Starting phenix.real_space_refine on Sat Aug 8 10:39:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p9s_71421/08_2026/9p9s_71421_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p9s_71421/08_2026/9p9s_71421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9p9s_71421/08_2026/9p9s_71421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p9s_71421/08_2026/9p9s_71421.map" model { file = "/net/cci-nas-00/data/ceres_data/9p9s_71421/08_2026/9p9s_71421_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p9s_71421/08_2026/9p9s_71421_trim.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians S 71 5.16 5 C 8474 2.51 5 N 2378 2.21 5 O 2722 1.98 5 H 12916 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26561 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 4946 Classifications: {'peptide': 325} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 16, 'TRANS': 308} Chain breaks: 1 Chain: "B" Number of atoms: 2666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 2666 Classifications: {'peptide': 169} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 168} Chain: "C" Number of atoms: 4948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 4948 Classifications: {'peptide': 325} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 16, 'TRANS': 308} Chain breaks: 1 Chain: "D" Number of atoms: 2666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 2666 Classifications: {'peptide': 169} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 168} Chain: "E" Number of atoms: 4985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 4985 Classifications: {'peptide': 328} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 16, 'TRANS': 311} Chain: "F" Number of atoms: 2666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 2666 Classifications: {'peptide': 169} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 168} Chain: "H" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1782 Classifications: {'peptide': 119} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1678 Classifications: {'peptide': 111} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.01, per 1000 atoms: 0.15 Number of scatterers: 26561 At special positions: 0 Unit cell: (89.964, 92.463, 175.763, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 71 16.00 O 2722 8.00 N 2378 7.00 C 8474 6.00 H 12916 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 296 " distance=2.05 Simple disulfide: pdb=" SG CYS A 72 " - pdb=" SG CYS A 84 " distance=2.03 Simple disulfide: pdb=" SG CYS A 105 " - pdb=" SG CYS A 147 " distance=2.05 Simple disulfide: pdb=" SG CYS A 300 " - pdb=" SG CYS A 324 " distance=2.03 Simple disulfide: pdb=" SG CYS B 493 " - pdb=" SG CYS B 497 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS D 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 296 " distance=2.03 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 84 " distance=2.03 Simple disulfide: pdb=" SG CYS C 105 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS C 300 " - pdb=" SG CYS C 324 " distance=2.03 Simple disulfide: pdb=" SG CYS D 493 " - pdb=" SG CYS D 497 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS F 486 " distance=2.03 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 296 " distance=2.03 Simple disulfide: pdb=" SG CYS E 72 " - pdb=" SG CYS E 84 " distance=2.03 Simple disulfide: pdb=" SG CYS E 105 " - pdb=" SG CYS E 147 " distance=2.03 Simple disulfide: pdb=" SG CYS E 300 " - pdb=" SG CYS E 324 " distance=2.03 Simple disulfide: pdb=" SG CYS F 493 " - pdb=" SG CYS F 497 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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=0, symmetry=0 Links applied NAG-ASN " NAG A 401 " - " ASN A 174 " " NAG A 402 " - " ASN A 46 " " NAG A 403 " - " ASN A 100 " " NAG B 601 " - " ASN B 431 " " NAG B 602 " - " ASN B 503 " " NAG B 603 " - " ASN B 507 " " NAG C 401 " - " ASN C 174 " " NAG C 402 " - " ASN C 46 " " NAG D 601 " - " ASN D 431 " " NAG D 602 " - " ASN D 507 " " NAG D 603 " - " ASN D 503 " " NAG E 401 " - " ASN E 46 " " NAG E 402 " - " ASN E 174 " " NAG F 601 " - " ASN F 431 " " NAG F 602 " - " ASN F 507 " " NAG F 603 " - " ASN F 503 " Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 756.9 milliseconds 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3126 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 36 sheets defined 22.8% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 75 through 80 removed outlier: 3.812A pdb=" N ILE A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.536A pdb=" N ASP A 85 " --> pdb=" O PRO A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 122 removed outlier: 3.841A pdb=" N GLU A 122 " --> pdb=" O GLN A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 204 Processing helix chain 'B' and resid 386 through 405 removed outlier: 4.370A pdb=" N GLY B 399 " --> pdb=" O ASP B 395 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS B 400 " --> pdb=" O GLN B 396 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ASN B 402 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU B 404 " --> pdb=" O LYS B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 476 Processing helix chain 'B' and resid 495 through 503 removed outlier: 3.820A pdb=" N GLU B 499 " --> pdb=" O ASP B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 521 removed outlier: 3.893A pdb=" N ILE B 520 " --> pdb=" O LEU B 516 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET B 521 " --> pdb=" O GLN B 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 80 removed outlier: 3.704A pdb=" N ILE C 79 " --> pdb=" O LEU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 85 Processing helix chain 'C' and resid 112 through 121 removed outlier: 3.544A pdb=" N LEU C 116 " --> pdb=" O ASN C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 148 removed outlier: 3.591A pdb=" N LYS C 148 " --> pdb=" O SER C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 205 Processing helix chain 'D' and resid 386 through 405 removed outlier: 4.330A pdb=" N GLY D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS D 400 " --> pdb=" O GLN D 396 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU D 401 " --> pdb=" O ILE D 397 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ASN D 402 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU D 404 " --> pdb=" O LYS D 400 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE D 405 " --> pdb=" O LEU D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 476 Processing helix chain 'D' and resid 477 through 479 No H-bonds generated for 'chain 'D' and resid 477 through 479' Processing helix chain 'D' and resid 494 through 503 Processing helix chain 'D' and resid 507 through 510 removed outlier: 3.691A pdb=" N GLU D 510 " --> pdb=" O ASN D 507 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 507 through 510' Processing helix chain 'D' and resid 511 through 521 Processing helix chain 'E' and resid 81 through 85 Processing helix chain 'E' and resid 112 through 122 removed outlier: 3.968A pdb=" N GLU E 122 " --> pdb=" O GLN E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 205 Processing helix chain 'F' and resid 386 through 405 removed outlier: 4.355A pdb=" N GLY F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS F 400 " --> pdb=" O GLN F 396 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU F 401 " --> pdb=" O ILE F 397 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ASN F 402 " --> pdb=" O THR F 398 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU F 404 " --> pdb=" O LYS F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 475 Processing helix chain 'F' and resid 494 through 503 Processing helix chain 'F' and resid 507 through 510 Processing helix chain 'F' and resid 511 through 520 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.844A pdb=" N THR L 83 " --> pdb=" O GLU L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 380 through 385 removed outlier: 3.529A pdb=" N GLY B 382 " --> pdb=" O HIS B 375 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU B 480 " --> pdb=" O GLU B 488 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 34 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 52 Processing sheet with id=AA5, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.168A pdb=" N VAL A 59 " --> pdb=" O ASP A 293 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 66 through 68 removed outlier: 3.581A pdb=" N VAL A 67 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE A 96 " --> pdb=" O VAL A 67 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 109 through 110 removed outlier: 6.626A pdb=" N ARG A 109 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N TRP A 243 " --> pdb=" O ARG A 109 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N VAL A 188 " --> pdb=" O PRO A 263 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA9, first strand: chain 'A' and resid 144 through 148 Processing sheet with id=AB1, first strand: chain 'A' and resid 176 through 178 removed outlier: 3.528A pdb=" N GLN A 220 " --> pdb=" O VAL A 213 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 305 through 307 removed outlier: 3.589A pdb=" N CYS A 300 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 23 through 25 Processing sheet with id=AB4, first strand: chain 'C' and resid 32 through 34 Processing sheet with id=AB5, first strand: chain 'C' and resid 47 through 48 Processing sheet with id=AB6, first strand: chain 'C' and resid 51 through 52 removed outlier: 3.515A pdb=" N GLU C 52 " --> pdb=" O PHE C 313 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 58 through 60 removed outlier: 3.708A pdb=" N ASP C 293 " --> pdb=" O VAL C 59 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 96 through 97 Processing sheet with id=AB9, first strand: chain 'C' and resid 108 through 110 Processing sheet with id=AC1, first strand: chain 'C' and resid 129 through 130 Processing sheet with id=AC2, first strand: chain 'C' and resid 173 through 178 Processing sheet with id=AC3, first strand: chain 'C' and resid 305 through 307 removed outlier: 3.547A pdb=" N GLY C 305 " --> pdb=" O TYR C 302 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR C 302 " --> pdb=" O GLY C 305 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N CYS C 300 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 371 through 376 removed outlier: 3.587A pdb=" N GLY E 24 " --> pdb=" O GLY F 372 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS E 22 " --> pdb=" O ARG F 374 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU F 480 " --> pdb=" O GLU F 488 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 32 through 34 Processing sheet with id=AC6, first strand: chain 'E' and resid 47 through 49 Processing sheet with id=AC7, first strand: chain 'E' and resid 51 through 52 Processing sheet with id=AC8, first strand: chain 'E' and resid 68 through 69 Processing sheet with id=AC9, first strand: chain 'E' and resid 108 through 110 removed outlier: 6.861A pdb=" N ARG E 109 " --> pdb=" O PHE E 241 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N TRP E 243 " --> pdb=" O ARG E 109 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU E 246 " --> pdb=" O ALA E 185 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL E 188 " --> pdb=" O ARG E 265 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ARG E 265 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU E 129 " --> pdb=" O ALA E 266 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 108 through 110 removed outlier: 6.861A pdb=" N ARG E 109 " --> pdb=" O PHE E 241 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N TRP E 243 " --> pdb=" O ARG E 109 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU E 246 " --> pdb=" O ALA E 185 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N VAL E 188 " --> pdb=" O PRO E 263 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 144 through 148 removed outlier: 4.224A pdb=" N CYS E 147 " --> pdb=" O SER E 153 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 173 through 178 Processing sheet with id=AD4, first strand: chain 'E' and resid 300 through 301 Processing sheet with id=AD5, first strand: chain 'H' and resid 18 through 20 removed outlier: 4.142A pdb=" N VAL H 18 " --> pdb=" O LEU H 82 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET H 20 " --> pdb=" O MET H 80 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET H 80 " --> pdb=" O MET H 20 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR H 70 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.693A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N TYR H 91 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.693A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N TYR H 91 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 20 through 23 removed outlier: 3.638A pdb=" N LEU L 73 " --> pdb=" O ILE L 21 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.838A pdb=" N LEU L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N LYS L 49 " --> pdb=" O MET L 33 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET L 33 " --> pdb=" O LYS L 49 " (cutoff:3.500A) 446 hydrogen bonds defined for protein. 1212 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: 6.48 Time building geometry restraints manager: 3.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 12914 1.04 - 1.24: 1923 1.24 - 1.44: 4193 1.44 - 1.64: 7688 1.64 - 1.84: 102 Bond restraints: 26820 Sorted by residual: bond pdb=" NZ LYS E 217 " pdb=" HZ2 LYS E 217 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS A 329 " pdb=" HZ3 LYS A 329 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS A 182 " pdb=" HZ2 LYS A 182 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS A 345 " pdb=" HZ1 LYS A 345 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS D 466 " pdb=" HZ2 LYS D 466 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 ... (remaining 26815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.61: 48143 8.61 - 17.21: 1 17.21 - 25.82: 0 25.82 - 34.42: 0 34.42 - 43.03: 2 Bond angle restraints: 48146 Sorted by residual: angle pdb=" CA GLU C 278 " pdb=" N GLU C 278 " pdb=" H GLU C 278 " ideal model delta sigma weight residual 114.00 157.03 -43.03 3.00e+00 1.11e-01 2.06e+02 angle pdb=" CA GLU A 278 " pdb=" N GLU A 278 " pdb=" H GLU A 278 " ideal model delta sigma weight residual 114.00 151.92 -37.92 3.00e+00 1.11e-01 1.60e+02 angle pdb=" N ILE A 316 " pdb=" CA ILE A 316 " pdb=" C ILE A 316 " ideal model delta sigma weight residual 111.67 108.72 2.95 9.50e-01 1.11e+00 9.67e+00 angle pdb=" C ARG A 149 " pdb=" N THR A 150 " pdb=" CA THR A 150 " ideal model delta sigma weight residual 121.54 127.46 -5.92 1.91e+00 2.74e-01 9.61e+00 angle pdb=" C2 NAG E 402 " pdb=" N2 NAG E 402 " pdb=" C7 NAG E 402 " ideal model delta sigma weight residual 124.56 133.69 -9.13 3.00e+00 1.11e-01 9.27e+00 ... (remaining 48141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 11951 17.94 - 35.88: 663 35.88 - 53.81: 215 53.81 - 71.75: 75 71.75 - 89.69: 12 Dihedral angle restraints: 12916 sinusoidal: 7204 harmonic: 5712 Sorted by residual: dihedral pdb=" CB CYS A 105 " pdb=" SG CYS A 105 " pdb=" SG CYS A 147 " pdb=" CB CYS A 147 " ideal model delta sinusoidal sigma weight residual -86.00 -0.89 -85.11 1 1.00e+01 1.00e-02 8.78e+01 dihedral pdb=" CB CYS D 493 " pdb=" SG CYS D 493 " pdb=" SG CYS D 497 " pdb=" CB CYS D 497 " ideal model delta sinusoidal sigma weight residual 93.00 142.67 -49.67 1 1.00e+01 1.00e-02 3.39e+01 dihedral pdb=" CB CYS B 493 " pdb=" SG CYS B 493 " pdb=" SG CYS B 497 " pdb=" CB CYS B 497 " ideal model delta sinusoidal sigma weight residual -86.00 -131.05 45.05 1 1.00e+01 1.00e-02 2.82e+01 ... (remaining 12913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1703 0.052 - 0.105: 285 0.105 - 0.157: 75 0.157 - 0.209: 2 0.209 - 0.262: 4 Chirality restraints: 2069 Sorted by residual: chirality pdb=" C1 NAG F 602 " pdb=" ND2 ASN F 507 " pdb=" C2 NAG F 602 " pdb=" O5 NAG F 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C2 NAG E 402 " pdb=" C1 NAG E 402 " pdb=" C3 NAG E 402 " pdb=" N2 NAG E 402 " both_signs ideal model delta sigma weight residual False -2.49 -2.26 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" C1 NAG B 603 " pdb=" ND2 ASN B 507 " pdb=" C2 NAG B 603 " pdb=" O5 NAG B 603 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 2066 not shown) Planarity restraints: 4124 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 100 " 0.002 2.00e-02 2.50e+03 2.25e-02 6.35e+00 pdb=" CG ASN A 100 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN A 100 " 0.025 2.00e-02 2.50e+03 pdb=" ND2 ASN A 100 " -0.029 2.00e-02 2.50e+03 pdb=" C1 NAG A 403 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 508 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.60e+00 pdb=" C HIS B 508 " 0.037 2.00e-02 2.50e+03 pdb=" O HIS B 508 " -0.014 2.00e-02 2.50e+03 pdb=" N THR B 509 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 67 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.22e+00 pdb=" C VAL A 67 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL A 67 " 0.013 2.00e-02 2.50e+03 pdb=" N ASP A 68 " 0.012 2.00e-02 2.50e+03 ... (remaining 4121 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 874 2.19 - 2.79: 53429 2.79 - 3.39: 71664 3.39 - 4.00: 96428 4.00 - 4.60: 148914 Nonbonded interactions: 371309 Sorted by model distance: nonbonded pdb="HG21 ILE A 126 " pdb=" HZ2 LYS A 128 " model vdw 1.586 2.270 nonbonded pdb=" HZ1 LYS C 91 " pdb=" H GLU C 278 " model vdw 1.800 2.100 nonbonded pdb=" HG2 LYS A 329 " pdb=" HG SER B 442 " model vdw 1.814 2.270 nonbonded pdb=" HZ2 LYS C 128 " pdb=" HB3 GLU C 157 " model vdw 1.817 2.270 nonbonded pdb="HD23 LEU A 75 " pdb="HD23 LEU A 116 " model vdw 1.833 2.440 ... (remaining 371304 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 19 through 402) selection = (chain 'C' and (resid 19 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ or name HB2 or name HB3)) or resid 101 through 402)) selection = (chain 'E' and (resid 19 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ or name HB2 or name HB3)) or resid 101 through 274 or resid 278 through 402)) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.150 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 24.060 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 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 : 0.004 0.040 13939 Z= 0.166 Angle : 0.710 14.662 18878 Z= 0.364 Chirality : 0.044 0.262 2069 Planarity : 0.004 0.052 2461 Dihedral : 12.391 89.691 5391 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.19), residues: 1695 helix: 1.31 (0.28), residues: 339 sheet: -2.76 (0.26), residues: 327 loop : -2.16 (0.17), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 229 TYR 0.018 0.001 TYR A 302 PHE 0.015 0.002 PHE A 260 TRP 0.008 0.001 TRP F 432 HIS 0.008 0.001 HIS C 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (13904) covalent geometry : angle 0.67163 / 0.35 (18792) SS BOND : bond 0.00564 / 0.28 ( 19) SS BOND : angle 2.40320 / 1.50 ( 38) hydrogen bonds : bond 0.20048 / 14.07 ( 430) hydrogen bonds : angle 8.37368 / 5.70 ( 1212) link_NAG-ASN : bond 0.00458 / 0.24 ( 16) link_NAG-ASN : angle 4.12750 / 2.26 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.7875 (t0) cc_final: 0.7532 (t0) REVERT: B 405 ILE cc_start: 0.8560 (pt) cc_final: 0.7905 (tp) REVERT: E 182 LYS cc_start: 0.8583 (mmtm) cc_final: 0.8043 (tptp) REVERT: F 435 ASP cc_start: 0.8836 (m-30) cc_final: 0.8593 (m-30) REVERT: L 11 LEU cc_start: 0.7359 (tp) cc_final: 0.6928 (tp) REVERT: L 94 ILE cc_start: 0.8108 (mt) cc_final: 0.7858 (mp) outliers start: 0 outliers final: 0 residues processed: 320 average time/residue: 0.2957 time to fit residues: 131.3194 Evaluate side-chains 201 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 424 GLN F 428 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.117454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.098961 restraints weight = 74689.080| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.47 r_work: 0.3236 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13939 Z= 0.118 Angle : 0.540 10.870 18878 Z= 0.278 Chirality : 0.041 0.254 2069 Planarity : 0.004 0.045 2461 Dihedral : 5.308 55.044 2194 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.62 % Allowed : 6.18 % Favored : 93.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.19), residues: 1695 helix: 1.72 (0.27), residues: 339 sheet: -2.56 (0.26), residues: 336 loop : -2.07 (0.17), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 40 TYR 0.008 0.001 TYR A 302 PHE 0.012 0.001 PHE A 110 TRP 0.007 0.001 TRP E 160 HIS 0.008 0.001 HIS B 508 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (13904) covalent geometry : angle 0.51896 / 0.27 (18792) SS BOND : bond 0.00278 / 0.16 ( 19) SS BOND : angle 1.44545 / 0.83 ( 38) hydrogen bonds : bond 0.04505 / 3.15 ( 430) hydrogen bonds : angle 6.10949 / 4.17 ( 1212) link_NAG-ASN : bond 0.00304 / 0.16 ( 16) link_NAG-ASN : angle 2.79006 / 1.54 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 212 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.7784 (t0) cc_final: 0.7479 (t0) REVERT: B 405 ILE cc_start: 0.8665 (pt) cc_final: 0.8054 (tp) REVERT: E 182 LYS cc_start: 0.8534 (mmtm) cc_final: 0.8002 (tptp) REVERT: F 435 ASP cc_start: 0.8780 (m-30) cc_final: 0.8548 (m-30) REVERT: F 482 ASP cc_start: 0.8370 (p0) cc_final: 0.8022 (p0) REVERT: L 11 LEU cc_start: 0.7327 (tp) cc_final: 0.6880 (tp) REVERT: L 62 PHE cc_start: 0.7943 (m-80) cc_final: 0.7709 (m-80) REVERT: L 94 ILE cc_start: 0.8131 (mt) cc_final: 0.7898 (mp) outliers start: 9 outliers final: 5 residues processed: 217 average time/residue: 0.2740 time to fit residues: 86.0169 Evaluate side-chains 196 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 191 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 37 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 146 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 118 GLN E 280 ASN F 424 GLN F 428 ASN F 454 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.112161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.093463 restraints weight = 76234.144| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.46 r_work: 0.3134 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 13939 Z= 0.235 Angle : 0.602 8.640 18878 Z= 0.314 Chirality : 0.043 0.266 2069 Planarity : 0.004 0.042 2461 Dihedral : 5.848 54.977 2194 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 1.10 % Allowed : 8.04 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.19), residues: 1695 helix: 1.57 (0.27), residues: 336 sheet: -2.73 (0.24), residues: 369 loop : -2.14 (0.17), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 40 TYR 0.013 0.002 TYR A 218 PHE 0.021 0.002 PHE A 110 TRP 0.008 0.001 TRP A 160 HIS 0.004 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.24 (13904) covalent geometry : angle 0.57913 / 0.31 (18792) SS BOND : bond 0.00386 / 0.22 ( 19) SS BOND : angle 1.81254 / 1.02 ( 38) hydrogen bonds : bond 0.04743 / 3.27 ( 430) hydrogen bonds : angle 5.78244 / 3.98 ( 1212) link_NAG-ASN : bond 0.00312 / 0.18 ( 16) link_NAG-ASN : angle 2.97270 / 1.84 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 184 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 405 ILE cc_start: 0.8703 (pt) cc_final: 0.8051 (tp) REVERT: E 182 LYS cc_start: 0.8561 (mmtm) cc_final: 0.7949 (tptp) REVERT: F 461 ASP cc_start: 0.8404 (t0) cc_final: 0.8143 (t0) REVERT: F 482 ASP cc_start: 0.8443 (p0) cc_final: 0.8226 (p0) REVERT: L 11 LEU cc_start: 0.7340 (tp) cc_final: 0.6918 (tp) REVERT: L 62 PHE cc_start: 0.7933 (m-80) cc_final: 0.7606 (m-80) REVERT: L 94 ILE cc_start: 0.8152 (mt) cc_final: 0.7917 (mp) outliers start: 16 outliers final: 12 residues processed: 192 average time/residue: 0.2561 time to fit residues: 72.0129 Evaluate side-chains 184 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 172 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain F residue 389 SER Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain F residue 511 TYR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 37 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 50 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 424 GLN F 428 ASN F 454 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.114627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.096085 restraints weight = 74550.466| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.46 r_work: 0.3186 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13939 Z= 0.144 Angle : 0.526 8.638 18878 Z= 0.273 Chirality : 0.041 0.228 2069 Planarity : 0.003 0.044 2461 Dihedral : 5.720 58.798 2194 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.17 % Allowed : 8.93 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.19), residues: 1695 helix: 1.70 (0.27), residues: 339 sheet: -2.61 (0.25), residues: 361 loop : -2.09 (0.17), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 472 TYR 0.009 0.001 TYR H 100A PHE 0.024 0.001 PHE A 110 TRP 0.007 0.001 TRP H 47 HIS 0.005 0.001 HIS B 508 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (13904) covalent geometry : angle 0.50477 / 0.27 (18792) SS BOND : bond 0.00315 / 0.20 ( 19) SS BOND : angle 1.63957 / 0.92 ( 38) hydrogen bonds : bond 0.04208 / 2.89 ( 430) hydrogen bonds : angle 5.49330 / 3.78 ( 1212) link_NAG-ASN : bond 0.00249 / 0.14 ( 16) link_NAG-ASN : angle 2.60744 / 1.57 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 181 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 405 ILE cc_start: 0.8708 (pt) cc_final: 0.8119 (tp) REVERT: E 182 LYS cc_start: 0.8589 (mmtm) cc_final: 0.7932 (tptp) REVERT: F 461 ASP cc_start: 0.8473 (t0) cc_final: 0.8226 (t0) REVERT: F 492 ARG cc_start: 0.7800 (tpp80) cc_final: 0.7591 (tpp80) REVERT: L 11 LEU cc_start: 0.7318 (tp) cc_final: 0.6890 (tp) REVERT: L 37 GLN cc_start: 0.8509 (tt0) cc_final: 0.7776 (tp-100) REVERT: L 62 PHE cc_start: 0.7828 (m-80) cc_final: 0.7505 (m-80) REVERT: L 94 ILE cc_start: 0.8177 (mt) cc_final: 0.7926 (mp) outliers start: 17 outliers final: 10 residues processed: 188 average time/residue: 0.2821 time to fit residues: 77.0226 Evaluate side-chains 187 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 177 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain F residue 486 CYS Chi-restraints excluded: chain F residue 511 TYR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 37 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 81 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 126 optimal weight: 0.0980 chunk 156 optimal weight: 10.0000 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 315 ASN F 454 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.112126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.093566 restraints weight = 75499.145| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.44 r_work: 0.3137 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 13939 Z= 0.239 Angle : 0.581 8.265 18878 Z= 0.304 Chirality : 0.042 0.238 2069 Planarity : 0.004 0.044 2461 Dihedral : 6.087 59.914 2194 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 1.24 % Allowed : 9.48 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.19), residues: 1695 helix: 1.49 (0.28), residues: 336 sheet: -2.70 (0.25), residues: 363 loop : -2.22 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 40 TYR 0.012 0.002 TYR H 100A PHE 0.030 0.002 PHE C 110 TRP 0.008 0.001 TRP A 243 HIS 0.006 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.24 (13904) covalent geometry : angle 0.55789 / 0.30 (18792) SS BOND : bond 0.00421 / 0.23 ( 19) SS BOND : angle 1.84125 / 1.02 ( 38) hydrogen bonds : bond 0.04575 / 3.13 ( 430) hydrogen bonds : angle 5.45770 / 3.77 ( 1212) link_NAG-ASN : bond 0.00283 / 0.16 ( 16) link_NAG-ASN : angle 2.90184 / 1.81 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 174 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 405 ILE cc_start: 0.8723 (pt) cc_final: 0.8108 (tp) REVERT: E 182 LYS cc_start: 0.8575 (mmtm) cc_final: 0.7923 (tptp) REVERT: F 407 LYS cc_start: 0.7716 (tptt) cc_final: 0.7440 (tptm) REVERT: F 461 ASP cc_start: 0.8456 (t0) cc_final: 0.8221 (t0) REVERT: L 11 LEU cc_start: 0.7321 (tp) cc_final: 0.6915 (tp) REVERT: L 62 PHE cc_start: 0.7834 (m-80) cc_final: 0.7519 (m-80) REVERT: L 94 ILE cc_start: 0.8175 (mt) cc_final: 0.7914 (mp) outliers start: 18 outliers final: 14 residues processed: 185 average time/residue: 0.2874 time to fit residues: 77.5438 Evaluate side-chains 178 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain F residue 511 TYR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 37 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 137 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 454 GLN F 424 GLN F 428 ASN F 454 GLN L 76 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.114097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.095654 restraints weight = 74855.676| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.42 r_work: 0.3175 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13939 Z= 0.120 Angle : 0.515 8.134 18878 Z= 0.268 Chirality : 0.041 0.224 2069 Planarity : 0.003 0.045 2461 Dihedral : 5.817 59.138 2194 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.03 % Allowed : 10.65 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.19), residues: 1695 helix: 1.59 (0.28), residues: 336 sheet: -2.54 (0.26), residues: 354 loop : -2.13 (0.17), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 40 TYR 0.008 0.001 TYR H 100A PHE 0.024 0.001 PHE A 110 TRP 0.009 0.001 TRP H 47 HIS 0.005 0.001 HIS B 508 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (13904) covalent geometry : angle 0.49504 / 0.26 (18792) SS BOND : bond 0.00276 / 0.16 ( 19) SS BOND : angle 1.63636 / 0.92 ( 38) hydrogen bonds : bond 0.04064 / 2.80 ( 430) hydrogen bonds : angle 5.27301 / 3.63 ( 1212) link_NAG-ASN : bond 0.00249 / 0.14 ( 16) link_NAG-ASN : angle 2.51102 / 1.53 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 405 ILE cc_start: 0.8736 (pt) cc_final: 0.8146 (tp) REVERT: F 407 LYS cc_start: 0.7571 (tptt) cc_final: 0.7308 (tptm) REVERT: F 461 ASP cc_start: 0.8373 (t0) cc_final: 0.8127 (t0) REVERT: L 11 LEU cc_start: 0.7245 (tp) cc_final: 0.6832 (tp) REVERT: L 37 GLN cc_start: 0.8501 (tt0) cc_final: 0.7789 (tp-100) REVERT: L 62 PHE cc_start: 0.7851 (m-80) cc_final: 0.7548 (m-80) REVERT: L 94 ILE cc_start: 0.8157 (mt) cc_final: 0.7906 (mp) outliers start: 15 outliers final: 13 residues processed: 189 average time/residue: 0.2859 time to fit residues: 77.7848 Evaluate side-chains 185 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 172 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain F residue 511 TYR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain L residue 17 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 141 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 61 optimal weight: 0.2980 chunk 165 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 424 GLN C 315 ASN F 424 GLN F 428 ASN F 454 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.114255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.095684 restraints weight = 74443.551| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.46 r_work: 0.3176 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13939 Z= 0.124 Angle : 0.505 7.955 18878 Z= 0.262 Chirality : 0.041 0.219 2069 Planarity : 0.003 0.045 2461 Dihedral : 5.598 59.789 2194 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.10 % Allowed : 10.99 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.19), residues: 1695 helix: 1.64 (0.28), residues: 336 sheet: -2.41 (0.26), residues: 352 loop : -2.12 (0.17), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 472 TYR 0.009 0.001 TYR H 79 PHE 0.021 0.001 PHE A 110 TRP 0.008 0.001 TRP H 47 HIS 0.004 0.001 HIS B 508 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (13904) covalent geometry : angle 0.48614 / 0.26 (18792) SS BOND : bond 0.00257 / 0.16 ( 19) SS BOND : angle 1.56821 / 0.87 ( 38) hydrogen bonds : bond 0.03976 / 2.74 ( 430) hydrogen bonds : angle 5.12019 / 3.53 ( 1212) link_NAG-ASN : bond 0.00218 / 0.13 ( 16) link_NAG-ASN : angle 2.40111 / 1.45 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 405 ILE cc_start: 0.8726 (pt) cc_final: 0.8130 (tp) REVERT: L 11 LEU cc_start: 0.7224 (tp) cc_final: 0.6802 (tp) REVERT: L 37 GLN cc_start: 0.8508 (tt0) cc_final: 0.7765 (tp-100) REVERT: L 62 PHE cc_start: 0.7827 (m-80) cc_final: 0.7494 (m-80) REVERT: L 94 ILE cc_start: 0.8149 (mt) cc_final: 0.7891 (mp) outliers start: 16 outliers final: 14 residues processed: 182 average time/residue: 0.2721 time to fit residues: 73.0965 Evaluate side-chains 181 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain F residue 511 TYR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain L residue 73 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 60 optimal weight: 0.0670 chunk 90 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 146 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.7324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 GLN B 424 GLN F 454 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.112945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.094242 restraints weight = 75560.744| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.47 r_work: 0.3149 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13939 Z= 0.183 Angle : 0.540 7.940 18878 Z= 0.281 Chirality : 0.041 0.223 2069 Planarity : 0.004 0.043 2461 Dihedral : 5.739 59.656 2194 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 1.37 % Allowed : 11.20 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.19), residues: 1695 helix: 1.56 (0.28), residues: 336 sheet: -2.43 (0.26), residues: 354 loop : -2.18 (0.17), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 40 TYR 0.016 0.001 TYR H 79 PHE 0.020 0.001 PHE A 110 TRP 0.006 0.001 TRP H 47 HIS 0.005 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (13904) covalent geometry : angle 0.51886 / 0.28 (18792) SS BOND : bond 0.00314 / 0.18 ( 19) SS BOND : angle 1.71082 / 0.96 ( 38) hydrogen bonds : bond 0.04230 / 2.89 ( 430) hydrogen bonds : angle 5.17667 / 3.58 ( 1212) link_NAG-ASN : bond 0.00219 / 0.13 ( 16) link_NAG-ASN : angle 2.63620 / 1.64 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 407 LYS cc_start: 0.7564 (tptt) cc_final: 0.7314 (tptm) REVERT: H 13 ARG cc_start: 0.6558 (mmt90) cc_final: 0.6067 (ttm170) REVERT: L 11 LEU cc_start: 0.7245 (tp) cc_final: 0.6836 (tp) REVERT: L 94 ILE cc_start: 0.8145 (mt) cc_final: 0.7894 (mp) outliers start: 20 outliers final: 16 residues processed: 184 average time/residue: 0.2807 time to fit residues: 75.3082 Evaluate side-chains 185 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain F residue 511 TYR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain L residue 73 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 124 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 424 GLN F 454 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.113223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.094567 restraints weight = 75296.635| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.46 r_work: 0.3156 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13939 Z= 0.165 Angle : 0.537 7.718 18878 Z= 0.280 Chirality : 0.041 0.225 2069 Planarity : 0.003 0.044 2461 Dihedral : 5.715 59.130 2194 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 1.24 % Allowed : 11.26 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.19), residues: 1695 helix: 1.54 (0.28), residues: 336 sheet: -2.38 (0.26), residues: 354 loop : -2.15 (0.17), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 472 TYR 0.009 0.001 TYR L 32 PHE 0.028 0.002 PHE E 110 TRP 0.007 0.001 TRP H 47 HIS 0.004 0.001 HIS B 508 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (13904) covalent geometry : angle 0.51502 / 0.27 (18792) SS BOND : bond 0.00335 / 0.21 ( 19) SS BOND : angle 1.92774 / 1.01 ( 38) hydrogen bonds : bond 0.04157 / 2.86 ( 430) hydrogen bonds : angle 5.17371 / 3.57 ( 1212) link_NAG-ASN : bond 0.00209 / 0.12 ( 16) link_NAG-ASN : angle 2.54791 / 1.58 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 407 LYS cc_start: 0.7567 (tptt) cc_final: 0.7320 (tptm) REVERT: H 13 ARG cc_start: 0.6567 (mmt90) cc_final: 0.6083 (ttm170) REVERT: L 11 LEU cc_start: 0.7270 (tp) cc_final: 0.6870 (tp) REVERT: L 94 ILE cc_start: 0.8140 (mt) cc_final: 0.7883 (mp) outliers start: 18 outliers final: 16 residues processed: 181 average time/residue: 0.2743 time to fit residues: 72.9782 Evaluate side-chains 183 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain F residue 511 TYR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain L residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 3.9990 chunk 21 optimal weight: 0.3980 chunk 122 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 424 GLN F 454 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.113579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.094908 restraints weight = 75229.879| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.45 r_work: 0.3165 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13939 Z= 0.145 Angle : 0.531 7.548 18878 Z= 0.277 Chirality : 0.041 0.221 2069 Planarity : 0.004 0.060 2461 Dihedral : 5.635 59.469 2194 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.17 % Allowed : 11.68 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.19), residues: 1695 helix: 1.57 (0.28), residues: 336 sheet: -2.40 (0.26), residues: 360 loop : -2.12 (0.17), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 40 TYR 0.008 0.001 TYR L 32 PHE 0.036 0.001 PHE E 110 TRP 0.009 0.001 TRP H 47 HIS 0.004 0.001 HIS B 508 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (13904) covalent geometry : angle 0.51124 / 0.27 (18792) SS BOND : bond 0.00276 / 0.15 ( 19) SS BOND : angle 1.73827 / 0.94 ( 38) hydrogen bonds : bond 0.04080 / 2.81 ( 430) hydrogen bonds : angle 5.13922 / 3.55 ( 1212) link_NAG-ASN : bond 0.00217 / 0.12 ( 16) link_NAG-ASN : angle 2.46242 / 1.53 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 407 LYS cc_start: 0.7533 (tptt) cc_final: 0.7290 (tptm) REVERT: F 461 ASP cc_start: 0.8412 (t0) cc_final: 0.8211 (t0) REVERT: F 488 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: H 13 ARG cc_start: 0.6558 (mmt90) cc_final: 0.6115 (ttm170) REVERT: L 11 LEU cc_start: 0.7275 (tp) cc_final: 0.6887 (tp) REVERT: L 94 ILE cc_start: 0.8134 (mt) cc_final: 0.7871 (mp) outliers start: 17 outliers final: 16 residues processed: 177 average time/residue: 0.2468 time to fit residues: 64.8638 Evaluate side-chains 183 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 488 GLU Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain F residue 511 TYR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain L residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 123 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 0.0770 chunk 128 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 27 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 424 GLN F 454 GLN H 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.114768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.096045 restraints weight = 74984.840| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.47 r_work: 0.3187 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13939 Z= 0.116 Angle : 0.510 7.187 18878 Z= 0.266 Chirality : 0.041 0.214 2069 Planarity : 0.003 0.061 2461 Dihedral : 5.469 59.392 2194 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.03 % Allowed : 11.88 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.20), residues: 1695 helix: 1.75 (0.28), residues: 333 sheet: -2.34 (0.26), residues: 364 loop : -2.02 (0.18), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 40 TYR 0.009 0.001 TYR C 302 PHE 0.043 0.001 PHE E 110 TRP 0.009 0.001 TRP H 47 HIS 0.006 0.001 HIS E 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (13904) covalent geometry : angle 0.49342 / 0.26 (18792) SS BOND : bond 0.00240 / 0.14 ( 19) SS BOND : angle 1.54384 / 0.84 ( 38) hydrogen bonds : bond 0.03890 / 2.69 ( 430) hydrogen bonds : angle 5.06662 / 3.50 ( 1212) link_NAG-ASN : bond 0.00221 / 0.13 ( 16) link_NAG-ASN : angle 2.24001 / 1.38 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5787.70 seconds wall clock time: 99 minutes 8.63 seconds (5948.63 seconds total)