Starting phenix.real_space_refine on Sun May 25 15:50:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fwq_29515/05_2025/8fwq_29515.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fwq_29515/05_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_29515/05_2025/8fwq_29515.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fwq_29515/05_2025/8fwq_29515.map" model { file = "/net/cci-nas-00/data/ceres_data/8fwq_29515/05_2025/8fwq_29515.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fwq_29515/05_2025/8fwq_29515.cif" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.96s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 16.17, per 1000 atoms: 0.60 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: 7.94 Conformation dependent library (CDL) restraints added in 3.3 seconds 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: 3.07 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: 9.17 Time building geometry restraints manager: 8.97 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: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 1.020 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 58.750 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.160 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.270 ------------------------------------------------------------------------------- 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 : 4.86 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.033 0.004 TRP C 134 HIS 0.013 0.003 HIS B 253 PHE 0.022 0.003 PHE B 446 TYR 0.023 0.003 TYR D 702 ARG 0.015 0.001 ARG D 184 Details of bonding type rmsd link_NAG-ASN : bond 0.01642 ( 32) link_NAG-ASN : angle 7.46095 ( 96) link_BETA1-4 : bond 0.02876 ( 26) link_BETA1-4 : angle 8.81418 ( 78) hydrogen bonds : bond 0.28287 ( 1024) hydrogen bonds : angle 9.46198 ( 2934) SS BOND : bond 0.03958 ( 10) SS BOND : angle 1.64473 ( 20) link_BETA1-3 : bond 0.01152 ( 4) link_BETA1-3 : angle 4.23343 ( 12) covalent geometry : bond 0.00948 (27408) covalent geometry : angle 1.21249 (37146) *********************** 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 : 2.914 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: 0.3776 time to fit residues: 338.4588 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 : 3.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 3.9990 chunk 245 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 253 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 189 optimal weight: 20.0000 chunk 294 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 GLN A 350 HIS A 456 ASN A 497 GLN A 591 ASN A 596 ASN A 604 ASN A 610 ASN ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN B 350 HIS B 456 ASN B 495 ASN B 604 ASN B 621 GLN B 802 ASN B 819 ASN C 136 HIS C 141 ASN C 165 GLN ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 GLN C 350 HIS C 456 ASN C 497 GLN C 591 ASN C 593 HIS C 596 ASN C 604 ASN C 610 ASN C 622 GLN ** 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: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.085071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.066071 restraints weight = 125102.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.066353 restraints weight = 74282.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.067244 restraints weight = 63108.865| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27480 Z= 0.193 Angle : 0.943 21.204 37352 Z= 0.434 Chirality : 0.056 0.661 4314 Planarity : 0.006 0.055 4618 Dihedral : 19.300 139.629 4834 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.69 % Favored : 91.97 % Rotamer: Outliers : 1.97 % Allowed : 10.25 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.13), residues: 3264 helix: -1.45 (0.11), residues: 1440 sheet: -2.56 (0.23), residues: 430 loop : -2.98 (0.15), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 706 HIS 0.006 0.001 HIS C 225 PHE 0.027 0.002 PHE D 579 TYR 0.025 0.001 TYR B 478 ARG 0.008 0.001 ARG C 713 Details of bonding type rmsd link_NAG-ASN : bond 0.00988 ( 32) link_NAG-ASN : angle 5.58174 ( 96) link_BETA1-4 : bond 0.02155 ( 26) link_BETA1-4 : angle 6.33764 ( 78) hydrogen bonds : bond 0.05914 ( 1024) hydrogen bonds : angle 5.38540 ( 2934) SS BOND : bond 0.01088 ( 10) SS BOND : angle 1.26210 ( 20) link_BETA1-3 : bond 0.01284 ( 4) link_BETA1-3 : angle 4.48217 ( 12) covalent geometry : bond 0.00416 (27408) covalent geometry : angle 0.84967 (37146) *********************** 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 394 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 338 time to evaluate : 2.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.6238 (mm-30) REVERT: A 57 PHE cc_start: 0.8816 (t80) cc_final: 0.8341 (t80) REVERT: A 155 SER cc_start: 0.9480 (m) cc_final: 0.9259 (p) REVERT: A 156 LEU cc_start: 0.9341 (mt) cc_final: 0.9103 (mt) REVERT: A 450 ASP cc_start: 0.7194 (p0) cc_final: 0.6887 (t70) REVERT: A 534 MET cc_start: 0.8561 (tpp) cc_final: 0.8015 (ttm) REVERT: A 565 MET cc_start: 0.8678 (mmt) cc_final: 0.7892 (mpp) REVERT: A 571 CYS cc_start: 0.9188 (m) cc_final: 0.8947 (t) REVERT: A 621 GLN cc_start: 0.8775 (mm-40) cc_final: 0.8451 (tp40) REVERT: A 649 SER cc_start: 0.9234 (m) cc_final: 0.8792 (t) REVERT: A 650 SER cc_start: 0.9045 (m) cc_final: 0.8837 (t) REVERT: A 704 LYS cc_start: 0.9445 (mmmt) cc_final: 0.9197 (tptm) REVERT: A 709 MET cc_start: 0.9066 (mtm) cc_final: 0.8850 (ptp) REVERT: B 223 GLU cc_start: 0.7341 (mt-10) cc_final: 0.6536 (mt-10) REVERT: B 234 MET cc_start: 0.8462 (mmp) cc_final: 0.8152 (mmp) REVERT: B 247 MET cc_start: 0.7486 (mtt) cc_final: 0.6905 (mmt) REVERT: B 248 MET cc_start: 0.8155 (mmm) cc_final: 0.7882 (mmm) REVERT: B 322 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9331 (mm) REVERT: B 536 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8319 (pt) REVERT: B 633 THR cc_start: 0.8729 (p) cc_final: 0.8445 (t) REVERT: B 665 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7234 (tm-30) REVERT: C 53 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.6332 (mm-30) REVERT: C 57 PHE cc_start: 0.8815 (t80) cc_final: 0.8251 (t80) REVERT: C 501 MET cc_start: 0.8623 (ttm) cc_final: 0.8159 (mmm) REVERT: C 528 ASP cc_start: 0.7740 (m-30) cc_final: 0.7479 (m-30) REVERT: C 565 MET cc_start: 0.8684 (mmt) cc_final: 0.7905 (mpp) REVERT: C 571 CYS cc_start: 0.9250 (m) cc_final: 0.8855 (t) REVERT: C 572 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9164 (mm) REVERT: C 709 MET cc_start: 0.9012 (mtm) cc_final: 0.8800 (ptp) REVERT: C 740 THR cc_start: 0.9302 (p) cc_final: 0.8965 (t) REVERT: C 741 THR cc_start: 0.8917 (p) cc_final: 0.8572 (t) REVERT: C 786 GLN cc_start: 0.8604 (tp40) cc_final: 0.8151 (tt0) REVERT: D 152 ASP cc_start: 0.7946 (t0) cc_final: 0.7555 (t0) REVERT: D 223 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6595 (mt-10) REVERT: D 234 MET cc_start: 0.8340 (mmp) cc_final: 0.8058 (ttm) REVERT: D 247 MET cc_start: 0.7474 (mtm) cc_final: 0.6788 (mtt) REVERT: D 248 MET cc_start: 0.8083 (mmm) cc_final: 0.7740 (mmm) REVERT: D 322 LEU cc_start: 0.9517 (OUTLIER) cc_final: 0.9291 (mm) REVERT: D 501 MET cc_start: 0.8937 (mmm) cc_final: 0.8357 (mmm) REVERT: D 536 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8393 (pt) REVERT: D 633 THR cc_start: 0.8882 (p) cc_final: 0.8513 (t) REVERT: D 665 GLU cc_start: 0.8411 (mt-10) cc_final: 0.7449 (pp20) REVERT: D 691 MET cc_start: 0.8819 (tmm) cc_final: 0.8608 (tmm) REVERT: D 705 MET cc_start: 0.8841 (mtp) cc_final: 0.8629 (mtp) outliers start: 56 outliers final: 23 residues processed: 376 average time/residue: 0.3674 time to fit residues: 232.4455 Evaluate side-chains 286 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 256 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 161 LEU 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 322 LEU 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 154 SER Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 672 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 309 optimal weight: 2.9990 chunk 297 optimal weight: 1.9990 chunk 192 optimal weight: 7.9990 chunk 255 optimal weight: 0.7980 chunk 279 optimal weight: 0.9980 chunk 222 optimal weight: 5.9990 chunk 285 optimal weight: 7.9990 chunk 310 optimal weight: 2.9990 chunk 276 optimal weight: 6.9990 chunk 282 optimal weight: 0.0970 chunk 252 optimal weight: 4.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 ASN 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 286 ASN C 508 HIS C 610 ASN ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.085095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.066767 restraints weight = 125547.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.066783 restraints weight = 80605.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.067742 restraints weight = 62197.130| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27480 Z= 0.156 Angle : 0.892 22.239 37352 Z= 0.396 Chirality : 0.052 0.549 4314 Planarity : 0.005 0.119 4618 Dihedral : 15.724 140.452 4834 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.20 % Favored : 92.52 % Rotamer: Outliers : 2.82 % Allowed : 11.13 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.14), residues: 3264 helix: -0.36 (0.13), residues: 1458 sheet: -2.29 (0.23), residues: 462 loop : -2.81 (0.15), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 706 HIS 0.007 0.001 HIS C 225 PHE 0.018 0.002 PHE C 693 TYR 0.050 0.001 TYR D 478 ARG 0.007 0.000 ARG A 712 Details of bonding type rmsd link_NAG-ASN : bond 0.00945 ( 32) link_NAG-ASN : angle 5.41871 ( 96) link_BETA1-4 : bond 0.02281 ( 26) link_BETA1-4 : angle 6.26705 ( 78) hydrogen bonds : bond 0.04404 ( 1024) hydrogen bonds : angle 4.71135 ( 2934) SS BOND : bond 0.01126 ( 10) SS BOND : angle 1.33030 ( 20) link_BETA1-3 : bond 0.01112 ( 4) link_BETA1-3 : angle 4.32017 ( 12) covalent geometry : bond 0.00320 (27408) covalent geometry : angle 0.79632 (37146) *********************** 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 375 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 295 time to evaluate : 2.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.8724 (t80) cc_final: 0.8240 (t80) REVERT: A 99 LEU cc_start: 0.8324 (mm) cc_final: 0.7935 (pp) REVERT: A 245 MET cc_start: 0.7479 (ttm) cc_final: 0.7159 (ttt) REVERT: A 450 ASP cc_start: 0.7129 (p0) cc_final: 0.6905 (t70) REVERT: A 565 MET cc_start: 0.8698 (mmt) cc_final: 0.7891 (mpp) REVERT: A 571 CYS cc_start: 0.9178 (m) cc_final: 0.8940 (t) REVERT: A 621 GLN cc_start: 0.8857 (mm-40) cc_final: 0.8647 (tp40) REVERT: A 649 SER cc_start: 0.9227 (m) cc_final: 0.8761 (t) REVERT: A 650 SER cc_start: 0.8987 (m) cc_final: 0.8705 (t) REVERT: A 691 MET cc_start: 0.8471 (ptp) cc_final: 0.8175 (ptp) REVERT: A 705 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8344 (mmm) REVERT: B 90 GLU cc_start: 0.8412 (tt0) cc_final: 0.7931 (tt0) REVERT: B 130 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8655 (tp) REVERT: B 223 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6288 (mt-10) REVERT: B 247 MET cc_start: 0.7516 (mtt) cc_final: 0.7015 (mmt) REVERT: B 322 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9264 (mm) REVERT: B 323 MET cc_start: 0.9002 (tpp) cc_final: 0.8458 (ttm) REVERT: B 536 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8442 (pt) REVERT: B 565 MET cc_start: 0.8132 (mmt) cc_final: 0.7878 (mmp) REVERT: B 627 MET cc_start: 0.8539 (mmm) cc_final: 0.8271 (mtt) REVERT: B 633 THR cc_start: 0.8657 (p) cc_final: 0.8369 (t) REVERT: B 665 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7139 (tm-30) REVERT: B 705 MET cc_start: 0.9102 (mtp) cc_final: 0.8847 (ptp) REVERT: C 57 PHE cc_start: 0.8760 (t80) cc_final: 0.8214 (t80) REVERT: C 450 ASP cc_start: 0.6919 (p0) cc_final: 0.6615 (t70) REVERT: C 565 MET cc_start: 0.8703 (mmt) cc_final: 0.7904 (mpp) REVERT: C 571 CYS cc_start: 0.9230 (m) cc_final: 0.8930 (t) REVERT: C 649 SER cc_start: 0.9273 (m) cc_final: 0.8921 (t) REVERT: C 740 THR cc_start: 0.9273 (p) cc_final: 0.8935 (t) REVERT: C 786 GLN cc_start: 0.8448 (tp40) cc_final: 0.8060 (tm-30) REVERT: D 90 GLU cc_start: 0.8529 (tt0) cc_final: 0.8089 (tt0) REVERT: D 152 ASP cc_start: 0.7802 (t0) cc_final: 0.7412 (t0) REVERT: D 223 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6176 (mt-10) REVERT: D 248 MET cc_start: 0.8106 (mmm) cc_final: 0.7885 (mmm) REVERT: D 322 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9171 (mm) REVERT: D 323 MET cc_start: 0.9002 (tpp) cc_final: 0.8545 (ttm) REVERT: D 536 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8500 (pt) REVERT: D 565 MET cc_start: 0.8061 (mmt) cc_final: 0.7832 (mmp) REVERT: D 627 MET cc_start: 0.8864 (mmm) cc_final: 0.8196 (mtt) REVERT: D 633 THR cc_start: 0.8799 (p) cc_final: 0.8405 (t) REVERT: D 665 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7328 (tm-30) REVERT: D 694 PHE cc_start: 0.8543 (m-80) cc_final: 0.8210 (m-80) REVERT: D 705 MET cc_start: 0.9057 (mtp) cc_final: 0.8551 (mtp) REVERT: D 794 MET cc_start: 0.9405 (mtt) cc_final: 0.9138 (mtp) outliers start: 80 outliers final: 33 residues processed: 348 average time/residue: 0.3284 time to fit residues: 193.5250 Evaluate side-chains 286 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 247 time to evaluate : 2.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 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 705 MET Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 322 LEU 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 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 636 VAL Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 650 SER 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 114 optimal weight: 6.9990 chunk 272 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 235 optimal weight: 9.9990 chunk 309 optimal weight: 0.0050 chunk 220 optimal weight: 6.9990 chunk 194 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 157 optimal weight: 0.6980 chunk 275 optimal weight: 0.7980 overall best weight: 1.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.084942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.066208 restraints weight = 127101.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.066656 restraints weight = 80667.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.067429 restraints weight = 63539.297| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3698 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= 0.148 Angle : 0.863 21.590 37352 Z= 0.381 Chirality : 0.051 0.519 4314 Planarity : 0.004 0.058 4618 Dihedral : 13.740 140.305 4834 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.95 % Favored : 92.74 % Rotamer: Outliers : 2.64 % Allowed : 12.32 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.14), residues: 3264 helix: 0.11 (0.13), residues: 1460 sheet: -2.02 (0.24), residues: 450 loop : -2.60 (0.15), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 169 HIS 0.006 0.001 HIS A 225 PHE 0.017 0.001 PHE B 579 TYR 0.042 0.001 TYR B 478 ARG 0.008 0.000 ARG C 712 Details of bonding type rmsd link_NAG-ASN : bond 0.00977 ( 32) link_NAG-ASN : angle 5.42818 ( 96) link_BETA1-4 : bond 0.02099 ( 26) link_BETA1-4 : angle 6.12158 ( 78) hydrogen bonds : bond 0.03959 ( 1024) hydrogen bonds : angle 4.51153 ( 2934) SS BOND : bond 0.00431 ( 10) SS BOND : angle 1.28073 ( 20) link_BETA1-3 : bond 0.01201 ( 4) link_BETA1-3 : angle 3.95153 ( 12) covalent geometry : bond 0.00315 (27408) covalent geometry : angle 0.76717 (37146) *********************** 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 348 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 273 time to evaluate : 2.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.8760 (t80) cc_final: 0.8276 (t80) REVERT: A 234 MET cc_start: 0.8812 (mpp) cc_final: 0.8239 (mpp) REVERT: A 245 MET cc_start: 0.7583 (ttm) cc_final: 0.7337 (ttp) REVERT: A 450 ASP cc_start: 0.7070 (p0) cc_final: 0.6857 (t70) REVERT: A 534 MET cc_start: 0.8576 (tpp) cc_final: 0.8147 (ttm) REVERT: A 565 MET cc_start: 0.8710 (mmt) cc_final: 0.7988 (mpp) REVERT: A 621 GLN cc_start: 0.8875 (mm-40) cc_final: 0.8652 (tp40) REVERT: A 649 SER cc_start: 0.9228 (m) cc_final: 0.8787 (t) REVERT: A 650 SER cc_start: 0.8973 (m) cc_final: 0.8663 (t) REVERT: A 691 MET cc_start: 0.8426 (ptp) cc_final: 0.8183 (ptp) REVERT: A 740 THR cc_start: 0.9300 (p) cc_final: 0.8921 (t) REVERT: B 90 GLU cc_start: 0.8407 (tt0) cc_final: 0.7953 (tt0) REVERT: B 130 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8701 (tp) REVERT: B 223 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6768 (mt-10) REVERT: B 247 MET cc_start: 0.7523 (mtt) cc_final: 0.6893 (mmt) REVERT: B 322 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9246 (mm) REVERT: B 536 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8493 (pt) REVERT: B 565 MET cc_start: 0.8134 (mmt) cc_final: 0.7901 (mmp) REVERT: B 633 THR cc_start: 0.8659 (p) cc_final: 0.8367 (t) REVERT: B 770 MET cc_start: 0.8780 (tpt) cc_final: 0.8525 (mmt) REVERT: C 57 PHE cc_start: 0.8747 (t80) cc_final: 0.8268 (t80) REVERT: C 147 VAL cc_start: 0.7894 (OUTLIER) cc_final: 0.7672 (m) REVERT: C 347 CYS cc_start: 0.5925 (OUTLIER) cc_final: 0.5378 (p) REVERT: C 450 ASP cc_start: 0.6874 (p0) cc_final: 0.6593 (t70) REVERT: C 534 MET cc_start: 0.8485 (tpp) cc_final: 0.8083 (ttm) REVERT: C 565 MET cc_start: 0.8699 (mmt) cc_final: 0.7893 (mpp) REVERT: C 571 CYS cc_start: 0.9152 (m) cc_final: 0.8936 (t) REVERT: C 649 SER cc_start: 0.9199 (m) cc_final: 0.8862 (t) REVERT: C 705 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8777 (mmm) REVERT: C 740 THR cc_start: 0.9283 (p) cc_final: 0.8916 (t) REVERT: C 786 GLN cc_start: 0.8399 (tp40) cc_final: 0.8148 (tm-30) REVERT: D 50 MET cc_start: 0.4601 (mtm) cc_final: 0.4343 (mtp) REVERT: D 152 ASP cc_start: 0.7773 (t0) cc_final: 0.7369 (t0) REVERT: D 247 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.6708 (mmt) REVERT: D 248 MET cc_start: 0.8159 (mmm) cc_final: 0.7948 (mmm) REVERT: D 322 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9179 (mm) REVERT: D 501 MET cc_start: 0.8923 (mmm) cc_final: 0.8652 (mmm) REVERT: D 536 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8534 (pt) REVERT: D 538 ILE cc_start: 0.9521 (mt) cc_final: 0.9165 (mt) REVERT: D 565 MET cc_start: 0.7982 (mmt) cc_final: 0.7762 (mmp) REVERT: D 627 MET cc_start: 0.8813 (mmm) cc_final: 0.8216 (mtt) REVERT: D 633 THR cc_start: 0.8836 (p) cc_final: 0.8442 (t) REVERT: D 665 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7298 (tm-30) REVERT: D 673 ASP cc_start: 0.8943 (t0) cc_final: 0.8673 (t0) REVERT: D 694 PHE cc_start: 0.8493 (m-80) cc_final: 0.8191 (m-80) REVERT: D 705 MET cc_start: 0.9070 (mtp) cc_final: 0.8572 (mtp) outliers start: 75 outliers final: 42 residues processed: 325 average time/residue: 0.3094 time to fit residues: 173.0297 Evaluate side-chains 294 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 243 time to evaluate : 2.748 ------------------------------------------------------------------------------- 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 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 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 274 VAL Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 322 LEU 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 147 VAL 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 635 ILE Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 650 SER Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 779 THR 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 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 430 ASN Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 635 ILE 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 74 optimal weight: 0.4980 chunk 45 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 chunk 318 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 279 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 192 optimal weight: 0.7980 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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** C 610 ASN ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.083642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.064793 restraints weight = 127129.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.065508 restraints weight = 78251.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.066143 restraints weight = 62780.808| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4015 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= 0.178 Angle : 0.853 21.016 37352 Z= 0.381 Chirality : 0.051 0.502 4314 Planarity : 0.004 0.071 4618 Dihedral : 12.527 140.836 4834 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.38 % Favored : 92.37 % Rotamer: Outliers : 3.03 % Allowed : 12.57 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.15), residues: 3264 helix: 0.39 (0.14), residues: 1458 sheet: -1.98 (0.23), residues: 466 loop : -2.41 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 169 HIS 0.006 0.001 HIS A 225 PHE 0.016 0.002 PHE D 579 TYR 0.036 0.001 TYR B 478 ARG 0.004 0.000 ARG C 712 Details of bonding type rmsd link_NAG-ASN : bond 0.00839 ( 32) link_NAG-ASN : angle 5.20690 ( 96) link_BETA1-4 : bond 0.01933 ( 26) link_BETA1-4 : angle 6.08021 ( 78) hydrogen bonds : bond 0.03834 ( 1024) hydrogen bonds : angle 4.51004 ( 2934) SS BOND : bond 0.00527 ( 10) SS BOND : angle 1.81905 ( 20) link_BETA1-3 : bond 0.01027 ( 4) link_BETA1-3 : angle 3.59466 ( 12) covalent geometry : bond 0.00383 (27408) covalent geometry : angle 0.76046 (37146) *********************** 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 338 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 252 time to evaluate : 3.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.8797 (t80) cc_final: 0.8304 (t80) REVERT: A 234 MET cc_start: 0.8843 (mpp) cc_final: 0.8261 (mpp) REVERT: A 245 MET cc_start: 0.7744 (ttm) cc_final: 0.7489 (ttp) REVERT: A 450 ASP cc_start: 0.6985 (p0) cc_final: 0.6767 (t70) REVERT: A 565 MET cc_start: 0.8706 (mmt) cc_final: 0.7979 (mpp) REVERT: A 649 SER cc_start: 0.9227 (m) cc_final: 0.8781 (t) REVERT: A 650 SER cc_start: 0.9044 (m) cc_final: 0.8736 (t) REVERT: B 90 GLU cc_start: 0.8566 (tt0) cc_final: 0.8104 (tt0) REVERT: B 130 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8771 (tp) REVERT: B 247 MET cc_start: 0.7360 (mtt) cc_final: 0.6821 (mmt) REVERT: B 322 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9216 (mm) REVERT: B 323 MET cc_start: 0.8942 (tpp) cc_final: 0.8621 (ttm) REVERT: B 536 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8646 (pt) REVERT: B 565 MET cc_start: 0.8106 (mmt) cc_final: 0.7872 (mmp) REVERT: B 633 THR cc_start: 0.8648 (p) cc_final: 0.8324 (t) REVERT: B 705 MET cc_start: 0.9065 (mtp) cc_final: 0.8857 (ptp) REVERT: C 57 PHE cc_start: 0.8809 (t80) cc_final: 0.8325 (t80) REVERT: C 245 MET cc_start: 0.8569 (ppp) cc_final: 0.7985 (ppp) REVERT: C 347 CYS cc_start: 0.5970 (OUTLIER) cc_final: 0.5529 (p) REVERT: C 450 ASP cc_start: 0.6848 (p0) cc_final: 0.6641 (t70) REVERT: C 565 MET cc_start: 0.8750 (mmt) cc_final: 0.7989 (mpp) REVERT: C 571 CYS cc_start: 0.9109 (m) cc_final: 0.8903 (t) REVERT: C 649 SER cc_start: 0.9244 (m) cc_final: 0.8958 (t) REVERT: C 677 GLN cc_start: 0.8210 (mp10) cc_final: 0.7925 (mp10) REVERT: C 705 MET cc_start: 0.8956 (mmm) cc_final: 0.8561 (mmm) REVERT: C 709 MET cc_start: 0.9026 (mtm) cc_final: 0.8378 (mtt) REVERT: C 738 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8736 (pm20) REVERT: C 740 THR cc_start: 0.9309 (p) cc_final: 0.9004 (t) REVERT: C 786 GLN cc_start: 0.8434 (tp40) cc_final: 0.8143 (tm-30) REVERT: D 90 GLU cc_start: 0.8562 (tt0) cc_final: 0.8087 (tt0) REVERT: D 152 ASP cc_start: 0.7829 (t0) cc_final: 0.7427 (t0) REVERT: D 228 PHE cc_start: 0.9285 (OUTLIER) cc_final: 0.9049 (m-10) REVERT: D 247 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.6733 (mmt) REVERT: D 322 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9168 (mm) REVERT: D 323 MET cc_start: 0.8950 (tpp) cc_final: 0.8461 (ttm) REVERT: D 501 MET cc_start: 0.9002 (mmm) cc_final: 0.8236 (mmm) REVERT: D 536 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8658 (pt) REVERT: D 538 ILE cc_start: 0.9519 (mt) cc_final: 0.9180 (mt) REVERT: D 565 MET cc_start: 0.7986 (mmt) cc_final: 0.7761 (mmp) REVERT: D 627 MET cc_start: 0.8849 (mmm) cc_final: 0.8222 (mtt) REVERT: D 633 THR cc_start: 0.8834 (p) cc_final: 0.8414 (t) REVERT: D 665 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7274 (pp20) REVERT: D 673 ASP cc_start: 0.8972 (t0) cc_final: 0.8703 (t0) outliers start: 86 outliers final: 49 residues processed: 312 average time/residue: 0.3140 time to fit residues: 168.0634 Evaluate side-chains 290 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 232 time to evaluate : 3.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 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 444 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 652 THR 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 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 130 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 322 LEU 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 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 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 540 ILE Chi-restraints excluded: chain C residue 572 LEU 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 650 SER Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 738 GLU Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 820 ILE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 168 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 250 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 207 optimal weight: 0.0970 chunk 92 optimal weight: 8.9990 chunk 197 optimal weight: 5.9990 chunk 140 optimal weight: 0.7980 chunk 24 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 overall best weight: 1.7582 ------------------------------------------------------------------------------- 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** C 288 GLN ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 754 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.083951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.065148 restraints weight = 126988.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.065803 restraints weight = 78955.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.066512 restraints weight = 62511.339| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27480 Z= 0.148 Angle : 0.828 20.906 37352 Z= 0.369 Chirality : 0.050 0.490 4314 Planarity : 0.004 0.066 4618 Dihedral : 11.739 140.599 4834 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.92 % Favored : 92.83 % Rotamer: Outliers : 2.85 % Allowed : 12.89 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.15), residues: 3264 helix: 0.65 (0.14), residues: 1452 sheet: -1.76 (0.24), residues: 454 loop : -2.31 (0.16), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 169 HIS 0.007 0.001 HIS A 225 PHE 0.015 0.001 PHE D 708 TYR 0.040 0.001 TYR B 478 ARG 0.003 0.000 ARG D 58 Details of bonding type rmsd link_NAG-ASN : bond 0.00846 ( 32) link_NAG-ASN : angle 4.95638 ( 96) link_BETA1-4 : bond 0.01806 ( 26) link_BETA1-4 : angle 5.92745 ( 78) hydrogen bonds : bond 0.03582 ( 1024) hydrogen bonds : angle 4.36772 ( 2934) SS BOND : bond 0.00884 ( 10) SS BOND : angle 1.49542 ( 20) link_BETA1-3 : bond 0.01059 ( 4) link_BETA1-3 : angle 3.20395 ( 12) covalent geometry : bond 0.00318 (27408) covalent geometry : angle 0.73957 (37146) *********************** 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 342 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 261 time to evaluate : 2.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9050 (mm) REVERT: A 57 PHE cc_start: 0.8804 (t80) cc_final: 0.8339 (t80) REVERT: A 219 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.8520 (ptpt) REVERT: A 234 MET cc_start: 0.8872 (mpp) cc_final: 0.8348 (mpp) REVERT: A 277 THR cc_start: 0.9118 (OUTLIER) cc_final: 0.8858 (p) REVERT: A 347 CYS cc_start: 0.6217 (OUTLIER) cc_final: 0.5805 (p) REVERT: A 501 MET cc_start: 0.8589 (mmm) cc_final: 0.8304 (tpt) REVERT: A 534 MET cc_start: 0.8355 (tpp) cc_final: 0.8016 (ttm) REVERT: A 565 MET cc_start: 0.8710 (mmt) cc_final: 0.7963 (mpp) REVERT: A 649 SER cc_start: 0.9176 (m) cc_final: 0.8848 (t) REVERT: A 650 SER cc_start: 0.9002 (m) cc_final: 0.8728 (t) REVERT: A 691 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8311 (ptp) REVERT: A 705 MET cc_start: 0.9035 (mmm) cc_final: 0.8463 (mmm) REVERT: A 740 THR cc_start: 0.9438 (p) cc_final: 0.9061 (t) REVERT: B 90 GLU cc_start: 0.8601 (tt0) cc_final: 0.8176 (tt0) REVERT: B 130 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8744 (tp) REVERT: B 228 PHE cc_start: 0.9234 (OUTLIER) cc_final: 0.8893 (m-10) REVERT: B 247 MET cc_start: 0.7322 (mtt) cc_final: 0.6793 (mmt) REVERT: B 322 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9195 (mm) REVERT: B 323 MET cc_start: 0.9017 (tpp) cc_final: 0.8668 (ttm) REVERT: B 536 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8554 (pt) REVERT: B 565 MET cc_start: 0.8099 (mmt) cc_final: 0.7866 (mmp) REVERT: B 633 THR cc_start: 0.8658 (p) cc_final: 0.8315 (t) REVERT: B 665 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7152 (pp20) REVERT: C 55 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9012 (mm) REVERT: C 57 PHE cc_start: 0.8829 (t80) cc_final: 0.8411 (t80) REVERT: C 245 MET cc_start: 0.8422 (ppp) cc_final: 0.7752 (ppp) REVERT: C 247 MET cc_start: 0.8262 (tpp) cc_final: 0.7502 (mpp) REVERT: C 323 MET cc_start: 0.8317 (tpp) cc_final: 0.7888 (mtt) REVERT: C 347 CYS cc_start: 0.6046 (OUTLIER) cc_final: 0.5548 (p) REVERT: C 534 MET cc_start: 0.8246 (tpp) cc_final: 0.8033 (ttm) REVERT: C 565 MET cc_start: 0.8685 (mmt) cc_final: 0.7943 (mpp) REVERT: C 649 SER cc_start: 0.9190 (m) cc_final: 0.8862 (t) REVERT: C 705 MET cc_start: 0.9150 (mmm) cc_final: 0.8825 (mmm) REVERT: C 709 MET cc_start: 0.8986 (mtm) cc_final: 0.8477 (mtt) REVERT: C 738 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8754 (pm20) REVERT: C 740 THR cc_start: 0.9376 (p) cc_final: 0.8989 (t) REVERT: D 90 GLU cc_start: 0.8587 (tt0) cc_final: 0.8130 (tt0) REVERT: D 152 ASP cc_start: 0.7695 (t0) cc_final: 0.7413 (t0) REVERT: D 228 PHE cc_start: 0.9259 (OUTLIER) cc_final: 0.8840 (m-10) REVERT: D 247 MET cc_start: 0.7269 (OUTLIER) cc_final: 0.6703 (mmt) REVERT: D 322 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9180 (mm) REVERT: D 323 MET cc_start: 0.8980 (tpp) cc_final: 0.8742 (ttm) REVERT: D 360 MET cc_start: 0.7847 (mmm) cc_final: 0.7639 (mmm) REVERT: D 501 MET cc_start: 0.9019 (mmm) cc_final: 0.8444 (mmm) REVERT: D 536 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8569 (pt) REVERT: D 538 ILE cc_start: 0.9516 (mt) cc_final: 0.9172 (mt) REVERT: D 627 MET cc_start: 0.8748 (mmm) cc_final: 0.8260 (mtt) REVERT: D 633 THR cc_start: 0.8814 (p) cc_final: 0.8394 (t) REVERT: D 673 ASP cc_start: 0.8959 (t0) cc_final: 0.8651 (t0) REVERT: D 705 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8503 (mpp) outliers start: 81 outliers final: 47 residues processed: 318 average time/residue: 0.3203 time to fit residues: 173.0372 Evaluate side-chains 292 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 228 time to evaluate : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 SER 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 277 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 691 MET 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 130 ILE Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 322 LEU 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 658 PHE Chi-restraints excluded: chain B residue 672 ASP 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 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 540 ILE Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 650 SER Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 738 GLU Chi-restraints excluded: chain C residue 820 ILE 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 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 Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 705 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 45 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 249 optimal weight: 4.9990 chunk 195 optimal weight: 20.0000 chunk 259 optimal weight: 0.9990 chunk 108 optimal weight: 0.0040 chunk 63 optimal weight: 0.4980 chunk 49 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 313 optimal weight: 2.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 ASN ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 ASN ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.084776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.066331 restraints weight = 125522.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.068477 restraints weight = 75178.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.068845 restraints weight = 54525.017| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27480 Z= 0.124 Angle : 0.819 20.577 37352 Z= 0.361 Chirality : 0.049 0.476 4314 Planarity : 0.004 0.058 4618 Dihedral : 11.057 140.633 4834 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.56 % Favored : 93.26 % Rotamer: Outliers : 2.61 % Allowed : 13.80 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.15), residues: 3264 helix: 0.85 (0.14), residues: 1444 sheet: -1.74 (0.25), residues: 456 loop : -2.05 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.001 TRP A 169 HIS 0.010 0.001 HIS A 225 PHE 0.013 0.001 PHE D 579 TYR 0.038 0.001 TYR B 478 ARG 0.003 0.000 ARG B 468 Details of bonding type rmsd link_NAG-ASN : bond 0.00871 ( 32) link_NAG-ASN : angle 4.83826 ( 96) link_BETA1-4 : bond 0.01771 ( 26) link_BETA1-4 : angle 5.74393 ( 78) hydrogen bonds : bond 0.03385 ( 1024) hydrogen bonds : angle 4.24320 ( 2934) SS BOND : bond 0.00408 ( 10) SS BOND : angle 1.50176 ( 20) link_BETA1-3 : bond 0.01004 ( 4) link_BETA1-3 : angle 2.87991 ( 12) covalent geometry : bond 0.00265 (27408) covalent geometry : angle 0.73525 (37146) *********************** 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 331 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 257 time to evaluate : 2.964 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: 0.8779 (t80) cc_final: 0.8286 (t80) REVERT: A 234 MET cc_start: 0.8848 (mpp) cc_final: 0.8345 (mpp) REVERT: A 277 THR cc_start: 0.9039 (OUTLIER) cc_final: 0.8767 (p) REVERT: A 347 CYS cc_start: 0.6143 (OUTLIER) cc_final: 0.5672 (p) REVERT: A 501 MET cc_start: 0.8556 (mmm) cc_final: 0.8128 (tpt) REVERT: A 534 MET cc_start: 0.8468 (tpp) cc_final: 0.8063 (ttm) REVERT: A 565 MET cc_start: 0.8617 (mmt) cc_final: 0.7893 (mpp) REVERT: A 649 SER cc_start: 0.9195 (m) cc_final: 0.8971 (t) REVERT: A 650 SER cc_start: 0.9017 (m) cc_final: 0.8713 (t) REVERT: A 740 THR cc_start: 0.9388 (p) cc_final: 0.9052 (t) REVERT: B 90 GLU cc_start: 0.8505 (tt0) cc_final: 0.8044 (tt0) REVERT: B 130 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8633 (tp) REVERT: B 152 ASP cc_start: 0.7571 (t0) cc_final: 0.7263 (t0) REVERT: B 157 SER cc_start: 0.8971 (m) cc_final: 0.8587 (t) REVERT: B 223 GLU cc_start: 0.7080 (mt-10) cc_final: 0.6473 (mt-10) REVERT: B 247 MET cc_start: 0.7265 (OUTLIER) cc_final: 0.6320 (mmt) REVERT: B 248 MET cc_start: 0.8132 (mmm) cc_final: 0.7676 (mmm) REVERT: B 322 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9118 (mm) REVERT: B 323 MET cc_start: 0.8912 (tpp) cc_final: 0.8626 (ttm) REVERT: B 501 MET cc_start: 0.8494 (mmm) cc_final: 0.7865 (mmm) REVERT: B 536 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8496 (pt) REVERT: B 629 LYS cc_start: 0.9281 (mmmt) cc_final: 0.8891 (ptmt) REVERT: B 633 THR cc_start: 0.8604 (p) cc_final: 0.8260 (t) REVERT: B 665 GLU cc_start: 0.7458 (mt-10) cc_final: 0.7195 (pp20) REVERT: B 692 THR cc_start: 0.8962 (p) cc_final: 0.8759 (t) REVERT: C 57 PHE cc_start: 0.8778 (t80) cc_final: 0.8293 (t80) REVERT: C 245 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7661 (ppp) REVERT: C 347 CYS cc_start: 0.5883 (OUTLIER) cc_final: 0.5414 (p) REVERT: C 501 MET cc_start: 0.8552 (mmm) cc_final: 0.8176 (tpt) REVERT: C 534 MET cc_start: 0.8415 (tpp) cc_final: 0.8162 (ttm) REVERT: C 565 MET cc_start: 0.8649 (mmt) cc_final: 0.7880 (mpp) REVERT: C 649 SER cc_start: 0.9198 (m) cc_final: 0.8923 (t) REVERT: C 691 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8068 (mpp) REVERT: C 738 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8523 (pm20) REVERT: C 740 THR cc_start: 0.9371 (p) cc_final: 0.9051 (t) REVERT: D 90 GLU cc_start: 0.8536 (tt0) cc_final: 0.8102 (tt0) REVERT: D 228 PHE cc_start: 0.9249 (OUTLIER) cc_final: 0.8827 (m-10) REVERT: D 247 MET cc_start: 0.6841 (OUTLIER) cc_final: 0.6622 (mmt) REVERT: D 322 LEU cc_start: 0.9384 (mm) cc_final: 0.9112 (mm) REVERT: D 360 MET cc_start: 0.7868 (mmm) cc_final: 0.7662 (mmm) REVERT: D 536 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8583 (pt) REVERT: D 538 ILE cc_start: 0.9460 (mt) cc_final: 0.9094 (mt) REVERT: D 633 THR cc_start: 0.8778 (p) cc_final: 0.8348 (t) REVERT: D 665 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7207 (pp20) REVERT: D 673 ASP cc_start: 0.8938 (t0) cc_final: 0.8646 (t0) outliers start: 74 outliers final: 44 residues processed: 310 average time/residue: 0.3292 time to fit residues: 175.1735 Evaluate side-chains 293 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 236 time to evaluate : 2.903 ------------------------------------------------------------------------------- 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 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 277 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 130 ILE 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 322 LEU Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 437 THR 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 658 PHE Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 245 MET 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 505 LEU Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 650 SER Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 738 GLU Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 466 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 645 LEU Chi-restraints excluded: chain D residue 658 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 23 optimal weight: 0.0970 chunk 240 optimal weight: 0.0670 chunk 138 optimal weight: 10.0000 chunk 318 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 chunk 226 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 chunk 299 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 202 optimal weight: 10.0000 overall best weight: 2.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 754 GLN ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.083732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.064918 restraints weight = 128338.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.065671 restraints weight = 80459.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.066258 restraints weight = 63680.674| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27480 Z= 0.159 Angle : 0.840 20.349 37352 Z= 0.374 Chirality : 0.050 0.476 4314 Planarity : 0.004 0.061 4618 Dihedral : 10.657 140.816 4834 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.11 % Favored : 92.65 % Rotamer: Outliers : 2.75 % Allowed : 14.08 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.15), residues: 3264 helix: 1.00 (0.14), residues: 1430 sheet: -1.72 (0.25), residues: 456 loop : -2.05 (0.16), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP A 169 HIS 0.005 0.001 HIS D 253 PHE 0.022 0.001 PHE C 279 TYR 0.038 0.001 TYR B 478 ARG 0.005 0.000 ARG A 634 Details of bonding type rmsd link_NAG-ASN : bond 0.00814 ( 32) link_NAG-ASN : angle 4.81191 ( 96) link_BETA1-4 : bond 0.01702 ( 26) link_BETA1-4 : angle 5.73047 ( 78) hydrogen bonds : bond 0.03433 ( 1024) hydrogen bonds : angle 4.29311 ( 2934) SS BOND : bond 0.00441 ( 10) SS BOND : angle 1.28397 ( 20) link_BETA1-3 : bond 0.00905 ( 4) link_BETA1-3 : angle 2.64905 ( 12) covalent geometry : bond 0.00348 (27408) covalent geometry : angle 0.75948 (37146) *********************** 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 317 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 239 time to evaluate : 2.734 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: 0.8807 (t80) cc_final: 0.8369 (t80) REVERT: A 234 MET cc_start: 0.8863 (mpp) cc_final: 0.8356 (mpp) REVERT: A 247 MET cc_start: 0.8038 (mmp) cc_final: 0.7143 (mmp) REVERT: A 277 THR cc_start: 0.9076 (OUTLIER) cc_final: 0.8740 (p) REVERT: A 347 CYS cc_start: 0.6025 (OUTLIER) cc_final: 0.5655 (p) REVERT: A 501 MET cc_start: 0.8535 (mmm) cc_final: 0.8117 (tpt) REVERT: A 534 MET cc_start: 0.8512 (tpp) cc_final: 0.8112 (ttm) REVERT: A 565 MET cc_start: 0.8669 (mmt) cc_final: 0.8072 (mpp) REVERT: A 649 SER cc_start: 0.9196 (m) cc_final: 0.8831 (t) REVERT: A 650 SER cc_start: 0.9035 (m) cc_final: 0.8698 (t) REVERT: A 740 THR cc_start: 0.9417 (p) cc_final: 0.9089 (t) REVERT: B 50 MET cc_start: 0.3607 (tmm) cc_final: 0.3386 (tmm) REVERT: B 90 GLU cc_start: 0.8596 (tt0) cc_final: 0.8149 (tt0) REVERT: B 130 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8700 (tp) REVERT: B 152 ASP cc_start: 0.7702 (t0) cc_final: 0.7319 (t0) REVERT: B 223 GLU cc_start: 0.7039 (mt-10) cc_final: 0.6591 (mt-10) REVERT: B 228 PHE cc_start: 0.9237 (OUTLIER) cc_final: 0.8868 (m-10) REVERT: B 247 MET cc_start: 0.7367 (OUTLIER) cc_final: 0.6890 (mmt) REVERT: B 322 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9175 (mm) REVERT: B 340 MET cc_start: 0.8305 (tpp) cc_final: 0.8019 (mmm) REVERT: B 536 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8575 (pt) REVERT: B 633 THR cc_start: 0.8689 (p) cc_final: 0.8329 (t) REVERT: B 665 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7160 (pp20) REVERT: B 737 MET cc_start: 0.7374 (tmm) cc_final: 0.7117 (tmm) REVERT: C 57 PHE cc_start: 0.8840 (t80) cc_final: 0.8414 (t80) REVERT: C 245 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7678 (ppp) REVERT: C 347 CYS cc_start: 0.5927 (OUTLIER) cc_final: 0.5526 (p) REVERT: C 501 MET cc_start: 0.8523 (mmm) cc_final: 0.8079 (tpt) REVERT: C 534 MET cc_start: 0.8438 (tpp) cc_final: 0.8131 (ttm) REVERT: C 565 MET cc_start: 0.8694 (mmt) cc_final: 0.8091 (mpp) REVERT: C 649 SER cc_start: 0.9156 (m) cc_final: 0.8820 (t) REVERT: C 691 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8080 (mpp) REVERT: C 705 MET cc_start: 0.8903 (mmm) cc_final: 0.8253 (mmm) REVERT: C 709 MET cc_start: 0.8996 (mtm) cc_final: 0.8477 (mtt) REVERT: C 737 MET cc_start: 0.8454 (ttp) cc_final: 0.7590 (ppp) REVERT: C 738 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8374 (pm20) REVERT: C 740 THR cc_start: 0.9354 (p) cc_final: 0.8938 (t) REVERT: D 90 GLU cc_start: 0.8564 (tt0) cc_final: 0.8113 (tt0) REVERT: D 152 ASP cc_start: 0.7892 (t0) cc_final: 0.7689 (t0) REVERT: D 228 PHE cc_start: 0.9258 (OUTLIER) cc_final: 0.8852 (m-10) REVERT: D 247 MET cc_start: 0.7319 (OUTLIER) cc_final: 0.6826 (mmt) REVERT: D 322 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9126 (mm) REVERT: D 360 MET cc_start: 0.7911 (mmm) cc_final: 0.7705 (mmm) REVERT: D 536 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8656 (pt) REVERT: D 538 ILE cc_start: 0.9493 (mt) cc_final: 0.9124 (mt) REVERT: D 619 LEU cc_start: 0.8828 (tt) cc_final: 0.8525 (tp) REVERT: D 620 MET cc_start: 0.9160 (mmt) cc_final: 0.8797 (mmp) REVERT: D 633 THR cc_start: 0.8823 (p) cc_final: 0.8381 (t) REVERT: D 665 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7106 (pp20) REVERT: D 673 ASP cc_start: 0.8957 (t0) cc_final: 0.8696 (t0) REVERT: D 705 MET cc_start: 0.9052 (mpp) cc_final: 0.8303 (mpp) outliers start: 78 outliers final: 53 residues processed: 294 average time/residue: 0.3007 time to fit residues: 151.8989 Evaluate side-chains 292 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 224 time to evaluate : 2.721 ------------------------------------------------------------------------------- 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 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 277 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 540 ILE 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 658 PHE 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 130 ILE 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 311 LEU Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 322 LEU 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 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 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 245 MET Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 650 SER Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 738 GLU Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 311 LEU 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 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 149 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 299 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 289 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 223 optimal weight: 3.9990 chunk 160 optimal weight: 0.9990 chunk 179 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 123 ASN ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.083127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.064413 restraints weight = 127983.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.065518 restraints weight = 78663.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.066270 restraints weight = 60707.623| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 27480 Z= 0.167 Angle : 0.846 20.220 37352 Z= 0.378 Chirality : 0.050 0.474 4314 Planarity : 0.004 0.066 4618 Dihedral : 10.335 140.860 4834 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.86 % Favored : 92.89 % Rotamer: Outliers : 2.78 % Allowed : 14.51 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.15), residues: 3264 helix: 1.04 (0.14), residues: 1416 sheet: -1.64 (0.25), residues: 446 loop : -1.97 (0.16), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.002 TRP D 613 HIS 0.006 0.001 HIS D 253 PHE 0.017 0.001 PHE D 708 TYR 0.027 0.001 TYR B 478 ARG 0.006 0.000 ARG C 634 Details of bonding type rmsd link_NAG-ASN : bond 0.00825 ( 32) link_NAG-ASN : angle 4.80849 ( 96) link_BETA1-4 : bond 0.01635 ( 26) link_BETA1-4 : angle 5.71704 ( 78) hydrogen bonds : bond 0.03483 ( 1024) hydrogen bonds : angle 4.32150 ( 2934) SS BOND : bond 0.00367 ( 10) SS BOND : angle 1.36021 ( 20) link_BETA1-3 : bond 0.00789 ( 4) link_BETA1-3 : angle 2.43678 ( 12) covalent geometry : bond 0.00365 (27408) covalent geometry : angle 0.76710 (37146) *********************** 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 312 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 233 time to evaluate : 2.962 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: 0.8795 (t80) cc_final: 0.8353 (t80) REVERT: A 234 MET cc_start: 0.8888 (mpp) cc_final: 0.8360 (mpp) REVERT: A 277 THR cc_start: 0.9152 (OUTLIER) cc_final: 0.8765 (p) REVERT: A 347 CYS cc_start: 0.5931 (OUTLIER) cc_final: 0.5586 (p) REVERT: A 501 MET cc_start: 0.8508 (mmm) cc_final: 0.8073 (tpt) REVERT: A 534 MET cc_start: 0.8529 (tpp) cc_final: 0.8105 (ttm) REVERT: A 565 MET cc_start: 0.8691 (mmt) cc_final: 0.8059 (mpp) REVERT: A 649 SER cc_start: 0.9166 (m) cc_final: 0.8781 (t) REVERT: A 650 SER cc_start: 0.9044 (m) cc_final: 0.8706 (t) REVERT: A 740 THR cc_start: 0.9429 (p) cc_final: 0.9117 (t) REVERT: B 50 MET cc_start: 0.3551 (tmm) cc_final: 0.3293 (tmm) REVERT: B 90 GLU cc_start: 0.8594 (tt0) cc_final: 0.8140 (tt0) REVERT: B 130 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8760 (tp) REVERT: B 152 ASP cc_start: 0.7753 (t0) cc_final: 0.7407 (t0) REVERT: B 223 GLU cc_start: 0.6974 (mt-10) cc_final: 0.6635 (mt-10) REVERT: B 228 PHE cc_start: 0.9257 (OUTLIER) cc_final: 0.8898 (m-10) REVERT: B 322 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9187 (mm) REVERT: B 323 MET cc_start: 0.8972 (tpp) cc_final: 0.8662 (ttt) REVERT: B 536 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8594 (pt) REVERT: B 629 LYS cc_start: 0.8986 (mmtp) cc_final: 0.8772 (ptmt) REVERT: B 633 THR cc_start: 0.8719 (p) cc_final: 0.8382 (t) REVERT: B 665 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7125 (pp20) REVERT: C 57 PHE cc_start: 0.8829 (t80) cc_final: 0.8419 (t80) REVERT: C 245 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7621 (ppp) REVERT: C 347 CYS cc_start: 0.5800 (OUTLIER) cc_final: 0.5440 (p) REVERT: C 501 MET cc_start: 0.8523 (mmm) cc_final: 0.8131 (tpt) REVERT: C 534 MET cc_start: 0.8455 (tpp) cc_final: 0.8102 (ttm) REVERT: C 565 MET cc_start: 0.8643 (mmt) cc_final: 0.8079 (mpp) REVERT: C 621 GLN cc_start: 0.9059 (tp40) cc_final: 0.8849 (tp-100) REVERT: C 649 SER cc_start: 0.9197 (m) cc_final: 0.8889 (t) REVERT: C 691 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8123 (mpp) REVERT: C 709 MET cc_start: 0.8988 (mtm) cc_final: 0.8482 (mtt) REVERT: C 737 MET cc_start: 0.8469 (ttp) cc_final: 0.7619 (ppp) REVERT: C 740 THR cc_start: 0.9368 (p) cc_final: 0.8967 (t) REVERT: D 90 GLU cc_start: 0.8598 (tt0) cc_final: 0.8140 (tt0) REVERT: D 152 ASP cc_start: 0.7878 (t0) cc_final: 0.7616 (t0) REVERT: D 228 PHE cc_start: 0.9277 (OUTLIER) cc_final: 0.8883 (m-10) REVERT: D 247 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.6934 (mmt) REVERT: D 322 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9081 (mm) REVERT: D 536 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8693 (pt) REVERT: D 538 ILE cc_start: 0.9494 (mt) cc_final: 0.9110 (mt) REVERT: D 633 THR cc_start: 0.8819 (p) cc_final: 0.8386 (t) REVERT: D 665 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7163 (pp20) REVERT: D 673 ASP cc_start: 0.8791 (t0) cc_final: 0.8536 (t0) REVERT: D 705 MET cc_start: 0.9105 (mpp) cc_final: 0.8623 (mpp) outliers start: 79 outliers final: 55 residues processed: 290 average time/residue: 0.3152 time to fit residues: 155.7214 Evaluate side-chains 288 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 220 time to evaluate : 2.715 ------------------------------------------------------------------------------- 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 78 TYR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 SER 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 277 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 540 ILE 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 658 PHE 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 130 ILE Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 322 LEU 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 C residue 35 VAL Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 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 658 PHE 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 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 311 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 43 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 264 optimal weight: 7.9990 chunk 254 optimal weight: 0.9980 chunk 322 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 35 optimal weight: 0.0980 chunk 151 optimal weight: 1.9990 chunk 257 optimal weight: 6.9990 chunk 72 optimal weight: 0.0670 overall best weight: 1.0322 ------------------------------------------------------------------------------- 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 ** 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 = 0.3873 r_free = 0.3873 target = 0.084229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.065611 restraints weight = 126105.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.066565 restraints weight = 82563.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.067117 restraints weight = 62011.250| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27480 Z= 0.131 Angle : 0.835 20.065 37352 Z= 0.370 Chirality : 0.049 0.475 4314 Planarity : 0.004 0.065 4618 Dihedral : 9.934 140.718 4834 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.83 % Favored : 92.95 % Rotamer: Outliers : 2.11 % Allowed : 15.14 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.15), residues: 3264 helix: 1.02 (0.14), residues: 1436 sheet: -1.56 (0.25), residues: 436 loop : -1.97 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.109 0.002 TRP D 613 HIS 0.006 0.001 HIS D 253 PHE 0.018 0.001 PHE D 708 TYR 0.027 0.001 TYR B 478 ARG 0.013 0.000 ARG A 634 Details of bonding type rmsd link_NAG-ASN : bond 0.00844 ( 32) link_NAG-ASN : angle 4.73272 ( 96) link_BETA1-4 : bond 0.01524 ( 26) link_BETA1-4 : angle 5.58758 ( 78) hydrogen bonds : bond 0.03437 ( 1024) hydrogen bonds : angle 4.23694 ( 2934) SS BOND : bond 0.00323 ( 10) SS BOND : angle 1.24568 ( 20) link_BETA1-3 : bond 0.00802 ( 4) link_BETA1-3 : angle 2.33555 ( 12) covalent geometry : bond 0.00285 (27408) covalent geometry : angle 0.75867 (37146) ********************** 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 303 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 243 time to evaluate : 2.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.8860 (t80) cc_final: 0.8399 (t80) REVERT: A 234 MET cc_start: 0.8872 (mpp) cc_final: 0.8340 (mpp) REVERT: A 277 THR cc_start: 0.9084 (OUTLIER) cc_final: 0.8658 (p) REVERT: A 279 PHE cc_start: 0.8621 (m-80) cc_final: 0.8366 (m-10) REVERT: A 347 CYS cc_start: 0.6009 (OUTLIER) cc_final: 0.5630 (p) REVERT: A 501 MET cc_start: 0.8518 (mmm) cc_final: 0.8209 (tpt) REVERT: A 534 MET cc_start: 0.8558 (tpp) cc_final: 0.8176 (ttm) REVERT: A 565 MET cc_start: 0.8680 (mmt) cc_final: 0.8072 (mpp) REVERT: A 649 SER cc_start: 0.9223 (m) cc_final: 0.8941 (t) REVERT: A 650 SER cc_start: 0.9090 (m) cc_final: 0.8770 (t) REVERT: A 709 MET cc_start: 0.8861 (mtm) cc_final: 0.8243 (mtt) REVERT: A 737 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7343 (ttp) REVERT: A 740 THR cc_start: 0.9369 (p) cc_final: 0.9046 (t) REVERT: B 50 MET cc_start: 0.3586 (tmm) cc_final: 0.3360 (tmm) REVERT: B 90 GLU cc_start: 0.8586 (tt0) cc_final: 0.8125 (tt0) REVERT: B 152 ASP cc_start: 0.7707 (t0) cc_final: 0.7422 (t0) REVERT: B 157 SER cc_start: 0.9020 (m) cc_final: 0.8634 (t) REVERT: B 223 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6612 (mt-10) REVERT: B 228 PHE cc_start: 0.9267 (OUTLIER) cc_final: 0.8884 (m-10) REVERT: B 247 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.7072 (mmt) REVERT: B 322 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9188 (mm) REVERT: B 323 MET cc_start: 0.8979 (tpp) cc_final: 0.8544 (ttt) REVERT: B 536 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8465 (pt) REVERT: B 608 LEU cc_start: 0.8340 (tp) cc_final: 0.7679 (pt) REVERT: B 633 THR cc_start: 0.8715 (p) cc_final: 0.8381 (t) REVERT: B 665 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7107 (pp20) REVERT: C 57 PHE cc_start: 0.8846 (t80) cc_final: 0.8426 (t80) REVERT: C 234 MET cc_start: 0.8613 (pmm) cc_final: 0.8374 (pmm) REVERT: C 245 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7518 (ppp) REVERT: C 347 CYS cc_start: 0.6055 (OUTLIER) cc_final: 0.5628 (p) REVERT: C 501 MET cc_start: 0.8501 (mmm) cc_final: 0.7821 (tpt) REVERT: C 534 MET cc_start: 0.8432 (tpp) cc_final: 0.8114 (ttm) REVERT: C 565 MET cc_start: 0.8639 (mmt) cc_final: 0.8062 (mpp) REVERT: C 649 SER cc_start: 0.9166 (m) cc_final: 0.8872 (t) REVERT: C 691 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.8141 (mpp) REVERT: C 709 MET cc_start: 0.9029 (mtm) cc_final: 0.8451 (mtt) REVERT: C 737 MET cc_start: 0.8507 (ttp) cc_final: 0.7569 (ppp) REVERT: C 738 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8431 (pm20) REVERT: C 740 THR cc_start: 0.9363 (p) cc_final: 0.8960 (t) REVERT: D 90 GLU cc_start: 0.8599 (tt0) cc_final: 0.8159 (tt0) REVERT: D 228 PHE cc_start: 0.9260 (OUTLIER) cc_final: 0.8807 (m-10) REVERT: D 247 MET cc_start: 0.7434 (OUTLIER) cc_final: 0.6847 (mmt) REVERT: D 322 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9077 (mm) REVERT: D 536 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8577 (pt) REVERT: D 538 ILE cc_start: 0.9467 (mt) cc_final: 0.8996 (mt) REVERT: D 633 THR cc_start: 0.8810 (p) cc_final: 0.8375 (t) REVERT: D 665 GLU cc_start: 0.7447 (mt-10) cc_final: 0.6921 (pp20) REVERT: D 673 ASP cc_start: 0.8830 (t0) cc_final: 0.8522 (t0) REVERT: D 705 MET cc_start: 0.9201 (mpp) cc_final: 0.8799 (mpp) outliers start: 60 outliers final: 40 residues processed: 285 average time/residue: 0.3287 time to fit residues: 160.3140 Evaluate side-chains 278 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 223 time to evaluate : 2.844 ------------------------------------------------------------------------------- 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 277 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 779 THR 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 274 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 322 LEU 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 562 ASP 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 50 MET Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 650 SER Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 738 GLU Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 311 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 120 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 172 optimal weight: 0.0020 chunk 271 optimal weight: 0.8980 chunk 191 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 319 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 289 optimal weight: 0.5980 chunk 6 optimal weight: 9.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- 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 ** 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 = 0.3877 r_free = 0.3877 target = 0.084323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.065616 restraints weight = 126298.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.066690 restraints weight = 76870.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.067437 restraints weight = 59620.298| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.5340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27480 Z= 0.128 Angle : 0.834 19.730 37352 Z= 0.370 Chirality : 0.048 0.465 4314 Planarity : 0.004 0.064 4618 Dihedral : 9.565 140.567 4834 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.50 % Favored : 93.29 % Rotamer: Outliers : 2.15 % Allowed : 15.63 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.15), residues: 3264 helix: 1.15 (0.14), residues: 1434 sheet: -1.38 (0.25), residues: 444 loop : -1.96 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.131 0.002 TRP B 613 HIS 0.005 0.001 HIS D 253 PHE 0.017 0.001 PHE D 579 TYR 0.026 0.001 TYR B 478 ARG 0.012 0.000 ARG A 133 Details of bonding type rmsd link_NAG-ASN : bond 0.00836 ( 32) link_NAG-ASN : angle 4.71884 ( 96) link_BETA1-4 : bond 0.01440 ( 26) link_BETA1-4 : angle 5.47928 ( 78) hydrogen bonds : bond 0.03402 ( 1024) hydrogen bonds : angle 4.20342 ( 2934) SS BOND : bond 0.00288 ( 10) SS BOND : angle 1.15367 ( 20) link_BETA1-3 : bond 0.00821 ( 4) link_BETA1-3 : angle 2.23666 ( 12) covalent geometry : bond 0.00277 (27408) covalent geometry : angle 0.75947 (37146) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7803.20 seconds wall clock time: 138 minutes 30.72 seconds (8310.72 seconds total)