 0.8427 (t) REVERT: D 665 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7450 (pp20) REVERT: D 705 MET cc_start: 0.8962 (mtp) cc_final: 0.8562 (mtp) REVERT: D 738 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8093 (mm-30) outliers start: 76 outliers final: 51 residues processed: 286 average time/residue: 0.1354 time to fit residues: 66.8999 Evaluate side-chains 275 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 215 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 155 SER 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 505 LEU Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 804 CYS 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 274 VAL Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 536 LEU 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 218 MET Chi-restraints excluded: chain C residue 219 LYS 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 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 650 SER Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 718 VAL 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 228 PHE Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 322 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 16 optimal weight: 0.7980 chunk 107 optimal weight: 9.9990 chunk 56 optimal weight: 0.3980 chunk 93 optimal weight: 7.9990 chunk 300 optimal weight: 7.9990 chunk 277 optimal weight: 0.5980 chunk 87 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 146 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3859 r_free = 0.3859 target = 0.083468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.064676 restraints weight = 125988.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.065759 restraints weight = 76227.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.066421 restraints weight = 60626.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.066550 restraints weight = 48170.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.066963 restraints weight = 45974.721| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.5170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27480 Z= 0.130 Angle : 0.838 20.574 37352 Z= 0.368 Chirality : 0.049 0.476 4314 Planarity : 0.004 0.061 4618 Dihedral : 10.391 140.384 4834 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.20 % Favored : 92.59 % Rotamer: Outliers : 2.25 % Allowed : 14.86 % Favored : 82.89 % 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 aren not related in a simple way. whole: -0.98 (0.15), residues: 3264 helix: 1.02 (0.14), residues: 1440 sheet: -1.69 (0.25), residues: 444 loop : -2.15 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 775 TYR 0.034 0.001 TYR B 478 PHE 0.013 0.001 PHE B 579 TRP 0.041 0.002 TRP C 169 HIS 0.006 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00285 (27408) covalent geometry : angle 0.76069 (37146) SS BOND : bond 0.00421 ( 10) SS BOND : angle 1.37417 ( 20) hydrogen bonds : bond 0.03386 ( 1024) hydrogen bonds : angle 4.27981 ( 2934) link_BETA1-3 : bond 0.00881 ( 4) link_BETA1-3 : angle 2.45757 ( 12) link_BETA1-4 : bond 0.01644 ( 26) link_BETA1-4 : angle 5.52843 ( 78) link_NAG-ASN : bond 0.00873 ( 32) link_NAG-ASN : angle 4.80505 ( 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 311 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 247 time to evaluate : 1.034 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: 0.8868 (t80) cc_final: 0.8377 (t80) REVERT: A 234 MET cc_start: 0.8920 (mpp) cc_final: 0.8472 (mpp) REVERT: A 245 MET cc_start: 0.8172 (ppp) cc_final: 0.7561 (ppp) REVERT: A 347 CYS cc_start: 0.6044 (OUTLIER) cc_final: 0.5699 (p) REVERT: A 501 MET cc_start: 0.8569 (mmm) cc_final: 0.8046 (tpt) REVERT: A 534 MET cc_start: 0.8430 (tpp) cc_final: 0.8138 (ttm) REVERT: A 565 MET cc_start: 0.8665 (mmt) cc_final: 0.8034 (mpp) REVERT: A 645 LEU cc_start: 0.8800 (tp) cc_final: 0.8493 (tt) REVERT: A 649 SER cc_start: 0.9279 (m) cc_final: 0.9047 (t) REVERT: A 650 SER cc_start: 0.9130 (m) cc_final: 0.8873 (t) REVERT: A 664 MET cc_start: 0.8684 (tpp) cc_final: 0.8424 (tpp) REVERT: A 691 MET cc_start: 0.8655 (ptp) cc_final: 0.8380 (pmm) REVERT: A 709 MET cc_start: 0.8867 (mtm) cc_final: 0.8292 (mtt) REVERT: A 737 MET cc_start: 0.7616 (ptp) cc_final: 0.7252 (ttp) REVERT: A 738 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8478 (mp0) REVERT: A 740 THR cc_start: 0.9436 (p) cc_final: 0.8999 (t) REVERT: B 50 MET cc_start: 0.3642 (tmm) cc_final: 0.3262 (tmm) REVERT: B 90 GLU cc_start: 0.8572 (tt0) cc_final: 0.8130 (tt0) REVERT: B 152 ASP cc_start: 0.7815 (t0) cc_final: 0.7509 (t0) REVERT: B 228 PHE cc_start: 0.9262 (OUTLIER) cc_final: 0.8891 (m-10) REVERT: B 247 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.6942 (mmt) REVERT: B 322 LEU cc_start: 0.9480 (mm) cc_final: 0.9147 (tp) REVERT: B 323 MET cc_start: 0.8933 (tpp) cc_final: 0.8626 (ttt) REVERT: B 340 MET cc_start: 0.8521 (tpp) cc_final: 0.8245 (mmm) REVERT: B 501 MET cc_start: 0.8619 (mmm) cc_final: 0.7717 (mmm) REVERT: B 536 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8510 (pt) REVERT: B 538 ILE cc_start: 0.9477 (mt) cc_final: 0.9017 (mt) REVERT: B 633 THR cc_start: 0.8690 (p) cc_final: 0.8407 (t) REVERT: B 665 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7147 (pp20) REVERT: C 57 PHE cc_start: 0.8850 (t80) cc_final: 0.8410 (t80) REVERT: C 245 MET cc_start: 0.8046 (ppp) cc_final: 0.7562 (ppp) REVERT: C 279 PHE cc_start: 0.8631 (m-80) cc_final: 0.8382 (m-10) REVERT: C 340 MET cc_start: 0.8500 (tmm) cc_final: 0.8043 (tmm) REVERT: C 347 CYS cc_start: 0.5928 (OUTLIER) cc_final: 0.5491 (p) REVERT: C 501 MET cc_start: 0.8481 (mmm) cc_final: 0.8145 (tpt) REVERT: C 534 MET cc_start: 0.8433 (tpp) cc_final: 0.8107 (ttm) REVERT: C 565 MET cc_start: 0.8621 (mmt) cc_final: 0.8041 (mpp) REVERT: C 621 GLN cc_start: 0.9073 (tp40) cc_final: 0.8840 (tp40) REVERT: C 649 SER cc_start: 0.9185 (m) cc_final: 0.8915 (t) REVERT: C 650 SER cc_start: 0.9114 (OUTLIER) cc_final: 0.8803 (t) REVERT: C 709 MET cc_start: 0.8820 (mtm) cc_final: 0.8328 (mtt) REVERT: C 737 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7555 (ttp) REVERT: C 740 THR cc_start: 0.9391 (p) cc_final: 0.9000 (t) REVERT: D 50 MET cc_start: 0.3217 (tmm) cc_final: 0.2783 (tmm) REVERT: D 90 GLU cc_start: 0.8609 (tt0) cc_final: 0.8176 (tt0) REVERT: D 228 PHE cc_start: 0.9249 (OUTLIER) cc_final: 0.8816 (m-10) REVERT: D 247 MET cc_start: 0.7333 (OUTLIER) cc_final: 0.6898 (mmt) REVERT: D 248 MET cc_start: 0.8192 (mmm) cc_final: 0.7921 (mmm) REVERT: D 322 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9093 (mm) REVERT: D 536 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8095 (pp) REVERT: D 538 ILE cc_start: 0.9527 (mt) cc_final: 0.9176 (mt) REVERT: D 627 MET cc_start: 0.8787 (mmm) cc_final: 0.8271 (ttm) REVERT: D 633 THR cc_start: 0.8784 (p) cc_final: 0.8354 (t) REVERT: D 665 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7283 (pp20) REVERT: D 705 MET cc_start: 0.8866 (mtp) cc_final: 0.8159 (mtp) REVERT: D 738 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8042 (mm-30) outliers start: 64 outliers final: 48 residues processed: 297 average time/residue: 0.1196 time to fit residues: 61.2367 Evaluate side-chains 293 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 233 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 50 MET 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 155 SER 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 450 ASP Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 644 THR 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 804 CYS 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 274 VAL 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 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 50 MET Chi-restraints excluded: chain C residue 55 LEU 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 345 LEU Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 650 SER Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 737 MET 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 322 LEU 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 645 LEU Chi-restraints excluded: chain D residue 658 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 239 optimal weight: 0.0270 chunk 167 optimal weight: 0.7980 chunk 293 optimal weight: 0.6980 chunk 140 optimal weight: 9.9990 chunk 214 optimal weight: 0.0270 chunk 54 optimal weight: 7.9990 chunk 274 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 292 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 237 optimal weight: 4.9990 overall best weight: 1.3098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 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 = 0.3855 r_free = 0.3855 target = 0.083406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.064584 restraints weight = 127095.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.065301 restraints weight = 79794.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.065917 restraints weight = 62196.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.066304 restraints weight = 50369.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.066704 restraints weight = 47324.973| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.5320 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= 0.137 Angle : 0.843 20.189 37352 Z= 0.372 Chirality : 0.049 0.461 4314 Planarity : 0.004 0.065 4618 Dihedral : 10.042 140.698 4834 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.32 % Favored : 92.46 % Rotamer: Outliers : 2.15 % Allowed : 15.77 % Favored : 82.08 % 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 aren not related in a simple way. whole: -0.84 (0.15), residues: 3264 helix: 1.13 (0.14), residues: 1426 sheet: -1.66 (0.25), residues: 446 loop : -2.01 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 775 TYR 0.034 0.001 TYR B 478 PHE 0.019 0.001 PHE A 584 TRP 0.064 0.002 TRP B 613 HIS 0.007 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00303 (27408) covalent geometry : angle 0.76727 (37146) SS BOND : bond 0.00352 ( 10) SS BOND : angle 1.28321 ( 20) hydrogen bonds : bond 0.03364 ( 1024) hydrogen bonds : angle 4.23362 ( 2934) link_BETA1-3 : bond 0.00825 ( 4) link_BETA1-3 : angle 2.34691 ( 12) link_BETA1-4 : bond 0.01575 ( 26) link_BETA1-4 : angle 5.52696 ( 78) link_NAG-ASN : bond 0.00840 ( 32) link_NAG-ASN : angle 4.79197 ( 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 300 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 239 time to evaluate : 1.091 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 57 PHE cc_start: 0.8918 (t80) cc_final: 0.8464 (t80) REVERT: A 234 MET cc_start: 0.8950 (mpp) cc_final: 0.8508 (mpp) REVERT: A 245 MET cc_start: 0.8155 (ppp) cc_final: 0.7587 (ppp) REVERT: A 347 CYS cc_start: 0.6112 (OUTLIER) cc_final: 0.5777 (p) REVERT: A 501 MET cc_start: 0.8672 (mmm) cc_final: 0.8119 (tpt) REVERT: A 534 MET cc_start: 0.8455 (tpp) cc_final: 0.8120 (ttm) REVERT: A 565 MET cc_start: 0.8649 (mmt) cc_final: 0.8042 (mpp) REVERT: A 649 SER cc_start: 0.9229 (m) cc_final: 0.8938 (t) REVERT: A 650 SER cc_start: 0.9137 (m) cc_final: 0.8860 (t) REVERT: A 691 MET cc_start: 0.8568 (ptp) cc_final: 0.8174 (pmm) REVERT: A 709 MET cc_start: 0.8941 (mtm) cc_final: 0.8441 (mtt) REVERT: A 737 MET cc_start: 0.7567 (ptp) cc_final: 0.7254 (ttp) REVERT: A 738 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8520 (mp0) REVERT: A 740 THR cc_start: 0.9412 (p) cc_final: 0.8985 (t) REVERT: B 50 MET cc_start: 0.3827 (tmm) cc_final: 0.3460 (tmm) REVERT: B 90 GLU cc_start: 0.8583 (tt0) cc_final: 0.8132 (tt0) REVERT: B 223 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6835 (mt-10) REVERT: B 228 PHE cc_start: 0.9286 (OUTLIER) cc_final: 0.8918 (m-10) REVERT: B 247 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.6955 (mmt) REVERT: B 322 LEU cc_start: 0.9484 (mm) cc_final: 0.9142 (tp) REVERT: B 323 MET cc_start: 0.8908 (tpp) cc_final: 0.8618 (ttt) REVERT: B 501 MET cc_start: 0.8654 (mmm) cc_final: 0.7822 (mmm) REVERT: B 536 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8537 (pt) REVERT: B 538 ILE cc_start: 0.9504 (mt) cc_final: 0.9183 (mt) REVERT: B 633 THR cc_start: 0.8720 (p) cc_final: 0.8442 (t) REVERT: B 665 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7131 (pp20) REVERT: B 691 MET cc_start: 0.8736 (tmm) cc_final: 0.8530 (ttm) REVERT: C 57 PHE cc_start: 0.8871 (t80) cc_final: 0.8434 (t80) REVERT: C 245 MET cc_start: 0.7996 (ppp) cc_final: 0.7614 (ppp) REVERT: C 340 MET cc_start: 0.8576 (tmm) cc_final: 0.8222 (tmm) REVERT: C 347 CYS cc_start: 0.5701 (OUTLIER) cc_final: 0.5324 (p) REVERT: C 501 MET cc_start: 0.8563 (mmm) cc_final: 0.8164 (tpt) REVERT: C 534 MET cc_start: 0.8505 (tpp) cc_final: 0.8145 (ttm) REVERT: C 649 SER cc_start: 0.9194 (m) cc_final: 0.8924 (t) REVERT: C 709 MET cc_start: 0.8867 (mtm) cc_final: 0.8402 (mtt) REVERT: C 740 THR cc_start: 0.9378 (p) cc_final: 0.8982 (t) REVERT: D 50 MET cc_start: 0.3438 (tmm) cc_final: 0.3003 (tmm) REVERT: D 90 GLU cc_start: 0.8618 (tt0) cc_final: 0.8189 (tt0) REVERT: D 152 ASP cc_start: 0.7900 (t0) cc_final: 0.7697 (t0) REVERT: D 228 PHE cc_start: 0.9282 (OUTLIER) cc_final: 0.8862 (m-10) REVERT: D 247 MET cc_start: 0.7265 (OUTLIER) cc_final: 0.6914 (mmt) REVERT: D 322 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9095 (mm) REVERT: D 536 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8192 (pp) REVERT: D 538 ILE cc_start: 0.9539 (mt) cc_final: 0.9155 (mt) REVERT: D 627 MET cc_start: 0.8892 (mmm) cc_final: 0.8315 (ttt) REVERT: D 633 THR cc_start: 0.8785 (p) cc_final: 0.8354 (t) REVERT: D 665 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7275 (pp20) REVERT: D 738 GLU cc_start: 0.8302 (mm-30) cc_final: 0.8059 (mm-30) outliers start: 61 outliers final: 45 residues processed: 284 average time/residue: 0.1512 time to fit residues: 74.5102 Evaluate side-chains 282 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 227 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 155 SER 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 644 THR 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 804 CYS 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 478 TYR 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 672 ASP Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 743 GLU 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 218 MET 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 572 LEU Chi-restraints excluded: chain C residue 650 SER Chi-restraints excluded: chain C residue 718 VAL 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 322 LEU 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 645 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 3 optimal weight: 6.9990 chunk 254 optimal weight: 0.8980 chunk 162 optimal weight: 20.0000 chunk 177 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 HIS ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 754 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.082103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.063251 restraints weight = 127632.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.064503 restraints weight = 78732.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.065178 restraints weight = 60167.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.065003 restraints weight = 49455.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.065358 restraints weight = 47435.501| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.5491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 27480 Z= 0.177 Angle : 0.857 20.146 37352 Z= 0.385 Chirality : 0.049 0.446 4314 Planarity : 0.005 0.067 4618 Dihedral : 9.777 140.603 4834 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.78 % Favored : 91.97 % Rotamer: Outliers : 2.15 % Allowed : 16.06 % Favored : 81.80 % 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 aren not related in a simple way. whole: -0.93 (0.15), residues: 3264 helix: 1.07 (0.14), residues: 1440 sheet: -1.67 (0.25), residues: 436 loop : -2.12 (0.16), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 634 TYR 0.034 0.001 TYR B 478 PHE 0.022 0.002 PHE B 584 TRP 0.098 0.002 TRP B 613 HIS 0.007 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00389 (27408) covalent geometry : angle 0.78454 (37146) SS BOND : bond 0.00343 ( 10) SS BOND : angle 1.30749 ( 20) hydrogen bonds : bond 0.03520 ( 1024) hydrogen bonds : angle 4.35649 ( 2934) link_BETA1-3 : bond 0.00750 ( 4) link_BETA1-3 : angle 2.21215 ( 12) link_BETA1-4 : bond 0.01455 ( 26) link_BETA1-4 : angle 5.44838 ( 78) link_NAG-ASN : bond 0.00733 ( 32) link_NAG-ASN : angle 4.76246 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3962.73 seconds wall clock time: 69 minutes 53.68 seconds (4193.68 seconds total)