Starting phenix.real_space_refine on Fri Aug 7 19:45:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z7x_73883/08_2026/9z7x_73883.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z7x_73883/08_2026/9z7x_73883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9z7x_73883/08_2026/9z7x_73883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z7x_73883/08_2026/9z7x_73883.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9z7x_73883/08_2026/9z7x_73883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z7x_73883/08_2026/9z7x_73883.map" } resolution = 2.9 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= 0.014 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 Zn 1 6.06 5 P 73 5.49 5 S 82 5.16 5 C 14517 2.51 5 N 3919 2.21 5 O 4484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23076 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 4665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4665 Classifications: {'peptide': 592} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 576} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 100 Planarities with less than four sites: {'GLU:plan': 13, 'ASP:plan': 12, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 94 Chain: "B" Number of atoms: 2686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2686 Classifications: {'peptide': 360} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 19, 'TRANS': 340} Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 10, 'ARG:plan': 2, 'GLU:plan': 10, 'GLN:plan1': 3, 'ASN:plan1': 3, 'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 105 Chain: "C" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2393 Classifications: {'peptide': 315} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 12, 'TRANS': 302} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 6, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "D" Number of atoms: 2402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2402 Classifications: {'peptide': 315} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 12, 'TRANS': 302} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 3, 'ASP:plan': 2, 'GLU:plan': 5, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 43 Chain: "E" Number of atoms: 2405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2405 Classifications: {'peptide': 315} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 12, 'TRANS': 302} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 7, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 49 Chain: "F" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1043 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 131} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 1040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1040 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 128} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 2296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2296 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 16, 'TRANS': 277} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 35 Chain: "J" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 751 Classifications: {'RNA': 36} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 11, 'rna3p_pyr': 21} Link IDs: {'rna2p': 4, 'rna3p': 31} Chain: "N" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 819 Classifications: {'RNA': 38} Modifications used: {'5*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 6, 'rna3p_pur': 12, 'rna3p_pyr': 6} Link IDs: {'rna2p': 19, 'rna3p': 18} Chain: "I" Number of atoms: 2555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2555 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 324} Chain breaks: 2 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 7, 'ASP:plan': 6, 'ASN:plan1': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 85 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1, 'water': 2} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1286 SG CYS A 166 42.299 54.285 161.642 1.00108.83 S ATOM 1306 SG CYS A 169 45.099 56.694 162.227 1.00112.80 S ATOM 1733 SG CYS A 222 42.432 56.302 164.921 1.00 99.75 S ATOM 1750 SG CYS A 225 41.466 58.024 161.804 1.00124.59 S Time building chain proxies: 4.34, per 1000 atoms: 0.19 Number of scatterers: 23076 At special positions: 0 Unit cell: (103.295, 111.45, 197.53, 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) Zn 1 29.99 S 82 16.00 P 73 15.00 O 4484 8.00 N 3919 7.00 C 14517 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 Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 805.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 222 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 166 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 225 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 169 " Number of angles added : 6 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5206 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 35 sheets defined 38.4% alpha, 18.1% beta 11 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 2.26 Creating SS restraints... Processing helix chain 'A' and resid 14 through 20 Processing helix chain 'A' and resid 23 through 47 removed outlier: 3.517A pdb=" N LEU A 27 " --> pdb=" O LYS A 23 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 77 Processing helix chain 'A' and resid 78 through 105 removed outlier: 3.721A pdb=" N VAL A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A 94 " --> pdb=" O GLU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 118 removed outlier: 3.710A pdb=" N SER A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 133 through 149 removed outlier: 3.511A pdb=" N ALA A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS A 149 " --> pdb=" O MET A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 193 Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 251 through 261 Processing helix chain 'A' and resid 263 through 266 Processing helix chain 'A' and resid 267 through 272 removed outlier: 3.697A pdb=" N ASP A 272 " --> pdb=" O ILE A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 281 removed outlier: 3.509A pdb=" N ILE A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A 280 " --> pdb=" O PRO A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 300 Processing helix chain 'A' and resid 302 through 312 removed outlier: 3.589A pdb=" N TYR A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 336 removed outlier: 3.537A pdb=" N TRP A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 366 removed outlier: 3.524A pdb=" N LYS A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR A 352 " --> pdb=" O HIS A 348 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY A 356 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 405 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 434 through 451 removed outlier: 3.623A pdb=" N VAL A 438 " --> pdb=" O PRO A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 497 removed outlier: 3.996A pdb=" N LEU A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET A 488 " --> pdb=" O THR A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 512 removed outlier: 4.029A pdb=" N LYS A 506 " --> pdb=" O ASN A 502 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 508 " --> pdb=" O PHE A 504 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 512 " --> pdb=" O LEU A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 537 removed outlier: 3.793A pdb=" N ILE A 528 " --> pdb=" O ASP A 524 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET A 537 " --> pdb=" O LYS A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 563 removed outlier: 3.911A pdb=" N GLN A 563 " --> pdb=" O ALA A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 571 removed outlier: 3.704A pdb=" N LEU A 567 " --> pdb=" O GLN A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 591 Processing helix chain 'B' and resid 35 through 49 removed outlier: 3.618A pdb=" N ILE B 39 " --> pdb=" O TYR B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 58 removed outlier: 6.262A pdb=" N SER B 53 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 55 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LYS B 56 " --> pdb=" O SER B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 150 Processing helix chain 'B' and resid 219 through 222 removed outlier: 3.637A pdb=" N GLY B 222 " --> pdb=" O GLY B 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 219 through 222' Processing helix chain 'B' and resid 331 through 336 removed outlier: 3.626A pdb=" N HIS B 336 " --> pdb=" O ILE B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 350 Processing helix chain 'C' and resid 43 through 57 removed outlier: 3.537A pdb=" N GLY C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 81 Processing helix chain 'C' and resid 117 through 129 Processing helix chain 'C' and resid 176 through 188 Processing helix chain 'C' and resid 197 through 202 Processing helix chain 'C' and resid 210 through 221 Processing helix chain 'C' and resid 271 through 275 removed outlier: 3.541A pdb=" N LYS C 275 " --> pdb=" O GLY C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 293 Processing helix chain 'D' and resid 44 through 58 removed outlier: 3.703A pdb=" N GLY D 50 " --> pdb=" O SER D 46 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA D 58 " --> pdb=" O ALA D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 81 Processing helix chain 'D' and resid 117 through 130 removed outlier: 3.790A pdb=" N LEU D 130 " --> pdb=" O SER D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 189 removed outlier: 4.147A pdb=" N PHE D 189 " --> pdb=" O SER D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 202 Processing helix chain 'D' and resid 210 through 221 Processing helix chain 'D' and resid 267 through 275 removed outlier: 3.548A pdb=" N GLU D 270 " --> pdb=" O LYS D 267 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS D 271 " --> pdb=" O ASP D 268 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLY D 272 " --> pdb=" O GLU D 269 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE D 273 " --> pdb=" O GLU D 270 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS D 275 " --> pdb=" O GLY D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 293 removed outlier: 3.522A pdb=" N LEU D 293 " --> pdb=" O PHE D 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 58 removed outlier: 3.508A pdb=" N LEU E 47 " --> pdb=" O GLU E 43 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA E 58 " --> pdb=" O ALA E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 82 Processing helix chain 'E' and resid 117 through 130 removed outlier: 4.020A pdb=" N LEU E 130 " --> pdb=" O SER E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 188 Processing helix chain 'E' and resid 196 through 202 Processing helix chain 'E' and resid 210 through 221 Processing helix chain 'E' and resid 267 through 275 removed outlier: 3.546A pdb=" N GLU E 270 " --> pdb=" O LYS E 267 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS E 271 " --> pdb=" O ASP E 268 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLY E 272 " --> pdb=" O GLU E 269 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE E 273 " --> pdb=" O GLU E 270 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS E 275 " --> pdb=" O GLY E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 293 Processing helix chain 'F' and resid 7 through 29 removed outlier: 3.643A pdb=" N ALA F 17 " --> pdb=" O GLU F 13 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA F 18 " --> pdb=" O ARG F 14 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE F 19 " --> pdb=" O GLN F 15 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS F 28 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER F 29 " --> pdb=" O GLU F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 41 removed outlier: 3.647A pdb=" N LYS F 41 " --> pdb=" O LYS F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 51 Processing helix chain 'F' and resid 51 through 62 Processing helix chain 'F' and resid 71 through 86 removed outlier: 3.560A pdb=" N LYS F 75 " --> pdb=" O GLY F 71 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 98 removed outlier: 3.814A pdb=" N ASN F 98 " --> pdb=" O TYR F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 107 removed outlier: 3.712A pdb=" N VAL F 107 " --> pdb=" O VAL F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 136 removed outlier: 3.816A pdb=" N TRP F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG F 130 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE F 136 " --> pdb=" O ALA F 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 27 removed outlier: 3.525A pdb=" N ALA G 18 " --> pdb=" O ARG G 14 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA G 26 " --> pdb=" O LYS G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 41 removed outlier: 3.606A pdb=" N TYR G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA G 38 " --> pdb=" O LYS G 34 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS G 41 " --> pdb=" O LYS G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 49 removed outlier: 4.050A pdb=" N LYS G 48 " --> pdb=" O PRO G 44 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR G 49 " --> pdb=" O MET G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 63 Processing helix chain 'G' and resid 71 through 86 removed outlier: 3.795A pdb=" N LYS G 75 " --> pdb=" O GLY G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 106 Processing helix chain 'G' and resid 110 through 136 removed outlier: 4.098A pdb=" N ARG G 115 " --> pdb=" O SER G 111 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA G 116 " --> pdb=" O ASP G 112 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL G 126 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N TRP G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 110 Processing helix chain 'H' and resid 134 through 138 removed outlier: 3.542A pdb=" N PHE H 138 " --> pdb=" O LEU H 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 134 through 138' Processing helix chain 'H' and resid 141 through 161 removed outlier: 3.567A pdb=" N ILE H 145 " --> pdb=" O ASN H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 220 removed outlier: 3.607A pdb=" N VAL H 206 " --> pdb=" O PRO H 202 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY H 220 " --> pdb=" O THR H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 227 Processing helix chain 'H' and resid 229 through 237 Processing helix chain 'H' and resid 273 through 278 removed outlier: 4.518A pdb=" N TYR H 277 " --> pdb=" O TYR H 273 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN H 278 " --> pdb=" O GLY H 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 273 through 278' Processing helix chain 'H' and resid 320 through 325 removed outlier: 3.902A pdb=" N VAL H 324 " --> pdb=" O GLN H 320 " (cutoff:3.500A) Processing helix chain 'H' and resid 330 through 335 removed outlier: 3.766A pdb=" N SER H 334 " --> pdb=" O SER H 330 " (cutoff:3.500A) Processing helix chain 'H' and resid 344 through 360 removed outlier: 3.700A pdb=" N ILE H 348 " --> pdb=" O ASN H 344 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA H 349 " --> pdb=" O LEU H 345 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE H 350 " --> pdb=" O HIS H 346 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS H 355 " --> pdb=" O SER H 351 " (cutoff:3.500A) Processing helix chain 'I' and resid 27 through 44 removed outlier: 3.971A pdb=" N ILE I 31 " --> pdb=" O ARG I 27 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA I 44 " --> pdb=" O ARG I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 60 removed outlier: 3.580A pdb=" N LYS I 53 " --> pdb=" O ASP I 49 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE I 58 " --> pdb=" O LYS I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 103 removed outlier: 3.569A pdb=" N PHE I 103 " --> pdb=" O TYR I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 145 removed outlier: 4.188A pdb=" N LEU I 131 " --> pdb=" O ASP I 127 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS I 132 " --> pdb=" O GLU I 128 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE I 133 " --> pdb=" O GLY I 129 " (cutoff:3.500A) Processing helix chain 'I' and resid 150 through 154 removed outlier: 4.008A pdb=" N GLY I 154 " --> pdb=" O ALA I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 203 Processing helix chain 'I' and resid 230 through 237 Processing helix chain 'I' and resid 239 through 247 Processing helix chain 'I' and resid 253 through 258 Processing helix chain 'I' and resid 331 through 341 removed outlier: 3.621A pdb=" N PHE I 335 " --> pdb=" O ILE I 331 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS I 341 " --> pdb=" O ALA I 337 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 55 removed outlier: 5.431A pdb=" N ILE A 53 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL A 70 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A 55 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE B 116 " --> pdb=" O PHE A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 200 through 202 Processing sheet with id=AA3, first strand: chain 'A' and resid 371 through 377 removed outlier: 7.003A pdb=" N LEU A 382 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA A 376 " --> pdb=" O ASP A 380 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ASP A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE A 381 " --> pdb=" O PHE A 325 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 325 " --> pdb=" O PHE A 381 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N PHE A 422 " --> pdb=" O ALA A 458 " (cutoff:3.500A) removed outlier: 9.085A pdb=" N ALA A 460 " --> pdb=" O PHE A 422 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA A 424 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N ALA A 462 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA A 426 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LEU A 464 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE A 428 " --> pdb=" O LEU A 464 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 160 through 161 removed outlier: 4.253A pdb=" N LEU B 80 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 13.178A pdb=" N ILE B 78 " --> pdb=" O PRO B 89 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ILE B 75 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ASP B 206 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLY B 77 " --> pdb=" O ASP B 204 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N THR B 199 " --> pdb=" O ALA B 8 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ALA B 8 " --> pdb=" O THR B 199 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG B 223 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY B 214 " --> pdb=" O PHE B 227 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 94 through 95 Processing sheet with id=AA6, first strand: chain 'B' and resid 166 through 176 removed outlier: 3.818A pdb=" N ALA B 175 " --> pdb=" O MET B 187 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N MET B 187 " --> pdb=" O ALA B 175 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 275 through 278 removed outlier: 4.300A pdb=" N TYR B 319 " --> pdb=" O ILE B 286 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ALA B 288 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL B 317 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS B 338 " --> pdb=" O ALA B 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 294 through 296 Processing sheet with id=AA9, first strand: chain 'B' and resid 299 through 300 Processing sheet with id=AB1, first strand: chain 'C' and resid 41 through 42 removed outlier: 3.595A pdb=" N ILE C 42 " --> pdb=" O ALA C 98 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL C 253 " --> pdb=" O LEU C 101 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 253 through 260 current: chain 'C' and resid 206 through 208 Processing sheet with id=AB2, first strand: chain 'C' and resid 93 through 95 removed outlier: 6.831A pdb=" N VAL C 253 " --> pdb=" O LEU C 101 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 98 through 106 current: chain 'C' and resid 309 through 314 Processing sheet with id=AB3, first strand: chain 'C' and resid 61 through 64 Processing sheet with id=AB4, first strand: chain 'C' and resid 144 through 145 Processing sheet with id=AB5, first strand: chain 'C' and resid 157 through 160 Processing sheet with id=AB6, first strand: chain 'C' and resid 223 through 230 removed outlier: 3.887A pdb=" N LYS C 229 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ALA C 241 " --> pdb=" O LYS C 229 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 41 through 42 removed outlier: 6.868A pdb=" N VAL D 253 " --> pdb=" O LEU D 101 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 253 through 260 current: chain 'D' and resid 206 through 208 Processing sheet with id=AB8, first strand: chain 'D' and resid 93 through 95 removed outlier: 6.868A pdb=" N VAL D 253 " --> pdb=" O LEU D 101 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 98 through 106 current: chain 'D' and resid 309 through 314 Processing sheet with id=AB9, first strand: chain 'D' and resid 61 through 64 Processing sheet with id=AC1, first strand: chain 'D' and resid 144 through 145 Processing sheet with id=AC2, first strand: chain 'D' and resid 157 through 159 Processing sheet with id=AC3, first strand: chain 'D' and resid 223 through 230 removed outlier: 3.885A pdb=" N LYS D 229 " --> pdb=" O ALA D 241 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ALA D 241 " --> pdb=" O LYS D 229 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 41 through 42 removed outlier: 6.737A pdb=" N VAL E 253 " --> pdb=" O LEU E 101 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 253 through 260 current: chain 'E' and resid 206 through 208 Processing sheet with id=AC5, first strand: chain 'E' and resid 93 through 95 removed outlier: 6.737A pdb=" N VAL E 253 " --> pdb=" O LEU E 101 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 98 through 106 current: chain 'E' and resid 309 through 314 Processing sheet with id=AC6, first strand: chain 'E' and resid 61 through 64 Processing sheet with id=AC7, first strand: chain 'E' and resid 144 through 145 Processing sheet with id=AC8, first strand: chain 'E' and resid 157 through 160 removed outlier: 3.700A pdb=" N TYR E 163 " --> pdb=" O LEU E 160 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 223 through 231 removed outlier: 11.047A pdb=" N GLU E 223 " --> pdb=" O THR E 244 " (cutoff:3.500A) removed outlier: 9.730A pdb=" N THR E 244 " --> pdb=" O GLU E 223 " (cutoff:3.500A) removed outlier: 11.298A pdb=" N ILE E 225 " --> pdb=" O LEU E 242 " (cutoff:3.500A) removed outlier: 10.032A pdb=" N LEU E 242 " --> pdb=" O ILE E 225 " (cutoff:3.500A) removed outlier: 10.113A pdb=" N ARG E 227 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 9.612A pdb=" N GLY E 240 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LYS E 229 " --> pdb=" O GLN E 238 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 122 through 124 removed outlier: 6.546A pdb=" N LYS H 123 " --> pdb=" O ILE H 131 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE H 131 " --> pdb=" O LYS H 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'H' and resid 251 through 253 Processing sheet with id=AD3, first strand: chain 'H' and resid 264 through 269 Processing sheet with id=AD4, first strand: chain 'H' and resid 281 through 282 Processing sheet with id=AD5, first strand: chain 'I' and resid 72 through 77 removed outlier: 6.917A pdb=" N GLY I 5 " --> pdb=" O VAL I 163 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL I 163 " --> pdb=" O GLY I 5 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR I 7 " --> pdb=" O ILE I 161 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 289 through 296 removed outlier: 6.143A pdb=" N TRP I 302 " --> pdb=" O GLY I 224 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG I 306 " --> pdb=" O ARG I 220 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ARG I 220 " --> pdb=" O ARG I 306 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N SER I 308 " --> pdb=" O PHE I 218 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N PHE I 218 " --> pdb=" O SER I 308 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER I 219 " --> pdb=" O LEU I 348 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 261 through 263 removed outlier: 4.008A pdb=" N VAL I 261 " --> pdb=" O VAL I 273 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE I 271 " --> pdb=" O HIS I 263 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY I 275 " --> pdb=" O PHE I 282 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 261 through 263 removed outlier: 4.008A pdb=" N VAL I 261 " --> pdb=" O VAL I 273 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE I 271 " --> pdb=" O HIS I 263 " (cutoff:3.500A) 853 hydrogen bonds defined for protein. 2421 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 3.71 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6269 1.33 - 1.46: 4591 1.46 - 1.58: 12539 1.58 - 1.70: 145 1.70 - 1.82: 132 Bond restraints: 23676 Sorted by residual: bond pdb=" CA ALA I 320 " pdb=" C ALA I 320 " ideal model delta sigma weight residual 1.533 1.522 0.012 5.60e-03 3.19e+04 4.24e+00 bond pdb=" C3' A N 32 " pdb=" C2' A N 32 " ideal model delta sigma weight residual 1.525 1.547 -0.022 1.10e-02 8.26e+03 3.99e+00 bond pdb=" CB GLU C 213 " pdb=" CG GLU C 213 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.05e+00 bond pdb=" CB GLU B 221 " pdb=" CG GLU B 221 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.88e+00 bond pdb=" CG ARG H 322 " pdb=" CD ARG H 322 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.85e+00 ... (remaining 23671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 31884 2.32 - 4.63: 429 4.63 - 6.95: 35 6.95 - 9.26: 5 9.26 - 11.58: 5 Bond angle restraints: 32358 Sorted by residual: angle pdb=" C LEU G 106 " pdb=" N VAL G 107 " pdb=" CA VAL G 107 " ideal model delta sigma weight residual 121.97 131.14 -9.17 1.80e+00 3.09e-01 2.59e+01 angle pdb=" O5' A N 22 " pdb=" C5' A N 22 " pdb=" C4' A N 22 " ideal model delta sigma weight residual 109.40 113.13 -3.73 8.00e-01 1.56e+00 2.18e+01 angle pdb=" O4' C J 24 " pdb=" C1' C J 24 " pdb=" N1 C J 24 " ideal model delta sigma weight residual 108.50 111.53 -3.03 7.00e-01 2.04e+00 1.88e+01 angle pdb=" CG1 VAL G 107 " pdb=" CB VAL G 107 " pdb=" CG2 VAL G 107 " ideal model delta sigma weight residual 110.80 101.40 9.40 2.20e+00 2.07e-01 1.83e+01 angle pdb=" CA ALA I 320 " pdb=" C ALA I 320 " pdb=" O ALA I 320 " ideal model delta sigma weight residual 117.94 120.41 -2.47 5.80e-01 2.97e+00 1.82e+01 ... (remaining 32353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 13685 35.80 - 71.61: 555 71.61 - 107.41: 37 107.41 - 143.21: 0 143.21 - 179.02: 6 Dihedral angle restraints: 14283 sinusoidal: 6205 harmonic: 8078 Sorted by residual: dihedral pdb=" O4' C N 20 " pdb=" C1' C N 20 " pdb=" N1 C N 20 " pdb=" C2 C N 20 " ideal model delta sinusoidal sigma weight residual 232.00 52.98 179.02 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C N 14 " pdb=" C1' C N 14 " pdb=" N1 C N 14 " pdb=" C2 C N 14 " ideal model delta sinusoidal sigma weight residual -128.00 42.07 -170.07 1 1.70e+01 3.46e-03 6.59e+01 dihedral pdb=" O4' U J 7 " pdb=" C1' U J 7 " pdb=" N1 U J 7 " pdb=" C2 U J 7 " ideal model delta sinusoidal sigma weight residual -128.00 40.72 -168.72 1 1.70e+01 3.46e-03 6.58e+01 ... (remaining 14280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 3287 0.074 - 0.149: 399 0.149 - 0.223: 17 0.223 - 0.298: 2 0.298 - 0.372: 1 Chirality restraints: 3706 Sorted by residual: chirality pdb=" CB ILE H 111 " pdb=" CA ILE H 111 " pdb=" CG1 ILE H 111 " pdb=" CG2 ILE H 111 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CB VAL G 107 " pdb=" CA VAL G 107 " pdb=" CG1 VAL G 107 " pdb=" CG2 VAL G 107 " both_signs ideal model delta sigma weight residual False -2.63 -2.87 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB ILE E 195 " pdb=" CA ILE E 195 " pdb=" CG1 ILE E 195 " pdb=" CG2 ILE E 195 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 3703 not shown) Planarity restraints: 3861 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A N 22 " 0.034 2.00e-02 2.50e+03 2.87e-02 2.26e+01 pdb=" N9 A N 22 " -0.077 2.00e-02 2.50e+03 pdb=" C8 A N 22 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A N 22 " 0.007 2.00e-02 2.50e+03 pdb=" C5 A N 22 " 0.003 2.00e-02 2.50e+03 pdb=" C6 A N 22 " 0.000 2.00e-02 2.50e+03 pdb=" N6 A N 22 " 0.003 2.00e-02 2.50e+03 pdb=" N1 A N 22 " -0.004 2.00e-02 2.50e+03 pdb=" C2 A N 22 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A N 22 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A N 22 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 255 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C PHE A 255 " 0.055 2.00e-02 2.50e+03 pdb=" O PHE A 255 " -0.021 2.00e-02 2.50e+03 pdb=" N LYS A 256 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 88 " 0.046 5.00e-02 4.00e+02 7.02e-02 7.89e+00 pdb=" N PRO H 89 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO H 89 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO H 89 " 0.039 5.00e-02 4.00e+02 ... (remaining 3858 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 8244 2.88 - 3.38: 18994 3.38 - 3.89: 34910 3.89 - 4.39: 39308 4.39 - 4.90: 70663 Nonbonded interactions: 172119 Sorted by model distance: nonbonded pdb=" O ASP I 164 " pdb=" OD1 ASP I 164 " model vdw 2.372 3.040 nonbonded pdb=" O ASN D 154 " pdb=" OD1 ASN D 154 " model vdw 2.388 3.040 nonbonded pdb=" O GLU A 561 " pdb=" OE1 GLU A 561 " model vdw 2.451 3.040 nonbonded pdb=" N GLU B 209 " pdb=" OE1 GLU B 209 " model vdw 2.519 3.120 nonbonded pdb=" OD1 ASP F 101 " pdb=" N MET F 102 " model vdw 2.529 3.120 ... (remaining 172114 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 'C' and (resid 1 through 21 or (resid 22 through 24 and (name N or name C \ A or name C or name O or name CB )) or resid 25 or (resid 26 and (name N or name \ CA or name C or name O or name CB )) or resid 27 through 58 or (resid 59 throug \ h 60 and (name N or name CA or name C or name O or name CB )) or resid 61 throug \ h 137 or (resid 138 and (name N or name CA or name C or name O or name CB )) or \ resid 139 through 195 or (resid 196 and (name N or name CA or name C or name O o \ r name CB )) or resid 197 through 222 or (resid 223 and (name N or name CA or na \ me C or name O or name CB )) or resid 224 through 265 or (resid 266 and (name N \ or name CA or name C or name O or name CB )) or resid 267 through 315)) selection = (chain 'D' and (resid 1 through 58 or (resid 59 through 60 and (name N or name C \ A or name C or name O or name CB )) or resid 61 through 73 or (resid 74 and (nam \ e N or name CA or name C or name O or name CB )) or resid 75 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 121 or (resid 122 and (name N or name CA or name C or name O or name CB )) or \ resid 123 through 137 or (resid 138 and (name N or name CA or name C or name O o \ r name CB )) or resid 139 through 147 or (resid 148 and (name N or name CA or na \ me C or name O or name CB )) or resid 149 through 153 or (resid 154 and (name N \ or name CA or name C or name O or name CB )) or resid 155 through 170 or (resid \ 171 and (name N or name CA or name C or name O or name CB )) or resid 172 throug \ h 211 or (resid 212 and (name N or name CA or name C or name O or name CB )) or \ resid 213 through 265 or (resid 266 and (name N or name CA or name C or name O o \ r name CB )) or resid 267 through 268 or (resid 269 and (name N or name CA or na \ me C or name O or name CB )) or resid 270 through 315)) selection = (chain 'E' and (resid 1 through 21 or (resid 22 through 24 and (name N or name C \ A or name C or name O or name CB )) or resid 25 or (resid 26 and (name N or name \ CA or name C or name O or name CB )) or resid 27 through 59 or (resid 60 and (n \ ame N or name CA or name C or name O or name CB )) or resid 61 through 73 or (re \ sid 74 and (name N or name CA or name C or name O or name CB )) or resid 75 thro \ ugh 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or \ resid 89 through 147 or (resid 148 and (name N or name CA or name C or name O or \ name CB )) or resid 149 through 153 or (resid 154 and (name N or name CA or nam \ e C or name O or name CB )) or resid 155 through 161 or (resid 162 and (name N o \ r name CA or name C or name O or name CB )) or resid 163 through 194 or (resid 1 \ 95 through 196 and (name N or name CA or name C or name O or name CB )) or resid \ 197 through 211 or (resid 212 and (name N or name CA or name C or name O or nam \ e CB )) or resid 213 through 222 or (resid 223 and (name N or name CA or name C \ or name O or name CB )) or resid 224 through 315)) } ncs_group { reference = (chain 'F' and ((resid 7 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 137)) selection = (chain 'G' and (resid 7 through 33 or (resid 34 and (name N or name CA or name C \ or name O or name CB )) or resid 35 through 87 or (resid 88 and (name N or name \ CA or name C or name O or name CB )) or resid 89 or (resid 90 and (name N or na \ me CA or name C or name O or name CB )) or resid 91 through 94 or (resid 95 thro \ ugh 96 and (name N or name CA or name C or name O or name CB )) or resid 97 thro \ ugh 137)) } 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: 8.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 22.440 Find NCS groups from input model: 0.310 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:6.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 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 : 0.002 0.043 23680 Z= 0.133 Angle : 0.633 11.578 32364 Z= 0.393 Chirality : 0.047 0.372 3706 Planarity : 0.005 0.070 3861 Dihedral : 17.904 179.018 9077 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.80 % Favored : 95.06 % Rotamer: Outliers : 0.91 % Allowed : 23.81 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % 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: -0.72 (0.16), residues: 2773 helix: 0.99 (0.18), residues: 929 sheet: 0.27 (0.24), residues: 444 loop : -1.83 (0.14), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 347 TYR 0.022 0.001 TYR I 86 PHE 0.014 0.001 PHE H 176 TRP 0.014 0.001 TRP G 84 HIS 0.008 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.13 (23676) covalent geometry : angle 0.63196 / 0.39 (32358) hydrogen bonds : bond 0.21226 / 13.75 ( 870) hydrogen bonds : angle 6.38650 / 4.31 ( 2477) metal coordination : bond 0.00154 / 0.08 ( 4) metal coordination : angle 2.88324 / 1.61 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7158 (t80) REVERT: B 267 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.7834 (tp40) REVERT: E 286 MET cc_start: 0.8829 (tpp) cc_final: 0.8524 (tpt) REVERT: I 14 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8212 (ttp) REVERT: I 25 GLU cc_start: 0.7103 (tt0) cc_final: 0.6315 (tt0) REVERT: I 220 ARG cc_start: 0.7981 (ptt-90) cc_final: 0.7612 (ptt-90) REVERT: I 225 ASN cc_start: 0.7880 (m-40) cc_final: 0.7668 (m110) outliers start: 20 outliers final: 5 residues processed: 161 average time/residue: 0.7467 time to fit residues: 135.2785 Evaluate side-chains 141 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 133 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain I residue 14 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.0670 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.8724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 480 ASN C 22 ASN D 298 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.076656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.057503 restraints weight = 51310.484| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 2.78 r_work: 0.2651 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 23680 Z= 0.236 Angle : 0.630 11.612 32364 Z= 0.342 Chirality : 0.048 0.585 3706 Planarity : 0.005 0.065 3861 Dihedral : 14.182 179.600 4115 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.75 % Favored : 96.14 % Rotamer: Outliers : 2.94 % Allowed : 21.00 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % 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: -0.48 (0.16), residues: 2773 helix: 1.28 (0.18), residues: 962 sheet: 0.34 (0.24), residues: 431 loop : -1.78 (0.14), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 322 TYR 0.026 0.002 TYR H 276 PHE 0.023 0.002 PHE G 56 TRP 0.015 0.001 TRP C 114 HIS 0.007 0.001 HIS A 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.24 (23676) covalent geometry : angle 0.62892 / 0.34 (32358) hydrogen bonds : bond 0.06726 / 4.44 ( 870) hydrogen bonds : angle 4.60213 / 3.14 ( 2477) metal coordination : bond 0.00459 / 0.23 ( 4) metal coordination : angle 2.16399 / 1.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 132 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 469 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: A 490 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8502 (mtmm) REVERT: B 247 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8508 (tp) REVERT: B 277 GLU cc_start: 0.8684 (pt0) cc_final: 0.8458 (pp20) REVERT: C 22 ASN cc_start: 0.7871 (m-40) cc_final: 0.7580 (m110) REVERT: E 148 ASP cc_start: 0.9184 (OUTLIER) cc_final: 0.8956 (m-30) REVERT: E 203 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.8985 (mtpt) REVERT: G 106 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8016 (pp) REVERT: H 177 ILE cc_start: 0.9632 (OUTLIER) cc_final: 0.9353 (tp) REVERT: I 25 GLU cc_start: 0.7177 (tt0) cc_final: 0.6071 (tt0) REVERT: I 64 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8431 (tt0) REVERT: I 110 ARG cc_start: 0.7743 (mtp-110) cc_final: 0.6873 (ptm160) REVERT: I 225 ASN cc_start: 0.7258 (OUTLIER) cc_final: 0.6887 (m-40) REVERT: I 284 ARG cc_start: 0.5722 (OUTLIER) cc_final: 0.5025 (ttp80) outliers start: 65 outliers final: 17 residues processed: 183 average time/residue: 0.6865 time to fit residues: 142.1481 Evaluate side-chains 157 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 177 CYS Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 350 ILE Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain I residue 225 ASN Chi-restraints excluded: chain I residue 284 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 101 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 chunk 152 optimal weight: 0.0870 chunk 57 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 262 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 248 optimal weight: 6.9990 chunk 179 optimal weight: 1.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.077110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.057869 restraints weight = 51269.692| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 2.79 r_work: 0.2660 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23680 Z= 0.161 Angle : 0.544 9.207 32364 Z= 0.297 Chirality : 0.045 0.576 3706 Planarity : 0.004 0.058 3861 Dihedral : 14.005 178.878 4101 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.61 % Favored : 96.29 % Rotamer: Outliers : 2.35 % Allowed : 22.05 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % 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: -0.25 (0.16), residues: 2773 helix: 1.52 (0.18), residues: 960 sheet: 0.58 (0.25), residues: 414 loop : -1.70 (0.15), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 322 TYR 0.013 0.001 TYR H 292 PHE 0.019 0.001 PHE G 56 TRP 0.012 0.001 TRP C 114 HIS 0.005 0.001 HIS A 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (23676) covalent geometry : angle 0.54297 / 0.30 (32358) hydrogen bonds : bond 0.05795 / 3.83 ( 870) hydrogen bonds : angle 4.28839 / 2.94 ( 2477) metal coordination : bond 0.00353 / 0.18 ( 4) metal coordination : angle 2.23553 / 1.25 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 133 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 469 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7407 (mp0) REVERT: A 490 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8395 (mtmm) REVERT: B 247 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8557 (tp) REVERT: B 277 GLU cc_start: 0.8719 (pt0) cc_final: 0.8485 (pp20) REVERT: C 227 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.7434 (mtm180) REVERT: C 266 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8785 (mp0) REVERT: D 182 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8473 (m-40) REVERT: E 148 ASP cc_start: 0.9148 (OUTLIER) cc_final: 0.8917 (m-30) REVERT: E 203 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.9016 (mtpt) REVERT: G 106 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8127 (pp) REVERT: H 177 ILE cc_start: 0.9627 (OUTLIER) cc_final: 0.9356 (tp) REVERT: I 25 GLU cc_start: 0.7116 (tt0) cc_final: 0.6043 (tt0) REVERT: I 26 LEU cc_start: 0.6147 (OUTLIER) cc_final: 0.5625 (tm) REVERT: I 64 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8410 (tt0) REVERT: I 110 ARG cc_start: 0.7757 (mtp-110) cc_final: 0.7030 (ptm160) REVERT: I 220 ARG cc_start: 0.7814 (ptt-90) cc_final: 0.7498 (ptt-90) REVERT: I 225 ASN cc_start: 0.7240 (OUTLIER) cc_final: 0.6894 (m-40) REVERT: I 284 ARG cc_start: 0.5630 (OUTLIER) cc_final: 0.4935 (ttp80) outliers start: 52 outliers final: 16 residues processed: 176 average time/residue: 0.7478 time to fit residues: 148.6162 Evaluate side-chains 158 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 177 CYS Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 350 ILE Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain I residue 225 ASN Chi-restraints excluded: chain I residue 284 ARG Chi-restraints excluded: chain I residue 287 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 29 optimal weight: 0.9980 chunk 238 optimal weight: 4.9990 chunk 222 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 275 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 280 optimal weight: 9.9990 chunk 219 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.077246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.058032 restraints weight = 51251.367| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 2.80 r_work: 0.2664 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 23680 Z= 0.144 Angle : 0.526 10.855 32364 Z= 0.285 Chirality : 0.044 0.565 3706 Planarity : 0.004 0.061 3861 Dihedral : 13.956 178.929 4098 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.57 % Favored : 96.32 % Rotamer: Outliers : 2.58 % Allowed : 22.18 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % 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: -0.08 (0.16), residues: 2773 helix: 1.64 (0.18), residues: 964 sheet: 0.68 (0.25), residues: 412 loop : -1.59 (0.15), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 322 TYR 0.012 0.001 TYR H 292 PHE 0.017 0.001 PHE G 56 TRP 0.010 0.001 TRP C 114 HIS 0.005 0.001 HIS A 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (23676) covalent geometry : angle 0.52544 / 0.28 (32358) hydrogen bonds : bond 0.05265 / 3.49 ( 870) hydrogen bonds : angle 4.12320 / 2.82 ( 2477) metal coordination : bond 0.00280 / 0.14 ( 4) metal coordination : angle 2.14466 / 1.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 132 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: A 469 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7414 (mp0) REVERT: A 490 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8386 (mtmm) REVERT: B 169 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8393 (mt-10) REVERT: B 277 GLU cc_start: 0.8757 (pt0) cc_final: 0.8515 (pp20) REVERT: C 227 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.7423 (mtm180) REVERT: D 182 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.8459 (m-40) REVERT: E 203 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.9018 (mtpt) REVERT: G 106 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8237 (pp) REVERT: H 177 ILE cc_start: 0.9634 (OUTLIER) cc_final: 0.9351 (tp) REVERT: I 25 GLU cc_start: 0.7014 (tt0) cc_final: 0.5942 (tt0) REVERT: I 64 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8416 (tt0) REVERT: I 110 ARG cc_start: 0.7791 (mtp-110) cc_final: 0.6972 (ptm160) REVERT: I 220 ARG cc_start: 0.7811 (ptt-90) cc_final: 0.7576 (ptt-90) REVERT: I 225 ASN cc_start: 0.7207 (OUTLIER) cc_final: 0.6853 (m-40) REVERT: I 284 ARG cc_start: 0.5662 (OUTLIER) cc_final: 0.4977 (ttp80) outliers start: 57 outliers final: 21 residues processed: 175 average time/residue: 0.7232 time to fit residues: 143.4280 Evaluate side-chains 159 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 509 ASN Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain E residue 177 CYS Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 336 CYS Chi-restraints excluded: chain H residue 350 ILE Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain I residue 225 ASN Chi-restraints excluded: chain I residue 284 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 115 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 177 optimal weight: 0.6980 chunk 141 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.077604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.058476 restraints weight = 50753.513| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 2.79 r_work: 0.2674 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23680 Z= 0.126 Angle : 0.501 10.475 32364 Z= 0.273 Chirality : 0.043 0.553 3706 Planarity : 0.004 0.059 3861 Dihedral : 13.920 178.734 4098 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.46 % Favored : 96.43 % Rotamer: Outliers : 2.35 % Allowed : 22.41 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % 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: 0.05 (0.16), residues: 2773 helix: 1.77 (0.18), residues: 966 sheet: 0.58 (0.25), residues: 433 loop : -1.51 (0.15), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 322 TYR 0.011 0.001 TYR H 292 PHE 0.016 0.001 PHE G 56 TRP 0.008 0.001 TRP I 302 HIS 0.004 0.001 HIS A 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (23676) covalent geometry : angle 0.50016 / 0.27 (32358) hydrogen bonds : bond 0.04847 / 3.21 ( 870) hydrogen bonds : angle 4.00158 / 2.75 ( 2477) metal coordination : bond 0.00240 / 0.12 ( 4) metal coordination : angle 2.00131 / 1.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 129 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: A 469 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7405 (mp0) REVERT: A 490 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8373 (mtmm) REVERT: B 277 GLU cc_start: 0.8786 (pt0) cc_final: 0.8547 (pp20) REVERT: C 227 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.7458 (mtm180) REVERT: C 266 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8790 (mp0) REVERT: E 203 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.9010 (mtpt) REVERT: G 106 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8195 (pp) REVERT: H 177 ILE cc_start: 0.9636 (OUTLIER) cc_final: 0.9355 (tp) REVERT: I 25 GLU cc_start: 0.7040 (tt0) cc_final: 0.5893 (tt0) REVERT: I 64 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8394 (tt0) REVERT: I 110 ARG cc_start: 0.7716 (mtp-110) cc_final: 0.6929 (ptm160) REVERT: I 220 ARG cc_start: 0.7856 (ptt-90) cc_final: 0.7567 (ptt-90) REVERT: I 284 ARG cc_start: 0.5715 (OUTLIER) cc_final: 0.5021 (ttp80) outliers start: 52 outliers final: 23 residues processed: 169 average time/residue: 0.7634 time to fit residues: 145.7740 Evaluate side-chains 158 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 509 ASN Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain E residue 177 CYS Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 246 GLU Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 336 CYS Chi-restraints excluded: chain H residue 350 ILE Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain I residue 284 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 43 optimal weight: 1.9990 chunk 178 optimal weight: 0.9980 chunk 273 optimal weight: 6.9990 chunk 123 optimal weight: 0.6980 chunk 266 optimal weight: 5.9990 chunk 165 optimal weight: 0.9980 chunk 231 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 238 optimal weight: 0.0770 chunk 163 optimal weight: 2.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.078221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.059125 restraints weight = 51061.760| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 2.79 r_work: 0.2689 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23680 Z= 0.110 Angle : 0.484 9.961 32364 Z= 0.262 Chirality : 0.043 0.539 3706 Planarity : 0.004 0.071 3861 Dihedral : 13.886 178.447 4098 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.35 % Favored : 96.54 % Rotamer: Outliers : 2.35 % Allowed : 22.14 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % 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: 0.14 (0.16), residues: 2773 helix: 1.85 (0.18), residues: 971 sheet: 0.58 (0.25), residues: 440 loop : -1.46 (0.15), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG H 322 TYR 0.010 0.001 TYR H 292 PHE 0.014 0.001 PHE G 56 TRP 0.008 0.001 TRP I 302 HIS 0.004 0.001 HIS A 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (23676) covalent geometry : angle 0.48333 / 0.26 (32358) hydrogen bonds : bond 0.04396 / 2.92 ( 870) hydrogen bonds : angle 3.88888 / 2.67 ( 2477) metal coordination : bond 0.00200 / 0.10 ( 4) metal coordination : angle 1.91796 / 1.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 133 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: A 469 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7380 (mp0) REVERT: A 490 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8366 (mtmm) REVERT: B 277 GLU cc_start: 0.8780 (pt0) cc_final: 0.8531 (pp20) REVERT: C 227 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.7477 (mtm180) REVERT: D 182 ASN cc_start: 0.8693 (OUTLIER) cc_final: 0.8447 (m-40) REVERT: E 63 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8668 (tptm) REVERT: E 203 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.8989 (mtpt) REVERT: G 106 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8251 (pp) REVERT: H 177 ILE cc_start: 0.9645 (OUTLIER) cc_final: 0.9368 (tp) REVERT: I 25 GLU cc_start: 0.7056 (tt0) cc_final: 0.5740 (tt0) REVERT: I 110 ARG cc_start: 0.7719 (mtp-110) cc_final: 0.6983 (ptm160) REVERT: I 220 ARG cc_start: 0.7874 (ptt-90) cc_final: 0.7542 (ptt-90) REVERT: I 284 ARG cc_start: 0.5733 (OUTLIER) cc_final: 0.5054 (ttp80) outliers start: 52 outliers final: 25 residues processed: 176 average time/residue: 0.7169 time to fit residues: 142.6844 Evaluate side-chains 161 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 509 ASN Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain E residue 63 LYS Chi-restraints excluded: chain E residue 177 CYS Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 246 GLU Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 336 CYS Chi-restraints excluded: chain H residue 350 ILE Chi-restraints excluded: chain H residue 368 VAL Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 284 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 235 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 218 optimal weight: 0.9990 chunk 263 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 274 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 243 optimal weight: 10.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.076965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.057799 restraints weight = 51277.563| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 2.80 r_work: 0.2659 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23680 Z= 0.149 Angle : 0.516 9.715 32364 Z= 0.278 Chirality : 0.044 0.560 3706 Planarity : 0.004 0.074 3861 Dihedral : 13.869 179.461 4097 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.75 % Favored : 96.14 % Rotamer: Outliers : 2.26 % Allowed : 22.45 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % 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: 0.13 (0.16), residues: 2773 helix: 1.82 (0.18), residues: 972 sheet: 0.61 (0.25), residues: 436 loop : -1.46 (0.15), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 322 TYR 0.010 0.001 TYR B 318 PHE 0.018 0.001 PHE G 56 TRP 0.007 0.001 TRP E 114 HIS 0.005 0.001 HIS A 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (23676) covalent geometry : angle 0.51499 / 0.28 (32358) hydrogen bonds : bond 0.05071 / 3.35 ( 870) hydrogen bonds : angle 3.91772 / 2.68 ( 2477) metal coordination : bond 0.00297 / 0.15 ( 4) metal coordination : angle 2.14899 / 1.20 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 125 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 469 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7415 (mp0) REVERT: A 490 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8388 (mtmm) REVERT: B 277 GLU cc_start: 0.8773 (pt0) cc_final: 0.8496 (pp20) REVERT: C 227 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.7491 (mtm180) REVERT: D 182 ASN cc_start: 0.8708 (OUTLIER) cc_final: 0.8458 (m-40) REVERT: E 203 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.9018 (mtpt) REVERT: G 106 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8286 (pp) REVERT: H 177 ILE cc_start: 0.9643 (OUTLIER) cc_final: 0.9343 (tp) REVERT: I 25 GLU cc_start: 0.7031 (tt0) cc_final: 0.5653 (tt0) REVERT: I 64 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8379 (tt0) REVERT: I 110 ARG cc_start: 0.7711 (mtp-110) cc_final: 0.6989 (ptm160) REVERT: I 220 ARG cc_start: 0.7894 (ptt-90) cc_final: 0.7530 (ptt-90) REVERT: I 284 ARG cc_start: 0.5677 (OUTLIER) cc_final: 0.5006 (ttp80) outliers start: 50 outliers final: 26 residues processed: 166 average time/residue: 0.7340 time to fit residues: 137.4755 Evaluate side-chains 158 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 509 ASN Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain E residue 177 CYS Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 246 GLU Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 336 CYS Chi-restraints excluded: chain H residue 368 VAL Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain I residue 284 ARG Chi-restraints excluded: chain I residue 287 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 146 optimal weight: 0.3980 chunk 240 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 196 optimal weight: 0.0870 chunk 259 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 92 optimal weight: 0.0010 chunk 99 optimal weight: 1.9990 chunk 234 optimal weight: 0.5980 overall best weight: 0.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.079073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.059953 restraints weight = 50675.220| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.79 r_work: 0.2710 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23680 Z= 0.091 Angle : 0.467 9.941 32364 Z= 0.252 Chirality : 0.042 0.520 3706 Planarity : 0.004 0.077 3861 Dihedral : 13.852 178.317 4097 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.43 % Favored : 96.47 % Rotamer: Outliers : 1.63 % Allowed : 22.86 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % 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: 0.25 (0.16), residues: 2773 helix: 1.93 (0.18), residues: 972 sheet: 0.61 (0.25), residues: 439 loop : -1.37 (0.15), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG H 322 TYR 0.011 0.001 TYR G 36 PHE 0.014 0.001 PHE D 2 TRP 0.010 0.001 TRP G 84 HIS 0.003 0.000 HIS A 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.09 (23676) covalent geometry : angle 0.46645 / 0.25 (32358) hydrogen bonds : bond 0.03873 / 2.58 ( 870) hydrogen bonds : angle 3.78775 / 2.61 ( 2477) metal coordination : bond 0.00141 / 0.07 ( 4) metal coordination : angle 1.67706 / 0.96 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 469 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7321 (mp0) REVERT: A 490 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8326 (mtmm) REVERT: B 217 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8298 (mtpt) REVERT: B 277 GLU cc_start: 0.8765 (pt0) cc_final: 0.8464 (pp20) REVERT: C 227 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.7502 (mtm180) REVERT: H 177 ILE cc_start: 0.9643 (OUTLIER) cc_final: 0.9347 (tp) REVERT: I 25 GLU cc_start: 0.7021 (tt0) cc_final: 0.5733 (tt0) REVERT: I 110 ARG cc_start: 0.7689 (mtp-110) cc_final: 0.7013 (ptm160) REVERT: I 220 ARG cc_start: 0.7878 (ptt-90) cc_final: 0.7368 (ptt-90) REVERT: I 284 ARG cc_start: 0.5732 (OUTLIER) cc_final: 0.5044 (ttp80) outliers start: 36 outliers final: 17 residues processed: 157 average time/residue: 0.7289 time to fit residues: 128.6612 Evaluate side-chains 149 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 509 ASN Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 177 CYS Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 246 GLU Chi-restraints excluded: chain H residue 336 CYS Chi-restraints excluded: chain H residue 368 VAL Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 284 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 19 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 234 optimal weight: 0.6980 chunk 186 optimal weight: 0.9990 chunk 214 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 88 optimal weight: 0.4980 chunk 243 optimal weight: 9.9990 chunk 113 optimal weight: 0.9990 chunk 277 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 215 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.077502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.058355 restraints weight = 51324.900| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 2.79 r_work: 0.2672 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23680 Z= 0.137 Angle : 0.508 17.738 32364 Z= 0.270 Chirality : 0.043 0.550 3706 Planarity : 0.004 0.079 3861 Dihedral : 13.836 179.938 4097 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.64 % Favored : 96.25 % Rotamer: Outliers : 1.40 % Allowed : 23.09 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % 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: 0.25 (0.16), residues: 2773 helix: 1.92 (0.18), residues: 972 sheet: 0.64 (0.25), residues: 436 loop : -1.38 (0.15), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG H 322 TYR 0.010 0.001 TYR B 318 PHE 0.017 0.001 PHE G 56 TRP 0.007 0.001 TRP E 114 HIS 0.004 0.001 HIS A 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (23676) covalent geometry : angle 0.50733 / 0.27 (32358) hydrogen bonds : bond 0.04726 / 3.13 ( 870) hydrogen bonds : angle 3.81097 / 2.61 ( 2477) metal coordination : bond 0.00256 / 0.13 ( 4) metal coordination : angle 2.11532 / 1.19 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: A 469 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: A 490 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8383 (mtmm) REVERT: B 277 GLU cc_start: 0.8758 (pt0) cc_final: 0.8462 (pp20) REVERT: C 227 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.7572 (mtm180) REVERT: D 182 ASN cc_start: 0.8699 (OUTLIER) cc_final: 0.8453 (m-40) REVERT: H 177 ILE cc_start: 0.9649 (OUTLIER) cc_final: 0.9353 (tp) REVERT: I 25 GLU cc_start: 0.7015 (tt0) cc_final: 0.5740 (tt0) REVERT: I 110 ARG cc_start: 0.7682 (mtp-110) cc_final: 0.7003 (ptm160) REVERT: I 220 ARG cc_start: 0.7870 (ptt-90) cc_final: 0.7498 (ptt-90) REVERT: I 284 ARG cc_start: 0.5646 (OUTLIER) cc_final: 0.4996 (ttp80) outliers start: 31 outliers final: 17 residues processed: 152 average time/residue: 0.7832 time to fit residues: 133.3559 Evaluate side-chains 147 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 509 ASN Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 177 CYS Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 336 CYS Chi-restraints excluded: chain H residue 368 VAL Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 284 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 50 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 98 optimal weight: 0.0970 chunk 54 optimal weight: 2.9990 chunk 191 optimal weight: 0.9990 chunk 109 optimal weight: 0.0970 chunk 87 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 40 optimal weight: 0.0570 overall best weight: 0.4094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.079415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.060305 restraints weight = 50958.413| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 2.80 r_work: 0.2717 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 23680 Z= 0.089 Angle : 0.474 16.837 32364 Z= 0.253 Chirality : 0.042 0.515 3706 Planarity : 0.004 0.085 3861 Dihedral : 13.821 178.281 4097 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.14 % Favored : 96.75 % Rotamer: Outliers : 1.09 % Allowed : 23.40 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % 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: 0.34 (0.16), residues: 2773 helix: 2.00 (0.18), residues: 973 sheet: 0.59 (0.25), residues: 454 loop : -1.31 (0.15), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG H 322 TYR 0.012 0.001 TYR G 36 PHE 0.013 0.001 PHE A 67 TRP 0.010 0.001 TRP G 84 HIS 0.003 0.000 HIS A 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00189 / 0.09 (23676) covalent geometry : angle 0.47353 / 0.25 (32358) hydrogen bonds : bond 0.03711 / 2.47 ( 870) hydrogen bonds : angle 3.71679 / 2.56 ( 2477) metal coordination : bond 0.00153 / 0.08 ( 4) metal coordination : angle 1.66055 / 0.95 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: A 490 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8339 (mtmm) REVERT: B 277 GLU cc_start: 0.8729 (pt0) cc_final: 0.8432 (pp20) REVERT: C 227 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.7513 (mtm180) REVERT: H 177 ILE cc_start: 0.9645 (OUTLIER) cc_final: 0.9346 (tp) REVERT: I 25 GLU cc_start: 0.6913 (tt0) cc_final: 0.5602 (tt0) REVERT: I 110 ARG cc_start: 0.7671 (mtp-110) cc_final: 0.7026 (ptm160) REVERT: I 220 ARG cc_start: 0.7864 (ptt-90) cc_final: 0.7349 (ptt-90) REVERT: I 284 ARG cc_start: 0.5707 (OUTLIER) cc_final: 0.5040 (ttp80) outliers start: 24 outliers final: 15 residues processed: 149 average time/residue: 0.7617 time to fit residues: 127.3959 Evaluate side-chains 143 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 509 ASN Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 177 CYS Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 336 CYS Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 284 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 281 optimal weight: 0.5980 chunk 126 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 233 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 chunk 53 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 132 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.079029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.059792 restraints weight = 50792.152| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.81 r_work: 0.2705 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23680 Z= 0.104 Angle : 0.486 17.556 32364 Z= 0.258 Chirality : 0.042 0.527 3706 Planarity : 0.004 0.083 3861 Dihedral : 13.801 178.501 4097 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.35 % Favored : 96.54 % Rotamer: Outliers : 1.13 % Allowed : 23.45 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % 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: 0.37 (0.16), residues: 2773 helix: 2.01 (0.18), residues: 974 sheet: 0.62 (0.24), residues: 459 loop : -1.29 (0.15), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG H 322 TYR 0.009 0.001 TYR H 292 PHE 0.014 0.001 PHE A 67 TRP 0.007 0.001 TRP I 302 HIS 0.003 0.001 HIS A 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (23676) covalent geometry : angle 0.48524 / 0.26 (32358) hydrogen bonds : bond 0.04015 / 2.67 ( 870) hydrogen bonds : angle 3.70331 / 2.55 ( 2477) metal coordination : bond 0.00182 / 0.09 ( 4) metal coordination : angle 1.89909 / 1.07 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5534.50 seconds wall clock time: 95 minutes 25.82 seconds (5725.82 seconds total)