Starting phenix.real_space_refine on Mon Jun 23 09:40:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fwq_29515/06_2025/8fwq_29515.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fwq_29515/06_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_29515/06_2025/8fwq_29515.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fwq_29515/06_2025/8fwq_29515.map" model { file = "/net/cci-nas-00/data/ceres_data/8fwq_29515/06_2025/8fwq_29515.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fwq_29515/06_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): 1.63s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 17.77, per 1000 atoms: 0.66 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: 7.35 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: 3.21 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: 10.22 Time building geometry restraints manager: 8.30 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: 4.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.130 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 61.720 Find NCS groups from input model: 2.010 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.730 ------------------------------------------------------------------------------- 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 : 2.819 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: 0.3918 time to fit residues: 349.9435 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 : 2.763 ------------------------------------------------------------------------------- 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 = 0.066070 restraints weight = 125102.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.066359 restraints weight = 74260.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.067248 restraints weight = 63060.157| |-----------------------------------------------------------------------------| 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 : 4.148 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: 0.9260 (p) REVERT: A 156 LEU cc_start: 0.9341 (mt) cc_final: 0.9103 (mt) REVERT: A 450 ASP cc_start: 0.7195 (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: 0.8793 (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: 0.8849 (ptp) REVERT: B 223 GLU cc_start: 0.7337 (mt-10) cc_final: 0.6533 (mt-10) REVERT: B 234 MET cc_start: 0.8462 (mmp) cc_final: 0.8152 (mmp) REVERT: B 247 MET cc_start: 0.7485 (mtt) cc_final: 0.6905 (mmt) REVERT: B 248 MET cc_start: 0.8154 (mmm) cc_final: 0.7881 (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: 0.8728 (p) cc_final: 0.8445 (t) REVERT: B 665 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7235 (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: 0.8160 (mmm) REVERT: C 528 ASP cc_start: 0.7740 (m-30) cc_final: 0.7479 (m-30) REVERT: C 565 MET cc_start: 0.8683 (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: 0.8603 (tp40) cc_final: 0.8150 (tt0) REVERT: D 152 ASP cc_start: 0.7947 (t0) cc_final: 0.7555 (t0) REVERT: D 223 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6593 (mt-10) REVERT: D 234 MET cc_start: 0.8341 (mmp) cc_final: 0.8058 (ttm) REVERT: D 247 MET cc_start: 0.7475 (mtm) cc_final: 0.6790 (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: 0.8512 (t) REVERT: D 665 GLU cc_start: 0.8411 (mt-10) cc_final: 0.7448 (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: 0.8630 (mtp) outliers start: 56 outliers final: 23 residues processed: 376 average time/residue: 0.3977 time to fit residues: 252.3973 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 : 2.849 ------------------------------------------------------------------------------- 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: 1.9990 chunk 297 optimal weight: 0.9980 chunk 192 optimal weight: 10.0000 chunk 255 optimal weight: 0.7980 chunk 279 optimal weight: 4.9990 chunk 222 optimal weight: 5.9990 chunk 285 optimal weight: 4.9990 chunk 310 optimal weight: 0.9980 chunk 276 optimal weight: 2.9990 chunk 282 optimal weight: 0.4980 chunk 252 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3905 r_free = 0.3905 target = 0.085414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.067083 restraints weight = 125302.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.067162 restraints weight = 79786.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.068166 restraints weight = 61470.567| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3276 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 : 0.889 22.379 37352 Z= 0.394 Chirality : 0.052 0.555 4314 Planarity : 0.005 0.127 4618 Dihedral : 15.852 140.533 4834 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.20 % Favored : 92.52 % Rotamer: Outliers : 2.71 % Allowed : 11.09 % Favored : 86.20 % 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: -2.41 (0.14), residues: 3264 helix: -0.38 (0.13), residues: 1446 sheet: -2.25 (0.23), residues: 452 loop : -2.70 (0.15), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 706 HIS 0.009 0.001 HIS C 225 PHE 0.018 0.002 PHE C 693 TYR 0.046 0.001 TYR D 478 ARG 0.006 0.000 ARG A 712 Details of bonding type rmsd link_NAG-ASN : bond 0.00982 ( 32) link_NAG-ASN : angle 5.42934 ( 96) link_BETA1-4 : bond 0.02132 ( 26) link_BETA1-4 : angle 6.23356 ( 78) hydrogen bonds : bond 0.04427 ( 1024) hydrogen bonds : angle 4.70101 ( 2934) SS BOND : bond 0.00729 ( 10) SS BOND : angle 1.27985 ( 20) link_BETA1-3 : bond 0.01176 ( 4) link_BETA1-3 : angle 4.33994 ( 12) covalent geometry : bond 0.00308 (27408) covalent geometry : angle 0.79340 (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 376 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 299 time to evaluate : 3.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.8728 (t80) cc_final: 0.8247 (t80) REVERT: A 245 MET cc_start: 0.7445 (ttm) cc_final: 0.7138 (ttt) REVERT: A 450 ASP cc_start: 0.7127 (p0) cc_final: 0.6902 (t70) REVERT: A 565 MET cc_start: 0.8704 (mmt) cc_final: 0.7875 (mpp) REVERT: A 571 CYS cc_start: 0.9181 (m) cc_final: 0.8943 (t) REVERT: A 621 GLN cc_start: 0.8840 (mm-40) cc_final: 0.8638 (tp40) REVERT: A 649 SER cc_start: 0.9223 (m) cc_final: 0.8838 (t) REVERT: A 650 SER cc_start: 0.8975 (m) cc_final: 0.8691 (t) REVERT: A 691 MET cc_start: 0.8536 (ptp) cc_final: 0.8185 (ptp) REVERT: A 740 THR cc_start: 0.9272 (p) cc_final: 0.8927 (t) REVERT: A 770 MET cc_start: 0.8136 (mmt) cc_final: 0.7933 (mmt) REVERT: B 90 GLU cc_start: 0.8410 (tt0) cc_final: 0.7946 (tt0) REVERT: B 130 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8645 (tp) REVERT: B 223 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6274 (mt-10) REVERT: B 247 MET cc_start: 0.7577 (mtt) cc_final: 0.7028 (mmt) REVERT: B 322 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9256 (mm) REVERT: B 323 MET cc_start: 0.8991 (tpp) cc_final: 0.8436 (ttm) REVERT: B 536 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8390 (pt) REVERT: B 565 MET cc_start: 0.8131 (mmt) cc_final: 0.7882 (mmp) REVERT: B 627 MET cc_start: 0.8515 (mmm) cc_final: 0.8246 (mtt) REVERT: B 633 THR cc_start: 0.8656 (p) cc_final: 0.8373 (t) REVERT: B 665 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7142 (tm-30) REVERT: C 57 PHE cc_start: 0.8759 (t80) cc_final: 0.8211 (t80) REVERT: C 450 ASP cc_start: 0.6919 (p0) cc_final: 0.6617 (t70) REVERT: C 565 MET cc_start: 0.8683 (mmt) cc_final: 0.7900 (mpp) REVERT: C 571 CYS cc_start: 0.9233 (m) cc_final: 0.8930 (t) REVERT: C 649 SER cc_start: 0.9273 (m) cc_final: 0.8908 (t) REVERT: C 740 THR cc_start: 0.9264 (p) cc_final: 0.8937 (t) REVERT: C 786 GLN cc_start: 0.8429 (tp40) cc_final: 0.8034 (tm-30) REVERT: D 90 GLU cc_start: 0.8537 (tt0) cc_final: 0.8095 (tt0) REVERT: D 152 ASP cc_start: 0.7800 (t0) cc_final: 0.7417 (t0) REVERT: D 234 MET cc_start: 0.8281 (mmp) cc_final: 0.8059 (ttm) REVERT: D 248 MET cc_start: 0.8077 (mmm) cc_final: 0.7827 (mmm) REVERT: D 322 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9157 (mm) REVERT: D 323 MET cc_start: 0.8995 (tpp) cc_final: 0.8527 (ttm) REVERT: D 536 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8491 (pt) REVERT: D 565 MET cc_start: 0.8059 (mmt) cc_final: 0.7830 (mmp) REVERT: D 627 MET cc_start: 0.8867 (mmm) cc_final: 0.8073 (mtt) REVERT: D 633 THR cc_start: 0.8781 (p) cc_final: 0.8391 (t) REVERT: D 665 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7308 (tm-30) REVERT: D 694 PHE cc_start: 0.8532 (m-80) cc_final: 0.8188 (m-80) REVERT: D 705 MET cc_start: 0.9063 (mtp) cc_final: 0.8549 (mtp) REVERT: D 794 MET cc_start: 0.9399 (mtt) cc_final: 0.9138 (mtp) outliers start: 77 outliers final: 30 residues processed: 350 average time/residue: 0.3410 time to fit residues: 200.1078 Evaluate side-chains 281 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 246 time to evaluate : 3.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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: 5.9990 chunk 272 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 235 optimal weight: 4.9990 chunk 309 optimal weight: 0.0370 chunk 220 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 275 optimal weight: 7.9990 overall best weight: 2.2064 ------------------------------------------------------------------------------- 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** 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 = 0.3879 r_free = 0.3879 target = 0.084124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.065335 restraints weight = 127547.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.066399 restraints weight = 76960.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.066890 restraints weight = 60564.386| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27480 Z= 0.174 Angle : 0.872 21.744 37352 Z= 0.388 Chirality : 0.052 0.535 4314 Planarity : 0.005 0.057 4618 Dihedral : 13.792 140.349 4834 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.20 % Favored : 92.49 % Rotamer: Outliers : 2.85 % Allowed : 12.18 % Favored : 84.96 % 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: -1.97 (0.14), residues: 3264 helix: 0.06 (0.13), residues: 1460 sheet: -2.04 (0.24), residues: 444 loop : -2.58 (0.15), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP C 169 HIS 0.004 0.001 HIS B 253 PHE 0.016 0.002 PHE D 708 TYR 0.039 0.001 TYR B 478 ARG 0.006 0.000 ARG A 712 Details of bonding type rmsd link_NAG-ASN : bond 0.00976 ( 32) link_NAG-ASN : angle 5.44637 ( 96) link_BETA1-4 : bond 0.02074 ( 26) link_BETA1-4 : angle 6.11853 ( 78) hydrogen bonds : bond 0.04070 ( 1024) hydrogen bonds : angle 4.59573 ( 2934) SS BOND : bond 0.00357 ( 10) SS BOND : angle 1.64918 ( 20) link_BETA1-3 : bond 0.01193 ( 4) link_BETA1-3 : angle 3.96157 ( 12) covalent geometry : bond 0.00376 (27408) covalent geometry : angle 0.77601 (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 335 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 254 time to evaluate : 2.814 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: 0.8769 (t80) cc_final: 0.8294 (t80) REVERT: A 219 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.7899 (ptpt) REVERT: A 229 ASP cc_start: 0.8047 (t0) cc_final: 0.7760 (t0) REVERT: A 234 MET cc_start: 0.8509 (mpp) cc_final: 0.8287 (mpp) REVERT: A 450 ASP cc_start: 0.7060 (p0) cc_final: 0.6841 (t70) REVERT: A 565 MET cc_start: 0.8683 (mmt) cc_final: 0.7978 (mpp) REVERT: A 649 SER cc_start: 0.9213 (m) cc_final: 0.8755 (t) REVERT: A 650 SER cc_start: 0.9040 (m) cc_final: 0.8746 (t) REVERT: B 90 GLU cc_start: 0.8430 (tt0) cc_final: 0.7970 (tt0) REVERT: B 130 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8714 (tp) REVERT: B 218 MET cc_start: 0.8206 (tpp) cc_final: 0.7886 (tpp) REVERT: B 223 GLU cc_start: 0.7021 (mt-10) cc_final: 0.6377 (mt-10) REVERT: B 247 MET cc_start: 0.7434 (mtt) cc_final: 0.6831 (mmt) REVERT: B 322 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9279 (mm) REVERT: B 536 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8572 (pt) REVERT: B 565 MET cc_start: 0.8137 (mmt) cc_final: 0.7902 (mmp) REVERT: B 627 MET cc_start: 0.8539 (mmm) cc_final: 0.8335 (mmm) REVERT: B 633 THR cc_start: 0.8668 (p) cc_final: 0.8360 (t) REVERT: B 770 MET cc_start: 0.8849 (tpt) cc_final: 0.8529 (mmt) REVERT: C 57 PHE cc_start: 0.8725 (t80) cc_final: 0.8248 (t80) REVERT: C 147 VAL cc_start: 0.7956 (OUTLIER) cc_final: 0.7726 (m) REVERT: C 347 CYS cc_start: 0.5795 (OUTLIER) cc_final: 0.5316 (p) REVERT: C 450 ASP cc_start: 0.6861 (p0) cc_final: 0.6611 (t70) REVERT: C 534 MET cc_start: 0.8508 (tpp) cc_final: 0.8048 (ttm) REVERT: C 565 MET cc_start: 0.8686 (mmt) cc_final: 0.7888 (mpp) REVERT: C 571 CYS cc_start: 0.9143 (m) cc_final: 0.8897 (t) REVERT: C 649 SER cc_start: 0.9284 (m) cc_final: 0.8971 (t) REVERT: C 740 THR cc_start: 0.9296 (p) cc_final: 0.8893 (t) REVERT: C 786 GLN cc_start: 0.8455 (tp40) cc_final: 0.8162 (tm-30) REVERT: D 50 MET cc_start: 0.4375 (mtm) cc_final: 0.4093 (mtp) REVERT: D 90 GLU cc_start: 0.8553 (tt0) cc_final: 0.8100 (tt0) REVERT: D 152 ASP cc_start: 0.7798 (t0) cc_final: 0.7403 (t0) REVERT: D 223 GLU cc_start: 0.7257 (mt-10) cc_final: 0.6265 (mt-10) REVERT: D 247 MET cc_start: 0.7191 (OUTLIER) cc_final: 0.6658 (mmt) REVERT: D 322 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9169 (mm) REVERT: D 501 MET cc_start: 0.8896 (mmm) cc_final: 0.8590 (mmm) REVERT: D 536 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8723 (pt) REVERT: D 538 ILE cc_start: 0.9527 (mt) cc_final: 0.9179 (mt) REVERT: D 565 MET cc_start: 0.8002 (mmt) cc_final: 0.7780 (mmp) REVERT: D 627 MET cc_start: 0.8800 (mmm) cc_final: 0.8191 (mtt) REVERT: D 633 THR cc_start: 0.8793 (p) cc_final: 0.8391 (t) REVERT: D 665 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7264 (tm-30) REVERT: D 673 ASP cc_start: 0.8951 (t0) cc_final: 0.8687 (t0) outliers start: 81 outliers final: 46 residues processed: 311 average time/residue: 0.3086 time to fit residues: 165.6219 Evaluate side-chains 297 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 242 time to evaluate : 3.100 ------------------------------------------------------------------------------- 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 219 LYS 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 820 ILE Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 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 644 THR Chi-restraints excluded: chain C residue 650 SER Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 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 247 MET Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 645 LEU 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: 0.9990 chunk 45 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 318 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 chunk 279 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 192 optimal weight: 0.3980 overall best weight: 2.0788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.083839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.065029 restraints weight = 126333.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.065678 restraints weight = 77171.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.066305 restraints weight = 62575.992| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27480 Z= 0.165 Angle : 0.845 21.006 37352 Z= 0.378 Chirality : 0.051 0.500 4314 Planarity : 0.004 0.057 4618 Dihedral : 12.480 140.820 4834 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.14 % Favored : 92.62 % Rotamer: Outliers : 2.85 % Allowed : 12.43 % Favored : 84.72 % 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: -1.62 (0.15), residues: 3264 helix: 0.42 (0.14), residues: 1456 sheet: -1.98 (0.23), residues: 466 loop : -2.43 (0.16), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 169 HIS 0.005 0.001 HIS D 253 PHE 0.015 0.001 PHE D 708 TYR 0.036 0.001 TYR B 478 ARG 0.005 0.000 ARG C 712 Details of bonding type rmsd link_NAG-ASN : bond 0.00831 ( 32) link_NAG-ASN : angle 5.19797 ( 96) link_BETA1-4 : bond 0.01870 ( 26) link_BETA1-4 : angle 6.08641 ( 78) hydrogen bonds : bond 0.03800 ( 1024) hydrogen bonds : angle 4.45996 ( 2934) SS BOND : bond 0.00580 ( 10) SS BOND : angle 1.78934 ( 20) link_BETA1-3 : bond 0.01115 ( 4) link_BETA1-3 : angle 3.59581 ( 12) covalent geometry : bond 0.00358 (27408) covalent geometry : angle 0.75164 (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 342 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 261 time to evaluate : 2.880 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: A 57 PHE cc_start: 0.8805 (t80) cc_final: 0.8286 (t80) REVERT: A 219 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8214 (ptpt) REVERT: A 234 MET cc_start: 0.8758 (mpp) cc_final: 0.8326 (mpp) REVERT: A 450 ASP cc_start: 0.6986 (p0) cc_final: 0.6777 (t70) REVERT: A 534 MET cc_start: 0.8510 (tpp) cc_final: 0.8026 (ttm) REVERT: A 565 MET cc_start: 0.8722 (mmt) cc_final: 0.7990 (mpp) REVERT: A 649 SER cc_start: 0.9227 (m) cc_final: 0.8851 (t) REVERT: A 650 SER cc_start: 0.9023 (m) cc_final: 0.8737 (t) REVERT: B 90 GLU cc_start: 0.8563 (tt0) cc_final: 0.8102 (tt0) REVERT: B 130 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8781 (tp) REVERT: B 218 MET cc_start: 0.8151 (tpp) cc_final: 0.7851 (tpp) REVERT: B 223 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6381 (mt-10) REVERT: B 247 MET cc_start: 0.7357 (mtt) cc_final: 0.6847 (mmt) REVERT: B 322 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9223 (mm) REVERT: B 323 MET cc_start: 0.8943 (tpp) cc_final: 0.8652 (ttm) REVERT: B 536 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8574 (pt) REVERT: B 565 MET cc_start: 0.8130 (mmt) cc_final: 0.7895 (mmp) REVERT: B 627 MET cc_start: 0.8615 (mmm) cc_final: 0.8393 (mmm) REVERT: B 633 THR cc_start: 0.8625 (p) cc_final: 0.8312 (t) REVERT: B 770 MET cc_start: 0.8834 (tpt) cc_final: 0.8495 (mmt) REVERT: C 57 PHE cc_start: 0.8808 (t80) cc_final: 0.8310 (t80) REVERT: C 245 MET cc_start: 0.8521 (ppp) cc_final: 0.8017 (ppp) REVERT: C 347 CYS cc_start: 0.6048 (OUTLIER) cc_final: 0.5615 (p) REVERT: C 565 MET cc_start: 0.8722 (mmt) cc_final: 0.7950 (mpp) REVERT: C 571 CYS cc_start: 0.9195 (m) cc_final: 0.8963 (t) REVERT: C 649 SER cc_start: 0.9261 (m) cc_final: 0.8934 (t) REVERT: C 705 MET cc_start: 0.9162 (mmm) cc_final: 0.8869 (mmm) REVERT: C 709 MET cc_start: 0.9058 (mtm) cc_final: 0.8450 (mtt) REVERT: C 740 THR cc_start: 0.9323 (p) cc_final: 0.9019 (t) REVERT: C 786 GLN cc_start: 0.8421 (tp40) cc_final: 0.8186 (tm-30) REVERT: D 90 GLU cc_start: 0.8552 (tt0) cc_final: 0.8084 (tt0) REVERT: D 152 ASP cc_start: 0.7794 (t0) cc_final: 0.7406 (t0) REVERT: D 228 PHE cc_start: 0.9279 (OUTLIER) cc_final: 0.8979 (m-10) REVERT: D 247 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.6795 (mmt) REVERT: D 322 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9172 (mm) REVERT: D 323 MET cc_start: 0.8959 (tpp) cc_final: 0.8473 (ttm) REVERT: D 360 MET cc_start: 0.7895 (mmm) cc_final: 0.7639 (mmm) REVERT: D 501 MET cc_start: 0.8969 (mmm) cc_final: 0.8237 (mmm) REVERT: D 536 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8600 (pt) REVERT: D 538 ILE cc_start: 0.9534 (mt) cc_final: 0.9197 (mt) REVERT: D 565 MET cc_start: 0.7962 (mmt) cc_final: 0.7744 (mmp) REVERT: D 627 MET cc_start: 0.8839 (mmm) cc_final: 0.8217 (mtt) REVERT: D 633 THR cc_start: 0.8822 (p) cc_final: 0.8414 (t) REVERT: D 665 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7251 (pp20) REVERT: D 673 ASP cc_start: 0.8993 (t0) cc_final: 0.8713 (t0) REVERT: D 705 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8764 (mpp) outliers start: 81 outliers final: 48 residues processed: 319 average time/residue: 0.3706 time to fit residues: 203.4554 Evaluate side-chains 288 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 230 time to evaluate : 3.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 219 LYS 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 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 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 430 ASN Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 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 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 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 Chi-restraints excluded: chain D residue 705 MET Chi-restraints excluded: chain D residue 793 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 168 optimal weight: 5.9990 chunk 141 optimal weight: 0.7980 chunk 250 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 197 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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** D 754 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.083872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.065087 restraints weight = 126823.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.065810 restraints weight = 78485.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.066522 restraints weight = 61800.956| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 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 0.042 27480 Z= 0.146 Angle : 0.821 20.963 37352 Z= 0.366 Chirality : 0.050 0.493 4314 Planarity : 0.004 0.058 4618 Dihedral : 11.753 140.595 4834 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.99 % Favored : 92.77 % Rotamer: Outliers : 2.68 % Allowed : 13.24 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.36 (0.15), residues: 3264 helix: 0.62 (0.14), residues: 1462 sheet: -1.74 (0.24), residues: 454 loop : -2.34 (0.16), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP A 169 HIS 0.010 0.001 HIS A 225 PHE 0.014 0.001 PHE D 579 TYR 0.039 0.001 TYR B 478 ARG 0.003 0.000 ARG D 220 Details of bonding type rmsd link_NAG-ASN : bond 0.00842 ( 32) link_NAG-ASN : angle 4.94122 ( 96) link_BETA1-4 : bond 0.01802 ( 26) link_BETA1-4 : angle 5.94251 ( 78) hydrogen bonds : bond 0.03578 ( 1024) hydrogen bonds : angle 4.35460 ( 2934) SS BOND : bond 0.00423 ( 10) SS BOND : angle 1.52238 ( 20) link_BETA1-3 : bond 0.01049 ( 4) link_BETA1-3 : angle 3.22559 ( 12) covalent geometry : bond 0.00314 (27408) covalent geometry : angle 0.73227 (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 331 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 255 time to evaluate : 4.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.8819 (t80) cc_final: 0.8343 (t80) REVERT: A 219 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.8169 (mttm) REVERT: A 347 CYS cc_start: 0.6280 (OUTLIER) cc_final: 0.5900 (p) REVERT: A 534 MET cc_start: 0.8634 (tpp) cc_final: 0.8112 (ttm) REVERT: A 565 MET cc_start: 0.8725 (mmt) cc_final: 0.7972 (mpp) REVERT: A 649 SER cc_start: 0.9228 (m) cc_final: 0.8871 (t) REVERT: A 650 SER cc_start: 0.9022 (m) cc_final: 0.8732 (t) REVERT: A 740 THR cc_start: 0.9437 (p) cc_final: 0.9096 (t) REVERT: B 90 GLU cc_start: 0.8594 (tt0) cc_final: 0.8167 (tt0) REVERT: B 130 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8718 (tp) REVERT: B 218 MET cc_start: 0.8242 (tpp) cc_final: 0.7963 (tpp) REVERT: B 223 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6324 (mt-10) REVERT: B 228 PHE cc_start: 0.9248 (OUTLIER) cc_final: 0.8905 (m-10) REVERT: B 247 MET cc_start: 0.7320 (OUTLIER) cc_final: 0.6827 (mmt) REVERT: B 322 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9201 (mm) REVERT: B 323 MET cc_start: 0.9008 (tpp) cc_final: 0.8643 (ttm) REVERT: B 536 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8558 (pt) REVERT: B 565 MET cc_start: 0.8115 (mmt) cc_final: 0.7878 (mmp) REVERT: B 627 MET cc_start: 0.8601 (mmm) cc_final: 0.7966 (mmm) REVERT: B 633 THR cc_start: 0.8624 (p) cc_final: 0.8290 (t) REVERT: B 665 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7170 (pp20) REVERT: B 770 MET cc_start: 0.8782 (tpt) cc_final: 0.8460 (mmt) REVERT: C 57 PHE cc_start: 0.8826 (t80) cc_final: 0.8366 (t80) REVERT: C 245 MET cc_start: 0.8410 (ppp) cc_final: 0.7765 (ppp) REVERT: C 247 MET cc_start: 0.8269 (tpp) cc_final: 0.7449 (mpp) REVERT: C 347 CYS cc_start: 0.6014 (OUTLIER) cc_final: 0.5524 (p) REVERT: C 534 MET cc_start: 0.8234 (tpp) cc_final: 0.7957 (ttm) REVERT: C 565 MET cc_start: 0.8701 (mmt) cc_final: 0.8078 (mpp) REVERT: C 649 SER cc_start: 0.9219 (m) cc_final: 0.8921 (t) REVERT: C 691 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8111 (mpp) REVERT: C 740 THR cc_start: 0.9419 (p) cc_final: 0.9031 (t) REVERT: D 90 GLU cc_start: 0.8584 (tt0) cc_final: 0.8127 (tt0) REVERT: D 152 ASP cc_start: 0.7747 (t0) cc_final: 0.7458 (t0) REVERT: D 228 PHE cc_start: 0.9305 (OUTLIER) cc_final: 0.8929 (m-10) REVERT: D 247 MET cc_start: 0.7249 (OUTLIER) cc_final: 0.6743 (mmt) REVERT: D 322 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9192 (mm) REVERT: D 323 MET cc_start: 0.8964 (tpp) cc_final: 0.8748 (ttm) REVERT: D 360 MET cc_start: 0.7956 (mmm) cc_final: 0.7728 (mmm) REVERT: D 501 MET cc_start: 0.9014 (mmm) cc_final: 0.8457 (mmm) REVERT: D 536 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8627 (pt) REVERT: D 538 ILE cc_start: 0.9528 (mt) cc_final: 0.9159 (mt) REVERT: D 565 MET cc_start: 0.7953 (mmt) cc_final: 0.7722 (mmp) REVERT: D 627 MET cc_start: 0.8752 (mmm) cc_final: 0.8271 (mtt) REVERT: D 633 THR cc_start: 0.8805 (p) cc_final: 0.8385 (t) REVERT: D 673 ASP cc_start: 0.8960 (t0) cc_final: 0.8656 (t0) REVERT: D 705 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8552 (mpp) outliers start: 76 outliers final: 47 residues processed: 306 average time/residue: 0.4783 time to fit residues: 255.0749 Evaluate side-chains 293 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 232 time to evaluate : 6.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 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 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 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 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 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 691 MET Chi-restraints excluded: chain C residue 718 VAL 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 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 705 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 45 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 249 optimal weight: 5.9990 chunk 195 optimal weight: 20.0000 chunk 259 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 63 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 244 optimal weight: 0.9980 chunk 313 optimal weight: 10.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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** B 754 GLN 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 = 0.3838 r_free = 0.3838 target = 0.082514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.063606 restraints weight = 128491.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.064790 restraints weight = 77130.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.065407 restraints weight = 61399.214| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 27480 Z= 0.188 Angle : 0.854 20.691 37352 Z= 0.384 Chirality : 0.050 0.488 4314 Planarity : 0.004 0.065 4618 Dihedral : 11.318 140.900 4834 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.32 % Favored : 92.43 % Rotamer: Outliers : 3.03 % Allowed : 13.52 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.24 (0.15), residues: 3264 helix: 0.72 (0.14), residues: 1456 sheet: -1.77 (0.24), residues: 456 loop : -2.23 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP C 169 HIS 0.006 0.001 HIS B 253 PHE 0.017 0.002 PHE D 579 TYR 0.040 0.001 TYR B 478 ARG 0.004 0.000 ARG C 184 Details of bonding type rmsd link_NAG-ASN : bond 0.00755 ( 32) link_NAG-ASN : angle 4.88744 ( 96) link_BETA1-4 : bond 0.01738 ( 26) link_BETA1-4 : angle 5.81895 ( 78) hydrogen bonds : bond 0.03652 ( 1024) hydrogen bonds : angle 4.45286 ( 2934) SS BOND : bond 0.00409 ( 10) SS BOND : angle 1.54254 ( 20) link_BETA1-3 : bond 0.00945 ( 4) link_BETA1-3 : angle 2.94753 ( 12) covalent geometry : bond 0.00408 (27408) covalent geometry : angle 0.77190 (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 322 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 236 time to evaluate : 3.082 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: 0.8810 (t80) cc_final: 0.8350 (t80) REVERT: A 219 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.8217 (mttt) REVERT: A 234 MET cc_start: 0.8993 (mpp) cc_final: 0.8561 (mpp) REVERT: A 347 CYS cc_start: 0.6180 (OUTLIER) cc_final: 0.5774 (p) REVERT: A 501 MET cc_start: 0.8591 (mmm) cc_final: 0.8121 (tpt) REVERT: A 565 MET cc_start: 0.8693 (mmt) cc_final: 0.7976 (mpp) REVERT: A 649 SER cc_start: 0.9265 (m) cc_final: 0.8826 (t) REVERT: A 650 SER cc_start: 0.9048 (m) cc_final: 0.8737 (t) REVERT: A 740 THR cc_start: 0.9455 (p) cc_final: 0.9188 (t) REVERT: B 90 GLU cc_start: 0.8596 (tt0) cc_final: 0.8137 (tt0) REVERT: B 130 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8776 (tp) REVERT: B 218 MET cc_start: 0.8225 (tpp) cc_final: 0.7904 (tpp) REVERT: B 223 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6263 (mt-10) REVERT: B 228 PHE cc_start: 0.9227 (OUTLIER) cc_final: 0.8852 (m-10) REVERT: B 322 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9228 (mm) REVERT: B 536 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8680 (pt) REVERT: B 565 MET cc_start: 0.8076 (mmt) cc_final: 0.7845 (mmp) REVERT: B 633 THR cc_start: 0.8663 (p) cc_final: 0.8334 (t) REVERT: B 665 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7154 (pp20) REVERT: B 770 MET cc_start: 0.8824 (tpt) cc_final: 0.8521 (mmt) REVERT: C 57 PHE cc_start: 0.8806 (t80) cc_final: 0.8376 (t80) REVERT: C 245 MET cc_start: 0.8395 (ppp) cc_final: 0.7867 (ppp) REVERT: C 279 PHE cc_start: 0.8661 (m-80) cc_final: 0.8360 (m-10) REVERT: C 347 CYS cc_start: 0.6053 (OUTLIER) cc_final: 0.5658 (p) REVERT: C 501 MET cc_start: 0.8566 (mmm) cc_final: 0.8233 (tpt) REVERT: C 534 MET cc_start: 0.8407 (tpp) cc_final: 0.8084 (ttm) REVERT: C 565 MET cc_start: 0.8676 (mmt) cc_final: 0.8078 (mpp) REVERT: C 649 SER cc_start: 0.9247 (m) cc_final: 0.8885 (t) REVERT: C 737 MET cc_start: 0.7704 (ptp) cc_final: 0.7441 (ttp) REVERT: C 740 THR cc_start: 0.9414 (p) cc_final: 0.9059 (t) REVERT: D 90 GLU cc_start: 0.8618 (tt0) cc_final: 0.8221 (tt0) REVERT: D 152 ASP cc_start: 0.7818 (t0) cc_final: 0.7419 (t0) REVERT: D 228 PHE cc_start: 0.9296 (OUTLIER) cc_final: 0.8925 (m-10) REVERT: D 322 LEU cc_start: 0.9417 (mm) cc_final: 0.9138 (mm) REVERT: D 323 MET cc_start: 0.9059 (tpp) cc_final: 0.8826 (ttm) REVERT: D 536 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8704 (pt) REVERT: D 538 ILE cc_start: 0.9532 (mt) cc_final: 0.9154 (mt) REVERT: D 565 MET cc_start: 0.7892 (mmt) cc_final: 0.7662 (mmp) REVERT: D 633 THR cc_start: 0.8814 (p) cc_final: 0.8389 (t) REVERT: D 665 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7164 (pp20) REVERT: D 673 ASP cc_start: 0.8982 (t0) cc_final: 0.8694 (t0) REVERT: D 737 MET cc_start: 0.7058 (tmm) cc_final: 0.6806 (tmm) outliers start: 86 outliers final: 58 residues processed: 298 average time/residue: 0.3478 time to fit residues: 177.3245 Evaluate side-chains 286 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 219 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 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 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 569 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 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 718 VAL Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 820 ILE Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 658 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 23 optimal weight: 0.1980 chunk 240 optimal weight: 0.0770 chunk 138 optimal weight: 6.9990 chunk 318 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 184 optimal weight: 0.9990 chunk 226 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 299 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 chunk 202 optimal weight: 6.9990 overall best weight: 2.6544 ------------------------------------------------------------------------------- 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 123 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.082256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.063331 restraints weight = 127994.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.064420 restraints weight = 76725.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.065138 restraints weight = 60278.757| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.4865 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= 0.179 Angle : 0.851 20.680 37352 Z= 0.382 Chirality : 0.050 0.481 4314 Planarity : 0.004 0.066 4618 Dihedral : 10.871 140.819 4834 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.29 % Favored : 92.46 % Rotamer: Outliers : 2.75 % Allowed : 14.23 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.12 (0.15), residues: 3264 helix: 0.86 (0.14), residues: 1442 sheet: -1.79 (0.25), residues: 446 loop : -2.16 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 169 HIS 0.006 0.001 HIS B 253 PHE 0.018 0.001 PHE D 708 TYR 0.038 0.001 TYR B 478 ARG 0.004 0.000 ARG C 634 Details of bonding type rmsd link_NAG-ASN : bond 0.00772 ( 32) link_NAG-ASN : angle 4.85895 ( 96) link_BETA1-4 : bond 0.01671 ( 26) link_BETA1-4 : angle 5.68956 ( 78) hydrogen bonds : bond 0.03664 ( 1024) hydrogen bonds : angle 4.44415 ( 2934) SS BOND : bond 0.00383 ( 10) SS BOND : angle 1.43298 ( 20) link_BETA1-3 : bond 0.00890 ( 4) link_BETA1-3 : angle 2.65968 ( 12) covalent geometry : bond 0.00391 (27408) covalent geometry : angle 0.77148 (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 309 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 231 time to evaluate : 2.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.8849 (t80) cc_final: 0.8389 (t80) REVERT: A 234 MET cc_start: 0.9084 (mpp) cc_final: 0.8693 (mpp) REVERT: A 340 MET cc_start: 0.8521 (tmm) cc_final: 0.8005 (tmm) REVERT: A 347 CYS cc_start: 0.6090 (OUTLIER) cc_final: 0.5689 (p) REVERT: A 501 MET cc_start: 0.8554 (mmm) cc_final: 0.8074 (tpt) REVERT: A 534 MET cc_start: 0.8250 (tpp) cc_final: 0.7960 (ttm) REVERT: A 565 MET cc_start: 0.8674 (mmt) cc_final: 0.8100 (mpp) REVERT: A 649 SER cc_start: 0.9267 (m) cc_final: 0.8852 (t) REVERT: A 650 SER cc_start: 0.9089 (m) cc_final: 0.8792 (t) REVERT: A 740 THR cc_start: 0.9430 (p) cc_final: 0.9047 (t) REVERT: B 50 MET cc_start: 0.3481 (tmm) cc_final: 0.3004 (tmm) REVERT: B 90 GLU cc_start: 0.8611 (tt0) cc_final: 0.8163 (tt0) REVERT: B 130 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8798 (tp) REVERT: B 218 MET cc_start: 0.8236 (tpp) cc_final: 0.7912 (tpp) REVERT: B 223 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6277 (mt-10) REVERT: B 228 PHE cc_start: 0.9259 (OUTLIER) cc_final: 0.8905 (m-10) REVERT: B 322 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9231 (mm) REVERT: B 323 MET cc_start: 0.9019 (tpp) cc_final: 0.8721 (ttt) REVERT: B 536 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8686 (pt) REVERT: B 565 MET cc_start: 0.8100 (mmt) cc_final: 0.7865 (mmp) REVERT: B 633 THR cc_start: 0.8680 (p) cc_final: 0.8349 (t) REVERT: B 665 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7208 (tm-30) REVERT: C 57 PHE cc_start: 0.8846 (t80) cc_final: 0.8405 (t80) REVERT: C 245 MET cc_start: 0.8407 (ppp) cc_final: 0.7853 (ppp) REVERT: C 279 PHE cc_start: 0.8638 (m-80) cc_final: 0.8418 (m-10) REVERT: C 347 CYS cc_start: 0.5928 (OUTLIER) cc_final: 0.5540 (p) REVERT: C 501 MET cc_start: 0.8547 (mmm) cc_final: 0.8109 (tpt) REVERT: C 534 MET cc_start: 0.8428 (tpp) cc_final: 0.8094 (ttm) REVERT: C 565 MET cc_start: 0.8722 (mmt) cc_final: 0.8113 (mpp) REVERT: C 649 SER cc_start: 0.9275 (m) cc_final: 0.8919 (t) REVERT: C 705 MET cc_start: 0.8955 (mmm) cc_final: 0.8598 (mmm) REVERT: C 709 MET cc_start: 0.8915 (mtm) cc_final: 0.8255 (mtt) REVERT: C 740 THR cc_start: 0.9426 (p) cc_final: 0.9068 (t) REVERT: D 90 GLU cc_start: 0.8634 (tt0) cc_final: 0.8173 (tt0) REVERT: D 152 ASP cc_start: 0.7853 (t0) cc_final: 0.7469 (t0) REVERT: D 228 PHE cc_start: 0.9308 (OUTLIER) cc_final: 0.8910 (m-10) REVERT: D 322 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9223 (mm) REVERT: D 323 MET cc_start: 0.9085 (tpp) cc_final: 0.8840 (ttm) REVERT: D 536 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8695 (pt) REVERT: D 538 ILE cc_start: 0.9534 (mt) cc_final: 0.9130 (mt) REVERT: D 633 THR cc_start: 0.8835 (p) cc_final: 0.8403 (t) REVERT: D 665 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7021 (tm-30) REVERT: D 673 ASP cc_start: 0.8968 (t0) cc_final: 0.8666 (t0) REVERT: D 705 MET cc_start: 0.9093 (mpp) cc_final: 0.8679 (mpp) REVERT: D 737 MET cc_start: 0.6975 (tmm) cc_final: 0.6718 (tmm) outliers start: 78 outliers final: 59 residues processed: 289 average time/residue: 0.3125 time to fit residues: 156.1256 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 : 2.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 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 718 VAL Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 783 LEU 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 466 LEU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain 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 505 LEU Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 635 ILE 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 658 PHE 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 149 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 299 optimal weight: 5.9990 chunk 35 optimal weight: 20.0000 chunk 56 optimal weight: 0.0470 chunk 289 optimal weight: 7.9990 chunk 189 optimal weight: 6.9990 chunk 223 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 chunk 179 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 HIS ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 HIS ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.081609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.062776 restraints weight = 128732.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.063963 restraints weight = 77821.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.064354 restraints weight = 60840.943| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 27480 Z= 0.196 Angle : 0.871 20.527 37352 Z= 0.393 Chirality : 0.050 0.470 4314 Planarity : 0.004 0.066 4618 Dihedral : 10.532 140.975 4834 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.81 % Favored : 91.91 % Rotamer: Outliers : 2.64 % Allowed : 14.61 % Favored : 82.75 % 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: -1.19 (0.15), residues: 3264 helix: 0.75 (0.14), residues: 1476 sheet: -1.75 (0.24), residues: 458 loop : -2.22 (0.16), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 169 HIS 0.006 0.001 HIS D 253 PHE 0.022 0.002 PHE D 708 TYR 0.024 0.001 TYR B 478 ARG 0.007 0.000 ARG B 663 Details of bonding type rmsd link_NAG-ASN : bond 0.00753 ( 32) link_NAG-ASN : angle 4.91043 ( 96) link_BETA1-4 : bond 0.01585 ( 26) link_BETA1-4 : angle 5.77063 ( 78) hydrogen bonds : bond 0.03687 ( 1024) hydrogen bonds : angle 4.52887 ( 2934) SS BOND : bond 0.00364 ( 10) SS BOND : angle 1.43367 ( 20) link_BETA1-3 : bond 0.00823 ( 4) link_BETA1-3 : angle 2.46690 ( 12) covalent geometry : bond 0.00424 (27408) covalent geometry : angle 0.79192 (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 297 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 222 time to evaluate : 2.913 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: 0.8944 (t80) cc_final: 0.8506 (t80) REVERT: A 234 MET cc_start: 0.9087 (mpp) cc_final: 0.8651 (mpp) REVERT: A 347 CYS cc_start: 0.6200 (OUTLIER) cc_final: 0.5844 (p) REVERT: A 501 MET cc_start: 0.8535 (mmm) cc_final: 0.8069 (tpt) REVERT: A 534 MET cc_start: 0.8439 (tpp) cc_final: 0.8028 (ttm) REVERT: A 565 MET cc_start: 0.8700 (mmt) cc_final: 0.8135 (mpp) REVERT: A 649 SER cc_start: 0.9344 (m) cc_final: 0.8891 (t) REVERT: A 650 SER cc_start: 0.9148 (m) cc_final: 0.8894 (t) REVERT: A 740 THR cc_start: 0.9421 (p) cc_final: 0.9057 (t) REVERT: B 50 MET cc_start: 0.3610 (tmm) cc_final: 0.3191 (tmm) REVERT: B 90 GLU cc_start: 0.8648 (tt0) cc_final: 0.8202 (tt0) REVERT: B 130 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8789 (tp) REVERT: B 218 MET cc_start: 0.8213 (tpp) cc_final: 0.7891 (tpp) REVERT: B 223 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6231 (mt-10) REVERT: B 228 PHE cc_start: 0.9285 (OUTLIER) cc_final: 0.8963 (m-10) REVERT: B 247 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.7125 (mmt) REVERT: B 322 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9243 (mm) REVERT: B 323 MET cc_start: 0.9073 (tpp) cc_final: 0.8658 (ttt) REVERT: B 501 MET cc_start: 0.8595 (mmm) cc_final: 0.7800 (mmm) REVERT: B 536 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8646 (pt) REVERT: B 565 MET cc_start: 0.8087 (mmt) cc_final: 0.7859 (mmp) REVERT: B 633 THR cc_start: 0.8707 (p) cc_final: 0.8369 (t) REVERT: B 665 GLU cc_start: 0.7506 (mt-10) cc_final: 0.6853 (tm-30) REVERT: B 770 MET cc_start: 0.8865 (tpt) cc_final: 0.8645 (mmt) REVERT: C 57 PHE cc_start: 0.8876 (t80) cc_final: 0.8465 (t80) REVERT: C 245 MET cc_start: 0.8379 (ppp) cc_final: 0.7784 (ppp) REVERT: C 347 CYS cc_start: 0.5759 (OUTLIER) cc_final: 0.5377 (p) REVERT: C 501 MET cc_start: 0.8542 (mmm) cc_final: 0.8111 (tpt) REVERT: C 534 MET cc_start: 0.8493 (tpp) cc_final: 0.8120 (ttm) REVERT: C 565 MET cc_start: 0.8705 (mmt) cc_final: 0.8118 (mpp) REVERT: C 649 SER cc_start: 0.9303 (m) cc_final: 0.8916 (t) REVERT: C 709 MET cc_start: 0.8904 (mtm) cc_final: 0.8265 (mtt) REVERT: C 737 MET cc_start: 0.8423 (ttp) cc_final: 0.7578 (ppp) REVERT: C 740 THR cc_start: 0.9406 (p) cc_final: 0.9062 (t) REVERT: D 90 GLU cc_start: 0.8673 (tt0) cc_final: 0.8208 (tt0) REVERT: D 152 ASP cc_start: 0.7919 (t0) cc_final: 0.7557 (t0) REVERT: D 228 PHE cc_start: 0.9295 (OUTLIER) cc_final: 0.8901 (m-10) REVERT: D 247 MET cc_start: 0.7424 (OUTLIER) cc_final: 0.6958 (mmt) REVERT: D 322 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9244 (mm) REVERT: D 323 MET cc_start: 0.9151 (tpp) cc_final: 0.8891 (ttm) REVERT: D 501 MET cc_start: 0.8709 (mmm) cc_final: 0.7991 (mmm) REVERT: D 536 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8720 (pt) REVERT: D 538 ILE cc_start: 0.9528 (mt) cc_final: 0.9115 (mt) REVERT: D 633 THR cc_start: 0.8832 (p) cc_final: 0.8399 (t) REVERT: D 665 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7098 (tm-30) REVERT: D 673 ASP cc_start: 0.8937 (t0) cc_final: 0.8638 (t0) REVERT: D 705 MET cc_start: 0.9265 (mpp) cc_final: 0.8872 (mpp) REVERT: D 737 MET cc_start: 0.6904 (tmm) cc_final: 0.6599 (tmm) REVERT: D 738 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8064 (mm-30) outliers start: 75 outliers final: 60 residues processed: 280 average time/residue: 0.3177 time to fit residues: 153.1098 Evaluate side-chains 289 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 218 time to evaluate : 2.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 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 783 LEU Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 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 658 PHE 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 230 CYS Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 648 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 718 VAL Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 820 ILE Chi-restraints excluded: chain D residue 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 360 MET Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 658 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 43 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 chunk 264 optimal weight: 0.0570 chunk 254 optimal weight: 6.9990 chunk 322 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 chunk 151 optimal weight: 8.9990 chunk 257 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3834 r_free = 0.3834 target = 0.082345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.063450 restraints weight = 127659.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.064412 restraints weight = 78658.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.064905 restraints weight = 61480.544| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 27480 Z= 0.159 Angle : 0.851 20.382 37352 Z= 0.380 Chirality : 0.049 0.472 4314 Planarity : 0.004 0.067 4618 Dihedral : 10.114 140.856 4834 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.72 % Favored : 92.03 % Rotamer: Outliers : 2.50 % Allowed : 15.11 % Favored : 82.39 % 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: -1.02 (0.15), residues: 3264 helix: 0.95 (0.14), residues: 1446 sheet: -1.72 (0.25), residues: 448 loop : -2.13 (0.16), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 169 HIS 0.006 0.001 HIS D 253 PHE 0.015 0.001 PHE D 579 TYR 0.026 0.001 TYR B 478 ARG 0.005 0.000 ARG D 663 Details of bonding type rmsd link_NAG-ASN : bond 0.00781 ( 32) link_NAG-ASN : angle 4.82077 ( 96) link_BETA1-4 : bond 0.01489 ( 26) link_BETA1-4 : angle 5.64941 ( 78) hydrogen bonds : bond 0.03545 ( 1024) hydrogen bonds : angle 4.44079 ( 2934) SS BOND : bond 0.00350 ( 10) SS BOND : angle 1.37677 ( 20) link_BETA1-3 : bond 0.00815 ( 4) link_BETA1-3 : angle 2.32344 ( 12) covalent geometry : bond 0.00347 (27408) covalent geometry : angle 0.77354 (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 300 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 229 time to evaluate : 2.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.7065 (tmm) cc_final: 0.6801 (tmm) REVERT: A 57 PHE cc_start: 0.8958 (t80) cc_final: 0.8506 (t80) REVERT: A 234 MET cc_start: 0.9141 (mpp) cc_final: 0.8696 (mpp) REVERT: A 347 CYS cc_start: 0.6155 (OUTLIER) cc_final: 0.5835 (p) REVERT: A 501 MET cc_start: 0.8556 (mmm) cc_final: 0.8114 (tpt) REVERT: A 534 MET cc_start: 0.8361 (tpp) cc_final: 0.8071 (ttm) REVERT: A 565 MET cc_start: 0.8709 (mmt) cc_final: 0.8104 (mpp) REVERT: A 621 GLN cc_start: 0.8962 (tp40) cc_final: 0.8565 (tp40) REVERT: A 649 SER cc_start: 0.9231 (m) cc_final: 0.8814 (t) REVERT: A 650 SER cc_start: 0.9142 (m) cc_final: 0.8866 (t) REVERT: A 740 THR cc_start: 0.9391 (p) cc_final: 0.9011 (t) REVERT: B 50 MET cc_start: 0.3704 (tmm) cc_final: 0.3365 (tmm) REVERT: B 90 GLU cc_start: 0.8630 (tt0) cc_final: 0.8197 (tt0) REVERT: B 218 MET cc_start: 0.8249 (tpp) cc_final: 0.7952 (tpp) REVERT: B 223 GLU cc_start: 0.7078 (mt-10) cc_final: 0.6330 (mt-10) REVERT: B 228 PHE cc_start: 0.9285 (OUTLIER) cc_final: 0.8937 (m-10) REVERT: B 247 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.7100 (mmt) REVERT: B 322 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9241 (mm) REVERT: B 323 MET cc_start: 0.9064 (tpp) cc_final: 0.8699 (ttt) REVERT: B 501 MET cc_start: 0.8551 (mmm) cc_final: 0.7808 (mmm) REVERT: B 536 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8602 (pt) REVERT: B 565 MET cc_start: 0.8087 (mmt) cc_final: 0.7857 (mmp) REVERT: B 633 THR cc_start: 0.8687 (p) cc_final: 0.8344 (t) REVERT: B 665 GLU cc_start: 0.7508 (mt-10) cc_final: 0.6940 (tm-30) REVERT: B 770 MET cc_start: 0.8829 (tpt) cc_final: 0.8551 (mmt) REVERT: C 57 PHE cc_start: 0.8950 (t80) cc_final: 0.8541 (t80) REVERT: C 234 MET cc_start: 0.8686 (pmm) cc_final: 0.8418 (pmm) REVERT: C 245 MET cc_start: 0.8291 (ppp) cc_final: 0.7595 (ppp) REVERT: C 279 PHE cc_start: 0.8697 (m-80) cc_final: 0.8479 (m-10) REVERT: C 347 CYS cc_start: 0.5840 (OUTLIER) cc_final: 0.5435 (p) REVERT: C 501 MET cc_start: 0.8524 (mmm) cc_final: 0.8101 (tpt) REVERT: C 534 MET cc_start: 0.8431 (tpp) cc_final: 0.8128 (ttm) REVERT: C 565 MET cc_start: 0.8687 (mmt) cc_final: 0.8087 (mpp) REVERT: C 649 SER cc_start: 0.9288 (m) cc_final: 0.8950 (t) REVERT: C 709 MET cc_start: 0.8850 (mtm) cc_final: 0.8340 (mtt) REVERT: C 737 MET cc_start: 0.8321 (ttp) cc_final: 0.7968 (ttp) REVERT: C 740 THR cc_start: 0.9367 (p) cc_final: 0.9022 (t) REVERT: D 90 GLU cc_start: 0.8664 (tt0) cc_final: 0.8227 (tt0) REVERT: D 152 ASP cc_start: 0.7875 (t0) cc_final: 0.7605 (t0) REVERT: D 228 PHE cc_start: 0.9291 (OUTLIER) cc_final: 0.8846 (m-10) REVERT: D 247 MET cc_start: 0.7380 (OUTLIER) cc_final: 0.7063 (mmt) REVERT: D 322 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9250 (mm) REVERT: D 323 MET cc_start: 0.9156 (tpp) cc_final: 0.8898 (ttm) REVERT: D 340 MET cc_start: 0.8033 (mmm) cc_final: 0.7712 (mmm) REVERT: D 536 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8597 (pt) REVERT: D 538 ILE cc_start: 0.9532 (mt) cc_final: 0.9125 (mt) REVERT: D 627 MET cc_start: 0.8786 (mmm) cc_final: 0.8578 (mmm) REVERT: D 633 THR cc_start: 0.8832 (p) cc_final: 0.8388 (t) REVERT: D 665 GLU cc_start: 0.7580 (mt-10) cc_final: 0.6936 (tm-30) REVERT: D 673 ASP cc_start: 0.8901 (t0) cc_final: 0.8631 (t0) REVERT: D 705 MET cc_start: 0.9236 (mpp) cc_final: 0.8941 (mpp) REVERT: D 737 MET cc_start: 0.6965 (tmm) cc_final: 0.6726 (tmm) REVERT: D 738 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8097 (mm-30) outliers start: 71 outliers final: 57 residues processed: 283 average time/residue: 0.3241 time to fit residues: 155.5973 Evaluate side-chains 287 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 220 time to evaluate : 2.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 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 783 LEU Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 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 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 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 514 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 650 SER Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 820 ILE Chi-restraints excluded: chain D residue 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 360 MET Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 658 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 120 optimal weight: 0.1980 chunk 13 optimal weight: 0.9980 chunk 172 optimal weight: 0.9980 chunk 271 optimal weight: 0.2980 chunk 191 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 319 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 289 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3869 r_free = 0.3869 target = 0.083928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.065281 restraints weight = 127103.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.066541 restraints weight = 77087.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.067234 restraints weight = 59269.774| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.5489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 27480 Z= 0.122 Angle : 0.827 20.099 37352 Z= 0.365 Chirality : 0.047 0.462 4314 Planarity : 0.004 0.063 4618 Dihedral : 9.458 140.636 4834 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.89 % Favored : 92.95 % Rotamer: Outliers : 1.83 % Allowed : 15.88 % Favored : 82.29 % 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: -0.85 (0.15), residues: 3264 helix: 1.11 (0.14), residues: 1454 sheet: -1.50 (0.25), residues: 442 loop : -2.14 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 169 HIS 0.008 0.001 HIS D 253 PHE 0.012 0.001 PHE D 476 TYR 0.024 0.001 TYR B 478 ARG 0.003 0.000 ARG B 800 Details of bonding type rmsd link_NAG-ASN : bond 0.00875 ( 32) link_NAG-ASN : angle 4.78761 ( 96) link_BETA1-4 : bond 0.01343 ( 26) link_BETA1-4 : angle 5.35793 ( 78) hydrogen bonds : bond 0.03309 ( 1024) hydrogen bonds : angle 4.27369 ( 2934) SS BOND : bond 0.00337 ( 10) SS BOND : angle 1.29833 ( 20) link_BETA1-3 : bond 0.00840 ( 4) link_BETA1-3 : angle 2.23442 ( 12) covalent geometry : bond 0.00262 (27408) covalent geometry : angle 0.75218 (37146) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8686.90 seconds wall clock time: 155 minutes 31.03 seconds (9331.03 seconds total)