Starting phenix.real_space_refine on Mon Nov 18 18:02:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g78_29802/11_2024/8g78_29802.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g78_29802/11_2024/8g78_29802.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g78_29802/11_2024/8g78_29802.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g78_29802/11_2024/8g78_29802.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g78_29802/11_2024/8g78_29802.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g78_29802/11_2024/8g78_29802.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 10761 2.51 5 N 2855 2.21 5 O 3342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 17036 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3740 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 25, 'TRANS': 450} Chain breaks: 4 Chain: "B" Number of atoms: 3743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3743 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 24, 'TRANS': 451} Chain breaks: 4 Chain: "D" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3768 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 25, 'TRANS': 454} Chain breaks: 4 Chain: "J" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 872 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain: "F" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 893 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "G" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 893 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "H" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 872 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain: "I" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 872 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain: "E" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 893 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "D" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 10.64, per 1000 atoms: 0.62 Number of scatterers: 17036 At special positions: 0 Unit cell: (177.067, 170.869, 99.1573, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 3342 8.00 N 2855 7.00 C 10761 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.00 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 136 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.02 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.02 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.04 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 95 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 94 " distance=2.01 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 94 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 234 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 17 " " NAG A1306 " - " ASN A 61 " " NAG A1307 " - " ASN A 74 " " NAG A1308 " - " ASN A 165 " " NAG A1309 " - " ASN A 603 " " NAG A1310 " - " ASN A 122 " " NAG A1311 " - " ASN A 149 " " NAG A1312 " - " ASN A 282 " " NAG B1301 " - " ASN B 234 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 17 " " NAG B1306 " - " ASN B 61 " " NAG B1307 " - " ASN B 74 " " NAG B1308 " - " ASN B 165 " " NAG B1309 " - " ASN B 282 " " NAG B1310 " - " ASN B 122 " " NAG B1311 " - " ASN B 149 " " NAG D1301 " - " ASN D 61 " " NAG D1302 " - " ASN D 122 " " NAG D1303 " - " ASN D 282 " " NAG D1304 " - " ASN D 331 " " NAG D1305 " - " ASN D 616 " " NAG D1306 " - " ASN D 657 " " NAG D1307 " - " ASN D 17 " " NAG D1308 " - " ASN D 74 " " NAG D1309 " - " ASN D 165 " " NAG D1310 " - " ASN D 603 " " NAG D1311 " - " ASN D 149 " " NAG D1312 " - " ASN D 234 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.36 Conformation dependent library (CDL) restraints added in 2.1 seconds 4166 Ramachandran restraints generated. 2083 Oldfield, 0 Emsley, 2083 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3890 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 41 sheets defined 5.0% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.43 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: 7.12 Time building geometry restraints manager: 4.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5236 1.34 - 1.46: 4071 1.46 - 1.58: 8009 1.58 - 1.70: 0 1.70 - 1.83: 102 Bond restraints: 17418 Sorted by residual: bond pdb=" C1 NAG A1310 " pdb=" O5 NAG A1310 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" N VAL E 23 " pdb=" CA VAL E 23 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.08e+01 bond pdb=" N VAL E 12 " pdb=" CA VAL E 12 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.17e-02 7.31e+03 9.14e+00 bond pdb=" N HIS E 95 " pdb=" CA HIS E 95 " ideal model delta sigma weight residual 1.452 1.490 -0.038 1.25e-02 6.40e+03 9.01e+00 bond pdb=" N LEU E 96 " pdb=" CA LEU E 96 " ideal model delta sigma weight residual 1.455 1.492 -0.038 1.26e-02 6.30e+03 8.98e+00 ... (remaining 17413 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 22975 2.31 - 4.62: 621 4.62 - 6.93: 48 6.93 - 9.25: 13 9.25 - 11.56: 2 Bond angle restraints: 23659 Sorted by residual: angle pdb=" N GLY E 109 " pdb=" CA GLY E 109 " pdb=" C GLY E 109 " ideal model delta sigma weight residual 112.83 121.00 -8.17 1.22e+00 6.72e-01 4.48e+01 angle pdb=" CA GLY E 9 " pdb=" C GLY E 9 " pdb=" O GLY E 9 " ideal model delta sigma weight residual 121.88 118.01 3.87 7.80e-01 1.64e+00 2.46e+01 angle pdb=" C GLN J 3 " pdb=" CA GLN J 3 " pdb=" CB GLN J 3 " ideal model delta sigma weight residual 115.89 109.36 6.53 1.32e+00 5.74e-01 2.45e+01 angle pdb=" CA GLY E 8 " pdb=" C GLY E 8 " pdb=" O GLY E 8 " ideal model delta sigma weight residual 121.88 118.15 3.73 7.80e-01 1.64e+00 2.29e+01 angle pdb=" C CYS E 22 " pdb=" CA CYS E 22 " pdb=" CB CYS E 22 " ideal model delta sigma weight residual 109.89 116.43 -6.54 1.60e+00 3.91e-01 1.67e+01 ... (remaining 23654 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.77: 9631 22.77 - 45.55: 892 45.55 - 68.32: 144 68.32 - 91.09: 28 91.09 - 113.86: 4 Dihedral angle restraints: 10699 sinusoidal: 4606 harmonic: 6093 Sorted by residual: dihedral pdb=" CB CYS D 617 " pdb=" SG CYS D 617 " pdb=" SG CYS D 649 " pdb=" CB CYS D 649 " ideal model delta sinusoidal sigma weight residual 93.00 29.88 63.12 1 1.00e+01 1.00e-02 5.26e+01 dihedral pdb=" CB CYS D 662 " pdb=" SG CYS D 662 " pdb=" SG CYS D 671 " pdb=" CB CYS D 671 " ideal model delta sinusoidal sigma weight residual -86.00 -32.51 -53.49 1 1.00e+01 1.00e-02 3.89e+01 dihedral pdb=" CB CYS D 538 " pdb=" SG CYS D 538 " pdb=" SG CYS D 590 " pdb=" CB CYS D 590 " ideal model delta sinusoidal sigma weight residual -86.00 -33.23 -52.77 1 1.00e+01 1.00e-02 3.79e+01 ... (remaining 10696 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2355 0.084 - 0.168: 354 0.168 - 0.252: 21 0.252 - 0.336: 3 0.336 - 0.421: 2 Chirality restraints: 2735 Sorted by residual: chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" C1 NAG D1311 " pdb=" ND2 ASN D 149 " pdb=" C2 NAG D1311 " pdb=" O5 NAG D1311 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.70 0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 2732 not shown) Planarity restraints: 3035 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 149 " 0.092 2.00e-02 2.50e+03 1.16e-01 1.67e+02 pdb=" CG ASN A 149 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN A 149 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN A 149 " -0.202 2.00e-02 2.50e+03 pdb=" C1 NAG A1311 " 0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 165 " -0.011 2.00e-02 2.50e+03 2.67e-02 8.88e+00 pdb=" CG ASN D 165 " 0.050 2.00e-02 2.50e+03 pdb=" OD1 ASN D 165 " -0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN D 165 " 0.001 2.00e-02 2.50e+03 pdb=" C1 NAG D1309 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 165 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.56e+00 pdb=" CG ASN D 165 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN D 165 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN D 165 " -0.016 2.00e-02 2.50e+03 ... (remaining 3032 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 134 2.49 - 3.09: 11941 3.09 - 3.69: 24707 3.69 - 4.30: 34642 4.30 - 4.90: 58696 Nonbonded interactions: 130120 Sorted by model distance: nonbonded pdb=" OE1 GLN B 607 " pdb=" O TRP H 100 " model vdw 1.884 3.040 nonbonded pdb=" OG SER A 31 " pdb=" O SER A 60 " model vdw 2.075 3.040 nonbonded pdb=" O ASP B 80 " pdb=" OH TYR B 265 " model vdw 2.094 3.040 nonbonded pdb=" OG1 THR D 323 " pdb=" NZ LYS D 537 " model vdw 2.153 3.120 nonbonded pdb=" N HIS A 69 " pdb=" O ARG A 78 " model vdw 2.165 3.120 ... (remaining 130115 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 178 or resid 184 through 333 or resid 524 throu \ gh 622 or resid 632 through 700 or resid 1301 through 1311)) selection = (chain 'B' and (resid 15 through 178 or resid 184 through 622 or resid 632 throu \ gh 676 or resid 690 through 700 or resid 1301 through 1311)) selection = (chain 'D' and (resid 15 through 333 or resid 524 through 622 or resid 632 throu \ gh 676 or resid 690 through 700 or resid 1301 through 1311)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.740 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 42.440 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.350 ------------------------------------------------------------------------------- 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 0.073 17418 Z= 0.443 Angle : 0.868 11.558 23659 Z= 0.482 Chirality : 0.058 0.421 2735 Planarity : 0.005 0.062 3000 Dihedral : 16.909 113.865 6740 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.55 % Favored : 90.83 % Rotamer: Outliers : 1.04 % Allowed : 26.57 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.17), residues: 2083 helix: 0.64 (0.79), residues: 33 sheet: -1.10 (0.19), residues: 724 loop : -1.75 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP D 104 HIS 0.009 0.002 HIS I 38 PHE 0.025 0.003 PHE B 86 TYR 0.026 0.002 TYR E 105 ARG 0.012 0.001 ARG J 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4166 Ramachandran restraints generated. 2083 Oldfield, 0 Emsley, 2083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4166 Ramachandran restraints generated. 2083 Oldfield, 0 Emsley, 2083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 220 time to evaluate : 1.917 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: 0.3177 time to fit residues: 108.8018 Evaluate side-chains 203 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 196 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 80 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 10.0000 chunk 157 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 121 optimal weight: 0.0770 chunk 188 optimal weight: 0.9980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17418 Z= 0.190 Angle : 0.678 14.071 23659 Z= 0.349 Chirality : 0.050 0.543 2735 Planarity : 0.004 0.049 3000 Dihedral : 8.820 89.246 3039 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.72 % Favored : 92.89 % Rotamer: Outliers : 3.22 % Allowed : 24.93 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.18), residues: 2083 helix: 1.47 (0.85), residues: 33 sheet: -0.64 (0.20), residues: 703 loop : -1.74 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 104 HIS 0.008 0.001 HIS E 95 PHE 0.020 0.002 PHE H 67 TYR 0.017 0.001 TYR E 105 ARG 0.005 0.000 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4166 Ramachandran restraints generated. 2083 Oldfield, 0 Emsley, 2083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4166 Ramachandran restraints generated. 2083 Oldfield, 0 Emsley, 2083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 215 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.7879 (ptp90) cc_final: 0.7501 (mtm110) REVERT: A 558 LYS cc_start: 0.8745 (mmtm) cc_final: 0.8302 (mmmm) REVERT: B 100 ILE cc_start: 0.8515 (mm) cc_final: 0.8222 (mt) REVERT: B 140 PHE cc_start: 0.7347 (p90) cc_final: 0.7033 (p90) REVERT: B 233 ILE cc_start: 0.7406 (pt) cc_final: 0.7131 (pt) REVERT: B 567 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8186 (ptp90) REVERT: D 131 CYS cc_start: 0.2395 (m) cc_final: 0.1980 (m) REVERT: D 229 LEU cc_start: 0.6064 (OUTLIER) cc_final: 0.5841 (tt) REVERT: J 32 GLU cc_start: 0.8444 (tm-30) cc_final: 0.7750 (pt0) REVERT: G 78 TYR cc_start: 0.5841 (m-80) cc_final: 0.5432 (m-80) REVERT: H 81 GLN cc_start: 0.6394 (pm20) cc_final: 0.5703 (pp30) REVERT: E 37 ARG cc_start: 0.6806 (ptm-80) cc_final: 0.6435 (ptm-80) outliers start: 59 outliers final: 33 residues processed: 262 average time/residue: 0.2980 time to fit residues: 117.9522 Evaluate side-chains 227 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 192 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 80 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 104 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 157 optimal weight: 8.9990 chunk 128 optimal weight: 0.9980 chunk 52 optimal weight: 0.3980 chunk 189 optimal weight: 5.9990 chunk 204 optimal weight: 8.9990 chunk 168 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS D 655 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 96 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 17418 Z= 0.394 Angle : 0.769 13.169 23659 Z= 0.398 Chirality : 0.052 0.377 2735 Planarity : 0.005 0.060 3000 Dihedral : 7.778 75.274 3031 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.88 % Favored : 90.73 % Rotamer: Outliers : 6.66 % Allowed : 23.24 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.17), residues: 2083 helix: 1.23 (0.83), residues: 33 sheet: -0.63 (0.20), residues: 662 loop : -1.77 (0.15), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 104 HIS 0.007 0.002 HIS A 49 PHE 0.028 0.003 PHE B 86 TYR 0.035 0.002 TYR E 105 ARG 0.009 0.001 ARG J 53 *********************** 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 335 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 213 time to evaluate : 1.785 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: 0.7630 (t0) cc_final: 0.7056 (t0) REVERT: A 108 THR cc_start: 0.7226 (p) cc_final: 0.6965 (p) REVERT: A 152 TRP cc_start: 0.6805 (t-100) cc_final: 0.6521 (t-100) REVERT: A 319 ARG cc_start: 0.8132 (ptp90) cc_final: 0.7782 (mtm110) REVERT: A 321 GLN cc_start: 0.8322 (mm110) cc_final: 0.7470 (pp30) REVERT: A 558 LYS cc_start: 0.8843 (mmtm) cc_final: 0.8417 (mmmt) REVERT: A 651 ILE cc_start: 0.8736 (pt) cc_final: 0.8464 (pt) REVERT: B 100 ILE cc_start: 0.8522 (mm) cc_final: 0.8239 (mt) REVERT: B 233 ILE cc_start: 0.7455 (pt) cc_final: 0.7220 (pt) REVERT: B 321 GLN cc_start: 0.7834 (pp30) cc_final: 0.7631 (pp30) REVERT: B 329 PHE cc_start: 0.6889 (t80) cc_final: 0.6580 (t80) REVERT: D 66 HIS cc_start: 0.7271 (OUTLIER) cc_final: 0.6466 (m90) REVERT: D 131 CYS cc_start: 0.2311 (m) cc_final: 0.1867 (m) REVERT: D 229 LEU cc_start: 0.6345 (OUTLIER) cc_final: 0.6043 (tt) REVERT: D 290 ASP cc_start: 0.8801 (OUTLIER) cc_final: 0.8589 (t0) REVERT: D 319 ARG cc_start: 0.8277 (ptp90) cc_final: 0.8024 (ttp-110) REVERT: D 630 THR cc_start: 0.7406 (OUTLIER) cc_final: 0.7172 (t) REVERT: J 46 GLU cc_start: 0.7717 (tp30) cc_final: 0.7164 (tp30) REVERT: F 38 GLN cc_start: 0.6625 (tm-30) cc_final: 0.6147 (tm-30) REVERT: G 78 TYR cc_start: 0.5919 (m-80) cc_final: 0.5602 (m-80) REVERT: H 81 GLN cc_start: 0.6465 (pm20) cc_final: 0.6104 (pp30) REVERT: H 98 ARG cc_start: 0.8279 (ttm170) cc_final: 0.7781 (ttp-110) REVERT: I 46 GLU cc_start: 0.7693 (tp30) cc_final: 0.7360 (tp30) REVERT: I 104 TRP cc_start: 0.7994 (OUTLIER) cc_final: 0.6029 (m-90) REVERT: I 109 GLN cc_start: 0.7975 (tp-100) cc_final: 0.7581 (tp-100) REVERT: E 84 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6621 (mt) outliers start: 122 outliers final: 78 residues processed: 313 average time/residue: 0.2768 time to fit residues: 134.7472 Evaluate side-chains 278 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 194 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 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 61 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 289 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 D residue 53 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 304 LYS Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 590 CYS Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain J residue 5 GLN Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 96 HIS Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 104 TRP Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 84 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 186 optimal weight: 0.0970 chunk 142 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 189 optimal weight: 0.8980 chunk 201 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 179 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 HIS B 87 ASN ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17418 Z= 0.174 Angle : 0.642 10.494 23659 Z= 0.331 Chirality : 0.048 0.370 2735 Planarity : 0.004 0.039 3000 Dihedral : 6.723 72.864 3028 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.14 % Favored : 93.52 % Rotamer: Outliers : 5.07 % Allowed : 25.75 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.18), residues: 2083 helix: 1.59 (0.86), residues: 33 sheet: -0.51 (0.20), residues: 685 loop : -1.69 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP D 104 HIS 0.010 0.001 HIS E 95 PHE 0.017 0.001 PHE A 59 TYR 0.019 0.001 TYR E 105 ARG 0.006 0.000 ARG E 65 *********************** 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 305 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 212 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7754 (t0) cc_final: 0.7215 (t0) REVERT: A 152 TRP cc_start: 0.6879 (t-100) cc_final: 0.6644 (t-100) REVERT: A 319 ARG cc_start: 0.8117 (ptp90) cc_final: 0.7765 (mtm110) REVERT: A 321 GLN cc_start: 0.8342 (mm110) cc_final: 0.7433 (pp30) REVERT: A 558 LYS cc_start: 0.8821 (mmtm) cc_final: 0.8403 (mmmt) REVERT: B 233 ILE cc_start: 0.7416 (pt) cc_final: 0.7163 (pt) REVERT: B 321 GLN cc_start: 0.7742 (pp30) cc_final: 0.7498 (pp30) REVERT: B 324 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.6391 (pm20) REVERT: B 329 PHE cc_start: 0.6775 (t80) cc_final: 0.6503 (t80) REVERT: B 532 ASN cc_start: 0.7893 (t0) cc_final: 0.7682 (m-40) REVERT: B 567 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.8087 (ptp90) REVERT: D 66 HIS cc_start: 0.7023 (OUTLIER) cc_final: 0.6333 (m90) REVERT: D 229 LEU cc_start: 0.6064 (OUTLIER) cc_final: 0.5638 (tt) REVERT: D 319 ARG cc_start: 0.8250 (ptp90) cc_final: 0.8001 (ttp-110) REVERT: D 321 GLN cc_start: 0.7574 (pp30) cc_final: 0.7157 (pp30) REVERT: D 630 THR cc_start: 0.7485 (OUTLIER) cc_final: 0.7234 (t) REVERT: J 32 GLU cc_start: 0.8380 (tm-30) cc_final: 0.7643 (pt0) REVERT: F 33 MET cc_start: 0.5111 (mmm) cc_final: 0.4488 (mmt) REVERT: F 38 GLN cc_start: 0.6587 (tm-30) cc_final: 0.6152 (tm-30) REVERT: G 78 TYR cc_start: 0.5941 (m-80) cc_final: 0.5664 (m-80) REVERT: H 81 GLN cc_start: 0.6468 (pm20) cc_final: 0.6029 (pp30) REVERT: H 98 ARG cc_start: 0.8183 (ttm170) cc_final: 0.7978 (ttp-170) REVERT: I 46 GLU cc_start: 0.7772 (tp30) cc_final: 0.7470 (tp30) REVERT: I 104 TRP cc_start: 0.7701 (OUTLIER) cc_final: 0.5859 (m-90) REVERT: I 109 GLN cc_start: 0.7891 (tp-100) cc_final: 0.7580 (tp-100) outliers start: 93 outliers final: 64 residues processed: 288 average time/residue: 0.3041 time to fit residues: 135.1514 Evaluate side-chains 259 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 189 time to evaluate : 1.768 ------------------------------------------------------------------------------- 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 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 306 PHE 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 585 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 567 ARG 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 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 227 VAL Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 304 LYS Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 590 CYS Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 640 SER Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain J residue 5 GLN Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 23 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 51 ILE Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 104 TRP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 80 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 167 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 149 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 171 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 102 optimal weight: 0.6980 chunk 180 optimal weight: 0.9990 chunk 50 optimal weight: 0.0870 overall best weight: 1.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 HIS E 57 HIS E 82 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17418 Z= 0.310 Angle : 0.693 14.810 23659 Z= 0.360 Chirality : 0.050 0.397 2735 Planarity : 0.004 0.067 3000 Dihedral : 6.707 69.632 3028 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.45 % Favored : 91.26 % Rotamer: Outliers : 7.20 % Allowed : 24.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.18), residues: 2083 helix: 1.46 (0.85), residues: 33 sheet: -0.41 (0.21), residues: 651 loop : -1.68 (0.16), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 104 HIS 0.013 0.002 HIS B 69 PHE 0.037 0.002 PHE B 86 TYR 0.028 0.002 TYR E 105 ARG 0.009 0.000 ARG J 53 *********************** 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 337 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 205 time to evaluate : 1.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7694 (t0) cc_final: 0.7056 (t0) REVERT: A 152 TRP cc_start: 0.6988 (t-100) cc_final: 0.6764 (t-100) REVERT: A 319 ARG cc_start: 0.8181 (ptp90) cc_final: 0.7843 (mtm110) REVERT: A 321 GLN cc_start: 0.8490 (mm110) cc_final: 0.7620 (pp30) REVERT: A 558 LYS cc_start: 0.8873 (mmtm) cc_final: 0.8458 (mmmt) REVERT: A 651 ILE cc_start: 0.8693 (pt) cc_final: 0.8470 (pt) REVERT: B 100 ILE cc_start: 0.8433 (mm) cc_final: 0.8133 (mt) REVERT: B 233 ILE cc_start: 0.7465 (pt) cc_final: 0.7203 (pt) REVERT: B 321 GLN cc_start: 0.7828 (pp30) cc_final: 0.7522 (pp30) REVERT: B 324 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.6335 (pm20) REVERT: B 329 PHE cc_start: 0.6859 (t80) cc_final: 0.6575 (t80) REVERT: B 567 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8234 (ptp90) REVERT: D 66 HIS cc_start: 0.7253 (OUTLIER) cc_final: 0.6467 (m90) REVERT: D 215 ASP cc_start: 0.7962 (p0) cc_final: 0.7554 (p0) REVERT: D 229 LEU cc_start: 0.6088 (OUTLIER) cc_final: 0.5705 (tt) REVERT: D 319 ARG cc_start: 0.8279 (ptp90) cc_final: 0.8050 (ttp-110) REVERT: D 321 GLN cc_start: 0.7704 (pp30) cc_final: 0.7253 (pp30) REVERT: D 582 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7421 (pp) REVERT: D 630 THR cc_start: 0.7569 (OUTLIER) cc_final: 0.7358 (t) REVERT: J 46 GLU cc_start: 0.7751 (tp30) cc_final: 0.7328 (tp30) REVERT: F 38 GLN cc_start: 0.6595 (tm-30) cc_final: 0.6346 (tm-30) REVERT: G 3 GLN cc_start: 0.5958 (OUTLIER) cc_final: 0.4147 (mp10) REVERT: G 78 TYR cc_start: 0.5928 (m-80) cc_final: 0.5675 (m-80) REVERT: H 81 GLN cc_start: 0.6602 (pm20) cc_final: 0.6366 (pp30) REVERT: H 98 ARG cc_start: 0.8368 (ttm170) cc_final: 0.7974 (ttp-110) REVERT: H 109 GLN cc_start: 0.7154 (tp40) cc_final: 0.6854 (tp-100) REVERT: I 104 TRP cc_start: 0.7924 (OUTLIER) cc_final: 0.6040 (m-90) REVERT: I 109 GLN cc_start: 0.7836 (tp-100) cc_final: 0.7542 (tp-100) REVERT: E 101 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7565 (tt) outliers start: 132 outliers final: 92 residues processed: 313 average time/residue: 0.2844 time to fit residues: 134.6393 Evaluate side-chains 294 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 193 time to evaluate : 1.919 ------------------------------------------------------------------------------- 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 306 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 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 210 ILE Chi-restraints excluded: chain D residue 227 VAL 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 316 SER Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 590 CYS Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 640 SER Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain J residue 5 GLN Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 96 HIS Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 35 GLU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 104 TRP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 101 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 67 optimal weight: 0.7980 chunk 181 optimal weight: 6.9990 chunk 39 optimal weight: 0.2980 chunk 118 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 201 optimal weight: 0.5980 chunk 167 optimal weight: 0.0670 chunk 93 optimal weight: 0.2980 chunk 16 optimal weight: 10.0000 chunk 66 optimal weight: 0.3980 chunk 105 optimal weight: 8.9990 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN B 607 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** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 GLN E 57 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17418 Z= 0.157 Angle : 0.635 13.516 23659 Z= 0.323 Chirality : 0.048 0.364 2735 Planarity : 0.004 0.072 3000 Dihedral : 6.095 67.433 3028 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.10 % Favored : 93.61 % Rotamer: Outliers : 5.73 % Allowed : 25.97 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.18), residues: 2083 helix: 1.64 (0.86), residues: 33 sheet: -0.39 (0.20), residues: 661 loop : -1.66 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 104 HIS 0.005 0.001 HIS G 82 PHE 0.015 0.001 PHE B 194 TYR 0.020 0.001 TYR H 59 ARG 0.004 0.000 ARG I 66 *********************** 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 323 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 218 time to evaluate : 1.766 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: 0.7815 (t0) cc_final: 0.7267 (t0) REVERT: A 319 ARG cc_start: 0.8100 (ptp90) cc_final: 0.7752 (mtm110) REVERT: A 321 GLN cc_start: 0.8419 (mm110) cc_final: 0.7540 (pp30) REVERT: A 558 LYS cc_start: 0.8796 (mmtm) cc_final: 0.8365 (mmmt) REVERT: B 96 GLU cc_start: 0.8479 (pt0) cc_final: 0.8156 (tt0) REVERT: B 218 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7797 (tt0) REVERT: B 233 ILE cc_start: 0.7403 (pt) cc_final: 0.7151 (pt) REVERT: B 321 GLN cc_start: 0.7848 (pp30) cc_final: 0.7558 (pp30) REVERT: B 324 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.6203 (pm20) REVERT: B 329 PHE cc_start: 0.6779 (t80) cc_final: 0.6555 (t80) REVERT: B 567 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8053 (ptp90) REVERT: D 66 HIS cc_start: 0.6873 (OUTLIER) cc_final: 0.6221 (m90) REVERT: D 79 PHE cc_start: 0.5179 (OUTLIER) cc_final: 0.4857 (m-10) REVERT: D 244 LEU cc_start: 0.6174 (OUTLIER) cc_final: 0.5969 (tp) REVERT: D 319 ARG cc_start: 0.8261 (ptp90) cc_final: 0.8037 (ttp-110) REVERT: D 321 GLN cc_start: 0.7711 (pp30) cc_final: 0.7265 (pp30) REVERT: D 582 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7446 (pp) REVERT: F 33 MET cc_start: 0.5080 (mmm) cc_final: 0.4343 (mmt) REVERT: F 81 MET cc_start: 0.5152 (ptt) cc_final: 0.4896 (ptm) REVERT: G 80 GLU cc_start: 0.4627 (tp30) cc_final: 0.4209 (pt0) REVERT: G 113 GLN cc_start: 0.3738 (OUTLIER) cc_final: 0.3459 (tp-100) REVERT: H 46 GLU cc_start: 0.7718 (tp30) cc_final: 0.7261 (tp30) REVERT: H 98 ARG cc_start: 0.8167 (ttm170) cc_final: 0.7800 (ttp-110) REVERT: H 106 ARG cc_start: 0.6665 (OUTLIER) cc_final: 0.5053 (mmt180) REVERT: H 109 GLN cc_start: 0.7121 (tp40) cc_final: 0.6853 (tp-100) REVERT: I 4 LEU cc_start: 0.7320 (pp) cc_final: 0.7111 (tt) REVERT: I 35 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6586 (pt0) REVERT: I 46 GLU cc_start: 0.7940 (tp30) cc_final: 0.7413 (tp30) REVERT: I 104 TRP cc_start: 0.7635 (OUTLIER) cc_final: 0.5922 (m-90) REVERT: I 109 GLN cc_start: 0.7756 (tp-100) cc_final: 0.7471 (tp-100) outliers start: 105 outliers final: 67 residues processed: 303 average time/residue: 0.3152 time to fit residues: 145.4073 Evaluate side-chains 265 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 187 time to evaluate : 1.873 ------------------------------------------------------------------------------- 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 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 306 PHE 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 585 LEU 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 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 136 CYS 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 318 PHE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 567 ARG 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 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 210 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 304 LYS Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 582 LEU 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 642 VAL Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain J residue 5 GLN Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 38 HIS 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 105 TYR Chi-restraints excluded: chain G residue 113 GLN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 96 HIS Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 35 GLU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 194 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 146 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 169 optimal weight: 30.0000 chunk 112 optimal weight: 0.9980 chunk 200 optimal weight: 9.9990 chunk 125 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 HIS D 690 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN E 57 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 17418 Z= 0.391 Angle : 0.758 13.844 23659 Z= 0.393 Chirality : 0.052 0.377 2735 Planarity : 0.005 0.061 3000 Dihedral : 6.768 66.792 3028 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.79 % Favored : 90.93 % Rotamer: Outliers : 6.93 % Allowed : 25.75 % Favored : 67.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.18), residues: 2083 helix: 1.17 (0.83), residues: 33 sheet: -0.47 (0.21), residues: 643 loop : -1.72 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 104 HIS 0.006 0.002 HIS A 49 PHE 0.025 0.003 PHE B 86 TYR 0.033 0.002 TYR E 105 ARG 0.013 0.001 ARG J 53 *********************** 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 336 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 209 time to evaluate : 1.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7558 (pp) REVERT: A 88 ASP cc_start: 0.7751 (t0) cc_final: 0.7022 (t0) REVERT: A 152 TRP cc_start: 0.6880 (t-100) cc_final: 0.6638 (t-100) REVERT: A 154 GLU cc_start: 0.6365 (tt0) cc_final: 0.5899 (tt0) REVERT: A 319 ARG cc_start: 0.8115 (ptp90) cc_final: 0.7636 (ttm110) REVERT: A 321 GLN cc_start: 0.8544 (mm110) cc_final: 0.7706 (pp30) REVERT: A 558 LYS cc_start: 0.8914 (mmtm) cc_final: 0.8514 (mmmt) REVERT: A 651 ILE cc_start: 0.8742 (pt) cc_final: 0.8536 (pt) REVERT: B 140 PHE cc_start: 0.8354 (p90) cc_final: 0.7925 (p90) REVERT: B 233 ILE cc_start: 0.7515 (pt) cc_final: 0.7250 (pt) REVERT: B 321 GLN cc_start: 0.8035 (pp30) cc_final: 0.7696 (pp30) REVERT: B 324 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.6269 (pm20) REVERT: B 567 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8244 (ptp90) REVERT: D 66 HIS cc_start: 0.7285 (OUTLIER) cc_final: 0.6502 (m90) REVERT: D 319 ARG cc_start: 0.8304 (ptp90) cc_final: 0.8083 (ttp-110) REVERT: D 321 GLN cc_start: 0.7914 (pp30) cc_final: 0.7447 (pp30) REVERT: D 630 THR cc_start: 0.7900 (OUTLIER) cc_final: 0.7649 (t) REVERT: J 46 GLU cc_start: 0.7839 (tp30) cc_final: 0.7482 (tp30) REVERT: F 33 MET cc_start: 0.5070 (mmm) cc_final: 0.4000 (mmt) REVERT: G 3 GLN cc_start: 0.5985 (OUTLIER) cc_final: 0.4183 (mp10) REVERT: H 46 GLU cc_start: 0.7830 (tp30) cc_final: 0.7477 (tp30) REVERT: H 98 ARG cc_start: 0.8375 (ttm170) cc_final: 0.8097 (ttm110) REVERT: I 46 GLU cc_start: 0.7976 (tp30) cc_final: 0.7582 (tp30) REVERT: I 104 TRP cc_start: 0.8054 (OUTLIER) cc_final: 0.6104 (m-90) REVERT: I 109 GLN cc_start: 0.7621 (tp-100) cc_final: 0.7316 (tp-100) REVERT: E 33 MET cc_start: 0.6235 (mmm) cc_final: 0.5592 (mmm) outliers start: 127 outliers final: 91 residues processed: 314 average time/residue: 0.2832 time to fit residues: 136.3751 Evaluate side-chains 293 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 195 time to evaluate : 1.957 ------------------------------------------------------------------------------- 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 63 THR Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 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 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 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 101 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain D residue 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 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 227 VAL Chi-restraints excluded: chain D residue 304 LYS Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 590 CYS Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 5 GLN Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 20 LEU 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 7 SER Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 3 GLN 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 106 ARG Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 35 GLU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 96 HIS Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 104 TRP Chi-restraints excluded: chain E residue 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 124 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 119 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 136 optimal weight: 0.0870 chunk 99 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 HIS D 658 ASN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 HIS ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 HIS ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 GLN E 57 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 17418 Z= 0.203 Angle : 0.664 12.531 23659 Z= 0.341 Chirality : 0.048 0.373 2735 Planarity : 0.004 0.049 3000 Dihedral : 6.278 65.174 3028 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.24 % Favored : 93.52 % Rotamer: Outliers : 5.56 % Allowed : 27.28 % Favored : 67.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.18), residues: 2083 helix: 1.49 (0.85), residues: 33 sheet: -0.38 (0.20), residues: 682 loop : -1.67 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP D 104 HIS 0.006 0.001 HIS G 82 PHE 0.015 0.001 PHE H 29 TYR 0.018 0.001 TYR E 105 ARG 0.004 0.000 ARG F 37 *********************** 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 305 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 203 time to evaluate : 1.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7745 (pp) REVERT: A 88 ASP cc_start: 0.7815 (t0) cc_final: 0.7333 (m-30) REVERT: A 154 GLU cc_start: 0.6367 (tt0) cc_final: 0.5779 (tt0) REVERT: A 319 ARG cc_start: 0.8046 (ptp90) cc_final: 0.7728 (mtm110) REVERT: A 321 GLN cc_start: 0.8514 (mm110) cc_final: 0.7677 (pp30) REVERT: A 558 LYS cc_start: 0.8855 (mmtm) cc_final: 0.8440 (mmmt) REVERT: B 96 GLU cc_start: 0.8440 (pt0) cc_final: 0.8199 (tt0) REVERT: B 233 ILE cc_start: 0.7455 (pt) cc_final: 0.7198 (pt) REVERT: B 321 GLN cc_start: 0.8032 (pp30) cc_final: 0.7692 (pp30) REVERT: B 324 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.6146 (pm20) REVERT: B 567 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8091 (ptp90) REVERT: D 66 HIS cc_start: 0.7036 (OUTLIER) cc_final: 0.6355 (m90) REVERT: D 146 HIS cc_start: 0.5682 (OUTLIER) cc_final: 0.5327 (m-70) REVERT: D 298 GLU cc_start: 0.8144 (tp30) cc_final: 0.7855 (tt0) REVERT: D 319 ARG cc_start: 0.8267 (ptp90) cc_final: 0.8050 (ttp-110) REVERT: D 321 GLN cc_start: 0.7860 (pp30) cc_final: 0.7379 (pp30) REVERT: J 13 GLN cc_start: 0.7109 (pp30) cc_final: 0.6792 (tp40) REVERT: J 46 GLU cc_start: 0.7780 (tp30) cc_final: 0.7367 (tp30) REVERT: F 81 MET cc_start: 0.5141 (ptt) cc_final: 0.4901 (ptm) REVERT: G 78 TYR cc_start: 0.5831 (m-80) cc_final: 0.5476 (m-80) REVERT: G 80 GLU cc_start: 0.4731 (tp30) cc_final: 0.4366 (pt0) REVERT: H 46 GLU cc_start: 0.7817 (tp30) cc_final: 0.7414 (tp30) REVERT: H 98 ARG cc_start: 0.8305 (ttm170) cc_final: 0.7994 (ttm110) REVERT: H 106 ARG cc_start: 0.6826 (OUTLIER) cc_final: 0.5406 (mmt180) REVERT: H 109 GLN cc_start: 0.7066 (tp40) cc_final: 0.6799 (tp-100) REVERT: I 46 GLU cc_start: 0.7976 (tp30) cc_final: 0.7512 (tp30) REVERT: I 104 TRP cc_start: 0.7826 (OUTLIER) cc_final: 0.6079 (m-90) REVERT: I 109 GLN cc_start: 0.7599 (tp-100) cc_final: 0.7298 (tp-100) REVERT: E 33 MET cc_start: 0.6620 (mmm) cc_final: 0.6339 (mmm) REVERT: E 37 ARG cc_start: 0.7041 (ptm160) cc_final: 0.6629 (ptm160) outliers start: 102 outliers final: 80 residues processed: 287 average time/residue: 0.2972 time to fit residues: 129.7417 Evaluate side-chains 279 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 192 time to evaluate : 2.029 ------------------------------------------------------------------------------- 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 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 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 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 567 ARG Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 146 HIS Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 304 LYS Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 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 38 HIS Chi-restraints excluded: chain J residue 48 VAL 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 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 106 ARG Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 35 GLU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 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 18 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 182 optimal weight: 0.7980 chunk 192 optimal weight: 0.0670 chunk 175 optimal weight: 7.9990 chunk 186 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 168 optimal weight: 0.8980 chunk 176 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN D 245 HIS ** 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** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 HIS ** E 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17418 Z= 0.207 Angle : 0.667 16.347 23659 Z= 0.341 Chirality : 0.048 0.369 2735 Planarity : 0.004 0.051 3000 Dihedral : 6.121 62.782 3028 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.15 % Favored : 92.61 % Rotamer: Outliers : 5.46 % Allowed : 27.66 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.18), residues: 2083 helix: 1.52 (0.86), residues: 33 sheet: -0.39 (0.20), residues: 690 loop : -1.66 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP D 104 HIS 0.005 0.001 HIS F 95 PHE 0.025 0.002 PHE A 32 TYR 0.022 0.001 TYR F 58 ARG 0.008 0.000 ARG J 53 *********************** 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 294 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 194 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7732 (pp) REVERT: A 88 ASP cc_start: 0.7854 (t0) cc_final: 0.7361 (m-30) REVERT: A 319 ARG cc_start: 0.8038 (ptp90) cc_final: 0.7553 (ttp-110) REVERT: A 558 LYS cc_start: 0.8865 (mmtm) cc_final: 0.8429 (mmmt) REVERT: B 96 GLU cc_start: 0.8332 (pt0) cc_final: 0.7962 (tt0) REVERT: B 233 ILE cc_start: 0.7467 (pt) cc_final: 0.7199 (pt) REVERT: B 324 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6011 (pm20) REVERT: B 537 LYS cc_start: 0.8244 (tttm) cc_final: 0.7965 (tttp) REVERT: B 567 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8254 (ptp90) REVERT: D 66 HIS cc_start: 0.6962 (OUTLIER) cc_final: 0.6313 (m90) REVERT: D 146 HIS cc_start: 0.5614 (OUTLIER) cc_final: 0.5268 (m-70) REVERT: D 319 ARG cc_start: 0.8255 (ptp90) cc_final: 0.8048 (ttp-110) REVERT: D 321 GLN cc_start: 0.7858 (pp30) cc_final: 0.7380 (pp30) REVERT: D 630 THR cc_start: 0.7980 (OUTLIER) cc_final: 0.7749 (t) REVERT: J 13 GLN cc_start: 0.7101 (pp30) cc_final: 0.6793 (tp40) REVERT: J 46 GLU cc_start: 0.7765 (tp30) cc_final: 0.7353 (tp30) REVERT: F 37 ARG cc_start: 0.7051 (tmt170) cc_final: 0.6824 (tmt170) REVERT: F 81 MET cc_start: 0.5070 (ptt) cc_final: 0.4850 (ptm) REVERT: G 19 ARG cc_start: 0.6085 (tpp80) cc_final: 0.5781 (tpp80) REVERT: G 78 TYR cc_start: 0.6052 (m-80) cc_final: 0.5550 (m-80) REVERT: G 80 GLU cc_start: 0.4759 (tp30) cc_final: 0.4351 (pt0) REVERT: H 46 GLU cc_start: 0.7837 (tp30) cc_final: 0.7455 (tp30) REVERT: H 98 ARG cc_start: 0.8321 (ttm170) cc_final: 0.8003 (ttp-110) REVERT: H 106 ARG cc_start: 0.6870 (OUTLIER) cc_final: 0.5451 (mmt180) REVERT: H 109 GLN cc_start: 0.7026 (tp40) cc_final: 0.6763 (tp-100) REVERT: I 46 GLU cc_start: 0.7940 (tp30) cc_final: 0.7494 (tp30) REVERT: I 82 MET cc_start: 0.6377 (ptp) cc_final: 0.5879 (mtm) REVERT: I 104 TRP cc_start: 0.7761 (OUTLIER) cc_final: 0.6046 (m-90) REVERT: I 109 GLN cc_start: 0.7571 (tp-100) cc_final: 0.7261 (tp-100) REVERT: E 33 MET cc_start: 0.6705 (mmm) cc_final: 0.6343 (mmm) REVERT: E 37 ARG cc_start: 0.7066 (ptm160) cc_final: 0.6688 (ptm160) outliers start: 100 outliers final: 83 residues processed: 277 average time/residue: 0.2855 time to fit residues: 119.7582 Evaluate side-chains 278 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 187 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 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 645 THR Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 74 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 567 ARG Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 587 ILE 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 130 VAL Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 146 HIS Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 304 LYS Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 590 CYS Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 640 SER Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain J residue 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 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 67 PHE 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 56 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 18 LEU 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 197 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 190 optimal weight: 6.9990 chunk 165 optimal weight: 20.0000 chunk 17 optimal weight: 0.7980 chunk 127 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 HIS E 57 HIS ** E 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17418 Z= 0.262 Angle : 0.686 15.300 23659 Z= 0.352 Chirality : 0.049 0.371 2735 Planarity : 0.004 0.066 3000 Dihedral : 6.223 60.688 3028 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.49 % Favored : 92.32 % Rotamer: Outliers : 5.24 % Allowed : 27.82 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.18), residues: 2083 helix: 1.39 (0.85), residues: 33 sheet: -0.38 (0.20), residues: 682 loop : -1.71 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP D 104 HIS 0.009 0.001 HIS E 95 PHE 0.062 0.002 PHE A 32 TYR 0.036 0.002 TYR F 58 ARG 0.013 0.000 ARG J 53 ********************** 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 285 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 189 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7699 (pp) REVERT: A 88 ASP cc_start: 0.7875 (t0) cc_final: 0.7357 (m-30) REVERT: A 319 ARG cc_start: 0.8042 (ptp90) cc_final: 0.7580 (ttp-110) REVERT: A 558 LYS cc_start: 0.8888 (mmtm) cc_final: 0.8449 (mmmt) REVERT: B 96 GLU cc_start: 0.8356 (pt0) cc_final: 0.7971 (tt0) REVERT: B 233 ILE cc_start: 0.7501 (pt) cc_final: 0.7245 (pt) REVERT: B 324 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6006 (pm20) REVERT: B 537 LYS cc_start: 0.8260 (tttm) cc_final: 0.7964 (tttp) REVERT: B 567 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8268 (ptp90) REVERT: D 66 HIS cc_start: 0.7004 (OUTLIER) cc_final: 0.6339 (m90) REVERT: D 145 TYR cc_start: 0.5729 (m-10) cc_final: 0.5319 (m-10) REVERT: D 146 HIS cc_start: 0.5627 (OUTLIER) cc_final: 0.5284 (m-70) REVERT: D 298 GLU cc_start: 0.8189 (tp30) cc_final: 0.7864 (tt0) REVERT: D 319 ARG cc_start: 0.8268 (ptp90) cc_final: 0.8057 (ttp-110) REVERT: D 321 GLN cc_start: 0.7872 (pp30) cc_final: 0.7384 (pp30) REVERT: D 630 THR cc_start: 0.8016 (OUTLIER) cc_final: 0.7797 (t) REVERT: J 13 GLN cc_start: 0.7118 (pp30) cc_final: 0.6821 (tp40) REVERT: J 46 GLU cc_start: 0.7806 (tp30) cc_final: 0.7399 (tp30) REVERT: F 33 MET cc_start: 0.5151 (mmm) cc_final: 0.3878 (mmt) REVERT: F 37 ARG cc_start: 0.7047 (tmt170) cc_final: 0.6788 (tmt170) REVERT: F 81 MET cc_start: 0.4994 (ptt) cc_final: 0.4769 (ptm) REVERT: G 19 ARG cc_start: 0.6121 (tpp80) cc_final: 0.5814 (tpp80) REVERT: G 78 TYR cc_start: 0.6065 (m-80) cc_final: 0.5587 (m-80) REVERT: G 80 GLU cc_start: 0.4767 (tp30) cc_final: 0.4371 (pt0) REVERT: H 46 GLU cc_start: 0.7860 (tp30) cc_final: 0.7455 (tp30) REVERT: H 98 ARG cc_start: 0.8299 (ttm170) cc_final: 0.7981 (ttp-110) REVERT: H 106 ARG cc_start: 0.6992 (OUTLIER) cc_final: 0.5483 (mmt180) REVERT: H 109 GLN cc_start: 0.6958 (tp40) cc_final: 0.6734 (tp-100) REVERT: I 46 GLU cc_start: 0.7904 (tp30) cc_final: 0.7465 (tp30) REVERT: I 104 TRP cc_start: 0.7852 (OUTLIER) cc_final: 0.6080 (m-90) REVERT: I 109 GLN cc_start: 0.7516 (tp-100) cc_final: 0.7223 (tp-100) REVERT: E 33 MET cc_start: 0.6733 (mmm) cc_final: 0.5999 (mmp) REVERT: E 37 ARG cc_start: 0.7083 (ptm160) cc_final: 0.6702 (ptm160) outliers start: 96 outliers final: 83 residues processed: 270 average time/residue: 0.2777 time to fit residues: 115.4425 Evaluate side-chains 276 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 185 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 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 B residue 47 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 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 567 ARG 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 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 130 VAL Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 146 HIS Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 304 LYS Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 590 CYS Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 640 SER Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 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 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 28 ILE Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 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 56 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 18 LEU 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 175 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 165 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 169 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 145 optimal weight: 0.7980 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 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 HIS D 658 ASN ** 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** ** E 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 = 0.4495 r_free = 0.4495 target = 0.205939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.158074 restraints weight = 24485.044| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 4.27 r_work: 0.3723 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17418 Z= 0.196 Angle : 0.645 14.540 23659 Z= 0.331 Chirality : 0.048 0.365 2735 Planarity : 0.004 0.047 3000 Dihedral : 5.942 55.894 3028 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.87 % Favored : 92.94 % Rotamer: Outliers : 5.07 % Allowed : 28.26 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.18), residues: 2083 helix: 1.50 (0.85), residues: 33 sheet: -0.35 (0.21), residues: 664 loop : -1.63 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 104 HIS 0.007 0.001 HIS E 95 PHE 0.047 0.001 PHE A 32 TYR 0.017 0.001 TYR E 105 ARG 0.009 0.000 ARG J 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4092.15 seconds wall clock time: 75 minutes 38.19 seconds (4538.19 seconds total)