Starting phenix.real_space_refine on Thu Feb 5 11:04:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g78_29802/02_2026/8g78_29802.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g78_29802/02_2026/8g78_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 { model { file = "/net/cci-nas-00/data/ceres_data/8g78_29802/02_2026/8g78_29802.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g78_29802/02_2026/8g78_29802.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g78_29802/02_2026/8g78_29802.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g78_29802/02_2026/8g78_29802.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/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: 4.44, per 1000 atoms: 0.26 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: 1.50 Conformation dependent library (CDL) restraints added in 802.8 milliseconds 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: 0.69 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: 2.67 Time building geometry restraints manager: 2.06 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 1311)) selection = (chain 'B' and (resid 15 through 178 or resid 184 through 622 or resid 632 throu \ gh 676 or resid 690 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 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: 5.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.150 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.480 ------------------------------------------------------------------------------- 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 : 14.61 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (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 ARG 0.012 0.001 ARG J 53 TYR 0.026 0.002 TYR E 105 PHE 0.025 0.003 PHE B 86 TRP 0.042 0.003 TRP D 104 HIS 0.009 0.002 HIS I 38 Details of bonding type rmsd covalent geometry : bond 0.00674 (17418) covalent geometry : angle 0.86834 (23659) SS BOND : bond 0.00983 ( 23) SS BOND : angle 2.03905 ( 46) hydrogen bonds : bond 0.13167 ( 486) hydrogen bonds : angle 7.16335 ( 1260) Misc. bond : bond 0.00002 ( 1) link_NAG-ASN : bond 0.04110 ( 35) link_NAG-ASN : angle 5.11018 ( 105) *********************** 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 : 0.650 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: 0.1289 time to fit residues: 44.7002 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 : 0.635 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.7980 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.6980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 641 ASN ** 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** E 75 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.197577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.134297 restraints weight = 24765.890| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 4.10 r_work: 0.3543 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17477 Z= 0.209 Angle : 0.802 15.530 23810 Z= 0.396 Chirality : 0.052 0.564 2735 Planarity : 0.005 0.053 3000 Dihedral : 8.677 82.939 3039 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.59 % Favored : 92.03 % Rotamer: Outliers : 5.56 % Allowed : 23.35 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.18), residues: 2083 helix: 1.10 (0.82), residues: 33 sheet: -0.85 (0.19), residues: 761 loop : -1.77 (0.16), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 53 TYR 0.029 0.002 TYR E 105 PHE 0.024 0.002 PHE A 32 TRP 0.025 0.002 TRP D 104 HIS 0.008 0.001 HIS E 95 Details of bonding type rmsd covalent geometry : bond 0.00497 (17418) covalent geometry : angle 0.74489 (23659) SS BOND : bond 0.00419 ( 23) SS BOND : angle 1.76661 ( 46) hydrogen bonds : bond 0.04446 ( 486) hydrogen bonds : angle 6.24659 ( 1260) Misc. bond : bond 0.00036 ( 1) link_NAG-ASN : bond 0.00482 ( 35) link_NAG-ASN : angle 4.41899 ( 105) *********************** 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 322 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 220 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.7075 (p) cc_final: 0.6763 (p) REVERT: A 152 TRP cc_start: 0.6766 (t-100) cc_final: 0.6500 (t-100) REVERT: A 319 ARG cc_start: 0.8253 (ptp90) cc_final: 0.7844 (mtm110) REVERT: A 321 GLN cc_start: 0.8125 (mm110) cc_final: 0.7350 (pp30) REVERT: A 558 LYS cc_start: 0.8868 (mmtm) cc_final: 0.8401 (mmmm) REVERT: B 100 ILE cc_start: 0.8486 (mm) cc_final: 0.8221 (mt) REVERT: B 233 ILE cc_start: 0.7622 (pt) cc_final: 0.7334 (pt) REVERT: B 567 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8328 (ptp90) REVERT: D 131 CYS cc_start: 0.2737 (m) cc_final: 0.2316 (m) REVERT: D 229 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6366 (tt) REVERT: G 78 TYR cc_start: 0.5829 (m-80) cc_final: 0.5421 (m-80) REVERT: I 104 TRP cc_start: 0.7909 (OUTLIER) cc_final: 0.5828 (m-90) outliers start: 102 outliers final: 60 residues processed: 306 average time/residue: 0.1186 time to fit residues: 55.5506 Evaluate side-chains 252 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 189 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 645 THR Chi-restraints excluded: chain A residue 696 THR 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 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 D residue 63 THR 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 266 TYR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 290 ASP 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 602 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 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 68 ILE 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 104 TRP Chi-restraints excluded: chain E residue 47 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 141 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 136 optimal weight: 0.6980 chunk 163 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 48 optimal weight: 0.0050 chunk 3 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 606 ASN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.201313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.139229 restraints weight = 24595.454| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 4.09 r_work: 0.3582 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17477 Z= 0.122 Angle : 0.687 12.866 23810 Z= 0.341 Chirality : 0.048 0.365 2735 Planarity : 0.004 0.043 3000 Dihedral : 7.128 72.575 3031 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.48 % Favored : 93.13 % Rotamer: Outliers : 4.26 % Allowed : 25.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.18), residues: 2083 helix: 1.63 (0.88), residues: 33 sheet: -0.67 (0.19), residues: 718 loop : -1.68 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 66 TYR 0.017 0.001 TYR E 105 PHE 0.016 0.001 PHE B 194 TRP 0.036 0.001 TRP D 104 HIS 0.007 0.001 HIS E 95 Details of bonding type rmsd covalent geometry : bond 0.00268 (17418) covalent geometry : angle 0.63869 (23659) SS BOND : bond 0.00305 ( 23) SS BOND : angle 1.27016 ( 46) hydrogen bonds : bond 0.03548 ( 486) hydrogen bonds : angle 5.82548 ( 1260) Misc. bond : bond 0.00014 ( 1) link_NAG-ASN : bond 0.00660 ( 35) link_NAG-ASN : angle 3.79475 ( 105) *********************** 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 300 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 222 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7985 (t0) cc_final: 0.7476 (t0) REVERT: A 319 ARG cc_start: 0.8249 (ptp90) cc_final: 0.7809 (mtm110) REVERT: A 558 LYS cc_start: 0.8798 (mmtm) cc_final: 0.8275 (mmmt) REVERT: B 233 ILE cc_start: 0.7523 (pt) cc_final: 0.7261 (pt) REVERT: B 329 PHE cc_start: 0.6724 (t80) cc_final: 0.6505 (t80) REVERT: B 532 ASN cc_start: 0.7749 (t0) cc_final: 0.7538 (m-40) REVERT: B 567 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8106 (ptp90) REVERT: D 66 HIS cc_start: 0.7073 (OUTLIER) cc_final: 0.6315 (m90) REVERT: D 145 TYR cc_start: 0.5157 (m-80) cc_final: 0.4829 (m-10) REVERT: D 229 LEU cc_start: 0.6188 (OUTLIER) cc_final: 0.5827 (tt) REVERT: J 32 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7899 (pt0) REVERT: J 46 GLU cc_start: 0.7714 (tp30) cc_final: 0.7102 (tp30) REVERT: F 38 GLN cc_start: 0.6385 (tm-30) cc_final: 0.5983 (tm-30) REVERT: G 78 TYR cc_start: 0.5998 (m-80) cc_final: 0.5795 (m-80) REVERT: H 81 GLN cc_start: 0.6619 (pm20) cc_final: 0.5947 (pp30) REVERT: I 35 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6572 (pt0) REVERT: I 46 GLU cc_start: 0.7605 (tp30) cc_final: 0.7280 (tp30) REVERT: I 104 TRP cc_start: 0.7664 (OUTLIER) cc_final: 0.5680 (m-90) REVERT: I 109 GLN cc_start: 0.8030 (tp-100) cc_final: 0.7732 (tp-100) REVERT: E 93 TYR cc_start: 0.5759 (m-80) cc_final: 0.5501 (m-80) outliers start: 78 outliers final: 47 residues processed: 277 average time/residue: 0.1171 time to fit residues: 49.2548 Evaluate side-chains 244 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 192 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 212 LEU Chi-restraints excluded: chain A residue 228 ASP 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 584 ILE Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 130 VAL 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 585 LEU Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 66 HIS 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 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 602 THR Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 697 MET 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 G residue 2 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 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 35 GLU 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 77 VAL Chi-restraints excluded: chain E residue 80 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 141 optimal weight: 0.4980 chunk 94 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 77 optimal weight: 8.9990 chunk 195 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 205 optimal weight: 0.6980 chunk 197 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 201 optimal weight: 20.0000 chunk 202 optimal weight: 8.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 607 GLN ** 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.199496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.136830 restraints weight = 25046.212| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 4.14 r_work: 0.3573 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17477 Z= 0.132 Angle : 0.682 13.088 23810 Z= 0.338 Chirality : 0.048 0.365 2735 Planarity : 0.004 0.039 3000 Dihedral : 6.418 70.917 3028 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.77 % Favored : 92.94 % Rotamer: Outliers : 6.22 % Allowed : 24.33 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.18), residues: 2083 helix: 1.69 (0.88), residues: 33 sheet: -0.38 (0.21), residues: 636 loop : -1.66 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 53 TYR 0.021 0.001 TYR A 144 PHE 0.016 0.002 PHE A 59 TRP 0.022 0.001 TRP D 104 HIS 0.007 0.001 HIS E 95 Details of bonding type rmsd covalent geometry : bond 0.00304 (17418) covalent geometry : angle 0.63260 (23659) SS BOND : bond 0.00319 ( 23) SS BOND : angle 1.33191 ( 46) hydrogen bonds : bond 0.03570 ( 486) hydrogen bonds : angle 5.63318 ( 1260) Misc. bond : bond 0.00010 ( 1) link_NAG-ASN : bond 0.00553 ( 35) link_NAG-ASN : angle 3.79420 ( 105) *********************** 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 324 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 210 time to evaluate : 0.427 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: 0.8136 (t0) cc_final: 0.7621 (t0) REVERT: A 152 TRP cc_start: 0.6865 (t-100) cc_final: 0.6513 (t-100) REVERT: A 154 GLU cc_start: 0.6207 (tt0) cc_final: 0.5634 (pp20) REVERT: A 319 ARG cc_start: 0.8359 (ptp90) cc_final: 0.7955 (mtm110) REVERT: A 321 GLN cc_start: 0.8321 (mm110) cc_final: 0.7423 (pp30) REVERT: A 558 LYS cc_start: 0.8887 (mmtm) cc_final: 0.8420 (mmmt) REVERT: B 233 ILE cc_start: 0.7616 (pt) cc_final: 0.7329 (pt) REVERT: B 329 PHE cc_start: 0.6943 (t80) cc_final: 0.6712 (t80) REVERT: D 66 HIS cc_start: 0.7106 (OUTLIER) cc_final: 0.6454 (m90) REVERT: D 145 TYR cc_start: 0.5287 (m-80) cc_final: 0.4967 (m-10) REVERT: D 229 LEU cc_start: 0.6450 (OUTLIER) cc_final: 0.6104 (tt) REVERT: D 321 GLN cc_start: 0.7608 (pp30) cc_final: 0.7219 (pp30) REVERT: J 34 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.6965 (ttm) REVERT: J 35 GLU cc_start: 0.8110 (pt0) cc_final: 0.7859 (pt0) REVERT: F 33 MET cc_start: 0.4680 (mmm) cc_final: 0.4158 (mmt) REVERT: F 38 GLN cc_start: 0.6506 (tm-30) cc_final: 0.6095 (tm-30) REVERT: G 78 TYR cc_start: 0.5987 (m-80) cc_final: 0.5705 (m-80) REVERT: G 113 GLN cc_start: 0.2807 (OUTLIER) cc_final: 0.2440 (tm-30) REVERT: H 81 GLN cc_start: 0.6322 (pm20) cc_final: 0.5812 (pp30) REVERT: H 98 ARG cc_start: 0.8296 (ttm170) cc_final: 0.7905 (ttp-110) REVERT: H 109 GLN cc_start: 0.7213 (tp40) cc_final: 0.6922 (tp-100) REVERT: I 35 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6745 (pt0) REVERT: I 104 TRP cc_start: 0.7843 (OUTLIER) cc_final: 0.5867 (m-90) REVERT: I 109 GLN cc_start: 0.8057 (tp-100) cc_final: 0.7727 (tp-100) outliers start: 114 outliers final: 75 residues processed: 304 average time/residue: 0.1151 time to fit residues: 54.0702 Evaluate side-chains 273 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 192 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 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 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 242 LEU Chi-restraints excluded: chain A residue 312 ILE 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 47 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 63 THR 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 316 SER Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU 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 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 304 LYS Chi-restraints excluded: chain D residue 549 THR 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 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 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 80 GLU Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 101 LEU 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 122 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 chunk 196 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 153 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 127 optimal weight: 0.9980 chunk 191 optimal weight: 0.0270 chunk 148 optimal weight: 0.0970 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 GLN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.201930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.139713 restraints weight = 25078.346| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 4.15 r_work: 0.3613 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17477 Z= 0.109 Angle : 0.656 15.778 23810 Z= 0.323 Chirality : 0.047 0.404 2735 Planarity : 0.004 0.062 3000 Dihedral : 5.971 67.677 3028 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.10 % Favored : 93.61 % Rotamer: Outliers : 5.35 % Allowed : 25.59 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.18), residues: 2083 helix: 1.73 (0.88), residues: 33 sheet: -0.38 (0.20), residues: 656 loop : -1.63 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 37 TYR 0.018 0.001 TYR H 59 PHE 0.016 0.001 PHE B 194 TRP 0.017 0.001 TRP D 104 HIS 0.006 0.001 HIS E 95 Details of bonding type rmsd covalent geometry : bond 0.00239 (17418) covalent geometry : angle 0.61118 (23659) SS BOND : bond 0.00352 ( 23) SS BOND : angle 1.09514 ( 46) hydrogen bonds : bond 0.03257 ( 486) hydrogen bonds : angle 5.47660 ( 1260) Misc. bond : bond 0.00007 ( 1) link_NAG-ASN : bond 0.00581 ( 35) link_NAG-ASN : angle 3.60060 ( 105) *********************** 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 303 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 205 time to evaluate : 0.541 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: 0.8176 (t0) cc_final: 0.7703 (t0) REVERT: A 154 GLU cc_start: 0.6233 (tt0) cc_final: 0.5785 (pp20) REVERT: A 319 ARG cc_start: 0.8344 (ptp90) cc_final: 0.7939 (mtm110) REVERT: A 558 LYS cc_start: 0.8887 (mmtm) cc_final: 0.8429 (mmmt) REVERT: B 96 GLU cc_start: 0.8500 (pt0) cc_final: 0.8186 (tt0) REVERT: B 233 ILE cc_start: 0.7568 (pt) cc_final: 0.7275 (pt) REVERT: B 324 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.6401 (pm20) REVERT: B 567 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8181 (ptp90) REVERT: D 63 THR cc_start: 0.8058 (OUTLIER) cc_final: 0.7769 (m) REVERT: D 66 HIS cc_start: 0.6999 (OUTLIER) cc_final: 0.6332 (m90) REVERT: D 145 TYR cc_start: 0.5278 (m-80) cc_final: 0.4932 (m-10) REVERT: D 229 LEU cc_start: 0.6255 (OUTLIER) cc_final: 0.5904 (tt) REVERT: D 321 GLN cc_start: 0.7711 (pp30) cc_final: 0.7291 (pp30) REVERT: J 35 GLU cc_start: 0.8049 (pt0) cc_final: 0.7795 (pt0) REVERT: F 38 GLN cc_start: 0.6594 (tm-30) cc_final: 0.6372 (tm-30) REVERT: F 81 MET cc_start: 0.4849 (ptt) cc_final: 0.4630 (ptm) REVERT: H 46 GLU cc_start: 0.7517 (tp30) cc_final: 0.7293 (tp30) REVERT: H 81 GLN cc_start: 0.6389 (pm20) cc_final: 0.5985 (pp30) REVERT: H 98 ARG cc_start: 0.8228 (ttm170) cc_final: 0.7938 (ttp-110) REVERT: H 106 ARG cc_start: 0.6482 (OUTLIER) cc_final: 0.5029 (mmt180) REVERT: H 109 GLN cc_start: 0.7096 (tp40) cc_final: 0.6829 (tp-100) REVERT: I 35 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6619 (pt0) REVERT: I 104 TRP cc_start: 0.7760 (OUTLIER) cc_final: 0.5826 (m-90) REVERT: I 109 GLN cc_start: 0.8056 (tp-100) cc_final: 0.7756 (tp-100) REVERT: E 6 GLU cc_start: 0.4768 (OUTLIER) cc_final: 0.2561 (pt0) outliers start: 98 outliers final: 67 residues processed: 282 average time/residue: 0.1207 time to fit residues: 52.1673 Evaluate side-chains 261 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 185 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 79 PHE 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 242 LEU Chi-restraints excluded: chain A residue 276 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 585 LEU Chi-restraints excluded: chain A residue 595 VAL 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 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 240 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 553 THR Chi-restraints excluded: chain B residue 567 ARG 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 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 290 ASP Chi-restraints excluded: chain D residue 304 LYS 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 645 THR Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain J residue 7 SER 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 F residue 7 SER Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain H residue 4 LEU 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 I residue 4 LEU 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 51 ILE Chi-restraints excluded: chain I residue 60 SER 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 6 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 93 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 183 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 178 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 B 30 ASN B 69 HIS ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 655 HIS D 690 GLN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.196662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.142776 restraints weight = 23926.750| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 3.60 r_work: 0.3549 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 17477 Z= 0.303 Angle : 0.850 16.591 23810 Z= 0.427 Chirality : 0.054 0.386 2735 Planarity : 0.005 0.075 3000 Dihedral : 7.031 67.041 3028 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.12 % Favored : 90.64 % Rotamer: Outliers : 7.26 % Allowed : 24.39 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.18), residues: 2083 helix: 1.18 (0.83), residues: 33 sheet: -0.43 (0.21), residues: 633 loop : -1.81 (0.15), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 53 TYR 0.035 0.003 TYR E 105 PHE 0.029 0.003 PHE H 29 TRP 0.027 0.002 TRP D 104 HIS 0.011 0.002 HIS G 71 Details of bonding type rmsd covalent geometry : bond 0.00734 (17418) covalent geometry : angle 0.80013 (23659) SS BOND : bond 0.00465 ( 23) SS BOND : angle 1.84333 ( 46) hydrogen bonds : bond 0.04853 ( 486) hydrogen bonds : angle 6.04806 ( 1260) Misc. bond : bond 0.00010 ( 1) link_NAG-ASN : bond 0.00626 ( 35) link_NAG-ASN : angle 4.23337 ( 105) *********************** 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 335 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 202 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8133 (t0) cc_final: 0.7583 (t0) REVERT: A 152 TRP cc_start: 0.7154 (t-100) cc_final: 0.6909 (t-100) REVERT: A 154 GLU cc_start: 0.6549 (tt0) cc_final: 0.6294 (pp20) REVERT: A 319 ARG cc_start: 0.8267 (ptp90) cc_final: 0.7874 (ttm110) REVERT: A 321 GLN cc_start: 0.8260 (mm110) cc_final: 0.7818 (pp30) REVERT: A 558 LYS cc_start: 0.8883 (mmtm) cc_final: 0.8589 (mmmt) REVERT: A 651 ILE cc_start: 0.8815 (pt) cc_final: 0.8545 (pt) REVERT: B 233 ILE cc_start: 0.7834 (pt) cc_final: 0.7544 (pt) REVERT: B 324 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.6753 (pm20) REVERT: D 66 HIS cc_start: 0.7218 (OUTLIER) cc_final: 0.6558 (m90) REVERT: D 79 PHE cc_start: 0.5715 (OUTLIER) cc_final: 0.5256 (m-10) REVERT: D 145 TYR cc_start: 0.5620 (m-80) cc_final: 0.5335 (m-10) REVERT: D 202 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7750 (mttm) REVERT: D 321 GLN cc_start: 0.7993 (pp30) cc_final: 0.7589 (pp30) REVERT: J 46 GLU cc_start: 0.7334 (tp30) cc_final: 0.7087 (tp30) REVERT: F 33 MET cc_start: 0.4694 (mmm) cc_final: 0.3579 (mmt) REVERT: F 38 GLN cc_start: 0.6911 (tm-30) cc_final: 0.6669 (tm-30) REVERT: G 3 GLN cc_start: 0.6243 (OUTLIER) cc_final: 0.4466 (mp10) REVERT: G 18 LEU cc_start: 0.3240 (OUTLIER) cc_final: 0.2457 (mt) REVERT: G 89 THR cc_start: 0.4767 (OUTLIER) cc_final: 0.4564 (p) REVERT: I 104 TRP cc_start: 0.8148 (OUTLIER) cc_final: 0.6311 (m-90) REVERT: I 109 GLN cc_start: 0.7783 (tp-100) cc_final: 0.7496 (tp-100) outliers start: 133 outliers final: 90 residues processed: 315 average time/residue: 0.1092 time to fit residues: 53.7378 Evaluate side-chains 284 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 186 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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 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 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 642 VAL 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 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 175 PHE Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 240 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 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 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 197 ILE Chi-restraints excluded: chain D residue 202 LYS Chi-restraints excluded: chain D residue 304 LYS 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 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 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 89 THR 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 106 ARG Chi-restraints excluded: chain I residue 4 LEU 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 60 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 113 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 108 optimal weight: 8.9990 chunk 139 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN D 658 ASN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN I 96 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.202388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.151089 restraints weight = 23912.345| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 3.80 r_work: 0.3620 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17477 Z= 0.133 Angle : 0.703 14.061 23810 Z= 0.349 Chirality : 0.049 0.379 2735 Planarity : 0.004 0.059 3000 Dihedral : 6.413 66.954 3028 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.48 % Favored : 93.28 % Rotamer: Outliers : 6.33 % Allowed : 25.48 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.18), residues: 2083 helix: 1.64 (0.87), residues: 33 sheet: -0.38 (0.21), residues: 652 loop : -1.71 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 53 TYR 0.021 0.001 TYR E 105 PHE 0.024 0.002 PHE B 32 TRP 0.048 0.002 TRP D 104 HIS 0.008 0.001 HIS E 95 Details of bonding type rmsd covalent geometry : bond 0.00306 (17418) covalent geometry : angle 0.65697 (23659) SS BOND : bond 0.00299 ( 23) SS BOND : angle 1.39504 ( 46) hydrogen bonds : bond 0.03611 ( 486) hydrogen bonds : angle 5.71443 ( 1260) Misc. bond : bond 0.00020 ( 1) link_NAG-ASN : bond 0.00547 ( 35) link_NAG-ASN : angle 3.75428 ( 105) *********************** 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 311 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 195 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8007 (pp) REVERT: A 88 ASP cc_start: 0.8107 (t0) cc_final: 0.7714 (m-30) REVERT: A 154 GLU cc_start: 0.6527 (tt0) cc_final: 0.6298 (pp20) REVERT: A 319 ARG cc_start: 0.8161 (ptp90) cc_final: 0.7747 (ttp-110) REVERT: A 321 GLN cc_start: 0.8275 (mm110) cc_final: 0.7798 (pp30) REVERT: A 558 LYS cc_start: 0.8804 (mmtm) cc_final: 0.8528 (mmmt) REVERT: B 233 ILE cc_start: 0.7768 (pt) cc_final: 0.7464 (pt) REVERT: B 324 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.6754 (pm20) REVERT: D 66 HIS cc_start: 0.7064 (OUTLIER) cc_final: 0.6445 (m90) REVERT: D 145 TYR cc_start: 0.5469 (m-80) cc_final: 0.5187 (m-10) REVERT: D 321 GLN cc_start: 0.7930 (pp30) cc_final: 0.7505 (pp30) REVERT: J 13 GLN cc_start: 0.7245 (pp30) cc_final: 0.6914 (tp40) REVERT: J 46 GLU cc_start: 0.7367 (tp30) cc_final: 0.7116 (tp30) REVERT: F 38 GLN cc_start: 0.6989 (tm-30) cc_final: 0.6743 (tm-30) REVERT: F 81 MET cc_start: 0.5328 (ptt) cc_final: 0.5065 (ptm) REVERT: G 78 TYR cc_start: 0.5482 (m-80) cc_final: 0.5238 (m-80) REVERT: H 46 GLU cc_start: 0.7367 (tp30) cc_final: 0.6971 (tp30) REVERT: H 81 GLN cc_start: 0.5967 (OUTLIER) cc_final: 0.5641 (pp30) REVERT: H 106 ARG cc_start: 0.6432 (OUTLIER) cc_final: 0.5012 (mmt180) REVERT: I 46 GLU cc_start: 0.7640 (tp30) cc_final: 0.7332 (tp30) REVERT: I 104 TRP cc_start: 0.7925 (OUTLIER) cc_final: 0.6231 (m-90) outliers start: 116 outliers final: 83 residues processed: 293 average time/residue: 0.1120 time to fit residues: 51.6093 Evaluate side-chains 273 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 184 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 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 642 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 87 ASN Chi-restraints excluded: chain B residue 105 ILE 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 218 GLN Chi-restraints excluded: chain B residue 240 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 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 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 304 LYS 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 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 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 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 81 GLN Chi-restraints excluded: chain H residue 96 HIS Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 60 SER 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 72 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 175 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 94 optimal weight: 20.0000 chunk 201 optimal weight: 10.0000 chunk 125 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 HIS ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN I 96 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.198962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.145875 restraints weight = 23869.407| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 3.44 r_work: 0.3574 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17477 Z= 0.183 Angle : 0.736 13.506 23810 Z= 0.367 Chirality : 0.050 0.379 2735 Planarity : 0.004 0.052 3000 Dihedral : 6.484 66.594 3028 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.55 % Favored : 91.26 % Rotamer: Outliers : 6.49 % Allowed : 25.75 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.18), residues: 2083 helix: 1.54 (0.87), residues: 33 sheet: -0.39 (0.21), residues: 661 loop : -1.76 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 37 TYR 0.026 0.002 TYR E 105 PHE 0.025 0.002 PHE H 29 TRP 0.044 0.002 TRP D 104 HIS 0.005 0.001 HIS F 95 Details of bonding type rmsd covalent geometry : bond 0.00438 (17418) covalent geometry : angle 0.68934 (23659) SS BOND : bond 0.00346 ( 23) SS BOND : angle 1.53624 ( 46) hydrogen bonds : bond 0.03920 ( 486) hydrogen bonds : angle 5.67207 ( 1260) Misc. bond : bond 0.00009 ( 1) link_NAG-ASN : bond 0.00556 ( 35) link_NAG-ASN : angle 3.84054 ( 105) *********************** 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 311 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 192 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7834 (pp) REVERT: A 88 ASP cc_start: 0.8200 (t0) cc_final: 0.7613 (t0) REVERT: A 319 ARG cc_start: 0.8193 (ptp90) cc_final: 0.7784 (ttp-110) REVERT: A 321 GLN cc_start: 0.8232 (mm110) cc_final: 0.7792 (pp30) REVERT: A 558 LYS cc_start: 0.8830 (mmtm) cc_final: 0.8574 (mmmt) REVERT: A 651 ILE cc_start: 0.8740 (pt) cc_final: 0.8519 (pt) REVERT: B 233 ILE cc_start: 0.7790 (pt) cc_final: 0.7474 (pt) REVERT: B 324 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.6697 (pm20) REVERT: D 66 HIS cc_start: 0.7123 (OUTLIER) cc_final: 0.6508 (m90) REVERT: D 145 TYR cc_start: 0.5369 (m-80) cc_final: 0.5161 (m-10) REVERT: D 202 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7766 (mttm) REVERT: D 233 ILE cc_start: 0.6756 (OUTLIER) cc_final: 0.6191 (tt) REVERT: D 321 GLN cc_start: 0.7988 (pp30) cc_final: 0.7593 (pp30) REVERT: J 46 GLU cc_start: 0.7460 (tp30) cc_final: 0.7208 (tp30) REVERT: F 33 MET cc_start: 0.4738 (mmm) cc_final: 0.4250 (mmt) REVERT: F 38 GLN cc_start: 0.7043 (tm-30) cc_final: 0.6813 (tm-30) REVERT: F 81 MET cc_start: 0.5270 (ptt) cc_final: 0.4975 (ptm) REVERT: G 3 GLN cc_start: 0.6252 (OUTLIER) cc_final: 0.4550 (mp10) REVERT: H 46 GLU cc_start: 0.7490 (tp30) cc_final: 0.7104 (tp30) REVERT: H 81 GLN cc_start: 0.5922 (OUTLIER) cc_final: 0.5546 (pp30) REVERT: I 46 GLU cc_start: 0.7692 (tp30) cc_final: 0.7419 (tp30) REVERT: I 81 GLN cc_start: 0.6229 (pp30) cc_final: 0.6020 (pp30) REVERT: I 104 TRP cc_start: 0.8034 (OUTLIER) cc_final: 0.6343 (m-90) REVERT: I 109 GLN cc_start: 0.7368 (tp-100) cc_final: 0.7112 (tp-100) REVERT: E 33 MET cc_start: 0.6603 (mmm) cc_final: 0.5859 (mmm) outliers start: 119 outliers final: 96 residues processed: 293 average time/residue: 0.1093 time to fit residues: 49.6487 Evaluate side-chains 288 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 184 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 79 PHE Chi-restraints excluded: chain A residue 84 LEU 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 642 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 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 175 PHE Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 240 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 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 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 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 202 LYS Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 304 LYS 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 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 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 81 GLN 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 4 LEU Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 60 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 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 34 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 190 optimal weight: 7.9990 chunk 180 optimal weight: 0.3980 chunk 176 optimal weight: 9.9990 chunk 195 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 658 ASN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.198111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.157946 restraints weight = 23809.859| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 5.24 r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17477 Z= 0.207 Angle : 0.766 14.357 23810 Z= 0.382 Chirality : 0.051 0.384 2735 Planarity : 0.004 0.069 3000 Dihedral : 6.662 67.210 3028 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.64 % Favored : 91.17 % Rotamer: Outliers : 6.33 % Allowed : 26.30 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.18), residues: 2083 helix: 1.42 (0.86), residues: 33 sheet: -0.54 (0.21), residues: 641 loop : -1.80 (0.15), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 53 TYR 0.029 0.002 TYR E 105 PHE 0.040 0.002 PHE A 32 TRP 0.041 0.002 TRP D 104 HIS 0.006 0.001 HIS F 57 Details of bonding type rmsd covalent geometry : bond 0.00498 (17418) covalent geometry : angle 0.71865 (23659) SS BOND : bond 0.00396 ( 23) SS BOND : angle 1.62797 ( 46) hydrogen bonds : bond 0.04076 ( 486) hydrogen bonds : angle 5.73212 ( 1260) Misc. bond : bond 0.00009 ( 1) link_NAG-ASN : bond 0.00505 ( 35) link_NAG-ASN : angle 3.93494 ( 105) *********************** 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 302 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 186 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.5530 (OUTLIER) cc_final: 0.4860 (m-10) REVERT: A 54 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7700 (pp) REVERT: A 88 ASP cc_start: 0.8047 (t0) cc_final: 0.7584 (t0) REVERT: B 233 ILE cc_start: 0.7701 (pt) cc_final: 0.7327 (pt) REVERT: B 324 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.6814 (pm20) REVERT: D 66 HIS cc_start: 0.6939 (OUTLIER) cc_final: 0.6366 (m90) REVERT: D 202 LYS cc_start: 0.7097 (OUTLIER) cc_final: 0.6817 (mttm) REVERT: D 321 GLN cc_start: 0.7964 (pp30) cc_final: 0.7619 (pp30) REVERT: J 5 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7803 (pt0) REVERT: F 33 MET cc_start: 0.4307 (mmm) cc_final: 0.3334 (mmt) REVERT: F 81 MET cc_start: 0.5984 (ptt) cc_final: 0.5756 (ptm) REVERT: G 3 GLN cc_start: 0.6289 (OUTLIER) cc_final: 0.4911 (mp10) REVERT: G 80 GLU cc_start: 0.3761 (tp30) cc_final: 0.3352 (pt0) REVERT: I 104 TRP cc_start: 0.7868 (OUTLIER) cc_final: 0.6441 (m-90) REVERT: I 109 GLN cc_start: 0.7408 (tp-100) cc_final: 0.7181 (tp-100) REVERT: E 33 MET cc_start: 0.6415 (mmm) cc_final: 0.5610 (mmm) outliers start: 116 outliers final: 94 residues processed: 283 average time/residue: 0.1116 time to fit residues: 49.1300 Evaluate side-chains 281 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 179 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 84 LEU 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 642 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 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 175 PHE Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 240 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 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 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 130 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 202 LYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 304 LYS 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 38 HIS Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 56 SER 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 99 THR Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain I residue 4 LEU 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 60 SER 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 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 170 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 168 optimal weight: 4.9990 chunk 115 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 121 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN D 658 ASN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 HIS ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.201088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.151664 restraints weight = 23648.658| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 3.44 r_work: 0.3627 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 17477 Z= 0.136 Angle : 0.717 13.696 23810 Z= 0.356 Chirality : 0.048 0.377 2735 Planarity : 0.004 0.071 3000 Dihedral : 6.339 64.103 3028 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.30 % Favored : 92.51 % Rotamer: Outliers : 5.40 % Allowed : 27.61 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.18), residues: 2083 helix: 1.56 (0.86), residues: 33 sheet: -0.40 (0.21), residues: 645 loop : -1.70 (0.16), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 53 TYR 0.023 0.001 TYR H 59 PHE 0.030 0.001 PHE A 32 TRP 0.031 0.002 TRP D 104 HIS 0.005 0.001 HIS F 95 Details of bonding type rmsd covalent geometry : bond 0.00318 (17418) covalent geometry : angle 0.67252 (23659) SS BOND : bond 0.00364 ( 23) SS BOND : angle 1.87079 ( 46) hydrogen bonds : bond 0.03404 ( 486) hydrogen bonds : angle 5.54213 ( 1260) Misc. bond : bond 0.00027 ( 1) link_NAG-ASN : bond 0.00456 ( 35) link_NAG-ASN : angle 3.63934 ( 105) ********************** 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 288 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 189 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.6000 (OUTLIER) cc_final: 0.5030 (m-10) REVERT: A 54 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7990 (pp) REVERT: A 88 ASP cc_start: 0.8193 (t0) cc_final: 0.7751 (m-30) REVERT: B 96 GLU cc_start: 0.8187 (pt0) cc_final: 0.7978 (tt0) REVERT: B 233 ILE cc_start: 0.7721 (pt) cc_final: 0.7407 (pt) REVERT: B 324 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.6406 (pm20) REVERT: D 66 HIS cc_start: 0.6988 (OUTLIER) cc_final: 0.6395 (m90) REVERT: D 202 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7761 (mttm) REVERT: D 321 GLN cc_start: 0.8007 (pp30) cc_final: 0.7598 (pp30) REVERT: J 5 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7889 (pt0) REVERT: J 13 GLN cc_start: 0.5881 (tp40) cc_final: 0.5458 (tp40) REVERT: F 33 MET cc_start: 0.4871 (mmm) cc_final: 0.3657 (mmt) REVERT: F 37 ARG cc_start: 0.7234 (tmt170) cc_final: 0.6991 (tmt170) REVERT: G 80 GLU cc_start: 0.4412 (tp30) cc_final: 0.3872 (pt0) REVERT: I 104 TRP cc_start: 0.7878 (OUTLIER) cc_final: 0.6304 (m-90) REVERT: I 109 GLN cc_start: 0.7418 (tp-100) cc_final: 0.7180 (tp-100) REVERT: E 33 MET cc_start: 0.6616 (mmm) cc_final: 0.5729 (mmm) REVERT: E 37 ARG cc_start: 0.7156 (ptm160) cc_final: 0.6696 (ptm-80) outliers start: 99 outliers final: 84 residues processed: 272 average time/residue: 0.1119 time to fit residues: 47.4987 Evaluate side-chains 269 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 178 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 32 PHE 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 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 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 175 PHE Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 240 THR 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 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 157 PHE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 202 LYS Chi-restraints excluded: chain D residue 304 LYS 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 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 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 99 THR Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 60 SER 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 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 99 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 137 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 162 optimal weight: 3.9990 chunk 181 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 197 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: D 245 HIS D 658 ASN ** 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 = 0.4354 r_free = 0.4354 target = 0.198899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.159099 restraints weight = 23695.103| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 5.06 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17477 Z= 0.183 Angle : 0.750 13.379 23810 Z= 0.374 Chirality : 0.050 0.377 2735 Planarity : 0.004 0.052 3000 Dihedral : 6.410 61.975 3028 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.64 % Favored : 91.17 % Rotamer: Outliers : 5.78 % Allowed : 27.17 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.18), residues: 2083 helix: 1.46 (0.86), residues: 33 sheet: -0.48 (0.20), residues: 662 loop : -1.75 (0.16), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 53 TYR 0.026 0.002 TYR E 105 PHE 0.035 0.002 PHE A 32 TRP 0.035 0.002 TRP D 104 HIS 0.015 0.001 HIS F 57 Details of bonding type rmsd covalent geometry : bond 0.00439 (17418) covalent geometry : angle 0.70570 (23659) SS BOND : bond 0.00368 ( 23) SS BOND : angle 1.78481 ( 46) hydrogen bonds : bond 0.03904 ( 486) hydrogen bonds : angle 5.60735 ( 1260) Misc. bond : bond 0.00022 ( 1) link_NAG-ASN : bond 0.00490 ( 35) link_NAG-ASN : angle 3.75334 ( 105) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3900.74 seconds wall clock time: 67 minutes 42.44 seconds (4062.44 seconds total)