Starting phenix.real_space_refine on Sat Jul 4 21:18:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7pm6_13522/07_2026/7pm6_13522.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pm6_13522/07_2026/7pm6_13522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7pm6_13522/07_2026/7pm6_13522.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7pm6_13522/07_2026/7pm6_13522.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pm6_13522/07_2026/7pm6_13522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pm6_13522/07_2026/7pm6_13522.map" model { file = "/net/cci-nas-00/data/ceres_data/7pm6_13522/07_2026/7pm6_13522.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pm6_13522/07_2026/7pm6_13522.cif" } resolution = 3.0 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: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 148 5.16 5 C 14835 2.51 5 N 3957 2.21 5 O 4379 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23334 Number of models: 1 Model: "" Number of chains: 18 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 6092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 6092 Classifications: {'peptide': 746} Link IDs: {'PTRANS': 27, 'TRANS': 718} Chain breaks: 4 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 6092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 6092 Classifications: {'peptide': 746} Link IDs: {'PTRANS': 27, 'TRANS': 718} Chain breaks: 4 Chain: "F" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.16, per 1000 atoms: 0.22 Number of scatterers: 23334 At special positions: 0 Unit cell: (171.72, 224.72, 177.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 148 16.00 P 10 15.00 Mg 5 11.99 O 4379 8.00 N 3957 7.00 C 14835 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 TRANS " TRP H 1 " - " ALA H 7 " " DTH H 4 " - " ALA H 3 " " TRP I 1 " - " ALA I 7 " " DTH I 4 " - " ALA I 3 " " TRP J 1 " - " ALA J 7 " " DTH J 4 " - " ALA J 3 " Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 1.1 seconds 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " pdb=" CB DTH I 4 " pdb=" CB DTH J 4 " Number of C-beta restraints generated: 5456 Finding SS restraints... Secondary structure from input PDB file: 151 helices and 35 sheets defined 54.8% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'B' and resid 5 through 19 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.213A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 53 Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 67 through 79 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 106 through 116 Processing helix chain 'B' and resid 121 through 130 Processing helix chain 'B' and resid 141 through 150 removed outlier: 3.572A pdb=" N SER B 150 " --> pdb=" O LYS B 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.628A pdb=" N LEU A 77 " --> pdb=" O LEU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 116 through 119 removed outlier: 4.502A pdb=" N TYR A 119 " --> pdb=" O LEU A 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 119' Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 138 through 153 removed outlier: 3.517A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 184 removed outlier: 3.576A pdb=" N PHE A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 207 removed outlier: 3.526A pdb=" N ASN A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 259 through 268 removed outlier: 4.203A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.522A pdb=" N LYS A 275 " --> pdb=" O PRO A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 4.205A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 removed outlier: 3.959A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 337 removed outlier: 3.869A pdb=" N ASN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'A' and resid 367 through 376 removed outlier: 3.909A pdb=" N CYS A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 424 Processing helix chain 'A' and resid 448 through 480 Processing helix chain 'A' and resid 483 through 487 removed outlier: 3.682A pdb=" N LEU A 486 " --> pdb=" O PRO A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 Processing helix chain 'A' and resid 504 through 515 removed outlier: 3.773A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 532 Processing helix chain 'A' and resid 563 through 569 removed outlier: 3.920A pdb=" N LYS A 567 " --> pdb=" O GLY A 563 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.506A pdb=" N ILE A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 594 removed outlier: 3.598A pdb=" N GLU A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 633 Processing helix chain 'A' and resid 635 through 653 removed outlier: 3.794A pdb=" N ALA A 653 " --> pdb=" O GLU A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.586A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 697 Processing helix chain 'A' and resid 704 through 712 Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 723 through 736 removed outlier: 3.881A pdb=" N GLU A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 754 through 792 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.550A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.870A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.264A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.542A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.689A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 194 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.749A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.521A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 283 Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.677A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 319 Processing helix chain 'C' and resid 337 through 349 removed outlier: 3.592A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.939A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.694A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 19 Processing helix chain 'E' and resid 29 through 39 removed outlier: 4.125A pdb=" N GLY E 33 " --> pdb=" O TYR E 29 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASP E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 53 Processing helix chain 'E' and resid 56 through 63 Processing helix chain 'E' and resid 67 through 79 Proline residue: E 72 - end of helix Processing helix chain 'E' and resid 87 through 95 Processing helix chain 'E' and resid 105 through 116 Processing helix chain 'E' and resid 121 through 130 Processing helix chain 'E' and resid 140 through 150 Processing helix chain 'D' and resid 73 through 77 removed outlier: 3.685A pdb=" N LEU D 77 " --> pdb=" O LEU D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 95 Processing helix chain 'D' and resid 116 through 119 removed outlier: 4.458A pdb=" N TYR D 119 " --> pdb=" O LEU D 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 116 through 119' Processing helix chain 'D' and resid 120 through 128 Processing helix chain 'D' and resid 138 through 153 removed outlier: 3.558A pdb=" N VAL D 142 " --> pdb=" O HIS D 138 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA D 151 " --> pdb=" O TYR D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 184 removed outlier: 3.653A pdb=" N PHE D 180 " --> pdb=" O ALA D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 207 removed outlier: 3.576A pdb=" N ASN D 200 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Proline residue: D 201 - end of helix Processing helix chain 'D' and resid 245 through 250 Processing helix chain 'D' and resid 259 through 268 removed outlier: 4.141A pdb=" N TYR D 263 " --> pdb=" O TYR D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 285 through 290 removed outlier: 4.244A pdb=" N GLN D 290 " --> pdb=" O HIS D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 315 removed outlier: 3.870A pdb=" N VAL D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 337 removed outlier: 3.916A pdb=" N ASN D 337 " --> pdb=" O LEU D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 365 Processing helix chain 'D' and resid 367 through 376 removed outlier: 3.814A pdb=" N CYS D 376 " --> pdb=" O ALA D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 424 Processing helix chain 'D' and resid 448 through 480 Processing helix chain 'D' and resid 483 through 487 removed outlier: 3.653A pdb=" N LEU D 486 " --> pdb=" O PRO D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 501 Processing helix chain 'D' and resid 504 through 515 removed outlier: 3.775A pdb=" N LYS D 514 " --> pdb=" O ASP D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 532 Processing helix chain 'D' and resid 563 through 569 removed outlier: 3.896A pdb=" N LYS D 567 " --> pdb=" O GLY D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 582 removed outlier: 3.554A pdb=" N ILE D 577 " --> pdb=" O TYR D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 594 removed outlier: 3.561A pdb=" N GLU D 591 " --> pdb=" O LYS D 587 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE D 593 " --> pdb=" O LEU D 589 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 633 Processing helix chain 'D' and resid 635 through 653 removed outlier: 3.664A pdb=" N ALA D 653 " --> pdb=" O GLU D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 685 removed outlier: 3.615A pdb=" N GLN D 680 " --> pdb=" O LYS D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 697 Processing helix chain 'D' and resid 704 through 712 Processing helix chain 'D' and resid 713 through 715 No H-bonds generated for 'chain 'D' and resid 713 through 715' Processing helix chain 'D' and resid 723 through 736 removed outlier: 3.987A pdb=" N GLU D 733 " --> pdb=" O LYS D 729 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 740 No H-bonds generated for 'chain 'D' and resid 738 through 740' Processing helix chain 'D' and resid 754 through 792 Processing helix chain 'F' and resid 55 through 62 Processing helix chain 'F' and resid 78 through 92 removed outlier: 3.550A pdb=" N MET F 82 " --> pdb=" O ASN F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.830A pdb=" N HIS F 101 " --> pdb=" O PRO F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 126 removed outlier: 4.228A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET F 123 " --> pdb=" O MET F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 removed outlier: 3.519A pdb=" N SER F 141 " --> pdb=" O GLN F 137 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR F 143 " --> pdb=" O VAL F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 175 removed outlier: 3.685A pdb=" N ILE F 175 " --> pdb=" O PRO F 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 172 through 175' Processing helix chain 'F' and resid 181 through 194 Processing helix chain 'F' and resid 195 through 197 No H-bonds generated for 'chain 'F' and resid 195 through 197' Processing helix chain 'F' and resid 202 through 217 removed outlier: 3.798A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP F 211 " --> pdb=" O GLU F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 233 Processing helix chain 'F' and resid 234 through 237 Processing helix chain 'F' and resid 252 through 257 removed outlier: 3.527A pdb=" N CYS F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 262 Processing helix chain 'F' and resid 263 through 268 Processing helix chain 'F' and resid 273 through 283 Processing helix chain 'F' and resid 289 through 295 removed outlier: 3.651A pdb=" N ALA F 295 " --> pdb=" O LYS F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 305 Processing helix chain 'F' and resid 308 through 319 Processing helix chain 'F' and resid 337 through 347 Processing helix chain 'F' and resid 348 through 349 No H-bonds generated for 'chain 'F' and resid 348 through 349' Processing helix chain 'F' and resid 350 through 355 removed outlier: 3.912A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 368 through 373 removed outlier: 3.689A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 61 Processing helix chain 'G' and resid 78 through 92 removed outlier: 3.618A pdb=" N MET G 82 " --> pdb=" O ASN G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 101 removed outlier: 3.816A pdb=" N HIS G 101 " --> pdb=" O PRO G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 126 removed outlier: 4.212A pdb=" N ARG G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU G 117 " --> pdb=" O LYS G 113 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET G 123 " --> pdb=" O MET G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 145 removed outlier: 3.529A pdb=" N SER G 141 " --> pdb=" O GLN G 137 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU G 142 " --> pdb=" O ALA G 138 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR G 143 " --> pdb=" O VAL G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 175 removed outlier: 3.767A pdb=" N ILE G 175 " --> pdb=" O PRO G 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 172 through 175' Processing helix chain 'G' and resid 181 through 194 Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 202 through 217 removed outlier: 3.726A pdb=" N GLU G 207 " --> pdb=" O THR G 203 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE G 208 " --> pdb=" O ALA G 204 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL G 209 " --> pdb=" O GLU G 205 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP G 211 " --> pdb=" O GLU G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 233 Processing helix chain 'G' and resid 252 through 257 removed outlier: 3.519A pdb=" N CYS G 257 " --> pdb=" O GLU G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 262 Processing helix chain 'G' and resid 263 through 268 Processing helix chain 'G' and resid 273 through 283 Processing helix chain 'G' and resid 284 through 285 No H-bonds generated for 'chain 'G' and resid 284 through 285' Processing helix chain 'G' and resid 286 through 288 No H-bonds generated for 'chain 'G' and resid 286 through 288' Processing helix chain 'G' and resid 289 through 295 removed outlier: 3.781A pdb=" N ALA G 295 " --> pdb=" O LYS G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 305 Processing helix chain 'G' and resid 308 through 319 Processing helix chain 'G' and resid 337 through 349 removed outlier: 3.588A pdb=" N SER G 348 " --> pdb=" O SER G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 355 removed outlier: 3.983A pdb=" N GLN G 354 " --> pdb=" O THR G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 366 Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.838A pdb=" N ARG G 372 " --> pdb=" O SER G 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 28 Processing sheet with id=AA2, first strand: chain 'B' and resid 103 through 105 Processing sheet with id=AA3, first strand: chain 'A' and resid 12 through 16 removed outlier: 3.544A pdb=" N LEU A 48 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 100 through 103 removed outlier: 6.419A pdb=" N GLN A 157 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N LEU A 436 " --> pdb=" O GLN A 157 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE A 159 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ILE A 438 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL A 161 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 209 Processing sheet with id=AA6, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.321A pdb=" N SER A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 377 through 381 Processing sheet with id=AA8, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA9, first strand: chain 'A' and resid 700 through 703 Processing sheet with id=AB1, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.880A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.334A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB7, first strand: chain 'E' and resid 26 through 28 Processing sheet with id=AB8, first strand: chain 'D' and resid 11 through 16 removed outlier: 3.753A pdb=" N ALA D 11 " --> pdb=" O LEU D 27 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 100 through 103 removed outlier: 6.466A pdb=" N GLN D 157 " --> pdb=" O GLY D 434 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LEU D 436 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE D 159 " --> pdb=" O LEU D 436 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ILE D 438 " --> pdb=" O ILE D 159 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL D 161 " --> pdb=" O ILE D 438 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY D 236 " --> pdb=" O GLY D 227 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 208 through 209 Processing sheet with id=AC2, first strand: chain 'D' and resid 341 through 344 removed outlier: 6.226A pdb=" N SER D 347 " --> pdb=" O ARG D 343 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 377 through 381 Processing sheet with id=AC4, first strand: chain 'D' and resid 538 through 539 Processing sheet with id=AC5, first strand: chain 'D' and resid 700 through 703 Processing sheet with id=AC6, first strand: chain 'F' and resid 29 through 32 removed outlier: 6.944A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AC8, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AC9, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AD1, first strand: chain 'F' and resid 169 through 170 removed outlier: 6.374A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AD3, first strand: chain 'G' and resid 29 through 32 removed outlier: 6.811A pdb=" N LEU G 8 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N THR G 106 " --> pdb=" O LEU G 8 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N CYS G 10 " --> pdb=" O THR G 106 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AD5, first strand: chain 'G' and resid 71 through 72 Processing sheet with id=AD6, first strand: chain 'G' and resid 169 through 170 Processing sheet with id=AD7, first strand: chain 'G' and resid 169 through 170 removed outlier: 6.273A pdb=" N ASN G 297 " --> pdb=" O ILE G 330 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 238 through 241 1180 hydrogen bonds defined for protein. 3249 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: 4.94 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3891 1.31 - 1.44: 6319 1.44 - 1.56: 13364 1.56 - 1.69: 15 1.69 - 1.82: 242 Bond restraints: 23831 Sorted by residual: bond pdb=" CA EEP I 2 " pdb=" C EEP I 2 " ideal model delta sigma weight residual 1.572 1.432 0.140 2.00e-02 2.50e+03 4.87e+01 bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.435 0.137 2.00e-02 2.50e+03 4.69e+01 bond pdb=" CA EEP J 2 " pdb=" C EEP J 2 " ideal model delta sigma weight residual 1.572 1.469 0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" CA TRP J 1 " pdb=" C TRP J 1 " ideal model delta sigma weight residual 1.525 1.441 0.084 2.10e-02 2.27e+03 1.60e+01 bond pdb=" C EEP I 2 " pdb=" O EEP I 2 " ideal model delta sigma weight residual 1.263 1.189 0.074 2.00e-02 2.50e+03 1.38e+01 ... (remaining 23826 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 31422 2.90 - 5.80: 706 5.80 - 8.70: 61 8.70 - 11.59: 22 11.59 - 14.49: 3 Bond angle restraints: 32214 Sorted by residual: angle pdb=" N TYR D 113 " pdb=" CA TYR D 113 " pdb=" CB TYR D 113 " ideal model delta sigma weight residual 113.15 103.69 9.46 1.63e+00 3.76e-01 3.37e+01 angle pdb=" C HYP J 6 " pdb=" N ALA J 7 " pdb=" CA ALA J 7 " ideal model delta sigma weight residual 121.70 111.40 10.30 1.80e+00 3.09e-01 3.27e+01 angle pdb=" N CYS I 5 " pdb=" CA CYS I 5 " pdb=" CB CYS I 5 " ideal model delta sigma weight residual 110.50 100.85 9.65 1.70e+00 3.46e-01 3.23e+01 angle pdb=" C HYP I 6 " pdb=" N ALA I 7 " pdb=" CA ALA I 7 " ideal model delta sigma weight residual 121.70 111.59 10.11 1.80e+00 3.09e-01 3.15e+01 angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 112.42 9.28 1.80e+00 3.09e-01 2.66e+01 ... (remaining 32209 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.86: 13858 27.86 - 55.73: 400 55.73 - 83.59: 67 83.59 - 111.46: 12 111.46 - 139.32: 12 Dihedral angle restraints: 14349 sinusoidal: 5875 harmonic: 8474 Sorted by residual: dihedral pdb=" O1B ADP G 401 " pdb=" O3A ADP G 401 " pdb=" PB ADP G 401 " pdb=" PA ADP G 401 " ideal model delta sinusoidal sigma weight residual -60.00 79.32 -139.32 1 2.00e+01 2.50e-03 4.22e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 79.28 -139.28 1 2.00e+01 2.50e-03 4.22e+01 dihedral pdb=" O1B ADP F 401 " pdb=" O3A ADP F 401 " pdb=" PB ADP F 401 " pdb=" PA ADP F 401 " ideal model delta sinusoidal sigma weight residual -60.00 79.04 -139.04 1 2.00e+01 2.50e-03 4.21e+01 ... (remaining 14346 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.024: 3520 1.024 - 2.048: 0 2.048 - 3.072: 0 3.072 - 4.097: 0 4.097 - 5.121: 6 Chirality restraints: 3526 Sorted by residual: chirality pdb=" CB DTH J 4 " pdb=" CA DTH J 4 " pdb=" OG1 DTH J 4 " pdb=" CG2 DTH J 4 " both_signs ideal model delta sigma weight residual False 2.55 -2.57 5.12 2.00e-01 2.50e+01 6.56e+02 chirality pdb=" CB DTH H 4 " pdb=" CA DTH H 4 " pdb=" OG1 DTH H 4 " pdb=" CG2 DTH H 4 " both_signs ideal model delta sigma weight residual False 2.55 -2.55 5.10 2.00e-01 2.50e+01 6.51e+02 chirality pdb=" CB DTH I 4 " pdb=" CA DTH I 4 " pdb=" OG1 DTH I 4 " pdb=" CG2 DTH I 4 " both_signs ideal model delta sigma weight residual False 2.55 -2.53 5.09 2.00e-01 2.50e+01 6.47e+02 ... (remaining 3523 not shown) Planarity restraints: 4115 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 113 " 0.057 2.00e-02 2.50e+03 4.60e-02 4.22e+01 pdb=" CG TYR D 113 " -0.106 2.00e-02 2.50e+03 pdb=" CD1 TYR D 113 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR D 113 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR D 113 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR D 113 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR D 113 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR D 113 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 677 " 0.077 9.50e-02 1.11e+02 4.67e-02 1.30e+01 pdb=" NE ARG A 677 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG A 677 " 0.060 2.00e-02 2.50e+03 pdb=" NH1 ARG A 677 " -0.021 2.00e-02 2.50e+03 pdb=" NH2 ARG A 677 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 677 " 0.079 9.50e-02 1.11e+02 4.69e-02 1.26e+01 pdb=" NE ARG D 677 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG D 677 " 0.059 2.00e-02 2.50e+03 pdb=" NH1 ARG D 677 " -0.021 2.00e-02 2.50e+03 pdb=" NH2 ARG D 677 " -0.017 2.00e-02 2.50e+03 ... (remaining 4112 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 38 2.36 - 2.99: 12842 2.99 - 3.63: 34361 3.63 - 4.26: 53661 4.26 - 4.90: 90888 Nonbonded interactions: 191790 Sorted by model distance: nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.724 3.620 nonbonded pdb=" CD1 TRP J 1 " pdb=" SG CYS J 5 " model vdw 1.727 3.620 nonbonded pdb=" CD1 TRP I 1 " pdb=" SG CYS I 5 " model vdw 1.731 3.620 nonbonded pdb="MG MG A1901 " pdb=" O1B ADP A1902 " model vdw 1.908 2.170 nonbonded pdb=" O2B ADP G 401 " pdb="MG MG G 402 " model vdw 1.968 2.170 ... (remaining 191785 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' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.980 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: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.810 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 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:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 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 : 0.012 0.140 23837 Z= 0.521 Angle : 1.075 14.493 32232 Z= 0.595 Chirality : 0.215 5.121 3526 Planarity : 0.007 0.047 4109 Dihedral : 14.848 139.320 8875 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 0.04 % Allowed : 0.52 % Favored : 99.44 % Cbeta Deviations : 0.15 % 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: -1.15 (0.14), residues: 2839 helix: -1.51 (0.12), residues: 1335 sheet: 0.01 (0.24), residues: 404 loop : 0.28 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.061 0.009 ARG A 677 TYR 0.106 0.006 TYR D 113 PHE 0.042 0.004 PHE D 564 TRP 0.046 0.005 TRP C 356 HIS 0.014 0.003 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.01219 / 0.52 (23831) covalent geometry : angle 1.07102 / 0.59 (32214) hydrogen bonds : bond 0.14481 / 9.54 ( 1174) hydrogen bonds : angle 6.91857 / 4.92 ( 3249) link_TRANS : bond 0.02174 / 1.13 ( 6) link_TRANS : angle 3.86711 / 2.30 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 266 time to evaluate : 0.989 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: C 355 MET cc_start: 0.8143 (mmm) cc_final: 0.7891 (mmt) REVERT: C 360 GLN cc_start: 0.8220 (tp40) cc_final: 0.7382 (tm-30) REVERT: E 120 MET cc_start: 0.4648 (mtm) cc_final: 0.4233 (mtt) REVERT: F 82 MET cc_start: 0.8444 (tpt) cc_final: 0.8142 (tpt) REVERT: G 360 GLN cc_start: 0.8238 (tp40) cc_final: 0.8011 (tp-100) outliers start: 1 outliers final: 3 residues processed: 267 average time/residue: 0.8876 time to fit residues: 263.4437 Evaluate side-chains 136 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 133 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 197 optimal weight: 0.0270 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN A 214 ASN A 264 GLN A 410 ASN A 463 GLN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN C 280 ASN E 75 GLN D 264 GLN D 310 GLN D 395 HIS D 410 ASN D 418 HIS ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN F 280 ASN G 280 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.088818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.056106 restraints weight = 84362.071| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.08 r_work: 0.2848 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23837 Z= 0.154 Angle : 0.696 11.046 32232 Z= 0.359 Chirality : 0.045 0.255 3526 Planarity : 0.004 0.044 4109 Dihedral : 10.128 138.037 3224 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.57 % Allowed : 6.00 % Favored : 92.43 % Cbeta Deviations : 0.11 % 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: 0.67 (0.15), residues: 2839 helix: 0.37 (0.14), residues: 1364 sheet: 0.43 (0.24), residues: 421 loop : 0.86 (0.19), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 64 TYR 0.046 0.002 TYR D 113 PHE 0.028 0.002 PHE C 255 TRP 0.015 0.002 TRP C 79 HIS 0.008 0.001 HIS F 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (23831) covalent geometry : angle 0.69568 / 0.36 (32214) hydrogen bonds : bond 0.04454 / 3.00 ( 1174) hydrogen bonds : angle 5.14637 / 3.70 ( 3249) link_TRANS : bond 0.00574 / 0.27 ( 6) link_TRANS : angle 0.80154 / 0.58 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 1.006 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 113 TYR cc_start: 0.8118 (OUTLIER) cc_final: 0.7861 (t80) REVERT: A 305 MET cc_start: 0.8553 (tmm) cc_final: 0.7998 (ppp) REVERT: A 346 ASP cc_start: 0.9093 (t70) cc_final: 0.8791 (t0) REVERT: A 364 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8439 (mpp) REVERT: A 507 ASP cc_start: 0.8426 (t0) cc_final: 0.8220 (t0) REVERT: C 176 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8209 (mpt) REVERT: C 269 MET cc_start: 0.8633 (mmm) cc_final: 0.7971 (ttm) REVERT: C 305 MET cc_start: 0.9291 (mmm) cc_final: 0.9058 (mmt) REVERT: C 355 MET cc_start: 0.9327 (mmm) cc_final: 0.9120 (mmt) REVERT: C 364 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8131 (mp0) REVERT: E 73 MET cc_start: 0.4324 (ptm) cc_final: 0.4048 (ptm) REVERT: D 715 MET cc_start: 0.3596 (OUTLIER) cc_final: 0.3265 (ptp) REVERT: F 314 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8684 (tt0) REVERT: G 47 MET cc_start: 0.8853 (mmm) cc_final: 0.8011 (ptm) outliers start: 39 outliers final: 5 residues processed: 181 average time/residue: 0.7391 time to fit residues: 151.7690 Evaluate side-chains 141 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 TYR Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 113 TYR Chi-restraints excluded: chain D residue 521 ASP Chi-restraints excluded: chain D residue 715 MET Chi-restraints excluded: chain F residue 314 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 84 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 228 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 231 optimal weight: 4.9990 chunk 179 optimal weight: 0.6980 chunk 209 optimal weight: 20.0000 chunk 166 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 207 optimal weight: 7.9990 chunk 142 optimal weight: 1.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 HIS A 730 ASN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.086464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.053433 restraints weight = 85090.263| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 3.02 r_work: 0.2773 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 23837 Z= 0.229 Angle : 0.673 11.902 32232 Z= 0.340 Chirality : 0.047 0.382 3526 Planarity : 0.004 0.043 4109 Dihedral : 9.242 144.639 3219 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.01 % Allowed : 7.49 % Favored : 90.49 % Cbeta Deviations : 0.11 % 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: 1.04 (0.16), residues: 2839 helix: 0.84 (0.14), residues: 1367 sheet: 0.64 (0.25), residues: 418 loop : 0.79 (0.20), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 95 TYR 0.033 0.002 TYR D 113 PHE 0.015 0.002 PHE D 470 TRP 0.016 0.002 TRP A 781 HIS 0.006 0.001 HIS D 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.23 (23831) covalent geometry : angle 0.67258 / 0.34 (32214) hydrogen bonds : bond 0.04238 / 2.84 ( 1174) hydrogen bonds : angle 4.82137 / 3.49 ( 3249) link_TRANS : bond 0.00332 / 0.17 ( 6) link_TRANS : angle 1.11195 / 0.81 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 134 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.8723 (tmm) cc_final: 0.8519 (ppp) REVERT: A 346 ASP cc_start: 0.9232 (t70) cc_final: 0.8913 (t0) REVERT: A 364 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8334 (mpp) REVERT: C 176 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8326 (mpt) REVERT: C 205 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8500 (mt-10) REVERT: C 269 MET cc_start: 0.8737 (mmm) cc_final: 0.8139 (ttm) REVERT: C 305 MET cc_start: 0.9385 (mmm) cc_final: 0.9116 (mmt) REVERT: C 355 MET cc_start: 0.9355 (mmm) cc_final: 0.9124 (mmt) REVERT: C 364 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8179 (mp0) REVERT: E 19 PHE cc_start: 0.5198 (m-80) cc_final: 0.4629 (m-80) REVERT: E 31 GLN cc_start: 0.7123 (tp-100) cc_final: 0.6791 (tp-100) REVERT: D 364 MET cc_start: 0.9210 (mmm) cc_final: 0.8361 (mpp) REVERT: D 561 CYS cc_start: 0.8748 (m) cc_final: 0.8465 (p) REVERT: D 715 MET cc_start: 0.3395 (OUTLIER) cc_final: 0.3167 (ptp) REVERT: F 12 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.8197 (m-40) REVERT: F 314 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.8776 (tt0) outliers start: 50 outliers final: 5 residues processed: 170 average time/residue: 0.6880 time to fit residues: 133.7647 Evaluate side-chains 136 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 521 ASP Chi-restraints excluded: chain D residue 715 MET Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain G residue 257 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 149 optimal weight: 0.8980 chunk 46 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 263 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 chunk 245 optimal weight: 1.9990 chunk 154 optimal weight: 8.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 755 GLN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 GLN ** D 775 GLN ** 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 = 0.3904 r_free = 0.3904 target = 0.086636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.053673 restraints weight = 85611.024| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.03 r_work: 0.2804 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23837 Z= 0.146 Angle : 0.605 10.774 32232 Z= 0.302 Chirality : 0.043 0.335 3526 Planarity : 0.004 0.049 4109 Dihedral : 8.713 148.069 3219 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.73 % Allowed : 8.78 % Favored : 89.48 % Cbeta Deviations : 0.11 % 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: 1.36 (0.16), residues: 2839 helix: 1.21 (0.14), residues: 1356 sheet: 0.82 (0.26), residues: 376 loop : 0.77 (0.20), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 95 TYR 0.023 0.001 TYR A 787 PHE 0.018 0.001 PHE D 750 TRP 0.019 0.002 TRP D 702 HIS 0.005 0.001 HIS F 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (23831) covalent geometry : angle 0.60476 / 0.30 (32214) hydrogen bonds : bond 0.03644 / 2.44 ( 1174) hydrogen bonds : angle 4.61873 / 3.34 ( 3249) link_TRANS : bond 0.00171 / 0.09 ( 6) link_TRANS : angle 0.75230 / 0.47 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 142 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.8744 (tmm) cc_final: 0.8508 (ppp) REVERT: A 346 ASP cc_start: 0.9239 (t70) cc_final: 0.8907 (t0) REVERT: A 364 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8332 (mpp) REVERT: C 176 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8296 (mpt) REVERT: C 269 MET cc_start: 0.8728 (mmm) cc_final: 0.8128 (ttm) REVERT: C 305 MET cc_start: 0.9358 (mmm) cc_final: 0.9125 (mmt) REVERT: C 355 MET cc_start: 0.9345 (mmm) cc_final: 0.9144 (mmm) REVERT: C 364 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8242 (mp0) REVERT: D 323 MET cc_start: 0.8798 (tpt) cc_final: 0.8442 (tpp) REVERT: D 364 MET cc_start: 0.9178 (mmm) cc_final: 0.8385 (mpp) REVERT: D 561 CYS cc_start: 0.8728 (m) cc_final: 0.8443 (p) REVERT: D 715 MET cc_start: 0.3374 (OUTLIER) cc_final: 0.2430 (ptp) REVERT: D 790 MET cc_start: 0.0015 (ppp) cc_final: -0.0221 (ppp) REVERT: F 123 MET cc_start: 0.9109 (mmp) cc_final: 0.8877 (mmt) outliers start: 43 outliers final: 8 residues processed: 173 average time/residue: 0.7488 time to fit residues: 147.1705 Evaluate side-chains 132 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 676 LYS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain D residue 521 ASP Chi-restraints excluded: chain D residue 715 MET Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 257 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 76 optimal weight: 0.9990 chunk 192 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 91 optimal weight: 0.0470 chunk 176 optimal weight: 4.9990 chunk 149 optimal weight: 0.0670 chunk 271 optimal weight: 3.9990 chunk 260 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 218 optimal weight: 0.8980 overall best weight: 1.0020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 HIS ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.087023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.054240 restraints weight = 84852.023| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.03 r_work: 0.2814 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23837 Z= 0.129 Angle : 0.591 10.722 32232 Z= 0.292 Chirality : 0.042 0.273 3526 Planarity : 0.004 0.045 4109 Dihedral : 8.378 149.158 3219 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.69 % Allowed : 10.03 % Favored : 88.28 % Cbeta Deviations : 0.11 % 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: 1.44 (0.16), residues: 2839 helix: 1.39 (0.15), residues: 1347 sheet: 0.77 (0.26), residues: 393 loop : 0.69 (0.20), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 779 TYR 0.024 0.001 TYR D 787 PHE 0.015 0.001 PHE E 19 TRP 0.020 0.002 TRP A 781 HIS 0.004 0.001 HIS G 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (23831) covalent geometry : angle 0.59075 / 0.29 (32214) hydrogen bonds : bond 0.03452 / 2.30 ( 1174) hydrogen bonds : angle 4.50316 / 3.26 ( 3249) link_TRANS : bond 0.00123 / 0.07 ( 6) link_TRANS : angle 0.38804 / 0.24 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 132 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.8752 (tmm) cc_final: 0.8506 (ppp) REVERT: A 364 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8354 (mpp) REVERT: C 176 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8293 (mpt) REVERT: C 276 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8444 (mt-10) REVERT: C 355 MET cc_start: 0.9309 (mmm) cc_final: 0.9101 (mmm) REVERT: C 364 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8275 (mp0) REVERT: D 113 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.8312 (t80) REVERT: D 203 MET cc_start: 0.8932 (mmm) cc_final: 0.8578 (mtt) REVERT: D 239 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7137 (tmm) REVERT: D 323 MET cc_start: 0.8731 (tpt) cc_final: 0.8348 (tpp) REVERT: D 364 MET cc_start: 0.9123 (mmm) cc_final: 0.8354 (mpp) REVERT: D 561 CYS cc_start: 0.8750 (m) cc_final: 0.8462 (p) REVERT: F 12 ASN cc_start: 0.8326 (OUTLIER) cc_final: 0.8081 (m-40) REVERT: G 314 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8631 (tt0) outliers start: 42 outliers final: 8 residues processed: 158 average time/residue: 0.7495 time to fit residues: 134.1214 Evaluate side-chains 139 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 676 LYS Chi-restraints excluded: chain A residue 702 TRP Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain D residue 113 TYR Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain G residue 314 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 88 optimal weight: 3.9990 chunk 206 optimal weight: 20.0000 chunk 110 optimal weight: 4.9990 chunk 193 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 chunk 223 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 203 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 418 HIS D 730 ASN ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.082160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.047737 restraints weight = 87899.899| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.25 r_work: 0.2773 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 23837 Z= 0.205 Angle : 0.628 9.995 32232 Z= 0.311 Chirality : 0.044 0.303 3526 Planarity : 0.004 0.044 4109 Dihedral : 8.338 146.655 3219 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.65 % Allowed : 11.08 % Favored : 87.27 % Cbeta Deviations : 0.11 % 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: 1.47 (0.16), residues: 2839 helix: 1.44 (0.14), residues: 1349 sheet: 0.72 (0.26), residues: 393 loop : 0.67 (0.20), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 177 TYR 0.024 0.001 TYR D 787 PHE 0.018 0.001 PHE B 96 TRP 0.016 0.002 TRP A 781 HIS 0.009 0.001 HIS D 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.21 (23831) covalent geometry : angle 0.62791 / 0.31 (32214) hydrogen bonds : bond 0.03615 / 2.43 ( 1174) hydrogen bonds : angle 4.54478 / 3.29 ( 3249) link_TRANS : bond 0.00266 / 0.14 ( 6) link_TRANS : angle 0.70114 / 0.46 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 MET cc_start: 0.8461 (tpp) cc_final: 0.8190 (tpp) REVERT: A 364 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8359 (mpp) REVERT: A 371 MET cc_start: 0.9303 (OUTLIER) cc_final: 0.8999 (mmp) REVERT: C 176 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8317 (mpt) REVERT: C 355 MET cc_start: 0.9327 (mmm) cc_final: 0.9105 (mmm) REVERT: C 364 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8401 (mp0) REVERT: D 113 TYR cc_start: 0.8651 (OUTLIER) cc_final: 0.8338 (m-80) REVERT: D 135 MET cc_start: 0.8863 (ttp) cc_final: 0.8364 (tmm) REVERT: D 203 MET cc_start: 0.9053 (mmm) cc_final: 0.8719 (mtt) REVERT: D 239 MET cc_start: 0.7861 (ttp) cc_final: 0.7572 (ttp) REVERT: D 323 MET cc_start: 0.8755 (tpt) cc_final: 0.8371 (tpp) REVERT: D 364 MET cc_start: 0.9178 (mmm) cc_final: 0.8423 (mpp) REVERT: D 561 CYS cc_start: 0.8797 (m) cc_final: 0.8535 (p) REVERT: D 715 MET cc_start: 0.3407 (mpt) cc_final: 0.3204 (mpt) REVERT: G 260 THR cc_start: 0.9509 (OUTLIER) cc_final: 0.9284 (t) REVERT: G 314 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8681 (tt0) outliers start: 41 outliers final: 13 residues processed: 150 average time/residue: 0.7528 time to fit residues: 127.8219 Evaluate side-chains 140 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 676 LYS Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 113 TYR Chi-restraints excluded: chain D residue 783 MET Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 314 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 79 optimal weight: 0.0770 chunk 94 optimal weight: 0.6980 chunk 43 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 127 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 221 optimal weight: 2.9990 chunk 273 optimal weight: 0.7980 chunk 163 optimal weight: 10.0000 chunk 151 optimal weight: 9.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.090906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.056916 restraints weight = 80172.522| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.36 r_work: 0.2814 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23837 Z= 0.116 Angle : 0.599 10.732 32232 Z= 0.293 Chirality : 0.042 0.233 3526 Planarity : 0.004 0.043 4109 Dihedral : 8.139 147.832 3219 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.29 % Allowed : 11.60 % Favored : 87.11 % Cbeta Deviations : 0.11 % 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: 1.53 (0.16), residues: 2839 helix: 1.53 (0.15), residues: 1351 sheet: 0.72 (0.26), residues: 393 loop : 0.67 (0.20), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 95 TYR 0.025 0.001 TYR A 787 PHE 0.015 0.001 PHE D 470 TRP 0.018 0.002 TRP A 781 HIS 0.007 0.001 HIS D 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (23831) covalent geometry : angle 0.59884 / 0.29 (32214) hydrogen bonds : bond 0.03307 / 2.21 ( 1174) hydrogen bonds : angle 4.43248 / 3.21 ( 3249) link_TRANS : bond 0.00095 / 0.05 ( 6) link_TRANS : angle 0.34398 / 0.20 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.8778 (tmm) cc_final: 0.8551 (ppp) REVERT: A 323 MET cc_start: 0.8371 (tpp) cc_final: 0.8081 (tpp) REVERT: A 364 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8366 (mpp) REVERT: C 176 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8320 (mpt) REVERT: C 364 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8307 (mp0) REVERT: E 120 MET cc_start: 0.6761 (tpp) cc_final: 0.6543 (tpp) REVERT: D 113 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.8207 (m-80) REVERT: D 135 MET cc_start: 0.8712 (ttp) cc_final: 0.8133 (tmm) REVERT: D 203 MET cc_start: 0.9051 (mmm) cc_final: 0.8746 (mtm) REVERT: D 364 MET cc_start: 0.9167 (mmm) cc_final: 0.8450 (mpp) REVERT: D 416 VAL cc_start: 0.8821 (OUTLIER) cc_final: 0.8612 (t) REVERT: D 561 CYS cc_start: 0.8742 (m) cc_final: 0.8438 (p) REVERT: D 715 MET cc_start: 0.3429 (mpt) cc_final: 0.2931 (mmt) REVERT: G 47 MET cc_start: 0.8789 (mmm) cc_final: 0.8186 (ptt) REVERT: G 314 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8620 (tt0) outliers start: 32 outliers final: 6 residues processed: 148 average time/residue: 0.7522 time to fit residues: 126.9089 Evaluate side-chains 130 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 676 LYS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain D residue 113 TYR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 783 MET Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain G residue 314 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 6 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 82 optimal weight: 7.9990 chunk 211 optimal weight: 4.9990 chunk 258 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 chunk 266 optimal weight: 0.5980 chunk 204 optimal weight: 10.0000 chunk 242 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.093838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.059903 restraints weight = 76724.699| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 4.05 r_work: 0.2763 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23837 Z= 0.155 Angle : 0.612 11.467 32232 Z= 0.300 Chirality : 0.043 0.248 3526 Planarity : 0.004 0.043 4109 Dihedral : 8.093 148.331 3219 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.13 % Allowed : 12.01 % Favored : 86.87 % Cbeta Deviations : 0.11 % 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: 1.56 (0.16), residues: 2839 helix: 1.59 (0.15), residues: 1349 sheet: 0.70 (0.25), residues: 413 loop : 0.64 (0.20), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 256 TYR 0.025 0.001 TYR A 787 PHE 0.014 0.001 PHE D 470 TRP 0.020 0.002 TRP D 781 HIS 0.007 0.001 HIS D 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (23831) covalent geometry : angle 0.61246 / 0.30 (32214) hydrogen bonds : bond 0.03384 / 2.26 ( 1174) hydrogen bonds : angle 4.43670 / 3.21 ( 3249) link_TRANS : bond 0.00168 / 0.09 ( 6) link_TRANS : angle 0.46197 / 0.29 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.8842 (tmm) cc_final: 0.8620 (ppp) REVERT: A 323 MET cc_start: 0.8451 (tpp) cc_final: 0.8139 (tpp) REVERT: A 364 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8381 (mpp) REVERT: C 176 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8369 (mpt) REVERT: C 364 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8438 (mp0) REVERT: D 113 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.8191 (m-80) REVERT: D 135 MET cc_start: 0.8725 (ttp) cc_final: 0.7857 (tmm) REVERT: D 203 MET cc_start: 0.9056 (mmm) cc_final: 0.8717 (mtm) REVERT: D 239 MET cc_start: 0.7845 (ttp) cc_final: 0.7093 (tmm) REVERT: D 364 MET cc_start: 0.9174 (mmm) cc_final: 0.8473 (mpp) REVERT: D 561 CYS cc_start: 0.8815 (m) cc_final: 0.8460 (p) REVERT: D 715 MET cc_start: 0.3464 (mpt) cc_final: 0.2908 (mmt) REVERT: F 355 MET cc_start: 0.9366 (OUTLIER) cc_final: 0.8916 (mmm) REVERT: G 180 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8857 (mp) REVERT: G 314 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8660 (tt0) outliers start: 28 outliers final: 8 residues processed: 142 average time/residue: 0.6788 time to fit residues: 109.7815 Evaluate side-chains 134 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 676 LYS Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain D residue 113 TYR Chi-restraints excluded: chain D residue 783 MET Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 355 MET Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain G residue 314 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 248 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 143 optimal weight: 9.9990 chunk 209 optimal weight: 30.0000 chunk 221 optimal weight: 0.8980 chunk 259 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 223 optimal weight: 0.5980 chunk 224 optimal weight: 0.9980 chunk 178 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN D 680 GLN ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.087937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.055043 restraints weight = 83749.482| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.10 r_work: 0.2824 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 23837 Z= 0.117 Angle : 0.599 12.331 32232 Z= 0.292 Chirality : 0.042 0.363 3526 Planarity : 0.003 0.043 4109 Dihedral : 7.908 151.860 3219 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.73 % Allowed : 12.49 % Favored : 86.78 % Cbeta Deviations : 0.11 % 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: 1.62 (0.16), residues: 2839 helix: 1.64 (0.15), residues: 1349 sheet: 0.78 (0.26), residues: 409 loop : 0.63 (0.20), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 683 TYR 0.027 0.001 TYR D 10 PHE 0.015 0.001 PHE D 470 TRP 0.021 0.002 TRP D 484 HIS 0.006 0.001 HIS D 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (23831) covalent geometry : angle 0.59916 / 0.29 (32214) hydrogen bonds : bond 0.03175 / 2.11 ( 1174) hydrogen bonds : angle 4.36585 / 3.17 ( 3249) link_TRANS : bond 0.00103 / 0.06 ( 6) link_TRANS : angle 0.28184 / 0.17 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.6401 (tpt) cc_final: 0.6100 (tpp) REVERT: A 305 MET cc_start: 0.8792 (tmm) cc_final: 0.8568 (ppp) REVERT: A 323 MET cc_start: 0.8330 (tpp) cc_final: 0.8015 (tpp) REVERT: A 364 MET cc_start: 0.8981 (mpp) cc_final: 0.8358 (mpp) REVERT: A 715 MET cc_start: 0.3445 (mtt) cc_final: 0.1561 (mmt) REVERT: C 176 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8271 (mpt) REVERT: C 364 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8311 (mp0) REVERT: E 120 MET cc_start: 0.6590 (tpp) cc_final: 0.6345 (tpp) REVERT: D 113 TYR cc_start: 0.8510 (OUTLIER) cc_final: 0.8165 (m-10) REVERT: D 135 MET cc_start: 0.8656 (ttp) cc_final: 0.8096 (tmm) REVERT: D 203 MET cc_start: 0.9000 (mmm) cc_final: 0.8750 (mtm) REVERT: D 239 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7689 (ttp) REVERT: D 364 MET cc_start: 0.9096 (mmm) cc_final: 0.8482 (mpp) REVERT: D 561 CYS cc_start: 0.8803 (m) cc_final: 0.8426 (p) REVERT: D 715 MET cc_start: 0.3522 (mpt) cc_final: 0.3086 (mmt) REVERT: F 211 ASP cc_start: 0.9005 (t0) cc_final: 0.8656 (t70) REVERT: G 180 LEU cc_start: 0.9036 (mp) cc_final: 0.8800 (mp) REVERT: G 314 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8624 (tt0) outliers start: 18 outliers final: 8 residues processed: 141 average time/residue: 0.6797 time to fit residues: 108.7920 Evaluate side-chains 135 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 676 LYS Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain E residue 31 GLN Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain D residue 113 TYR Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 783 MET Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain G residue 314 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 170 optimal weight: 4.9990 chunk 126 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 chunk 163 optimal weight: 9.9990 chunk 248 optimal weight: 5.9990 chunk 152 optimal weight: 0.1980 chunk 65 optimal weight: 0.5980 chunk 227 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 262 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 HIS ** A 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN E 31 GLN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.086842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.053915 restraints weight = 84911.191| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.09 r_work: 0.2804 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23837 Z= 0.160 Angle : 0.631 13.062 32232 Z= 0.307 Chirality : 0.043 0.242 3526 Planarity : 0.004 0.042 4109 Dihedral : 7.935 149.745 3219 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.85 % Allowed : 12.81 % Favored : 86.34 % Cbeta Deviations : 0.11 % 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: 1.62 (0.16), residues: 2839 helix: 1.62 (0.15), residues: 1363 sheet: 0.77 (0.26), residues: 409 loop : 0.66 (0.20), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 177 TYR 0.044 0.001 TYR D 10 PHE 0.014 0.001 PHE D 470 TRP 0.025 0.002 TRP D 484 HIS 0.007 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (23831) covalent geometry : angle 0.63072 / 0.31 (32214) hydrogen bonds : bond 0.03325 / 2.22 ( 1174) hydrogen bonds : angle 4.40642 / 3.20 ( 3249) link_TRANS : bond 0.00167 / 0.09 ( 6) link_TRANS : angle 0.39717 / 0.24 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.5415 (mmt) cc_final: 0.3940 (tpp) REVERT: A 305 MET cc_start: 0.8799 (tmm) cc_final: 0.8577 (ppp) REVERT: A 323 MET cc_start: 0.8409 (tpp) cc_final: 0.8082 (tpp) REVERT: A 364 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8352 (mpp) REVERT: A 715 MET cc_start: 0.3713 (mtt) cc_final: 0.1725 (mmt) REVERT: C 176 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8312 (mpt) REVERT: C 305 MET cc_start: 0.9370 (mmm) cc_final: 0.9099 (mmt) REVERT: C 364 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8452 (mp0) REVERT: E 73 MET cc_start: 0.3584 (pp-130) cc_final: 0.3187 (ppp) REVERT: E 120 MET cc_start: 0.6659 (tpp) cc_final: 0.6379 (tpp) REVERT: D 113 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.8217 (m-80) REVERT: D 135 MET cc_start: 0.8656 (ttp) cc_final: 0.8135 (tmm) REVERT: D 203 MET cc_start: 0.9019 (mmm) cc_final: 0.8729 (mtm) REVERT: D 239 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7685 (ttp) REVERT: D 364 MET cc_start: 0.9084 (mmm) cc_final: 0.8483 (mpp) REVERT: D 561 CYS cc_start: 0.8759 (m) cc_final: 0.8444 (p) REVERT: D 715 MET cc_start: 0.3484 (mpt) cc_final: 0.2896 (mmt) REVERT: F 211 ASP cc_start: 0.9009 (t0) cc_final: 0.8666 (t70) REVERT: G 260 THR cc_start: 0.9500 (OUTLIER) cc_final: 0.9254 (t) REVERT: G 314 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8663 (tt0) outliers start: 21 outliers final: 11 residues processed: 136 average time/residue: 0.7534 time to fit residues: 116.3771 Evaluate side-chains 138 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 676 LYS Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain E residue 31 GLN Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain D residue 113 TYR Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 783 MET Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 314 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 2 optimal weight: 20.0000 chunk 162 optimal weight: 0.4980 chunk 151 optimal weight: 0.9990 chunk 224 optimal weight: 1.9990 chunk 238 optimal weight: 1.9990 chunk 258 optimal weight: 0.9990 chunk 137 optimal weight: 0.4980 chunk 271 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 189 optimal weight: 0.0980 chunk 51 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN E 31 GLN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN ** G 12 ASN ** 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 = 0.3932 r_free = 0.3932 target = 0.094204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.059131 restraints weight = 76556.632| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.69 r_work: 0.2823 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23837 Z= 0.106 Angle : 0.609 12.477 32232 Z= 0.295 Chirality : 0.042 0.231 3526 Planarity : 0.003 0.042 4109 Dihedral : 7.818 152.338 3219 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.85 % Allowed : 12.85 % Favored : 86.30 % Cbeta Deviations : 0.11 % 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: 1.64 (0.16), residues: 2839 helix: 1.64 (0.15), residues: 1365 sheet: 0.80 (0.26), residues: 409 loop : 0.66 (0.20), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 95 TYR 0.028 0.001 TYR A 787 PHE 0.015 0.001 PHE D 470 TRP 0.023 0.002 TRP D 484 HIS 0.006 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (23831) covalent geometry : angle 0.60929 / 0.29 (32214) hydrogen bonds : bond 0.03136 / 2.09 ( 1174) hydrogen bonds : angle 4.35492 / 3.17 ( 3249) link_TRANS : bond 0.00084 / 0.05 ( 6) link_TRANS : angle 0.32418 / 0.21 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9508.11 seconds wall clock time: 162 minutes 37.12 seconds (9757.12 seconds total)