Starting phenix.real_space_refine on Sun Jun 15 08:15:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g78_29802/06_2025/8g78_29802.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g78_29802/06_2025/8g78_29802.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g78_29802/06_2025/8g78_29802.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g78_29802/06_2025/8g78_29802.map" model { file = "/net/cci-nas-00/data/ceres_data/8g78_29802/06_2025/8g78_29802.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g78_29802/06_2025/8g78_29802.cif" } resolution = 3.4 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= 0.001 sd= 0.026 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: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 10761 2.51 5 N 2855 2.21 5 O 3342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17036 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3740 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 25, 'TRANS': 450} Chain breaks: 4 Chain: "B" Number of atoms: 3743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3743 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 24, 'TRANS': 451} Chain breaks: 4 Chain: "D" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3768 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 25, 'TRANS': 454} Chain breaks: 4 Chain: "J" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 872 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain: "F" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 893 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "G" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 893 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "H" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 872 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain: "I" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 872 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain: "E" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 893 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "D" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 11.36, per 1000 atoms: 0.67 Number of scatterers: 17036 At special positions: 0 Unit cell: (177.067, 170.869, 99.1573, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 3342 8.00 N 2855 7.00 C 10761 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.00 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 136 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.02 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.02 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.04 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 95 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 94 " distance=2.01 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 94 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 234 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 17 " " NAG A1306 " - " ASN A 61 " " NAG A1307 " - " ASN A 74 " " NAG A1308 " - " ASN A 165 " " NAG A1309 " - " ASN A 603 " " NAG A1310 " - " ASN A 122 " " NAG A1311 " - " ASN A 149 " " NAG A1312 " - " ASN A 282 " " NAG B1301 " - " ASN B 234 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 17 " " NAG B1306 " - " ASN B 61 " " NAG B1307 " - " ASN B 74 " " NAG B1308 " - " ASN B 165 " " NAG B1309 " - " ASN B 282 " " NAG B1310 " - " ASN B 122 " " NAG B1311 " - " ASN B 149 " " NAG D1301 " - " ASN D 61 " " NAG D1302 " - " ASN D 122 " " NAG D1303 " - " ASN D 282 " " NAG D1304 " - " ASN D 331 " " NAG D1305 " - " ASN D 616 " " NAG D1306 " - " ASN D 657 " " NAG D1307 " - " ASN D 17 " " NAG D1308 " - " ASN D 74 " " NAG D1309 " - " ASN D 165 " " NAG D1310 " - " ASN D 603 " " NAG D1311 " - " ASN D 149 " " NAG D1312 " - " ASN D 234 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.28 Conformation dependent library (CDL) restraints added in 2.4 seconds 4166 Ramachandran restraints generated. 2083 Oldfield, 0 Emsley, 2083 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3890 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 41 sheets defined 5.0% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 257 through 261 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 619 through 624 removed outlier: 4.037A pdb=" N ILE B 624 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 642 removed outlier: 4.051A pdb=" N VAL B 642 " --> pdb=" O GLY B 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 637 through 641 removed outlier: 3.947A pdb=" N SER D 640 " --> pdb=" O SER D 637 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN D 641 " --> pdb=" O THR D 638 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 637 through 641' Processing helix chain 'J' and resid 27 through 31 removed outlier: 3.750A pdb=" N MET J 31 " --> pdb=" O ILE J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.772A pdb=" N LYS J 64 " --> pdb=" O ASP J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing helix chain 'J' and resid 86 through 90 Processing helix chain 'F' and resid 60 through 63 removed outlier: 3.638A pdb=" N LYS F 63 " --> pdb=" O ASP F 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 60 through 63' Processing helix chain 'F' and resid 85 through 89 removed outlier: 3.526A pdb=" N THR F 89 " --> pdb=" O PRO F 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 63 Processing helix chain 'G' and resid 85 through 89 removed outlier: 3.546A pdb=" N THR G 89 " --> pdb=" O PRO G 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'I' and resid 27 through 31 removed outlier: 3.520A pdb=" N ARG I 30 " --> pdb=" O SER I 27 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET I 31 " --> pdb=" O ILE I 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 27 through 31' Processing helix chain 'I' and resid 86 through 90 Processing helix chain 'E' and resid 85 through 89 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29 removed outlier: 4.228A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.365A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.262A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.491A pdb=" N PHE A 43 " --> pdb=" O ARG D 567 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLY D 566 " --> pdb=" O ASP D 574 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 50 removed outlier: 3.959A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA6, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.709A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.752A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 327 Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 327 removed outlier: 3.742A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.353A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.197A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.948A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 68 through 72 removed outlier: 6.914A pdb=" N THR B 76 " --> pdb=" O SER B 71 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.367A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.944A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.508A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.628A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N PHE B 565 " --> pdb=" O PHE D 43 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.152A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 28 through 30 removed outlier: 8.160A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) removed outlier: 9.644A pdb=" N HIS D 207 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 9.594A pdb=" N LEU D 223 " --> pdb=" O HIS D 207 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL D 36 " --> pdb=" O LEU D 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 47 through 55 removed outlier: 3.788A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 68 through 69 removed outlier: 4.387A pdb=" N ARG D 78 " --> pdb=" O HIS D 69 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 84 through 85 Processing sheet with id=AC5, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.756A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ALA D 243 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE D 101 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ILE D 128 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N PHE D 168 " --> pdb=" O ILE D 128 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N VAL D 130 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N CYS D 166 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER D 162 " --> pdb=" O GLN D 134 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 311 through 319 removed outlier: 5.334A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER D 316 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU D 650 " --> pdb=" O PHE D 643 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE D 643 " --> pdb=" O LEU D 650 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.345A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA D 672 " --> pdb=" O PRO D 665 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.645A pdb=" N MET J 34 " --> pdb=" O ILE J 51 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N HIS J 38 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N LEU J 47 " --> pdb=" O HIS J 38 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 17 through 20 Processing sheet with id=AD1, first strand: chain 'J' and resid 97 through 98 removed outlier: 3.667A pdb=" N ALA J 97 " --> pdb=" O TYR J 103 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 18 through 21 Processing sheet with id=AD3, first strand: chain 'F' and resid 56 through 58 removed outlier: 5.560A pdb=" N LEU F 46 " --> pdb=" O ARG F 37 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ARG F 37 " --> pdb=" O LEU F 46 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 17 through 22 removed outlier: 3.712A pdb=" N VAL G 77 " --> pdb=" O CYS G 22 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 56 through 58 removed outlier: 5.578A pdb=" N LEU G 46 " --> pdb=" O ARG G 37 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ARG G 37 " --> pdb=" O LEU G 46 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.228A pdb=" N GLY H 10 " --> pdb=" O THR H 111 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N SER H 113 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL H 12 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU H 33 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N MET H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N THR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.228A pdb=" N GLY H 10 " --> pdb=" O THR H 111 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N SER H 113 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL H 12 " --> pdb=" O SER H 113 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 17 through 18 Processing sheet with id=AD9, first strand: chain 'H' and resid 21 through 23 removed outlier: 3.769A pdb=" N CYS H 22 " --> pdb=" O VAL H 78 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.204A pdb=" N GLY I 10 " --> pdb=" O THR I 111 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N SER I 113 " --> pdb=" O GLY I 10 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL I 12 " --> pdb=" O SER I 113 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU I 33 " --> pdb=" O ARG I 98 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N MET I 34 " --> pdb=" O THR I 50 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N THR I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.204A pdb=" N GLY I 10 " --> pdb=" O THR I 111 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N SER I 113 " --> pdb=" O GLY I 10 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL I 12 " --> pdb=" O SER I 113 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 17 through 23 removed outlier: 3.847A pdb=" N LEU I 20 " --> pdb=" O LEU I 80 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU I 80 " --> pdb=" O LEU I 20 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N CYS I 22 " --> pdb=" O VAL I 78 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN I 81 " --> pdb=" O ILE I 68 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE I 68 " --> pdb=" O GLN I 81 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 17 through 22 removed outlier: 3.895A pdb=" N VAL E 77 " --> pdb=" O CYS E 22 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 56 through 58 removed outlier: 5.751A pdb=" N LEU E 46 " --> pdb=" O ARG E 37 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY E 34 " --> pdb=" O HIS E 95 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS E 95 " --> pdb=" O GLY E 34 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR E 36 " --> pdb=" O TYR E 93 " (cutoff:3.500A) 504 hydrogen bonds defined for protein. 1260 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.28 Time building geometry restraints manager: 4.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5236 1.34 - 1.46: 4071 1.46 - 1.58: 8009 1.58 - 1.70: 0 1.70 - 1.83: 102 Bond restraints: 17418 Sorted by residual: bond pdb=" C1 NAG A1310 " pdb=" O5 NAG A1310 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" N VAL E 23 " pdb=" CA VAL E 23 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.08e+01 bond pdb=" N VAL E 12 " pdb=" CA VAL E 12 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.17e-02 7.31e+03 9.14e+00 bond pdb=" N HIS E 95 " pdb=" CA HIS E 95 " ideal model delta sigma weight residual 1.452 1.490 -0.038 1.25e-02 6.40e+03 9.01e+00 bond pdb=" N LEU E 96 " pdb=" CA LEU E 96 " ideal model delta sigma weight residual 1.455 1.492 -0.038 1.26e-02 6.30e+03 8.98e+00 ... (remaining 17413 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 22975 2.31 - 4.62: 621 4.62 - 6.93: 48 6.93 - 9.25: 13 9.25 - 11.56: 2 Bond angle restraints: 23659 Sorted by residual: angle pdb=" N GLY E 109 " pdb=" CA GLY E 109 " pdb=" C GLY E 109 " ideal model delta sigma weight residual 112.83 121.00 -8.17 1.22e+00 6.72e-01 4.48e+01 angle pdb=" CA GLY E 9 " pdb=" C GLY E 9 " pdb=" O GLY E 9 " ideal model delta sigma weight residual 121.88 118.01 3.87 7.80e-01 1.64e+00 2.46e+01 angle pdb=" C GLN J 3 " pdb=" CA GLN J 3 " pdb=" CB GLN J 3 " ideal model delta sigma weight residual 115.89 109.36 6.53 1.32e+00 5.74e-01 2.45e+01 angle pdb=" CA GLY E 8 " pdb=" C GLY E 8 " pdb=" O GLY E 8 " ideal model delta sigma weight residual 121.88 118.15 3.73 7.80e-01 1.64e+00 2.29e+01 angle pdb=" C CYS E 22 " pdb=" CA CYS E 22 " pdb=" CB CYS E 22 " ideal model delta sigma weight residual 109.89 116.43 -6.54 1.60e+00 3.91e-01 1.67e+01 ... (remaining 23654 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.77: 9631 22.77 - 45.55: 892 45.55 - 68.32: 144 68.32 - 91.09: 28 91.09 - 113.86: 4 Dihedral angle restraints: 10699 sinusoidal: 4606 harmonic: 6093 Sorted by residual: dihedral pdb=" CB CYS D 617 " pdb=" SG CYS D 617 " pdb=" SG CYS D 649 " pdb=" CB CYS D 649 " ideal model delta sinusoidal sigma weight residual 93.00 29.88 63.12 1 1.00e+01 1.00e-02 5.26e+01 dihedral pdb=" CB CYS D 662 " pdb=" SG CYS D 662 " pdb=" SG CYS D 671 " pdb=" CB CYS D 671 " ideal model delta sinusoidal sigma weight residual -86.00 -32.51 -53.49 1 1.00e+01 1.00e-02 3.89e+01 dihedral pdb=" CB CYS D 538 " pdb=" SG CYS D 538 " pdb=" SG CYS D 590 " pdb=" CB CYS D 590 " ideal model delta sinusoidal sigma weight residual -86.00 -33.23 -52.77 1 1.00e+01 1.00e-02 3.79e+01 ... (remaining 10696 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2355 0.084 - 0.168: 354 0.168 - 0.252: 21 0.252 - 0.336: 3 0.336 - 0.421: 2 Chirality restraints: 2735 Sorted by residual: chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" C1 NAG D1311 " pdb=" ND2 ASN D 149 " pdb=" C2 NAG D1311 " pdb=" O5 NAG D1311 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.70 0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 2732 not shown) Planarity restraints: 3035 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 149 " 0.092 2.00e-02 2.50e+03 1.16e-01 1.67e+02 pdb=" CG ASN A 149 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN A 149 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN A 149 " -0.202 2.00e-02 2.50e+03 pdb=" C1 NAG A1311 " 0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 165 " -0.011 2.00e-02 2.50e+03 2.67e-02 8.88e+00 pdb=" CG ASN D 165 " 0.050 2.00e-02 2.50e+03 pdb=" OD1 ASN D 165 " -0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN D 165 " 0.001 2.00e-02 2.50e+03 pdb=" C1 NAG D1309 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 165 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.56e+00 pdb=" CG ASN D 165 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN D 165 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN D 165 " -0.016 2.00e-02 2.50e+03 ... (remaining 3032 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 134 2.49 - 3.09: 11941 3.09 - 3.69: 24707 3.69 - 4.30: 34642 4.30 - 4.90: 58696 Nonbonded interactions: 130120 Sorted by model distance: nonbonded pdb=" OE1 GLN B 607 " pdb=" O TRP H 100 " model vdw 1.884 3.040 nonbonded pdb=" OG SER A 31 " pdb=" O SER A 60 " model vdw 2.075 3.040 nonbonded pdb=" O ASP B 80 " pdb=" OH TYR B 265 " model vdw 2.094 3.040 nonbonded pdb=" OG1 THR D 323 " pdb=" NZ LYS D 537 " model vdw 2.153 3.120 nonbonded pdb=" N HIS A 69 " pdb=" O ARG A 78 " model vdw 2.165 3.120 ... (remaining 130115 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 15 through 178 or resid 184 through 333 or resid 524 throu \ gh 622 or resid 632 through 700 or resid 1301 through 1311)) selection = (chain 'B' and (resid 15 through 178 or resid 184 through 622 or resid 632 throu \ gh 676 or resid 690 through 700 or resid 1301 through 1311)) selection = (chain 'D' and (resid 15 through 333 or resid 524 through 622 or resid 632 throu \ gh 676 or resid 690 through 700 or resid 1301 through 1311)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 39.190 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 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 : 0.007 0.209 17477 Z= 0.339 Angle : 0.934 23.155 23810 Z= 0.495 Chirality : 0.058 0.421 2735 Planarity : 0.005 0.062 3000 Dihedral : 16.909 113.865 6740 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.55 % Favored : 90.83 % Rotamer: Outliers : 1.04 % Allowed : 26.57 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.17 (0.17), residues: 2083 helix: 0.64 (0.79), residues: 33 sheet: -1.10 (0.19), residues: 724 loop : -1.75 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP D 104 HIS 0.009 0.002 HIS I 38 PHE 0.025 0.003 PHE B 86 TYR 0.026 0.002 TYR E 105 ARG 0.012 0.001 ARG J 53 Details of bonding type rmsd link_NAG-ASN : bond 0.04110 ( 35) link_NAG-ASN : angle 5.11018 ( 105) hydrogen bonds : bond 0.13167 ( 486) hydrogen bonds : angle 7.16335 ( 1260) SS BOND : bond 0.00983 ( 23) SS BOND : angle 2.03905 ( 46) covalent geometry : bond 0.00674 (17418) covalent geometry : angle 0.86834 (23659) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4166 Ramachandran restraints generated. 2083 Oldfield, 0 Emsley, 2083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4166 Ramachandran restraints generated. 2083 Oldfield, 0 Emsley, 2083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 220 time to evaluate : 1.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6005 (mtt) cc_final: 0.5790 (mtt) REVERT: A 321 GLN cc_start: 0.8145 (mm110) cc_final: 0.7141 (pp30) REVERT: A 558 LYS cc_start: 0.8768 (mmtm) cc_final: 0.8290 (mmmt) REVERT: B 100 ILE cc_start: 0.8478 (mm) cc_final: 0.8230 (mt) REVERT: B 587 ILE cc_start: 0.8632 (pt) cc_final: 0.8409 (pt) REVERT: D 169 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7823 (tm-30) REVERT: J 64 LYS cc_start: 0.6615 (mmtt) cc_final: 0.6361 (mmtt) REVERT: G 78 TYR cc_start: 0.5934 (m-80) cc_final: 0.5397 (m-80) REVERT: E 23 VAL cc_start: 0.7406 (OUTLIER) cc_final: 0.7070 (m) outliers start: 19 outliers final: 6 residues processed: 232 average time/residue: 0.3113 time to fit residues: 107.6155 Evaluate side-chains 203 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 196 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 80 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 10.0000 chunk 157 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 121 optimal weight: 0.0770 chunk 188 optimal weight: 0.9980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 ASN ** 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 = 0.4372 r_free = 0.4372 target = 0.202633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.140376 restraints weight = 24496.520| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 4.48 r_work: 0.3575 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17477 Z= 0.132 Angle : 0.738 17.584 23810 Z= 0.362 Chirality : 0.050 0.543 2735 Planarity : 0.004 0.049 3000 Dihedral : 8.820 89.246 3039 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.72 % Favored : 92.89 % Rotamer: Outliers : 3.22 % Allowed : 24.93 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.88 (0.18), residues: 2083 helix: 1.47 (0.85), residues: 33 sheet: -0.64 (0.20), residues: 703 loop : -1.74 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 104 HIS 0.008 0.001 HIS E 95 PHE 0.020 0.002 PHE H 67 TYR 0.017 0.001 TYR E 105 ARG 0.005 0.000 ARG H 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00423 ( 35) link_NAG-ASN : angle 4.38832 ( 105) hydrogen bonds : bond 0.03764 ( 486) hydrogen bonds : angle 6.16371 ( 1260) SS BOND : bond 0.00411 ( 23) SS BOND : angle 1.43401 ( 46) covalent geometry : bond 0.00293 (17418) covalent geometry : angle 0.67769 (23659) Misc. bond : bond 0.00038 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4166 Ramachandran restraints generated. 2083 Oldfield, 0 Emsley, 2083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4166 Ramachandran restraints generated. 2083 Oldfield, 0 Emsley, 2083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 215 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.8324 (pt0) cc_final: 0.8066 (pt0) REVERT: A 319 ARG cc_start: 0.8076 (ptp90) cc_final: 0.7618 (mtm110) REVERT: A 558 LYS cc_start: 0.8709 (mmtm) cc_final: 0.8173 (mmmm) REVERT: B 100 ILE cc_start: 0.8206 (mm) cc_final: 0.7983 (mt) REVERT: B 140 PHE cc_start: 0.7583 (p90) cc_final: 0.7246 (p90) REVERT: B 233 ILE cc_start: 0.7486 (pt) cc_final: 0.7221 (pt) REVERT: B 567 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8166 (ptp90) REVERT: D 131 CYS cc_start: 0.2587 (m) cc_final: 0.2147 (m) REVERT: D 229 LEU cc_start: 0.6010 (OUTLIER) cc_final: 0.5721 (tt) REVERT: J 32 GLU cc_start: 0.8386 (tm-30) cc_final: 0.7678 (pt0) REVERT: G 78 TYR cc_start: 0.5907 (m-80) cc_final: 0.5490 (m-80) REVERT: H 81 GLN cc_start: 0.6522 (pm20) cc_final: 0.5803 (pp30) REVERT: E 37 ARG cc_start: 0.6401 (ptm-80) cc_final: 0.6068 (ptm-80) outliers start: 59 outliers final: 33 residues processed: 262 average time/residue: 0.2835 time to fit residues: 112.5488 Evaluate side-chains 228 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 80 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 90 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 chunk 178 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 203 optimal weight: 20.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 655 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 96 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.195948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.134048 restraints weight = 24261.990| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 3.95 r_work: 0.3534 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17477 Z= 0.214 Angle : 0.781 13.683 23810 Z= 0.388 Chirality : 0.051 0.371 2735 Planarity : 0.005 0.053 3000 Dihedral : 7.623 75.310 3031 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.55 % Favored : 91.07 % Rotamer: Outliers : 6.27 % Allowed : 23.30 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.90 (0.17), residues: 2083 helix: 1.42 (0.85), residues: 33 sheet: -0.62 (0.20), residues: 664 loop : -1.74 (0.15), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 104 HIS 0.007 0.002 HIS G 95 PHE 0.024 0.002 PHE B 86 TYR 0.031 0.002 TYR E 105 ARG 0.011 0.001 ARG J 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00779 ( 35) link_NAG-ASN : angle 4.26117 ( 105) hydrogen bonds : bond 0.04411 ( 486) hydrogen bonds : angle 6.05477 ( 1260) SS BOND : bond 0.00395 ( 23) SS BOND : angle 1.77884 ( 46) covalent geometry : bond 0.00506 (17418) covalent geometry : angle 0.72626 (23659) Misc. bond : bond 0.00023 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4166 Ramachandran restraints generated. 2083 Oldfield, 0 Emsley, 2083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4166 Ramachandran restraints generated. 2083 Oldfield, 0 Emsley, 2083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 210 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8037 (t0) cc_final: 0.7537 (t0) REVERT: A 108 THR cc_start: 0.7170 (p) cc_final: 0.6922 (p) REVERT: A 152 TRP cc_start: 0.6817 (t-100) cc_final: 0.6589 (t-100) REVERT: A 319 ARG cc_start: 0.8313 (ptp90) cc_final: 0.7908 (mtm110) REVERT: A 321 GLN cc_start: 0.8314 (mm110) cc_final: 0.7516 (pp30) REVERT: A 558 LYS cc_start: 0.8874 (mmtm) cc_final: 0.8395 (mmmt) REVERT: A 651 ILE cc_start: 0.8661 (pt) cc_final: 0.8383 (pt) REVERT: B 100 ILE cc_start: 0.8378 (mm) cc_final: 0.8133 (mt) REVERT: B 233 ILE cc_start: 0.7626 (pt) cc_final: 0.7374 (pt) REVERT: B 329 PHE cc_start: 0.6987 (t80) cc_final: 0.6716 (t80) REVERT: D 66 HIS cc_start: 0.7347 (OUTLIER) cc_final: 0.6577 (m90) REVERT: D 131 CYS cc_start: 0.2444 (m) cc_final: 0.2048 (m) REVERT: D 229 LEU cc_start: 0.6724 (OUTLIER) cc_final: 0.6361 (tt) REVERT: D 319 ARG cc_start: 0.8525 (ptp90) cc_final: 0.8254 (ttp-110) REVERT: D 630 THR cc_start: 0.7454 (OUTLIER) cc_final: 0.7176 (t) REVERT: F 33 MET cc_start: 0.4793 (mmm) cc_final: 0.4481 (mmt) REVERT: G 78 TYR cc_start: 0.5925 (m-80) cc_final: 0.5629 (m-80) REVERT: H 81 GLN cc_start: 0.6488 (pm20) cc_final: 0.6110 (pp30) REVERT: I 46 GLU cc_start: 0.7620 (tp30) cc_final: 0.7271 (tp30) REVERT: I 104 TRP cc_start: 0.7962 (OUTLIER) cc_final: 0.5891 (m-90) REVERT: I 109 GLN cc_start: 0.8114 (tp-100) cc_final: 0.7806 (tp-100) REVERT: E 84 LEU cc_start: 0.6742 (OUTLIER) cc_final: 0.6423 (mt) outliers start: 115 outliers final: 79 residues processed: 304 average time/residue: 0.2652 time to fit residues: 125.7171 Evaluate side-chains 281 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 197 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 304 LYS Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 590 CYS Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain J residue 5 GLN Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 96 HIS Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 104 TRP Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 84 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 57 optimal weight: 1.9990 chunk 113 optimal weight: 0.3980 chunk 101 optimal weight: 0.4980 chunk 36 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 65 optimal weight: 0.4980 chunk 1 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 607 GLN ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 HIS E 82 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.201525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.140039 restraints weight = 24402.341| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 4.02 r_work: 0.3582 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17477 Z= 0.114 Angle : 0.677 13.683 23810 Z= 0.335 Chirality : 0.048 0.366 2735 Planarity : 0.004 0.038 3000 Dihedral : 6.489 71.415 3028 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.05 % Favored : 93.61 % Rotamer: Outliers : 4.58 % Allowed : 25.75 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.76 (0.18), residues: 2083 helix: 1.66 (0.87), residues: 33 sheet: -0.52 (0.20), residues: 689 loop : -1.67 (0.16), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP D 104 HIS 0.010 0.001 HIS E 95 PHE 0.021 0.001 PHE F 100 TYR 0.015 0.001 TYR E 36 ARG 0.005 0.000 ARG E 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00598 ( 35) link_NAG-ASN : angle 3.70239 ( 105) hydrogen bonds : bond 0.03419 ( 486) hydrogen bonds : angle 5.70426 ( 1260) SS BOND : bond 0.00286 ( 23) SS BOND : angle 1.18837 ( 46) covalent geometry : bond 0.00254 (17418) covalent geometry : angle 0.63066 (23659) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4166 Ramachandran restraints generated. 2083 Oldfield, 0 Emsley, 2083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4166 Ramachandran restraints generated. 2083 Oldfield, 0 Emsley, 2083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 217 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8021 (t0) cc_final: 0.7436 (t0) REVERT: A 319 ARG cc_start: 0.8285 (ptp90) cc_final: 0.7860 (mtm110) REVERT: A 558 LYS cc_start: 0.8796 (mmtm) cc_final: 0.8264 (mmmt) REVERT: B 96 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8289 (tt0) REVERT: B 233 ILE cc_start: 0.7495 (pt) cc_final: 0.7249 (pt) REVERT: B 329 PHE cc_start: 0.6764 (t80) cc_final: 0.6526 (t80) REVERT: B 532 ASN cc_start: 0.7795 (t0) cc_final: 0.7589 (m-40) REVERT: B 567 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.8033 (ptp90) REVERT: D 66 HIS cc_start: 0.6989 (OUTLIER) cc_final: 0.6270 (m90) REVERT: D 145 TYR cc_start: 0.5180 (m-80) cc_final: 0.4810 (m-10) REVERT: D 215 ASP cc_start: 0.7809 (p0) cc_final: 0.7400 (p0) REVERT: D 229 LEU cc_start: 0.6010 (OUTLIER) cc_final: 0.5606 (tt) REVERT: D 319 ARG cc_start: 0.8480 (ptp90) cc_final: 0.8168 (ttp-110) REVERT: D 321 GLN cc_start: 0.7554 (pp30) cc_final: 0.7152 (pp30) REVERT: F 37 ARG cc_start: 0.7003 (tmt170) cc_final: 0.6635 (tmt170) REVERT: F 38 GLN cc_start: 0.6138 (tm-30) cc_final: 0.5779 (tm-30) REVERT: G 78 TYR cc_start: 0.6046 (m-80) cc_final: 0.5791 (m-80) REVERT: H 81 GLN cc_start: 0.6552 (pm20) cc_final: 0.6102 (pp30) REVERT: H 98 ARG cc_start: 0.8071 (ttm170) cc_final: 0.7799 (ttp-170) REVERT: I 46 GLU cc_start: 0.7798 (tp30) cc_final: 0.7449 (tp30) REVERT: I 104 TRP cc_start: 0.7523 (OUTLIER) cc_final: 0.5657 (m-90) REVERT: I 109 GLN cc_start: 0.8034 (tp-100) cc_final: 0.7752 (tp-100) outliers start: 84 outliers final: 53 residues processed: 283 average time/residue: 0.2681 time to fit residues: 116.3746 Evaluate side-chains 248 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 190 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 304 LYS Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 590 CYS Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain J residue 5 GLN Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 96 HIS Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 104 TRP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 95 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 52 optimal weight: 0.9980 chunk 162 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 206 optimal weight: 5.9990 chunk 41 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.196318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.133636 restraints weight = 25149.290| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 4.11 r_work: 0.3537 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17477 Z= 0.177 Angle : 0.720 13.444 23810 Z= 0.359 Chirality : 0.049 0.370 2735 Planarity : 0.004 0.066 3000 Dihedral : 6.500 68.740 3028 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.78 % Favored : 91.93 % Rotamer: Outliers : 6.66 % Allowed : 24.60 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.71 (0.18), residues: 2083 helix: 1.54 (0.86), residues: 33 sheet: -0.45 (0.21), residues: 649 loop : -1.63 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 104 HIS 0.010 0.001 HIS E 95 PHE 0.041 0.002 PHE B 86 TYR 0.025 0.002 TYR E 105 ARG 0.008 0.000 ARG J 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00594 ( 35) link_NAG-ASN : angle 3.83131 ( 105) hydrogen bonds : bond 0.03914 ( 486) hydrogen bonds : angle 5.69373 ( 1260) SS BOND : bond 0.00420 ( 23) SS BOND : angle 1.53302 ( 46) covalent geometry : bond 0.00418 (17418) covalent geometry : angle 0.67195 (23659) Misc. bond : bond 0.00109 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4166 Ramachandran restraints generated. 2083 Oldfield, 0 Emsley, 2083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4166 Ramachandran restraints generated. 2083 Oldfield, 0 Emsley, 2083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 207 time to evaluate : 1.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8340 (m) REVERT: A 88 ASP cc_start: 0.8139 (t0) cc_final: 0.7575 (t0) REVERT: A 152 TRP cc_start: 0.6998 (t-100) cc_final: 0.6665 (t-100) REVERT: A 319 ARG cc_start: 0.8404 (ptp90) cc_final: 0.8004 (mtm110) REVERT: A 321 GLN cc_start: 0.8451 (mm110) cc_final: 0.7602 (pp30) REVERT: A 558 LYS cc_start: 0.8906 (mmtm) cc_final: 0.8454 (mmmt) REVERT: A 651 ILE cc_start: 0.8629 (pt) cc_final: 0.8406 (pt) REVERT: B 96 GLU cc_start: 0.8507 (pt0) cc_final: 0.8279 (tt0) REVERT: B 233 ILE cc_start: 0.7634 (pt) cc_final: 0.7346 (pt) REVERT: B 324 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.6443 (pm20) REVERT: B 329 PHE cc_start: 0.6966 (t80) cc_final: 0.6722 (t80) REVERT: B 567 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8319 (ptp90) REVERT: D 66 HIS cc_start: 0.7213 (OUTLIER) cc_final: 0.6526 (m90) REVERT: D 229 LEU cc_start: 0.6649 (OUTLIER) cc_final: 0.6250 (tt) REVERT: D 319 ARG cc_start: 0.8557 (ptp90) cc_final: 0.8306 (ttp-110) REVERT: D 321 GLN cc_start: 0.7779 (pp30) cc_final: 0.7352 (pp30) REVERT: D 582 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7473 (pp) REVERT: D 630 THR cc_start: 0.7727 (OUTLIER) cc_final: 0.7490 (t) REVERT: F 38 GLN cc_start: 0.6589 (tm-30) cc_final: 0.6340 (tm-30) REVERT: G 78 TYR cc_start: 0.6020 (m-80) cc_final: 0.5703 (m-80) REVERT: G 113 GLN cc_start: 0.2970 (OUTLIER) cc_final: 0.2732 (tm-30) REVERT: H 81 GLN cc_start: 0.6524 (pm20) cc_final: 0.6282 (pp30) REVERT: H 98 ARG cc_start: 0.8437 (ttm170) cc_final: 0.8089 (ttp-110) REVERT: H 109 GLN cc_start: 0.7130 (tp40) cc_final: 0.6822 (tp-100) REVERT: I 104 TRP cc_start: 0.7900 (OUTLIER) cc_final: 0.5987 (m-90) REVERT: I 109 GLN cc_start: 0.8017 (tp-100) cc_final: 0.7743 (tp-100) REVERT: E 101 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7450 (tt) outliers start: 122 outliers final: 86 residues processed: 308 average time/residue: 0.2792 time to fit residues: 132.4861 Evaluate side-chains 286 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 190 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 304 LYS Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 590 CYS Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 640 SER Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain J residue 5 GLN Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 113 GLN Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 96 HIS Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 35 GLU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 104 TRP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 101 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 151 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 188 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 149 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 HIS D 690 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** 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 = 0.4426 r_free = 0.4426 target = 0.200690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.141972 restraints weight = 24580.808| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 4.04 r_work: 0.3621 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17477 Z= 0.197 Angle : 0.754 16.711 23810 Z= 0.374 Chirality : 0.050 0.377 2735 Planarity : 0.004 0.079 3000 Dihedral : 6.626 66.233 3028 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.59 % Favored : 92.13 % Rotamer: Outliers : 7.64 % Allowed : 24.33 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.76 (0.18), residues: 2083 helix: 1.38 (0.85), residues: 33 sheet: -0.43 (0.21), residues: 652 loop : -1.70 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 104 HIS 0.010 0.002 HIS E 95 PHE 0.020 0.002 PHE H 29 TYR 0.028 0.002 TYR E 105 ARG 0.010 0.001 ARG J 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00562 ( 35) link_NAG-ASN : angle 3.90186 ( 105) hydrogen bonds : bond 0.04094 ( 486) hydrogen bonds : angle 5.75535 ( 1260) SS BOND : bond 0.00373 ( 23) SS BOND : angle 1.62054 ( 46) covalent geometry : bond 0.00471 (17418) covalent geometry : angle 0.70643 (23659) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4166 Ramachandran restraints generated. 2083 Oldfield, 0 Emsley, 2083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4166 Ramachandran restraints generated. 2083 Oldfield, 0 Emsley, 2083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 211 time to evaluate : 1.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8320 (t0) cc_final: 0.7760 (t0) REVERT: A 154 GLU cc_start: 0.6657 (tt0) cc_final: 0.6188 (pp20) REVERT: A 319 ARG cc_start: 0.8332 (ptp90) cc_final: 0.8022 (mtm110) REVERT: A 321 GLN cc_start: 0.8375 (mm110) cc_final: 0.7739 (pp30) REVERT: A 558 LYS cc_start: 0.8943 (mmtm) cc_final: 0.8550 (mmmt) REVERT: A 651 ILE cc_start: 0.8772 (pt) cc_final: 0.8549 (pt) REVERT: B 233 ILE cc_start: 0.7779 (pt) cc_final: 0.7497 (pt) REVERT: B 324 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.6651 (pm20) REVERT: B 567 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8343 (ptp90) REVERT: D 66 HIS cc_start: 0.7109 (OUTLIER) cc_final: 0.6412 (m90) REVERT: D 79 PHE cc_start: 0.5492 (OUTLIER) cc_final: 0.4983 (m-10) REVERT: D 321 GLN cc_start: 0.8051 (pp30) cc_final: 0.7631 (pp30) REVERT: J 46 GLU cc_start: 0.7561 (tp30) cc_final: 0.7264 (tp30) REVERT: F 33 MET cc_start: 0.4770 (mmm) cc_final: 0.4133 (mmt) REVERT: F 38 GLN cc_start: 0.6746 (tm-30) cc_final: 0.6523 (tm-30) REVERT: G 3 GLN cc_start: 0.6213 (OUTLIER) cc_final: 0.4439 (mp10) REVERT: G 18 LEU cc_start: 0.3115 (OUTLIER) cc_final: 0.2370 (mt) REVERT: G 78 TYR cc_start: 0.5919 (m-80) cc_final: 0.5583 (m-80) REVERT: G 113 GLN cc_start: 0.2874 (OUTLIER) cc_final: 0.2452 (tp-100) REVERT: H 46 GLU cc_start: 0.7735 (tp30) cc_final: 0.7296 (tp30) REVERT: H 98 ARG cc_start: 0.8568 (ttm170) cc_final: 0.8303 (ttm110) REVERT: I 46 GLU cc_start: 0.7856 (tp30) cc_final: 0.7518 (tp30) REVERT: I 104 TRP cc_start: 0.7938 (OUTLIER) cc_final: 0.6099 (m-90) REVERT: I 109 GLN cc_start: 0.7851 (tp-100) cc_final: 0.7546 (tp-100) REVERT: E 101 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7649 (tt) outliers start: 140 outliers final: 96 residues processed: 329 average time/residue: 0.2933 time to fit residues: 146.9675 Evaluate side-chains 295 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 190 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 304 LYS Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 590 CYS Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 640 SER Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain J residue 5 GLN Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 113 GLN Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 96 HIS Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 35 GLU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 104 TRP Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 101 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 46 optimal weight: 0.9990 chunk 184 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 147 optimal weight: 5.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 HIS ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 GLN H 81 GLN E 57 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.200032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.140827 restraints weight = 24496.869| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 4.08 r_work: 0.3623 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 17477 Z= 0.197 Angle : 0.758 14.563 23810 Z= 0.377 Chirality : 0.050 0.382 2735 Planarity : 0.004 0.059 3000 Dihedral : 6.676 66.308 3028 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.40 % Favored : 91.41 % Rotamer: Outliers : 7.20 % Allowed : 25.64 % Favored : 67.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.82 (0.18), residues: 2083 helix: 1.35 (0.85), residues: 33 sheet: -0.44 (0.21), residues: 660 loop : -1.76 (0.16), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 104 HIS 0.006 0.001 HIS F 57 PHE 0.026 0.002 PHE A 32 TYR 0.027 0.002 TYR E 105 ARG 0.008 0.001 ARG J 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00517 ( 35) link_NAG-ASN : angle 3.93181 ( 105) hydrogen bonds : bond 0.04116 ( 486) hydrogen bonds : angle 5.82812 ( 1260) SS BOND : bond 0.00368 ( 23) SS BOND : angle 1.81069 ( 46) covalent geometry : bond 0.00470 (17418) covalent geometry : angle 0.70894 (23659) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4166 Ramachandran restraints generated. 2083 Oldfield, 0 Emsley, 2083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4166 Ramachandran restraints generated. 2083 Oldfield, 0 Emsley, 2083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 203 time to evaluate : 1.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7872 (pp) REVERT: A 88 ASP cc_start: 0.8324 (t0) cc_final: 0.7705 (t0) REVERT: A 319 ARG cc_start: 0.8300 (ptp90) cc_final: 0.7841 (ttp-110) REVERT: A 321 GLN cc_start: 0.8392 (mm110) cc_final: 0.7787 (pp30) REVERT: A 558 LYS cc_start: 0.8914 (mmtm) cc_final: 0.8543 (mmmt) REVERT: A 651 ILE cc_start: 0.8767 (pt) cc_final: 0.8564 (pt) REVERT: B 96 GLU cc_start: 0.8367 (pt0) cc_final: 0.8030 (tt0) REVERT: B 233 ILE cc_start: 0.7801 (pt) cc_final: 0.7498 (pt) REVERT: B 324 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.6604 (pm20) REVERT: B 567 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8410 (ptp90) REVERT: D 66 HIS cc_start: 0.7062 (OUTLIER) cc_final: 0.6415 (m90) REVERT: D 146 HIS cc_start: 0.5988 (OUTLIER) cc_final: 0.5606 (m-70) REVERT: D 321 GLN cc_start: 0.8095 (pp30) cc_final: 0.7669 (pp30) REVERT: J 46 GLU cc_start: 0.7669 (tp30) cc_final: 0.7375 (tp30) REVERT: F 38 GLN cc_start: 0.6854 (tm-30) cc_final: 0.6626 (tm-30) REVERT: G 3 GLN cc_start: 0.6264 (OUTLIER) cc_final: 0.4531 (mp10) REVERT: G 18 LEU cc_start: 0.3121 (OUTLIER) cc_final: 0.2426 (mt) REVERT: G 78 TYR cc_start: 0.5910 (m-80) cc_final: 0.5406 (m-80) REVERT: H 46 GLU cc_start: 0.7719 (tp30) cc_final: 0.7411 (tp30) REVERT: H 98 ARG cc_start: 0.8635 (ttm170) cc_final: 0.8426 (ttp-110) REVERT: I 46 GLU cc_start: 0.7806 (tp30) cc_final: 0.7540 (tp30) REVERT: I 104 TRP cc_start: 0.8046 (OUTLIER) cc_final: 0.6208 (m-90) REVERT: I 109 GLN cc_start: 0.7713 (tp-100) cc_final: 0.7416 (tp-100) REVERT: E 33 MET cc_start: 0.6681 (mmm) cc_final: 0.6150 (mmm) REVERT: E 101 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7641 (tt) outliers start: 132 outliers final: 102 residues processed: 315 average time/residue: 0.2645 time to fit residues: 127.9670 Evaluate side-chains 298 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 187 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 146 HIS Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 304 LYS Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 590 CYS Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 640 SER Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain J residue 5 GLN Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 57 HIS Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 96 HIS Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 35 GLU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 96 HIS Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 104 TRP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 101 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 118 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 117 optimal weight: 9.9990 chunk 152 optimal weight: 0.9990 chunk 79 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 136 optimal weight: 7.9990 chunk 173 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN D 658 ASN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 GLN E 57 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.204900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.156139 restraints weight = 24397.496| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 4.05 r_work: 0.3702 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17477 Z= 0.143 Angle : 0.717 13.924 23810 Z= 0.356 Chirality : 0.049 0.379 2735 Planarity : 0.004 0.047 3000 Dihedral : 6.424 65.491 3028 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.11 % Favored : 92.70 % Rotamer: Outliers : 6.71 % Allowed : 26.46 % Favored : 66.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.75 (0.18), residues: 2083 helix: 1.52 (0.86), residues: 33 sheet: -0.40 (0.21), residues: 652 loop : -1.70 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 104 HIS 0.005 0.001 HIS F 95 PHE 0.023 0.002 PHE B 643 TYR 0.022 0.002 TYR E 105 ARG 0.006 0.000 ARG D 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00472 ( 35) link_NAG-ASN : angle 3.73405 ( 105) hydrogen bonds : bond 0.03631 ( 486) hydrogen bonds : angle 5.69813 ( 1260) SS BOND : bond 0.00391 ( 23) SS BOND : angle 1.62721 ( 46) covalent geometry : bond 0.00333 (17418) covalent geometry : angle 0.67111 (23659) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4166 Ramachandran restraints generated. 2083 Oldfield, 0 Emsley, 2083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4166 Ramachandran restraints generated. 2083 Oldfield, 0 Emsley, 2083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 200 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7962 (pp) REVERT: A 88 ASP cc_start: 0.8286 (t0) cc_final: 0.7816 (m-30) REVERT: A 319 ARG cc_start: 0.8258 (ptp90) cc_final: 0.7825 (ttp-110) REVERT: A 558 LYS cc_start: 0.8873 (mmtm) cc_final: 0.8511 (mmmt) REVERT: B 233 ILE cc_start: 0.7769 (pt) cc_final: 0.7471 (pt) REVERT: B 324 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.6473 (pm20) REVERT: D 66 HIS cc_start: 0.6974 (OUTLIER) cc_final: 0.6347 (m90) REVERT: D 146 HIS cc_start: 0.5973 (OUTLIER) cc_final: 0.5683 (m-70) REVERT: D 202 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7590 (mttm) REVERT: D 321 GLN cc_start: 0.8077 (pp30) cc_final: 0.7661 (pp30) REVERT: J 13 GLN cc_start: 0.7156 (pp30) cc_final: 0.6819 (tp40) REVERT: J 46 GLU cc_start: 0.7548 (tp30) cc_final: 0.7273 (tp30) REVERT: F 33 MET cc_start: 0.4834 (mmm) cc_final: 0.3553 (mmt) REVERT: F 38 GLN cc_start: 0.6896 (tm-30) cc_final: 0.6673 (tm-30) REVERT: G 3 GLN cc_start: 0.6166 (OUTLIER) cc_final: 0.4484 (mp10) REVERT: G 80 GLU cc_start: 0.4596 (tp30) cc_final: 0.4034 (pt0) REVERT: H 46 GLU cc_start: 0.7652 (tp30) cc_final: 0.7378 (tp30) REVERT: H 98 ARG cc_start: 0.8496 (ttm170) cc_final: 0.8283 (ttp-110) REVERT: H 106 ARG cc_start: 0.6702 (OUTLIER) cc_final: 0.5244 (mmt180) REVERT: H 109 GLN cc_start: 0.7001 (tp40) cc_final: 0.6778 (tp-100) REVERT: I 46 GLU cc_start: 0.7774 (tp30) cc_final: 0.7493 (tp30) REVERT: I 104 TRP cc_start: 0.7918 (OUTLIER) cc_final: 0.6168 (m-90) REVERT: I 109 GLN cc_start: 0.7734 (tp-100) cc_final: 0.7459 (tp-100) REVERT: E 6 GLU cc_start: 0.3470 (tp30) cc_final: 0.2542 (mt-10) REVERT: E 33 MET cc_start: 0.6756 (mmm) cc_final: 0.6423 (mmm) outliers start: 123 outliers final: 91 residues processed: 304 average time/residue: 0.2683 time to fit residues: 124.9355 Evaluate side-chains 289 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 190 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 146 HIS Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 202 LYS Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 304 LYS Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 590 CYS Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 640 SER Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 5 GLN Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 96 HIS Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 35 GLU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 96 HIS Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 104 TRP Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 82 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 153 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 186 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 658 ASN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 HIS ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.202564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.154755 restraints weight = 24627.057| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 4.25 r_work: 0.3677 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17477 Z= 0.168 Angle : 0.733 13.218 23810 Z= 0.365 Chirality : 0.049 0.380 2735 Planarity : 0.004 0.054 3000 Dihedral : 6.461 64.178 3028 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.02 % Favored : 91.79 % Rotamer: Outliers : 6.38 % Allowed : 26.79 % Favored : 66.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.78 (0.18), residues: 2083 helix: 1.35 (0.85), residues: 33 sheet: -0.42 (0.21), residues: 661 loop : -1.73 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 104 HIS 0.005 0.001 HIS F 95 PHE 0.024 0.002 PHE B 329 TYR 0.025 0.002 TYR E 105 ARG 0.007 0.000 ARG J 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00484 ( 35) link_NAG-ASN : angle 3.75073 ( 105) hydrogen bonds : bond 0.03783 ( 486) hydrogen bonds : angle 5.69179 ( 1260) SS BOND : bond 0.00353 ( 23) SS BOND : angle 1.62085 ( 46) covalent geometry : bond 0.00399 (17418) covalent geometry : angle 0.68827 (23659) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4166 Ramachandran restraints generated. 2083 Oldfield, 0 Emsley, 2083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4166 Ramachandran restraints generated. 2083 Oldfield, 0 Emsley, 2083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 194 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7811 (pp) REVERT: A 88 ASP cc_start: 0.8308 (t0) cc_final: 0.7742 (t0) REVERT: A 319 ARG cc_start: 0.8282 (ptp90) cc_final: 0.7865 (ttp-110) REVERT: A 558 LYS cc_start: 0.8903 (mmtm) cc_final: 0.8517 (mmmt) REVERT: A 651 ILE cc_start: 0.8738 (pt) cc_final: 0.8521 (pt) REVERT: B 233 ILE cc_start: 0.7750 (pt) cc_final: 0.7436 (pt) REVERT: B 324 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.6414 (pm20) REVERT: D 66 HIS cc_start: 0.6923 (OUTLIER) cc_final: 0.6305 (m90) REVERT: D 146 HIS cc_start: 0.5933 (OUTLIER) cc_final: 0.5586 (m-70) REVERT: D 202 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7584 (mttm) REVERT: D 321 GLN cc_start: 0.8098 (pp30) cc_final: 0.7686 (pp30) REVERT: J 13 GLN cc_start: 0.7160 (pp30) cc_final: 0.6822 (tp40) REVERT: J 46 GLU cc_start: 0.7573 (tp30) cc_final: 0.7302 (tp30) REVERT: F 33 MET cc_start: 0.4937 (mmm) cc_final: 0.3722 (mmt) REVERT: F 37 ARG cc_start: 0.7159 (tmt170) cc_final: 0.6883 (tmt170) REVERT: F 38 GLN cc_start: 0.6887 (tm-30) cc_final: 0.6653 (tm-30) REVERT: G 3 GLN cc_start: 0.6212 (OUTLIER) cc_final: 0.4514 (mp10) REVERT: G 18 LEU cc_start: 0.3314 (OUTLIER) cc_final: 0.1181 (mt) REVERT: G 33 MET cc_start: 0.7147 (tpt) cc_final: 0.6852 (tpt) REVERT: G 80 GLU cc_start: 0.4641 (tp30) cc_final: 0.4074 (pt0) REVERT: H 46 GLU cc_start: 0.7678 (tp30) cc_final: 0.7400 (tp30) REVERT: H 98 ARG cc_start: 0.8536 (ttm170) cc_final: 0.8307 (ttp-110) REVERT: I 46 GLU cc_start: 0.7780 (tp30) cc_final: 0.7493 (tp30) REVERT: I 104 TRP cc_start: 0.7949 (OUTLIER) cc_final: 0.6152 (m-90) REVERT: I 109 GLN cc_start: 0.7705 (tp-100) cc_final: 0.7439 (tp-100) REVERT: E 33 MET cc_start: 0.6959 (mmm) cc_final: 0.6708 (mmp) outliers start: 117 outliers final: 101 residues processed: 293 average time/residue: 0.2566 time to fit residues: 117.0399 Evaluate side-chains 297 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 188 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 146 HIS Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 202 LYS Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 304 LYS Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 590 CYS Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 640 SER Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 5 GLN Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 57 HIS Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 96 HIS Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 35 GLU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 96 HIS Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 104 TRP Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 82 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 96 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 170 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 190 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 82 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 658 ASN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 HIS E 57 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.204017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.156948 restraints weight = 24498.088| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 4.23 r_work: 0.3686 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17477 Z= 0.140 Angle : 0.711 12.680 23810 Z= 0.353 Chirality : 0.049 0.370 2735 Planarity : 0.004 0.079 3000 Dihedral : 6.300 61.418 3028 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.11 % Favored : 92.70 % Rotamer: Outliers : 6.00 % Allowed : 27.06 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.74 (0.18), residues: 2083 helix: 1.46 (0.86), residues: 33 sheet: -0.44 (0.20), residues: 687 loop : -1.69 (0.16), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 104 HIS 0.005 0.001 HIS F 95 PHE 0.062 0.002 PHE A 32 TYR 0.023 0.002 TYR F 58 ARG 0.016 0.000 ARG J 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00474 ( 35) link_NAG-ASN : angle 3.63539 ( 105) hydrogen bonds : bond 0.03477 ( 486) hydrogen bonds : angle 5.60933 ( 1260) SS BOND : bond 0.00314 ( 23) SS BOND : angle 1.47201 ( 46) covalent geometry : bond 0.00325 (17418) covalent geometry : angle 0.66728 (23659) Misc. bond : bond 0.00002 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4166 Ramachandran restraints generated. 2083 Oldfield, 0 Emsley, 2083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4166 Ramachandran restraints generated. 2083 Oldfield, 0 Emsley, 2083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 198 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8000 (pp) REVERT: A 88 ASP cc_start: 0.8336 (t0) cc_final: 0.7836 (m-30) REVERT: A 319 ARG cc_start: 0.8318 (ptp90) cc_final: 0.8071 (mtm110) REVERT: A 558 LYS cc_start: 0.8899 (mmtm) cc_final: 0.8509 (mmmt) REVERT: B 233 ILE cc_start: 0.7748 (pt) cc_final: 0.7450 (pt) REVERT: B 281 GLU cc_start: 0.7667 (pp20) cc_final: 0.7310 (pm20) REVERT: B 324 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.6354 (pm20) REVERT: D 66 HIS cc_start: 0.6882 (OUTLIER) cc_final: 0.6313 (m90) REVERT: D 146 HIS cc_start: 0.5624 (OUTLIER) cc_final: 0.5355 (m-70) REVERT: D 202 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7776 (mttm) REVERT: D 321 GLN cc_start: 0.8095 (pp30) cc_final: 0.7678 (pp30) REVERT: J 13 GLN cc_start: 0.7145 (pp30) cc_final: 0.6837 (tp40) REVERT: J 46 GLU cc_start: 0.7572 (tp30) cc_final: 0.7285 (tp30) REVERT: F 33 MET cc_start: 0.5044 (mmm) cc_final: 0.3847 (mmt) REVERT: F 37 ARG cc_start: 0.7193 (tmt170) cc_final: 0.6917 (tmt170) REVERT: F 38 GLN cc_start: 0.6893 (tm-30) cc_final: 0.6660 (tm-30) REVERT: G 3 GLN cc_start: 0.6138 (OUTLIER) cc_final: 0.4456 (mp10) REVERT: G 18 LEU cc_start: 0.3290 (OUTLIER) cc_final: 0.2650 (mt) REVERT: G 33 MET cc_start: 0.7127 (tpt) cc_final: 0.6841 (tpt) REVERT: H 46 GLU cc_start: 0.7697 (tp30) cc_final: 0.7420 (tp30) REVERT: H 106 ARG cc_start: 0.6691 (OUTLIER) cc_final: 0.5283 (mmt180) REVERT: I 46 GLU cc_start: 0.7767 (tp30) cc_final: 0.7466 (tp30) REVERT: I 104 TRP cc_start: 0.7875 (OUTLIER) cc_final: 0.6163 (m-90) REVERT: I 109 GLN cc_start: 0.7661 (tp-100) cc_final: 0.7365 (tp-100) REVERT: E 33 MET cc_start: 0.6954 (mmm) cc_final: 0.6646 (mmp) REVERT: E 50 ILE cc_start: 0.6979 (pt) cc_final: 0.6623 (tp) outliers start: 110 outliers final: 94 residues processed: 288 average time/residue: 0.2695 time to fit residues: 120.2616 Evaluate side-chains 292 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 189 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 146 HIS Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 202 LYS Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 304 LYS Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 590 CYS Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 640 SER Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 5 GLN Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 96 HIS Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain I residue 13 GLN Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 35 GLU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 96 HIS Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 104 TRP Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 82 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 11 optimal weight: 1.9990 chunk 157 optimal weight: 8.9990 chunk 37 optimal weight: 0.7980 chunk 197 optimal weight: 0.0970 chunk 70 optimal weight: 0.0370 chunk 115 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 200 optimal weight: 10.0000 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 658 ASN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 HIS ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.205965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.157847 restraints weight = 24439.189| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 4.28 r_work: 0.3715 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17477 Z= 0.125 Angle : 0.685 12.313 23810 Z= 0.341 Chirality : 0.048 0.367 2735 Planarity : 0.004 0.044 3000 Dihedral : 5.954 55.114 3028 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.82 % Favored : 92.99 % Rotamer: Outliers : 5.78 % Allowed : 27.66 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.65 (0.18), residues: 2083 helix: 1.52 (0.86), residues: 33 sheet: -0.36 (0.21), residues: 655 loop : -1.62 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 152 HIS 0.008 0.001 HIS D 146 PHE 0.044 0.002 PHE A 32 TYR 0.017 0.001 TYR D 145 ARG 0.009 0.000 ARG J 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00496 ( 35) link_NAG-ASN : angle 3.50630 ( 105) hydrogen bonds : bond 0.03263 ( 486) hydrogen bonds : angle 5.46035 ( 1260) SS BOND : bond 0.00276 ( 23) SS BOND : angle 1.34200 ( 46) covalent geometry : bond 0.00286 (17418) covalent geometry : angle 0.64402 (23659) Misc. bond : bond 0.00162 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9833.03 seconds wall clock time: 168 minutes 54.90 seconds (10134.90 seconds total)