Starting phenix.real_space_refine on Sat Jun 28 10:12:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oz6_17299/06_2025/8oz6_17299.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oz6_17299/06_2025/8oz6_17299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8oz6_17299/06_2025/8oz6_17299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oz6_17299/06_2025/8oz6_17299.map" model { file = "/net/cci-nas-00/data/ceres_data/8oz6_17299/06_2025/8oz6_17299.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oz6_17299/06_2025/8oz6_17299.cif" } resolution = 3.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1220 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 132 5.49 5 S 96 5.16 5 C 20236 2.51 5 N 5300 2.21 5 O 6240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 32004 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "B" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "I" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "J" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "C" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "D" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "K" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "L" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "E" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "F" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "G" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "H" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "M" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "N" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "O" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "P" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Time building chain proxies: 18.86, per 1000 atoms: 0.59 Number of scatterers: 32004 At special positions: 0 Unit cell: (177.87, 208.12, 165.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 132 15.00 O 6240 8.00 N 5300 7.00 C 20236 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: 6.89 Conformation dependent library (CDL) restraints added in 3.7 seconds 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6792 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 28 sheets defined 39.3% alpha, 14.3% beta 11 base pairs and 87 stacking pairs defined. Time for finding SS restraints: 9.67 Creating SS restraints... Processing helix chain 'A' and resid 14 through 28 Processing helix chain 'A' and resid 44 through 56 removed outlier: 3.825A pdb=" N GLU A 50 " --> pdb=" O TRP A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 89 Processing helix chain 'A' and resid 109 through 114 removed outlier: 4.081A pdb=" N ARG A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 138 Processing helix chain 'A' and resid 146 through 158 removed outlier: 4.037A pdb=" N SER A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.512A pdb=" N GLU A 202 " --> pdb=" O ASP A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 233 removed outlier: 4.118A pdb=" N THR A 232 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.522A pdb=" N LYS A 237 " --> pdb=" O HIS A 234 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 238 " --> pdb=" O LYS A 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 234 through 238' Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 257 through 280 removed outlier: 3.682A pdb=" N ARG A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE A 265 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 353 through 366 Processing helix chain 'A' and resid 369 through 384 removed outlier: 3.865A pdb=" N THR A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS A 376 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 22 through 30 Processing helix chain 'B' and resid 46 through 62 removed outlier: 3.695A pdb=" N LYS B 51 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 97 through 106 removed outlier: 3.695A pdb=" N TYR B 106 " --> pdb=" O GLY B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 132 removed outlier: 4.083A pdb=" N LYS B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 150 removed outlier: 3.546A pdb=" N TYR B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 214 Processing helix chain 'B' and resid 215 through 218 Processing helix chain 'B' and resid 230 through 234 removed outlier: 3.537A pdb=" N ASP B 233 " --> pdb=" O ALA B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 331 through 351 removed outlier: 4.672A pdb=" N GLN B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 377 removed outlier: 3.716A pdb=" N TRP B 370 " --> pdb=" O ASN B 366 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 463 removed outlier: 3.824A pdb=" N LEU B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER B 461 " --> pdb=" O LYS B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 490 removed outlier: 3.529A pdb=" N ASP B 484 " --> pdb=" O LEU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.526A pdb=" N TYR B 505 " --> pdb=" O ALA B 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 28 Processing helix chain 'C' and resid 44 through 56 Processing helix chain 'C' and resid 71 through 89 Processing helix chain 'C' and resid 109 through 115 removed outlier: 3.928A pdb=" N LEU C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 138 removed outlier: 3.558A pdb=" N GLY C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 158 Processing helix chain 'C' and resid 190 through 194 Processing helix chain 'C' and resid 219 through 224 removed outlier: 4.168A pdb=" N PHE C 223 " --> pdb=" O ALA C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 233 removed outlier: 4.300A pdb=" N THR C 232 " --> pdb=" O LYS C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 238 removed outlier: 3.541A pdb=" N THR C 238 " --> pdb=" O LYS C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 249 Processing helix chain 'C' and resid 257 through 280 removed outlier: 3.537A pdb=" N LYS C 262 " --> pdb=" O ASN C 258 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE C 265 " --> pdb=" O CYS C 261 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL C 266 " --> pdb=" O LYS C 262 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN C 267 " --> pdb=" O ARG C 263 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 304 Processing helix chain 'C' and resid 353 through 366 removed outlier: 3.557A pdb=" N GLN C 357 " --> pdb=" O SER C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 385 removed outlier: 3.797A pdb=" N LYS C 376 " --> pdb=" O THR C 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 17 No H-bonds generated for 'chain 'D' and resid 15 through 17' Processing helix chain 'D' and resid 23 through 30 Processing helix chain 'D' and resid 46 through 62 removed outlier: 4.095A pdb=" N LYS D 51 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE D 52 " --> pdb=" O GLN D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 83 Processing helix chain 'D' and resid 97 through 106 removed outlier: 3.642A pdb=" N PHE D 104 " --> pdb=" O ASP D 100 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR D 106 " --> pdb=" O GLY D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 132 removed outlier: 3.702A pdb=" N LYS D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU D 132 " --> pdb=" O ALA D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 151 Processing helix chain 'D' and resid 158 through 162 removed outlier: 3.568A pdb=" N VAL D 162 " --> pdb=" O LYS D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 214 removed outlier: 3.523A pdb=" N GLN D 209 " --> pdb=" O GLN D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 265 removed outlier: 3.841A pdb=" N ALA D 259 " --> pdb=" O THR D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 351 removed outlier: 3.858A pdb=" N SER D 345 " --> pdb=" O GLN D 341 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR D 346 " --> pdb=" O SER D 342 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLN D 349 " --> pdb=" O SER D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 377 removed outlier: 3.852A pdb=" N TRP D 370 " --> pdb=" O ASN D 366 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU D 375 " --> pdb=" O ASP D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 463 removed outlier: 3.710A pdb=" N ASP D 458 " --> pdb=" O GLN D 454 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE D 459 " --> pdb=" O VAL D 455 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU D 460 " --> pdb=" O LEU D 456 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER D 461 " --> pdb=" O LYS D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 491 removed outlier: 3.789A pdb=" N ASP D 484 " --> pdb=" O LEU D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 506 removed outlier: 3.718A pdb=" N TYR D 505 " --> pdb=" O ALA D 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 29 Processing helix chain 'E' and resid 44 through 56 removed outlier: 3.626A pdb=" N GLU E 50 " --> pdb=" O TRP E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 89 Processing helix chain 'E' and resid 90 through 94 removed outlier: 3.838A pdb=" N PHE E 93 " --> pdb=" O ASP E 90 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE E 94 " --> pdb=" O ASP E 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 90 through 94' Processing helix chain 'E' and resid 109 through 114 removed outlier: 4.528A pdb=" N ARG E 114 " --> pdb=" O ILE E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 138 Processing helix chain 'E' and resid 146 through 157 removed outlier: 3.654A pdb=" N SER E 150 " --> pdb=" O ASP E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 194 Processing helix chain 'E' and resid 227 through 233 removed outlier: 4.056A pdb=" N THR E 232 " --> pdb=" O LYS E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 238 removed outlier: 3.548A pdb=" N THR E 238 " --> pdb=" O LYS E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 249 Processing helix chain 'E' and resid 257 through 280 removed outlier: 3.950A pdb=" N ILE E 265 " --> pdb=" O CYS E 261 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN E 267 " --> pdb=" O ARG E 263 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU E 268 " --> pdb=" O LEU E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 302 No H-bonds generated for 'chain 'E' and resid 300 through 302' Processing helix chain 'E' and resid 353 through 366 Processing helix chain 'E' and resid 369 through 385 removed outlier: 4.527A pdb=" N LYS E 376 " --> pdb=" O THR E 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 17 No H-bonds generated for 'chain 'F' and resid 15 through 17' Processing helix chain 'F' and resid 22 through 30 Processing helix chain 'F' and resid 46 through 62 removed outlier: 4.086A pdb=" N LYS F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE F 52 " --> pdb=" O GLN F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 83 Processing helix chain 'F' and resid 97 through 104 removed outlier: 3.778A pdb=" N PHE F 104 " --> pdb=" O ASP F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 132 removed outlier: 4.173A pdb=" N LYS F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 151 removed outlier: 3.549A pdb=" N TYR F 148 " --> pdb=" O PRO F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 214 removed outlier: 3.692A pdb=" N GLN F 209 " --> pdb=" O GLN F 205 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU F 214 " --> pdb=" O PHE F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 218 Processing helix chain 'F' and resid 230 through 234 removed outlier: 3.750A pdb=" N ASP F 233 " --> pdb=" O ALA F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 264 removed outlier: 3.505A pdb=" N ALA F 259 " --> pdb=" O THR F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 348 removed outlier: 3.518A pdb=" N TYR F 346 " --> pdb=" O SER F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 377 removed outlier: 3.596A pdb=" N VAL F 376 " --> pdb=" O ALA F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 430 Processing helix chain 'F' and resid 451 through 463 removed outlier: 3.837A pdb=" N LEU F 460 " --> pdb=" O LEU F 456 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER F 461 " --> pdb=" O LYS F 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 477 through 491 removed outlier: 3.550A pdb=" N ASP F 484 " --> pdb=" O LEU F 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 502 through 506 Processing helix chain 'G' and resid 10 through 13 removed outlier: 3.801A pdb=" N ASP G 13 " --> pdb=" O ALA G 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 10 through 13' Processing helix chain 'G' and resid 14 through 27 removed outlier: 3.939A pdb=" N THR G 18 " --> pdb=" O ASP G 14 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP G 20 " --> pdb=" O ASP G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 56 Processing helix chain 'G' and resid 65 through 70 removed outlier: 4.612A pdb=" N GLN G 70 " --> pdb=" O SER G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 89 Processing helix chain 'G' and resid 104 through 108 removed outlier: 3.729A pdb=" N ILE G 108 " --> pdb=" O TYR G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 115 removed outlier: 3.898A pdb=" N LEU G 115 " --> pdb=" O ASP G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 138 removed outlier: 3.913A pdb=" N GLY G 127 " --> pdb=" O SER G 123 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU G 128 " --> pdb=" O TRP G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 158 removed outlier: 3.678A pdb=" N PHE G 158 " --> pdb=" O TYR G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 194 Processing helix chain 'G' and resid 219 through 224 removed outlier: 3.684A pdb=" N ASP G 222 " --> pdb=" O TRP G 219 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N PHE G 223 " --> pdb=" O ALA G 220 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR G 224 " --> pdb=" O TYR G 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 219 through 224' Processing helix chain 'G' and resid 227 through 233 removed outlier: 3.575A pdb=" N GLU G 231 " --> pdb=" O PRO G 228 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR G 232 " --> pdb=" O LYS G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 238 Processing helix chain 'G' and resid 242 through 249 removed outlier: 3.519A pdb=" N ILE G 246 " --> pdb=" O PRO G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 280 removed outlier: 4.233A pdb=" N LEU G 264 " --> pdb=" O GLU G 260 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE G 265 " --> pdb=" O CYS G 261 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL G 266 " --> pdb=" O LYS G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 300 through 302 No H-bonds generated for 'chain 'G' and resid 300 through 302' Processing helix chain 'G' and resid 353 through 367 removed outlier: 4.180A pdb=" N ASN G 367 " --> pdb=" O ARG G 363 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 385 removed outlier: 3.905A pdb=" N THR G 375 " --> pdb=" O ASN G 371 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS G 376 " --> pdb=" O THR G 372 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 18 removed outlier: 3.637A pdb=" N GLY H 17 " --> pdb=" O PHE H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 31 Processing helix chain 'H' and resid 46 through 62 removed outlier: 3.737A pdb=" N ILE H 52 " --> pdb=" O GLN H 48 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE H 53 " --> pdb=" O GLY H 49 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS H 62 " --> pdb=" O ASP H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 82 Processing helix chain 'H' and resid 97 through 106 Processing helix chain 'H' and resid 109 through 132 removed outlier: 4.028A pdb=" N LYS H 124 " --> pdb=" O LEU H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 151 removed outlier: 4.170A pdb=" N TYR H 148 " --> pdb=" O PRO H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 162 Processing helix chain 'H' and resid 205 through 214 removed outlier: 3.679A pdb=" N LEU H 214 " --> pdb=" O PHE H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 234 Processing helix chain 'H' and resid 248 through 265 removed outlier: 3.590A pdb=" N ALA H 259 " --> pdb=" O THR H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 331 through 348 removed outlier: 3.660A pdb=" N TYR H 346 " --> pdb=" O SER H 342 " (cutoff:3.500A) Processing helix chain 'H' and resid 366 through 377 removed outlier: 3.550A pdb=" N TRP H 370 " --> pdb=" O ASN H 366 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL H 376 " --> pdb=" O ALA H 372 " (cutoff:3.500A) Processing helix chain 'H' and resid 451 through 463 removed outlier: 3.578A pdb=" N ASP H 458 " --> pdb=" O GLN H 454 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU H 460 " --> pdb=" O LEU H 456 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER H 461 " --> pdb=" O LYS H 457 " (cutoff:3.500A) Processing helix chain 'H' and resid 477 through 491 removed outlier: 3.630A pdb=" N ASP H 484 " --> pdb=" O LEU H 480 " (cutoff:3.500A) Processing helix chain 'H' and resid 502 through 506 removed outlier: 3.788A pdb=" N TYR H 505 " --> pdb=" O ALA H 502 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 33 removed outlier: 5.902A pdb=" N ILE A 5 " --> pdb=" O TRP A 33 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS A 4 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LEU A 61 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE A 6 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL A 63 " --> pdb=" O PHE A 6 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N SER A 8 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU A 62 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ILE A 118 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 165 through 178 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 165 through 178 current: chain 'A' and resid 291 through 294 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 291 through 294 current: chain 'A' and resid 317 through 328 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 334 through 344 current: chain 'A' and resid 400 through 415 removed outlier: 8.367A pdb=" N LEU B 4 " --> pdb=" O LYS A 409 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LYS A 411 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N TYR B 6 " --> pdb=" O LYS A 411 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ASN A 413 " --> pdb=" O TYR B 6 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 3 through 6 current: chain 'B' and resid 297 through 301 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 315 through 316 current: chain 'B' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 382 through 389 current: chain 'B' and resid 417 through 420 Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 210 Processing sheet with id=AA4, first strand: chain 'A' and resid 304 through 305 removed outlier: 3.583A pdb=" N PHE A 305 " --> pdb=" O THR A 308 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 18 through 20 removed outlier: 3.513A pdb=" N GLN B 18 " --> pdb=" O PHE B 14 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 92 through 95 removed outlier: 3.671A pdb=" N THR B 92 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLY B 42 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ILE B 142 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE B 44 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TRP B 139 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N PHE B 224 " --> pdb=" O TRP B 139 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL B 141 " --> pdb=" O PHE B 224 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 304 through 305 removed outlier: 3.655A pdb=" N PHE B 304 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 312 " --> pdb=" O PHE B 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 32 through 33 removed outlier: 5.584A pdb=" N LYS C 4 " --> pdb=" O THR C 57 " (cutoff:3.500A) removed outlier: 8.896A pdb=" N ILE C 95 " --> pdb=" O CYS C 58 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N PHE C 60 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU C 97 " --> pdb=" O PHE C 60 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU C 62 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ILE C 118 " --> pdb=" O ILE C 94 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 169 through 172 removed outlier: 8.431A pdb=" N LEU D 4 " --> pdb=" O LYS C 409 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LYS C 411 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N TYR D 6 " --> pdb=" O LYS C 411 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 3 through 6 current: chain 'D' and resid 298 through 305 removed outlier: 3.539A pdb=" N PHE D 304 " --> pdb=" O VAL D 312 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 312 " --> pdb=" O PHE D 304 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 311 through 315 current: chain 'D' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 382 through 389 current: chain 'D' and resid 417 through 420 Processing sheet with id=AB1, first strand: chain 'C' and resid 283 through 286 removed outlier: 6.297A pdb=" N THR C 291 " --> pdb=" O GLY C 325 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY C 325 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 334 " --> pdb=" O LYS C 328 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER C 177 " --> pdb=" O SER C 404 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N PHE C 402 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL C 401 " --> pdb=" O LEU C 393 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 208 through 210 Processing sheet with id=AB3, first strand: chain 'D' and resid 19 through 20 Processing sheet with id=AB4, first strand: chain 'D' and resid 92 through 95 removed outlier: 3.588A pdb=" N THR D 92 " --> pdb=" O SER D 41 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLY D 42 " --> pdb=" O PHE D 140 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE D 142 " --> pdb=" O GLY D 42 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE D 44 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 425 through 426 removed outlier: 3.803A pdb=" N VAL D 426 " --> pdb=" O THR D 431 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 32 through 33 removed outlier: 5.831A pdb=" N ILE E 5 " --> pdb=" O TRP E 33 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LYS E 4 " --> pdb=" O CYS E 58 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N PHE E 60 " --> pdb=" O LYS E 4 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE E 6 " --> pdb=" O PHE E 60 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LEU E 62 " --> pdb=" O PHE E 6 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N SER E 8 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N SER E 64 " --> pdb=" O SER E 8 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 115 through 116 Processing sheet with id=AB8, first strand: chain 'E' and resid 169 through 180 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 169 through 180 current: chain 'E' and resid 291 through 294 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 291 through 294 current: chain 'E' and resid 317 through 328 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 334 through 344 current: chain 'E' and resid 400 through 412 removed outlier: 8.672A pdb=" N LEU F 4 " --> pdb=" O LYS E 409 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LYS E 411 " --> pdb=" O LEU F 4 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N TYR F 6 " --> pdb=" O LYS E 411 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 3 through 6 current: chain 'F' and resid 297 through 305 removed outlier: 3.534A pdb=" N PHE F 304 " --> pdb=" O VAL F 312 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL F 312 " --> pdb=" O PHE F 304 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 311 through 315 current: chain 'F' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 382 through 389 current: chain 'F' and resid 417 through 420 Processing sheet with id=AB9, first strand: chain 'E' and resid 208 through 210 Processing sheet with id=AC1, first strand: chain 'E' and resid 304 through 305 Processing sheet with id=AC2, first strand: chain 'F' and resid 18 through 20 removed outlier: 3.589A pdb=" N GLN F 18 " --> pdb=" O PHE F 14 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 92 through 95 removed outlier: 6.328A pdb=" N GLY F 42 " --> pdb=" O PHE F 140 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE F 142 " --> pdb=" O GLY F 42 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE F 44 " --> pdb=" O ILE F 142 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 425 through 426 removed outlier: 3.921A pdb=" N THR F 431 " --> pdb=" O VAL F 426 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 32 through 33 removed outlier: 5.622A pdb=" N ILE G 5 " --> pdb=" O TRP G 33 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LYS G 4 " --> pdb=" O LYS G 59 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU G 61 " --> pdb=" O LYS G 4 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N PHE G 6 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL G 63 " --> pdb=" O PHE G 6 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER G 8 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ILE G 118 " --> pdb=" O ILE G 94 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 165 through 178 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 165 through 178 current: chain 'G' and resid 291 through 294 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 291 through 294 current: chain 'G' and resid 317 through 328 removed outlier: 3.639A pdb=" N VAL G 334 " --> pdb=" O LYS G 328 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 334 through 344 current: chain 'G' and resid 400 through 415 removed outlier: 4.302A pdb=" N ASN G 413 " --> pdb=" O LEU H 4 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N TYR H 6 " --> pdb=" O ASN G 413 " (cutoff:3.500A) removed outlier: 10.585A pdb=" N SER G 415 " --> pdb=" O TYR H 6 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 2 through 6 current: chain 'H' and resid 297 through 305 removed outlier: 3.527A pdb=" N PHE H 304 " --> pdb=" O VAL H 312 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 311 through 316 current: chain 'H' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 382 through 389 current: chain 'H' and resid 417 through 420 Processing sheet with id=AC7, first strand: chain 'G' and resid 186 through 188 Processing sheet with id=AC8, first strand: chain 'G' and resid 304 through 305 Processing sheet with id=AC9, first strand: chain 'H' and resid 12 through 13 Processing sheet with id=AD1, first strand: chain 'H' and resid 92 through 95 removed outlier: 7.099A pdb=" N SER H 41 " --> pdb=" O THR H 92 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N LYS H 94 " --> pdb=" O SER H 41 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL H 43 " --> pdb=" O LYS H 94 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N GLY H 42 " --> pdb=" O PHE H 140 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE H 142 " --> pdb=" O GLY H 42 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE H 44 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TRP H 139 " --> pdb=" O GLN H 222 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N PHE H 224 " --> pdb=" O TRP H 139 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL H 141 " --> pdb=" O PHE H 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 999 hydrogen bonds defined for protein. 2754 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 87 stacking parallelities Total time for adding SS restraints: 10.87 Time building geometry restraints manager: 8.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.24: 3965 1.24 - 1.38: 8709 1.38 - 1.53: 15872 1.53 - 1.67: 4370 1.67 - 1.81: 148 Bond restraints: 33064 Sorted by residual: bond pdb=" CG PRO D 378 " pdb=" CD PRO D 378 " ideal model delta sigma weight residual 1.503 1.098 0.405 3.40e-02 8.65e+02 1.42e+02 bond pdb=" CG PRO D 76 " pdb=" CD PRO D 76 " ideal model delta sigma weight residual 1.503 1.113 0.390 3.40e-02 8.65e+02 1.31e+02 bond pdb=" CG PRO F 158 " pdb=" CD PRO F 158 " ideal model delta sigma weight residual 1.503 1.151 0.352 3.40e-02 8.65e+02 1.07e+02 bond pdb=" CG PRO D 500 " pdb=" CD PRO D 500 " ideal model delta sigma weight residual 1.503 1.305 0.198 3.40e-02 8.65e+02 3.40e+01 bond pdb=" N PRO D 378 " pdb=" CD PRO D 378 " ideal model delta sigma weight residual 1.473 1.538 -0.065 1.40e-02 5.10e+03 2.14e+01 ... (remaining 33059 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.33: 45141 4.33 - 8.66: 99 8.66 - 12.99: 9 12.99 - 17.33: 4 17.33 - 21.66: 3 Bond angle restraints: 45256 Sorted by residual: angle pdb=" N PRO D 378 " pdb=" CD PRO D 378 " pdb=" CG PRO D 378 " ideal model delta sigma weight residual 103.20 81.54 21.66 1.50e+00 4.44e-01 2.08e+02 angle pdb=" N PRO D 76 " pdb=" CD PRO D 76 " pdb=" CG PRO D 76 " ideal model delta sigma weight residual 103.20 82.69 20.51 1.50e+00 4.44e-01 1.87e+02 angle pdb=" N PRO F 158 " pdb=" CD PRO F 158 " pdb=" CG PRO F 158 " ideal model delta sigma weight residual 103.20 83.55 19.65 1.50e+00 4.44e-01 1.72e+02 angle pdb=" CA PRO D 378 " pdb=" N PRO D 378 " pdb=" CD PRO D 378 " ideal model delta sigma weight residual 112.00 98.26 13.74 1.40e+00 5.10e-01 9.64e+01 angle pdb=" CA PRO D 76 " pdb=" N PRO D 76 " pdb=" CD PRO D 76 " ideal model delta sigma weight residual 112.00 99.32 12.68 1.40e+00 5.10e-01 8.20e+01 ... (remaining 45251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.69: 19247 35.69 - 71.37: 645 71.37 - 107.06: 33 107.06 - 142.74: 8 142.74 - 178.43: 7 Dihedral angle restraints: 19940 sinusoidal: 9432 harmonic: 10508 Sorted by residual: dihedral pdb=" O4' U N 9 " pdb=" C1' U N 9 " pdb=" N1 U N 9 " pdb=" C2 U N 9 " ideal model delta sinusoidal sigma weight residual 200.00 21.57 178.43 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U M 9 " pdb=" C1' U M 9 " pdb=" N1 U M 9 " pdb=" C2 U M 9 " ideal model delta sinusoidal sigma weight residual -160.00 -7.26 -152.74 1 1.50e+01 4.44e-03 8.06e+01 dihedral pdb=" O4' U K 9 " pdb=" C1' U K 9 " pdb=" N1 U K 9 " pdb=" C2 U K 9 " ideal model delta sinusoidal sigma weight residual 200.00 48.79 151.21 1 1.50e+01 4.44e-03 8.01e+01 ... (remaining 19937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 3585 0.038 - 0.076: 1001 0.076 - 0.114: 312 0.114 - 0.152: 64 0.152 - 0.190: 6 Chirality restraints: 4968 Sorted by residual: chirality pdb=" CB ILE G 239 " pdb=" CA ILE G 239 " pdb=" CG1 ILE G 239 " pdb=" CG2 ILE G 239 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.98e-01 chirality pdb=" CA PRO D 427 " pdb=" N PRO D 427 " pdb=" C PRO D 427 " pdb=" CB PRO D 427 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.72e-01 chirality pdb=" CA TYR D 56 " pdb=" N TYR D 56 " pdb=" C TYR D 56 " pdb=" CB TYR D 56 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.33e-01 ... (remaining 4965 not shown) Planarity restraints: 5236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 499 " -0.065 5.00e-02 4.00e+02 9.05e-02 1.31e+01 pdb=" N PRO D 500 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO D 500 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 500 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 254 " -0.019 2.00e-02 2.50e+03 2.26e-02 1.28e+01 pdb=" CG TRP D 254 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP D 254 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP D 254 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 254 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 254 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 254 " -0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 254 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 254 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 254 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU F 157 " -0.063 5.00e-02 4.00e+02 8.89e-02 1.26e+01 pdb=" N PRO F 158 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO F 158 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO F 158 " -0.048 5.00e-02 4.00e+02 ... (remaining 5233 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 631 2.65 - 3.22: 30314 3.22 - 3.78: 52738 3.78 - 4.34: 73379 4.34 - 4.90: 112902 Nonbonded interactions: 269964 Sorted by model distance: nonbonded pdb=" OG SER C 354 " pdb=" O2' U K 8 " model vdw 2.093 3.040 nonbonded pdb=" OH TYR A 416 " pdb=" O THR B 404 " model vdw 2.122 3.040 nonbonded pdb=" OD1 ASN A 151 " pdb=" NE2 GLN A 155 " model vdw 2.131 3.120 nonbonded pdb=" OH TYR C 190 " pdb=" O ALA C 220 " model vdw 2.134 3.040 nonbonded pdb=" OH TYR G 221 " pdb=" O TYR G 233 " model vdw 2.140 3.040 ... (remaining 269959 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'O' selection = chain 'P' } 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 group one per residue 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: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.030 Extract box with map and model: 1.110 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 72.440 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.160 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5954 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 : 0.005 0.405 33064 Z= 0.195 Angle : 0.734 21.656 45256 Z= 0.433 Chirality : 0.040 0.190 4968 Planarity : 0.005 0.091 5236 Dihedral : 16.726 178.426 13148 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.95 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.14), residues: 3532 helix: 0.11 (0.15), residues: 1190 sheet: -1.09 (0.21), residues: 612 loop : -1.13 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP D 254 HIS 0.007 0.001 HIS E 358 PHE 0.031 0.002 PHE E 135 TYR 0.035 0.001 TYR D 56 ARG 0.008 0.001 ARG B 407 Details of bonding type rmsd hydrogen bonds : bond 0.21413 ( 1021) hydrogen bonds : angle 7.98308 ( 2798) covalent geometry : bond 0.00507 (33064) covalent geometry : angle 0.73387 (45256) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 3.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.7500 (mt) cc_final: 0.7210 (mm) REVERT: A 156 GLN cc_start: 0.7743 (mt0) cc_final: 0.7165 (mp10) REVERT: A 210 TYR cc_start: 0.7786 (t80) cc_final: 0.7569 (t80) REVERT: B 118 VAL cc_start: 0.7046 (t) cc_final: 0.6820 (t) REVERT: B 478 VAL cc_start: 0.7524 (p) cc_final: 0.7262 (m) REVERT: C 122 MET cc_start: 0.6943 (tmm) cc_final: 0.6714 (tmm) REVERT: C 162 LYS cc_start: 0.6753 (mptt) cc_final: 0.5963 (mmmt) REVERT: D 290 LYS cc_start: 0.7512 (tptt) cc_final: 0.7130 (tptp) REVERT: E 287 MET cc_start: 0.3500 (tmm) cc_final: 0.3217 (tmm) REVERT: E 305 PHE cc_start: 0.8034 (t80) cc_final: 0.7646 (t80) REVERT: F 390 LYS cc_start: 0.7176 (tmtt) cc_final: 0.6937 (tmtt) REVERT: G 62 LEU cc_start: 0.8220 (tp) cc_final: 0.7976 (tp) REVERT: G 192 TRP cc_start: 0.6359 (p-90) cc_final: 0.5188 (t60) REVERT: G 193 MET cc_start: 0.5917 (mpp) cc_final: 0.3739 (mtt) REVERT: G 393 LEU cc_start: 0.8649 (mt) cc_final: 0.8302 (tp) REVERT: H 86 TRP cc_start: 0.6116 (t60) cc_final: 0.5134 (t60) outliers start: 0 outliers final: 0 residues processed: 422 average time/residue: 0.4357 time to fit residues: 297.3092 Evaluate side-chains 276 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 3.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 20.0000 chunk 272 optimal weight: 7.9990 chunk 151 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 184 optimal weight: 30.0000 chunk 145 optimal weight: 7.9990 chunk 282 optimal weight: 0.5980 chunk 109 optimal weight: 9.9990 chunk 171 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 chunk 326 optimal weight: 5.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN B 135 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 HIS D 446 ASN ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 GLN G 109 ASN ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 ASN H 329 HIS H 349 GLN ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.110952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.094478 restraints weight = 200885.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.095885 restraints weight = 145231.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.096750 restraints weight = 115178.965| |-----------------------------------------------------------------------------| r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6330 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 33064 Z= 0.202 Angle : 0.709 8.607 45256 Z= 0.373 Chirality : 0.044 0.199 4968 Planarity : 0.005 0.060 5236 Dihedral : 17.447 159.006 5860 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.75 % Favored : 93.94 % Rotamer: Outliers : 1.50 % Allowed : 9.17 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.14), residues: 3532 helix: 0.09 (0.15), residues: 1228 sheet: -1.32 (0.21), residues: 602 loop : -1.18 (0.14), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP D 254 HIS 0.012 0.002 HIS E 358 PHE 0.025 0.002 PHE G 223 TYR 0.021 0.002 TYR D 56 ARG 0.010 0.001 ARG E 2 Details of bonding type rmsd hydrogen bonds : bond 0.06000 ( 1021) hydrogen bonds : angle 6.03114 ( 2798) covalent geometry : bond 0.00449 (33064) covalent geometry : angle 0.70887 (45256) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 319 time to evaluate : 3.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 TYR cc_start: 0.7864 (t80) cc_final: 0.7634 (t80) REVERT: B 74 MET cc_start: 0.5424 (tpp) cc_final: 0.4892 (tpp) REVERT: B 118 VAL cc_start: 0.7358 (t) cc_final: 0.7139 (t) REVERT: C 122 MET cc_start: 0.7349 (tmm) cc_final: 0.6941 (tmm) REVERT: C 162 LYS cc_start: 0.6586 (mptt) cc_final: 0.5950 (mmmt) REVERT: C 217 PHE cc_start: 0.6870 (m-80) cc_final: 0.5576 (m-10) REVERT: C 410 PHE cc_start: 0.6509 (m-10) cc_final: 0.5966 (m-80) REVERT: D 435 MET cc_start: -0.0296 (ttp) cc_final: -0.0584 (ttp) REVERT: E 287 MET cc_start: 0.5052 (tmm) cc_final: 0.4584 (tmm) REVERT: E 373 TRP cc_start: 0.5746 (m100) cc_final: 0.5433 (m100) REVERT: F 390 LYS cc_start: 0.7377 (tmtt) cc_final: 0.7163 (tmtt) REVERT: F 435 MET cc_start: 0.6562 (mmm) cc_final: 0.6181 (mmm) REVERT: G 192 TRP cc_start: 0.6315 (p-90) cc_final: 0.5135 (t60) REVERT: G 193 MET cc_start: 0.4968 (mpp) cc_final: 0.4054 (mtt) REVERT: G 393 LEU cc_start: 0.8823 (mt) cc_final: 0.8562 (tp) REVERT: H 86 TRP cc_start: 0.6558 (t60) cc_final: 0.5528 (t60) REVERT: H 106 TYR cc_start: 0.4870 (m-80) cc_final: 0.4646 (m-10) REVERT: H 303 MET cc_start: 0.4970 (ttm) cc_final: 0.4499 (ttt) REVERT: H 429 ILE cc_start: 0.7403 (mm) cc_final: 0.7145 (mp) outliers start: 48 outliers final: 31 residues processed: 338 average time/residue: 0.4309 time to fit residues: 239.2017 Evaluate side-chains 295 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 264 time to evaluate : 3.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 279 CYS Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 454 GLN Chi-restraints excluded: chain E residue 234 HIS Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain G residue 34 CYS Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain H residue 141 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 72 optimal weight: 8.9990 chunk 232 optimal weight: 9.9990 chunk 245 optimal weight: 20.0000 chunk 328 optimal weight: 9.9990 chunk 200 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 chunk 154 optimal weight: 0.1980 chunk 148 optimal weight: 4.9990 chunk 246 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 GLN F 135 ASN F 454 GLN G 109 ASN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 270 ASN ** G 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 135 ASN H 322 ASN ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.108684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.092230 restraints weight = 202785.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.093593 restraints weight = 146382.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.094712 restraints weight = 116448.261| |-----------------------------------------------------------------------------| r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6407 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 33064 Z= 0.184 Angle : 0.672 9.483 45256 Z= 0.354 Chirality : 0.043 0.154 4968 Planarity : 0.005 0.062 5236 Dihedral : 17.632 161.584 5860 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.55 % Favored : 94.14 % Rotamer: Outliers : 2.22 % Allowed : 12.08 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.14), residues: 3532 helix: 0.22 (0.15), residues: 1202 sheet: -1.45 (0.21), residues: 584 loop : -1.23 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 254 HIS 0.012 0.001 HIS G 358 PHE 0.038 0.002 PHE H 373 TYR 0.029 0.002 TYR H 397 ARG 0.009 0.001 ARG G 374 Details of bonding type rmsd hydrogen bonds : bond 0.05331 ( 1021) hydrogen bonds : angle 5.78707 ( 2798) covalent geometry : bond 0.00408 (33064) covalent geometry : angle 0.67159 (45256) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 286 time to evaluate : 3.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 MET cc_start: 0.5837 (tpp) cc_final: 0.5118 (tpp) REVERT: B 118 VAL cc_start: 0.7300 (t) cc_final: 0.7055 (t) REVERT: C 122 MET cc_start: 0.7512 (tmm) cc_final: 0.7126 (tmm) REVERT: C 410 PHE cc_start: 0.6477 (m-10) cc_final: 0.5940 (m-80) REVERT: E 93 PHE cc_start: 0.7072 (t80) cc_final: 0.6537 (t80) REVERT: E 175 TRP cc_start: 0.4996 (m-10) cc_final: 0.4744 (m-10) REVERT: E 257 ARG cc_start: 0.6790 (tpt90) cc_final: 0.6331 (tpt90) REVERT: E 373 TRP cc_start: 0.5827 (m100) cc_final: 0.5616 (m100) REVERT: F 81 VAL cc_start: 0.7588 (m) cc_final: 0.7234 (p) REVERT: G 1 MET cc_start: 0.5810 (ppp) cc_final: 0.5594 (ppp) REVERT: G 393 LEU cc_start: 0.8688 (mt) cc_final: 0.8444 (tp) REVERT: H 86 TRP cc_start: 0.6717 (t60) cc_final: 0.5623 (t60) REVERT: H 106 TYR cc_start: 0.4853 (m-80) cc_final: 0.4634 (m-80) REVERT: H 262 TYR cc_start: 0.7855 (t80) cc_final: 0.7646 (t80) REVERT: H 303 MET cc_start: 0.4581 (ttm) cc_final: 0.4317 (ttm) REVERT: H 489 ILE cc_start: 0.6251 (tp) cc_final: 0.5995 (tp) outliers start: 71 outliers final: 43 residues processed: 327 average time/residue: 0.4181 time to fit residues: 225.7602 Evaluate side-chains 289 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 246 time to evaluate : 3.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 279 CYS Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 234 HIS Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 484 ASP Chi-restraints excluded: chain G residue 34 CYS Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 283 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 347 optimal weight: 9.9990 chunk 275 optimal weight: 10.0000 chunk 186 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 282 optimal weight: 5.9990 chunk 299 optimal weight: 20.0000 chunk 15 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN B 468 ASN C 174 ASN D 293 ASN D 468 ASN ** E 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 ASN ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 HIS ** F 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 ASN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 ASN H 296 ASN ** H 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.103447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.087599 restraints weight = 206416.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.088906 restraints weight = 148527.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.089710 restraints weight = 117976.875| |-----------------------------------------------------------------------------| r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 33064 Z= 0.255 Angle : 0.776 13.224 45256 Z= 0.411 Chirality : 0.046 0.188 4968 Planarity : 0.006 0.065 5236 Dihedral : 17.931 163.305 5860 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 25.82 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.88 % Favored : 92.81 % Rotamer: Outliers : 3.38 % Allowed : 14.46 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.14), residues: 3532 helix: -0.27 (0.14), residues: 1232 sheet: -1.78 (0.21), residues: 554 loop : -1.46 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP G 33 HIS 0.010 0.002 HIS E 188 PHE 0.032 0.003 PHE H 373 TYR 0.027 0.002 TYR H 397 ARG 0.011 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.05931 ( 1021) hydrogen bonds : angle 6.08659 ( 2798) covalent geometry : bond 0.00555 (33064) covalent geometry : angle 0.77553 (45256) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 267 time to evaluate : 3.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8237 (pt0) REVERT: B 118 VAL cc_start: 0.7424 (t) cc_final: 0.7189 (t) REVERT: B 303 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7549 (mmm) REVERT: C 122 MET cc_start: 0.7322 (tmm) cc_final: 0.7024 (tmm) REVERT: C 388 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7356 (p0) REVERT: C 410 PHE cc_start: 0.6605 (m-10) cc_final: 0.6402 (m-10) REVERT: D 137 ASP cc_start: 0.7186 (OUTLIER) cc_final: 0.6623 (t0) REVERT: E 175 TRP cc_start: 0.5361 (m-10) cc_final: 0.4690 (m-10) REVERT: E 257 ARG cc_start: 0.7253 (tpt90) cc_final: 0.6852 (tpt90) REVERT: F 81 VAL cc_start: 0.7785 (m) cc_final: 0.7368 (p) REVERT: F 353 TYR cc_start: 0.6916 (OUTLIER) cc_final: 0.6078 (m-10) REVERT: G 133 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8774 (pt0) REVERT: G 287 MET cc_start: 0.0653 (tpt) cc_final: 0.0405 (tpt) REVERT: G 393 LEU cc_start: 0.8830 (mt) cc_final: 0.8582 (tp) REVERT: H 86 TRP cc_start: 0.7011 (t60) cc_final: 0.5879 (t60) REVERT: H 161 MET cc_start: 0.2108 (mpp) cc_final: 0.1667 (ttm) REVERT: H 243 ARG cc_start: 0.5578 (mtp180) cc_final: 0.4142 (ptp90) outliers start: 108 outliers final: 72 residues processed: 342 average time/residue: 0.4041 time to fit residues: 229.3765 Evaluate side-chains 319 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 242 time to evaluate : 3.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 468 ASN Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 279 CYS Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 454 GLN Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 234 HIS Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 308 THR Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 86 TRP Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain F residue 353 TYR Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 484 ASP Chi-restraints excluded: chain G residue 34 CYS Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 341 GLN Chi-restraints excluded: chain H residue 411 TYR Chi-restraints excluded: chain H residue 426 VAL Chi-restraints excluded: chain H residue 478 VAL Chi-restraints excluded: chain H residue 501 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 106 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 157 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 220 optimal weight: 8.9990 chunk 158 optimal weight: 4.9990 chunk 217 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 286 optimal weight: 5.9990 chunk 272 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 70 GLN A 109 ASN ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 ASN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 HIS D 468 ASN ** E 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 370 ASN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 302 GLN ** H 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.105042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.089090 restraints weight = 202774.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.090482 restraints weight = 145444.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.091458 restraints weight = 114975.912| |-----------------------------------------------------------------------------| r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 33064 Z= 0.167 Angle : 0.666 10.400 45256 Z= 0.349 Chirality : 0.043 0.254 4968 Planarity : 0.005 0.069 5236 Dihedral : 17.836 164.446 5860 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.23 % Favored : 93.49 % Rotamer: Outliers : 3.16 % Allowed : 15.89 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.14), residues: 3532 helix: 0.06 (0.15), residues: 1236 sheet: -1.75 (0.21), residues: 544 loop : -1.38 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 192 HIS 0.012 0.001 HIS G 358 PHE 0.038 0.002 PHE F 121 TYR 0.021 0.002 TYR D 346 ARG 0.010 0.001 ARG E 114 Details of bonding type rmsd hydrogen bonds : bond 0.04831 ( 1021) hydrogen bonds : angle 5.69946 ( 2798) covalent geometry : bond 0.00374 (33064) covalent geometry : angle 0.66612 (45256) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 276 time to evaluate : 3.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 TYR cc_start: 0.7134 (t80) cc_final: 0.6835 (t80) REVERT: A 268 LEU cc_start: 0.7671 (mm) cc_final: 0.7438 (mm) REVERT: B 118 VAL cc_start: 0.7435 (t) cc_final: 0.7171 (t) REVERT: B 303 MET cc_start: 0.7644 (mmm) cc_final: 0.6805 (ttm) REVERT: C 122 MET cc_start: 0.7254 (tmm) cc_final: 0.6769 (tmm) REVERT: C 388 ASP cc_start: 0.7642 (OUTLIER) cc_final: 0.7211 (p0) REVERT: C 410 PHE cc_start: 0.6487 (m-10) cc_final: 0.5937 (m-80) REVERT: D 137 ASP cc_start: 0.7120 (OUTLIER) cc_final: 0.6473 (t0) REVERT: D 398 LYS cc_start: 0.6673 (pttm) cc_final: 0.6059 (tmmt) REVERT: E 93 PHE cc_start: 0.7127 (t80) cc_final: 0.6657 (t80) REVERT: E 257 ARG cc_start: 0.7093 (tpt90) cc_final: 0.6628 (tpt90) REVERT: E 287 MET cc_start: 0.5398 (tmm) cc_final: 0.5173 (tmm) REVERT: F 81 VAL cc_start: 0.7586 (m) cc_final: 0.7202 (p) REVERT: F 101 ILE cc_start: 0.6030 (pp) cc_final: 0.5781 (pp) REVERT: F 353 TYR cc_start: 0.6588 (OUTLIER) cc_final: 0.5953 (m-10) REVERT: G 133 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8794 (pt0) REVERT: G 143 GLU cc_start: 0.8119 (pp20) cc_final: 0.7874 (tp30) REVERT: G 287 MET cc_start: -0.0538 (tpt) cc_final: -0.0825 (tpt) REVERT: G 391 PHE cc_start: 0.8344 (p90) cc_final: 0.8072 (p90) REVERT: G 393 LEU cc_start: 0.8661 (mt) cc_final: 0.8423 (tp) REVERT: H 86 TRP cc_start: 0.6997 (t60) cc_final: 0.6241 (t60) REVERT: H 161 MET cc_start: 0.1932 (mpp) cc_final: 0.1452 (ttt) REVERT: H 243 ARG cc_start: 0.5622 (mtp180) cc_final: 0.4204 (ptp90) REVERT: H 262 TYR cc_start: 0.7915 (t80) cc_final: 0.7488 (t80) REVERT: H 504 LYS cc_start: 0.7596 (mtmt) cc_final: 0.7286 (mtmm) outliers start: 101 outliers final: 68 residues processed: 347 average time/residue: 0.4131 time to fit residues: 235.8762 Evaluate side-chains 322 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 251 time to evaluate : 3.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 416 TYR Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 279 CYS Chi-restraints excluded: chain D residue 299 CYS Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 454 GLN Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 234 HIS Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 321 PHE Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 86 TRP Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 299 CYS Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain F residue 353 TYR Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 484 ASP Chi-restraints excluded: chain G residue 34 CYS Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 67 TYR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 362 ARG Chi-restraints excluded: chain G residue 370 ASN Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 223 ILE Chi-restraints excluded: chain H residue 341 GLN Chi-restraints excluded: chain H residue 411 TYR Chi-restraints excluded: chain H residue 426 VAL Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 478 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 133 optimal weight: 0.8980 chunk 193 optimal weight: 0.9980 chunk 328 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 190 optimal weight: 8.9990 chunk 188 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 chunk 187 optimal weight: 6.9990 chunk 228 optimal weight: 1.9990 chunk 263 optimal weight: 0.6980 chunk 125 optimal weight: 8.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN D 439 ASN ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 ASN ** F 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.106445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.090398 restraints weight = 201912.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.091839 restraints weight = 144541.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.092860 restraints weight = 113848.327| |-----------------------------------------------------------------------------| r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6472 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 33064 Z= 0.135 Angle : 0.638 10.564 45256 Z= 0.331 Chirality : 0.043 0.256 4968 Planarity : 0.005 0.063 5236 Dihedral : 17.732 165.921 5860 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.23 % Favored : 93.49 % Rotamer: Outliers : 2.82 % Allowed : 16.99 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.14), residues: 3532 helix: 0.28 (0.15), residues: 1240 sheet: -1.65 (0.21), residues: 556 loop : -1.29 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 294 HIS 0.011 0.001 HIS G 358 PHE 0.029 0.002 PHE H 373 TYR 0.025 0.001 TYR H 346 ARG 0.009 0.001 ARG E 114 Details of bonding type rmsd hydrogen bonds : bond 0.04503 ( 1021) hydrogen bonds : angle 5.47329 ( 2798) covalent geometry : bond 0.00305 (33064) covalent geometry : angle 0.63757 (45256) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 284 time to evaluate : 3.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 TYR cc_start: 0.7229 (t80) cc_final: 0.6952 (t80) REVERT: A 268 LEU cc_start: 0.7489 (mm) cc_final: 0.7209 (mm) REVERT: B 118 VAL cc_start: 0.7310 (t) cc_final: 0.7051 (t) REVERT: B 303 MET cc_start: 0.7553 (tmm) cc_final: 0.6793 (ttm) REVERT: C 122 MET cc_start: 0.7187 (tmm) cc_final: 0.6720 (tmm) REVERT: C 388 ASP cc_start: 0.7561 (OUTLIER) cc_final: 0.7109 (p0) REVERT: C 410 PHE cc_start: 0.6442 (m-10) cc_final: 0.5872 (m-80) REVERT: D 137 ASP cc_start: 0.7101 (OUTLIER) cc_final: 0.6558 (t0) REVERT: E 93 PHE cc_start: 0.7394 (t80) cc_final: 0.6934 (t80) REVERT: E 257 ARG cc_start: 0.7049 (tpt90) cc_final: 0.6673 (tpt90) REVERT: E 287 MET cc_start: 0.5585 (OUTLIER) cc_final: 0.5378 (tmm) REVERT: F 81 VAL cc_start: 0.7296 (m) cc_final: 0.6968 (p) REVERT: G 133 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8952 (pt0) REVERT: G 143 GLU cc_start: 0.7980 (pp20) cc_final: 0.7695 (tp30) REVERT: G 287 MET cc_start: -0.0716 (tpt) cc_final: -0.1052 (tpt) REVERT: G 391 PHE cc_start: 0.8189 (p90) cc_final: 0.7952 (p90) REVERT: G 393 LEU cc_start: 0.8691 (mt) cc_final: 0.8443 (tp) REVERT: H 86 TRP cc_start: 0.6958 (t60) cc_final: 0.6283 (t60) REVERT: H 106 TYR cc_start: 0.4314 (m-80) cc_final: 0.3839 (m-10) REVERT: H 243 ARG cc_start: 0.5862 (mtp180) cc_final: 0.4465 (ptp90) REVERT: H 262 TYR cc_start: 0.7872 (t80) cc_final: 0.7604 (t80) REVERT: H 484 ASP cc_start: 0.4923 (OUTLIER) cc_final: 0.4406 (t70) outliers start: 90 outliers final: 54 residues processed: 344 average time/residue: 0.4162 time to fit residues: 235.5530 Evaluate side-chains 312 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 254 time to evaluate : 3.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 416 TYR Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 279 CYS Chi-restraints excluded: chain D residue 299 CYS Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 234 HIS Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 321 PHE Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 86 TRP Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 299 CYS Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain G residue 67 TYR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 341 GLN Chi-restraints excluded: chain H residue 411 TYR Chi-restraints excluded: chain H residue 426 VAL Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 484 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 245 optimal weight: 20.0000 chunk 141 optimal weight: 9.9990 chunk 358 optimal weight: 10.0000 chunk 143 optimal weight: 7.9990 chunk 260 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 356 optimal weight: 20.0000 chunk 136 optimal weight: 8.9990 chunk 299 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN B 16 HIS ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 HIS B 360 HIS ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 ASN D 59 HIS ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 318 ASN ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 HIS F 382 ASN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 370 ASN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 ASN ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 430 GLN ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.100245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.084024 restraints weight = 200290.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.085205 restraints weight = 150238.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.085922 restraints weight = 122958.239| |-----------------------------------------------------------------------------| r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 33064 Z= 0.248 Angle : 0.778 10.991 45256 Z= 0.411 Chirality : 0.047 0.273 4968 Planarity : 0.006 0.068 5236 Dihedral : 18.008 166.223 5860 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 26.93 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.98 % Favored : 91.79 % Rotamer: Outliers : 3.69 % Allowed : 17.40 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.14), residues: 3532 helix: -0.15 (0.14), residues: 1228 sheet: -2.03 (0.20), residues: 578 loop : -1.54 (0.15), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 175 HIS 0.011 0.002 HIS G 358 PHE 0.028 0.003 PHE H 373 TYR 0.028 0.002 TYR C 293 ARG 0.011 0.001 ARG E 263 Details of bonding type rmsd hydrogen bonds : bond 0.05693 ( 1021) hydrogen bonds : angle 6.03756 ( 2798) covalent geometry : bond 0.00548 (33064) covalent geometry : angle 0.77849 (45256) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 252 time to evaluate : 3.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 LEU cc_start: 0.7610 (mm) cc_final: 0.7355 (mm) REVERT: A 336 MET cc_start: 0.6729 (mmp) cc_final: 0.6511 (mmp) REVERT: B 118 VAL cc_start: 0.7374 (t) cc_final: 0.7131 (t) REVERT: B 303 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.7185 (ttm) REVERT: B 331 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.5891 (mm-30) REVERT: C 122 MET cc_start: 0.7316 (tmm) cc_final: 0.6816 (tmm) REVERT: C 185 LEU cc_start: 0.8725 (tt) cc_final: 0.8487 (tp) REVERT: C 217 PHE cc_start: 0.7334 (OUTLIER) cc_final: 0.5390 (m-10) REVERT: C 388 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.7365 (p0) REVERT: D 398 LYS cc_start: 0.6977 (pttm) cc_final: 0.6412 (tmmt) REVERT: E 175 TRP cc_start: 0.5163 (m-10) cc_final: 0.4667 (m-10) REVERT: E 287 MET cc_start: 0.5800 (OUTLIER) cc_final: 0.5486 (tmm) REVERT: E 321 PHE cc_start: 0.1112 (OUTLIER) cc_final: 0.0784 (t80) REVERT: E 336 MET cc_start: 0.7205 (mpp) cc_final: 0.6903 (mpp) REVERT: E 395 MET cc_start: 0.7097 (tmm) cc_final: 0.6833 (ppp) REVERT: F 81 VAL cc_start: 0.7409 (m) cc_final: 0.6988 (p) REVERT: F 86 TRP cc_start: 0.6584 (OUTLIER) cc_final: 0.6245 (t60) REVERT: F 249 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8146 (mt-10) REVERT: F 405 ILE cc_start: 0.6622 (OUTLIER) cc_final: 0.6201 (mm) REVERT: G 287 MET cc_start: -0.0945 (tpt) cc_final: -0.1269 (tpt) REVERT: H 86 TRP cc_start: 0.7102 (t60) cc_final: 0.6337 (t60) REVERT: H 161 MET cc_start: 0.2117 (mpp) cc_final: 0.1688 (ttm) REVERT: H 435 MET cc_start: 0.4860 (tmm) cc_final: 0.0468 (ptp) REVERT: H 504 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.7064 (mtmm) outliers start: 118 outliers final: 87 residues processed: 330 average time/residue: 0.4245 time to fit residues: 230.8297 Evaluate side-chains 333 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 236 time to evaluate : 3.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TRP Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain C residue 416 TYR Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 65 TYR Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 279 CYS Chi-restraints excluded: chain D residue 299 CYS Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 234 HIS Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 321 PHE Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 86 TRP Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 299 CYS Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 484 ASP Chi-restraints excluded: chain G residue 34 CYS Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 67 TYR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 278 LYS Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 223 ILE Chi-restraints excluded: chain H residue 316 GLU Chi-restraints excluded: chain H residue 341 GLN Chi-restraints excluded: chain H residue 411 TYR Chi-restraints excluded: chain H residue 426 VAL Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 430 GLN Chi-restraints excluded: chain H residue 459 ILE Chi-restraints excluded: chain H residue 478 VAL Chi-restraints excluded: chain H residue 504 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 313 optimal weight: 0.9980 chunk 291 optimal weight: 0.0000 chunk 178 optimal weight: 20.0000 chunk 242 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 126 optimal weight: 9.9990 chunk 195 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 269 optimal weight: 0.8980 chunk 260 optimal weight: 2.9990 chunk 344 optimal weight: 4.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 191 ASN A 314 GLN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 382 ASN ** G 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 446 ASN ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.105509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.089776 restraints weight = 203007.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.091137 restraints weight = 145121.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.091975 restraints weight = 112966.825| |-----------------------------------------------------------------------------| r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 moved from start: 0.5212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 33064 Z= 0.135 Angle : 0.671 15.120 45256 Z= 0.345 Chirality : 0.044 0.251 4968 Planarity : 0.005 0.131 5236 Dihedral : 17.870 170.389 5860 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.78 % Favored : 94.00 % Rotamer: Outliers : 2.41 % Allowed : 19.18 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.14), residues: 3532 helix: 0.29 (0.15), residues: 1234 sheet: -1.78 (0.21), residues: 526 loop : -1.42 (0.15), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 175 HIS 0.010 0.001 HIS G 358 PHE 0.026 0.002 PHE C 17 TYR 0.034 0.001 TYR H 106 ARG 0.010 0.001 ARG E 114 Details of bonding type rmsd hydrogen bonds : bond 0.04350 ( 1021) hydrogen bonds : angle 5.47326 ( 2798) covalent geometry : bond 0.00298 (33064) covalent geometry : angle 0.67117 (45256) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 273 time to evaluate : 3.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 LEU cc_start: 0.7658 (mm) cc_final: 0.7362 (mm) REVERT: A 336 MET cc_start: 0.6558 (mmp) cc_final: 0.6165 (mmp) REVERT: B 118 VAL cc_start: 0.7260 (t) cc_final: 0.6981 (t) REVERT: B 303 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.6874 (ttm) REVERT: B 503 PHE cc_start: 0.6444 (m-10) cc_final: 0.6146 (m-80) REVERT: C 122 MET cc_start: 0.7039 (tmm) cc_final: 0.6627 (tmm) REVERT: C 185 LEU cc_start: 0.8562 (tt) cc_final: 0.8302 (tp) REVERT: C 217 PHE cc_start: 0.7127 (OUTLIER) cc_final: 0.5302 (m-10) REVERT: C 388 ASP cc_start: 0.7526 (OUTLIER) cc_final: 0.7164 (p0) REVERT: C 410 PHE cc_start: 0.6472 (m-10) cc_final: 0.6013 (m-10) REVERT: C 411 LYS cc_start: 0.6761 (pttp) cc_final: 0.6420 (pttm) REVERT: D 74 MET cc_start: 0.6722 (tpp) cc_final: 0.6513 (tpt) REVERT: D 398 LYS cc_start: 0.6809 (pttm) cc_final: 0.6278 (tmmt) REVERT: E 93 PHE cc_start: 0.7455 (t80) cc_final: 0.6982 (t80) REVERT: E 257 ARG cc_start: 0.7001 (tpt90) cc_final: 0.6767 (tpt90) REVERT: E 287 MET cc_start: 0.5845 (OUTLIER) cc_final: 0.5602 (tmm) REVERT: F 81 VAL cc_start: 0.7001 (m) cc_final: 0.6660 (p) REVERT: G 287 MET cc_start: -0.1184 (tpt) cc_final: -0.1537 (tpt) REVERT: G 393 LEU cc_start: 0.8741 (mt) cc_final: 0.8499 (tp) REVERT: H 86 TRP cc_start: 0.6898 (t60) cc_final: 0.6241 (t60) REVERT: H 262 TYR cc_start: 0.7944 (t80) cc_final: 0.7432 (t80) REVERT: H 435 MET cc_start: 0.4755 (tmm) cc_final: 0.0601 (ptp) outliers start: 77 outliers final: 56 residues processed: 324 average time/residue: 0.4999 time to fit residues: 267.7222 Evaluate side-chains 309 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 249 time to evaluate : 5.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 416 TYR Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 65 TYR Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 279 CYS Chi-restraints excluded: chain D residue 299 CYS Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 447 LYS Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 234 HIS Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 308 THR Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 86 TRP Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 299 CYS Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 67 TYR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 340 HIS Chi-restraints excluded: chain G residue 395 MET Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 341 GLN Chi-restraints excluded: chain H residue 411 TYR Chi-restraints excluded: chain H residue 426 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 248 optimal weight: 9.9990 chunk 339 optimal weight: 20.0000 chunk 228 optimal weight: 5.9990 chunk 300 optimal weight: 30.0000 chunk 125 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 219 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 258 optimal weight: 30.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 HIS ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 HIS ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 HIS ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 370 ASN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 302 GLN H 430 GLN ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.100919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.084876 restraints weight = 198421.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.086064 restraints weight = 148874.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.086804 restraints weight = 121480.480| |-----------------------------------------------------------------------------| r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.5662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 33064 Z= 0.214 Angle : 0.735 13.800 45256 Z= 0.384 Chirality : 0.045 0.269 4968 Planarity : 0.005 0.065 5236 Dihedral : 17.980 169.667 5860 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 24.06 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.64 % Favored : 92.13 % Rotamer: Outliers : 2.91 % Allowed : 19.37 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.14), residues: 3532 helix: 0.06 (0.15), residues: 1228 sheet: -2.08 (0.21), residues: 546 loop : -1.52 (0.15), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 369 HIS 0.009 0.002 HIS G 358 PHE 0.026 0.002 PHE H 373 TYR 0.038 0.002 TYR D 321 ARG 0.025 0.001 ARG D 295 Details of bonding type rmsd hydrogen bonds : bond 0.05092 ( 1021) hydrogen bonds : angle 5.80798 ( 2798) covalent geometry : bond 0.00474 (33064) covalent geometry : angle 0.73494 (45256) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 244 time to evaluate : 3.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 LEU cc_start: 0.7687 (mm) cc_final: 0.7403 (mm) REVERT: A 336 MET cc_start: 0.6516 (mmp) cc_final: 0.6057 (mmp) REVERT: B 118 VAL cc_start: 0.7370 (t) cc_final: 0.7136 (t) REVERT: B 219 ILE cc_start: 0.7094 (mt) cc_final: 0.6555 (mt) REVERT: B 303 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7272 (ttm) REVERT: C 19 ARG cc_start: 0.7249 (ptp90) cc_final: 0.7038 (ptp90) REVERT: C 122 MET cc_start: 0.7229 (tmm) cc_final: 0.6691 (tmm) REVERT: C 185 LEU cc_start: 0.8693 (tt) cc_final: 0.8483 (tp) REVERT: C 217 PHE cc_start: 0.7252 (OUTLIER) cc_final: 0.5379 (m-10) REVERT: C 388 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.7402 (p0) REVERT: C 410 PHE cc_start: 0.6708 (m-10) cc_final: 0.6373 (m-10) REVERT: E 287 MET cc_start: 0.5983 (OUTLIER) cc_final: 0.5659 (tmm) REVERT: E 321 PHE cc_start: 0.0289 (OUTLIER) cc_final: 0.0034 (t80) REVERT: E 336 MET cc_start: 0.7269 (mpp) cc_final: 0.6667 (mpp) REVERT: F 86 TRP cc_start: 0.6503 (OUTLIER) cc_final: 0.6169 (t60) REVERT: F 405 ILE cc_start: 0.6461 (OUTLIER) cc_final: 0.6059 (mm) REVERT: G 287 MET cc_start: -0.1336 (tpt) cc_final: -0.1559 (tpt) REVERT: G 393 LEU cc_start: 0.8714 (mt) cc_final: 0.8418 (pt) REVERT: H 86 TRP cc_start: 0.6998 (t60) cc_final: 0.6262 (t60) REVERT: H 243 ARG cc_start: 0.6201 (mtp180) cc_final: 0.4569 (mtm-85) REVERT: H 435 MET cc_start: 0.4729 (tmm) cc_final: 0.0653 (ptp) outliers start: 93 outliers final: 74 residues processed: 308 average time/residue: 0.4133 time to fit residues: 210.8306 Evaluate side-chains 314 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 233 time to evaluate : 3.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TRP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 416 TYR Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 65 TYR Chi-restraints excluded: chain D residue 279 CYS Chi-restraints excluded: chain D residue 299 CYS Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 447 LYS Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 234 HIS Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 308 THR Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 321 PHE Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 86 TRP Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 299 CYS Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain G residue 67 TYR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 223 ILE Chi-restraints excluded: chain H residue 341 GLN Chi-restraints excluded: chain H residue 411 TYR Chi-restraints excluded: chain H residue 426 VAL Chi-restraints excluded: chain H residue 430 GLN Chi-restraints excluded: chain H residue 478 VAL Chi-restraints excluded: chain H residue 484 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 302 optimal weight: 20.0000 chunk 206 optimal weight: 6.9990 chunk 182 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 234 optimal weight: 5.9990 chunk 16 optimal weight: 30.0000 chunk 79 optimal weight: 9.9990 chunk 345 optimal weight: 7.9990 chunk 205 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 HIS ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 430 GLN ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.101374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.085502 restraints weight = 198012.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.086565 restraints weight = 150489.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.087323 restraints weight = 121395.991| |-----------------------------------------------------------------------------| r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.5866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 33064 Z= 0.184 Angle : 0.716 14.056 45256 Z= 0.372 Chirality : 0.045 0.267 4968 Planarity : 0.005 0.065 5236 Dihedral : 18.075 172.534 5860 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 22.35 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.16 % Favored : 92.64 % Rotamer: Outliers : 2.78 % Allowed : 19.49 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.14), residues: 3532 helix: 0.07 (0.15), residues: 1230 sheet: -2.14 (0.21), residues: 546 loop : -1.53 (0.15), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 175 HIS 0.011 0.002 HIS G 358 PHE 0.028 0.002 PHE C 17 TYR 0.027 0.002 TYR H 106 ARG 0.011 0.001 ARG E 114 Details of bonding type rmsd hydrogen bonds : bond 0.04740 ( 1021) hydrogen bonds : angle 5.72913 ( 2798) covalent geometry : bond 0.00411 (33064) covalent geometry : angle 0.71624 (45256) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 247 time to evaluate : 3.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 LEU cc_start: 0.7753 (mm) cc_final: 0.7464 (mm) REVERT: A 336 MET cc_start: 0.6393 (mmp) cc_final: 0.5865 (mmp) REVERT: B 25 ASP cc_start: 0.7437 (m-30) cc_final: 0.7227 (m-30) REVERT: B 118 VAL cc_start: 0.7276 (t) cc_final: 0.7057 (t) REVERT: B 219 ILE cc_start: 0.7015 (mt) cc_final: 0.6467 (mt) REVERT: B 303 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7219 (ttm) REVERT: B 435 MET cc_start: 0.1208 (mmt) cc_final: 0.0696 (ttp) REVERT: C 122 MET cc_start: 0.7078 (tmm) cc_final: 0.6646 (tmm) REVERT: C 217 PHE cc_start: 0.7248 (OUTLIER) cc_final: 0.5389 (m-10) REVERT: C 388 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.7391 (p0) REVERT: C 410 PHE cc_start: 0.6697 (m-10) cc_final: 0.6404 (m-10) REVERT: E 257 ARG cc_start: 0.7129 (tpt90) cc_final: 0.6845 (tpt90) REVERT: E 287 MET cc_start: 0.5929 (OUTLIER) cc_final: 0.5667 (tmm) REVERT: E 321 PHE cc_start: 0.0402 (OUTLIER) cc_final: 0.0102 (t80) REVERT: E 336 MET cc_start: 0.7321 (mpp) cc_final: 0.6677 (mpp) REVERT: F 81 VAL cc_start: 0.6801 (m) cc_final: 0.6498 (p) REVERT: F 86 TRP cc_start: 0.6561 (OUTLIER) cc_final: 0.6162 (t60) REVERT: F 405 ILE cc_start: 0.6365 (OUTLIER) cc_final: 0.5961 (mm) REVERT: H 86 TRP cc_start: 0.6941 (t60) cc_final: 0.6267 (t60) REVERT: H 243 ARG cc_start: 0.6346 (mtp180) cc_final: 0.4730 (mtm-85) REVERT: H 313 PHE cc_start: 0.7086 (OUTLIER) cc_final: 0.6731 (p90) outliers start: 89 outliers final: 71 residues processed: 306 average time/residue: 0.4459 time to fit residues: 224.5797 Evaluate side-chains 311 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 232 time to evaluate : 3.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TRP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 416 TYR Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 65 TYR Chi-restraints excluded: chain D residue 279 CYS Chi-restraints excluded: chain D residue 299 CYS Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 447 LYS Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 234 HIS Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 308 THR Chi-restraints excluded: chain E residue 321 PHE Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 86 TRP Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 299 CYS Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain G residue 67 TYR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 313 PHE Chi-restraints excluded: chain H residue 411 TYR Chi-restraints excluded: chain H residue 426 VAL Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 430 GLN Chi-restraints excluded: chain H residue 478 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 30.0000 chunk 136 optimal weight: 6.9990 chunk 277 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 217 optimal weight: 9.9990 chunk 344 optimal weight: 0.4980 chunk 46 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 307 optimal weight: 5.9990 chunk 311 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 GLN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 HIS F 382 ASN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 430 GLN ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.102441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.087328 restraints weight = 206922.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.088573 restraints weight = 150711.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.089305 restraints weight = 120561.190| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.6039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 33064 Z= 0.178 Angle : 0.716 13.917 45256 Z= 0.371 Chirality : 0.045 0.261 4968 Planarity : 0.005 0.065 5236 Dihedral : 18.127 173.109 5860 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 22.10 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.84 % Favored : 91.96 % Rotamer: Outliers : 2.78 % Allowed : 19.65 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.14), residues: 3532 helix: 0.08 (0.15), residues: 1230 sheet: -2.20 (0.21), residues: 544 loop : -1.53 (0.15), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 175 HIS 0.010 0.001 HIS G 358 PHE 0.031 0.002 PHE G 158 TYR 0.027 0.002 TYR H 106 ARG 0.012 0.001 ARG D 407 Details of bonding type rmsd hydrogen bonds : bond 0.04714 ( 1021) hydrogen bonds : angle 5.72308 ( 2798) covalent geometry : bond 0.00398 (33064) covalent geometry : angle 0.71554 (45256) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11271.54 seconds wall clock time: 199 minutes 41.08 seconds (11981.08 seconds total)