Starting phenix.real_space_refine on Tue Aug 26 03:15:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oz6_17299/08_2025/8oz6_17299.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oz6_17299/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8oz6_17299/08_2025/8oz6_17299.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oz6_17299/08_2025/8oz6_17299.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8oz6_17299/08_2025/8oz6_17299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oz6_17299/08_2025/8oz6_17299.map" } resolution = 3.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 8.92, per 1000 atoms: 0.28 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: 2.93 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 4.16 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: 6.47 Time building geometry restraints manager: 4.05 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: 0.01 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: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.050 Extract box with map and model: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 35.550 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.480 ------------------------------------------------------------------------------- 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 : 14.93 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.001 ARG B 407 TYR 0.035 0.001 TYR D 56 PHE 0.031 0.002 PHE E 135 TRP 0.060 0.002 TRP D 254 HIS 0.007 0.001 HIS E 358 Details of bonding type rmsd covalent geometry : bond 0.00507 (33064) covalent geometry : angle 0.73387 (45256) hydrogen bonds : bond 0.21413 ( 1021) hydrogen bonds : angle 7.98308 ( 2798) *********************** 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 : 1.375 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: A 112 ILE cc_start: 0.7500 (mt) cc_final: 0.7209 (mm) REVERT: A 210 TYR cc_start: 0.7786 (t80) cc_final: 0.7570 (t80) REVERT: B 118 VAL cc_start: 0.7046 (t) cc_final: 0.6819 (t) REVERT: B 478 VAL cc_start: 0.7524 (p) cc_final: 0.7266 (m) REVERT: C 122 MET cc_start: 0.6943 (tmm) cc_final: 0.6717 (tmm) REVERT: C 162 LYS cc_start: 0.6753 (mptt) cc_final: 0.5962 (mmmt) REVERT: D 290 LYS cc_start: 0.7512 (tptt) cc_final: 0.7129 (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: 0.7645 (t80) REVERT: F 390 LYS cc_start: 0.7176 (tmtt) cc_final: 0.6936 (tmtt) REVERT: G 62 LEU cc_start: 0.8220 (tp) cc_final: 0.7975 (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: 0.3738 (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: 0.2153 time to fit residues: 147.3480 Evaluate side-chains 273 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 50.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 0.0470 overall best weight: 4.5484 ------------------------------------------------------------------------------- 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 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 ASN A 267 GLN B 18 GLN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS D 18 GLN 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 H 129 ASN H 329 HIS H 349 GLN H 468 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.110490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.093986 restraints weight = 202444.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.095386 restraints weight = 146238.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.096246 restraints weight = 115922.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.096962 restraints weight = 99358.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 65)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.097564 restraints weight = 88847.255| |-----------------------------------------------------------------------------| r_work (final): 0.4223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6302 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 33064 Z= 0.211 Angle : 0.718 8.777 45256 Z= 0.378 Chirality : 0.044 0.188 4968 Planarity : 0.005 0.061 5236 Dihedral : 17.450 159.072 5860 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.75 % Favored : 93.94 % Rotamer: Outliers : 1.47 % Allowed : 9.23 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.14), residues: 3532 helix: 0.05 (0.15), residues: 1228 sheet: -1.40 (0.21), residues: 606 loop : -1.18 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 2 TYR 0.021 0.002 TYR D 56 PHE 0.026 0.003 PHE H 373 TRP 0.067 0.002 TRP D 254 HIS 0.013 0.002 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00474 (33064) covalent geometry : angle 0.71798 (45256) hydrogen bonds : bond 0.06082 ( 1021) hydrogen bonds : angle 6.08786 ( 2798) *********************** 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 361 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 314 time to evaluate : 1.243 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: 0.7880 (t80) cc_final: 0.7654 (t80) REVERT: B 74 MET cc_start: 0.5433 (tpp) cc_final: 0.4900 (tpp) REVERT: B 118 VAL cc_start: 0.7441 (t) cc_final: 0.7230 (t) REVERT: C 122 MET cc_start: 0.7281 (tmm) cc_final: 0.6874 (tmm) REVERT: C 162 LYS cc_start: 0.6638 (mptt) cc_final: 0.5980 (mmmt) REVERT: C 395 MET cc_start: 0.5801 (OUTLIER) cc_final: 0.5234 (ppp) REVERT: C 410 PHE cc_start: 0.6474 (m-10) cc_final: 0.5950 (m-80) REVERT: D 290 LYS cc_start: 0.7791 (tptt) cc_final: 0.7148 (tptp) REVERT: D 435 MET cc_start: -0.0236 (ttp) cc_final: -0.0533 (ttp) REVERT: E 287 MET cc_start: 0.5096 (tmm) cc_final: 0.4597 (tmm) REVERT: E 373 TRP cc_start: 0.5802 (m100) cc_final: 0.5459 (m100) REVERT: F 272 SER cc_start: 0.4883 (p) cc_final: 0.4667 (t) REVERT: F 435 MET cc_start: 0.6585 (mmm) cc_final: 0.6207 (mmm) REVERT: G 192 TRP cc_start: 0.6225 (p-90) cc_final: 0.5077 (t60) REVERT: G 193 MET cc_start: 0.4995 (mpp) cc_final: 0.4331 (mtt) REVERT: G 393 LEU cc_start: 0.8641 (mt) cc_final: 0.8405 (tp) REVERT: H 86 TRP cc_start: 0.6526 (t60) cc_final: 0.5483 (t60) REVERT: H 106 TYR cc_start: 0.4797 (m-80) cc_final: 0.4544 (m-10) REVERT: H 303 MET cc_start: 0.5039 (ttm) cc_final: 0.4568 (ttt) outliers start: 47 outliers final: 29 residues processed: 337 average time/residue: 0.2074 time to fit residues: 115.0824 Evaluate side-chains 289 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 259 time to evaluate : 1.251 ------------------------------------------------------------------------------- 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 C residue 395 MET 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 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 97 THR 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 304 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 28 optimal weight: 0.0980 chunk 305 optimal weight: 10.0000 chunk 150 optimal weight: 8.9990 chunk 232 optimal weight: 9.9990 chunk 230 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 112 optimal weight: 30.0000 chunk 153 optimal weight: 9.9990 chunk 319 optimal weight: 20.0000 overall best weight: 4.2188 ------------------------------------------------------------------------------- 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 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 ASN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 GLN F 409 ASN G 109 ASN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 322 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.108108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.091776 restraints weight = 203293.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.093243 restraints weight = 146230.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.094255 restraints weight = 115933.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.094816 restraints weight = 98328.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.095073 restraints weight = 88482.890| |-----------------------------------------------------------------------------| r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6406 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 33064 Z= 0.199 Angle : 0.684 9.878 45256 Z= 0.361 Chirality : 0.044 0.152 4968 Planarity : 0.005 0.061 5236 Dihedral : 17.646 160.887 5860 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.80 % Favored : 93.88 % Rotamer: Outliers : 2.32 % Allowed : 12.20 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.14), residues: 3532 helix: 0.10 (0.15), residues: 1230 sheet: -1.53 (0.21), residues: 570 loop : -1.28 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 19 TYR 0.029 0.002 TYR H 397 PHE 0.038 0.002 PHE H 373 TRP 0.034 0.002 TRP D 254 HIS 0.011 0.001 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00433 (33064) covalent geometry : angle 0.68429 (45256) hydrogen bonds : bond 0.05425 ( 1021) hydrogen bonds : angle 5.88751 ( 2798) *********************** 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 358 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 284 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 MET cc_start: 0.5847 (tpp) cc_final: 0.5141 (tpp) REVERT: B 118 VAL cc_start: 0.7346 (t) cc_final: 0.7104 (t) REVERT: B 303 MET cc_start: 0.7604 (mmm) cc_final: 0.7394 (mmm) REVERT: C 122 MET cc_start: 0.7550 (tmm) cc_final: 0.7137 (tmm) REVERT: C 395 MET cc_start: 0.5728 (OUTLIER) cc_final: 0.5246 (tmm) REVERT: C 410 PHE cc_start: 0.6463 (m-10) cc_final: 0.5923 (m-80) REVERT: D 290 LYS cc_start: 0.7906 (tptt) cc_final: 0.7227 (tptp) REVERT: D 398 LYS cc_start: 0.6718 (pttt) cc_final: 0.6203 (pptt) REVERT: E 93 PHE cc_start: 0.6980 (t80) cc_final: 0.6480 (t80) REVERT: E 175 TRP cc_start: 0.5089 (m-10) cc_final: 0.4643 (m-10) REVERT: E 257 ARG cc_start: 0.7087 (tpt90) cc_final: 0.6588 (tpt90) REVERT: F 81 VAL cc_start: 0.7620 (m) cc_final: 0.7243 (p) REVERT: G 1 MET cc_start: 0.5847 (ppp) cc_final: 0.5621 (ppp) REVERT: G 393 LEU cc_start: 0.8666 (mt) cc_final: 0.8442 (tp) REVERT: H 86 TRP cc_start: 0.6645 (t60) cc_final: 0.5481 (t60) REVERT: H 106 TYR cc_start: 0.4836 (m-80) cc_final: 0.4632 (m-80) REVERT: H 262 TYR cc_start: 0.7892 (t80) cc_final: 0.7595 (t80) REVERT: H 303 MET cc_start: 0.4682 (ttm) cc_final: 0.4440 (ttm) REVERT: H 504 LYS cc_start: 0.7338 (mtmt) cc_final: 0.6880 (mtmm) outliers start: 74 outliers final: 45 residues processed: 329 average time/residue: 0.1823 time to fit residues: 99.1398 Evaluate side-chains 298 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 252 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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 309 MET 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 C residue 273 PHE Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain D residue 56 TYR 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 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 86 TRP 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 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 G residue 34 CYS Chi-restraints excluded: chain G residue 56 ASP 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 107 optimal weight: 9.9990 chunk 299 optimal weight: 10.0000 chunk 258 optimal weight: 10.0000 chunk 310 optimal weight: 1.9990 chunk 146 optimal weight: 0.0050 chunk 152 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 235 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 87 optimal weight: 0.0670 chunk 138 optimal weight: 4.9990 overall best weight: 2.6138 ------------------------------------------------------------------------------- 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 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN B 409 ASN D 322 ASN E 116 ASN ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 135 ASN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.108555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.092261 restraints weight = 201564.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.093696 restraints weight = 144939.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.094649 restraints weight = 115002.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.095407 restraints weight = 97814.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.095819 restraints weight = 87097.920| |-----------------------------------------------------------------------------| r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6371 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33064 Z= 0.147 Angle : 0.633 12.042 45256 Z= 0.330 Chirality : 0.042 0.168 4968 Planarity : 0.005 0.063 5236 Dihedral : 17.611 162.447 5860 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.69 % Favored : 94.00 % Rotamer: Outliers : 2.22 % Allowed : 13.86 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.14), residues: 3532 helix: 0.29 (0.15), residues: 1236 sheet: -1.52 (0.21), residues: 582 loop : -1.23 (0.15), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 114 TYR 0.020 0.001 TYR H 397 PHE 0.035 0.002 PHE H 373 TRP 0.034 0.002 TRP H 370 HIS 0.011 0.001 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00328 (33064) covalent geometry : angle 0.63252 (45256) hydrogen bonds : bond 0.04718 ( 1021) hydrogen bonds : angle 5.57147 ( 2798) *********************** 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 353 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 282 time to evaluate : 1.167 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: A 395 MET cc_start: 0.1069 (pmm) cc_final: 0.0827 (pmm) REVERT: B 118 VAL cc_start: 0.7292 (t) cc_final: 0.7027 (t) REVERT: C 122 MET cc_start: 0.7456 (tmm) cc_final: 0.7065 (tmm) REVERT: C 388 ASP cc_start: 0.7187 (m-30) cc_final: 0.6688 (p0) REVERT: C 395 MET cc_start: 0.5697 (OUTLIER) cc_final: 0.5143 (tmm) REVERT: C 410 PHE cc_start: 0.6338 (m-10) cc_final: 0.5953 (m-80) REVERT: D 137 ASP cc_start: 0.7110 (OUTLIER) cc_final: 0.6605 (t0) REVERT: D 290 LYS cc_start: 0.7932 (tptt) cc_final: 0.7268 (tptp) REVERT: E 93 PHE cc_start: 0.6992 (t80) cc_final: 0.6387 (t80) REVERT: E 175 TRP cc_start: 0.5042 (m-10) cc_final: 0.4458 (m-10) REVERT: F 81 VAL cc_start: 0.7647 (m) cc_final: 0.7213 (p) REVERT: G 393 LEU cc_start: 0.8648 (mt) cc_final: 0.8410 (tp) REVERT: H 86 TRP cc_start: 0.6783 (t60) cc_final: 0.5773 (t60) REVERT: H 262 TYR cc_start: 0.7973 (t80) cc_final: 0.7692 (t80) REVERT: H 303 MET cc_start: 0.4316 (ttm) cc_final: 0.4021 (ttm) REVERT: H 504 LYS cc_start: 0.7400 (mtmt) cc_final: 0.6795 (mtmm) outliers start: 71 outliers final: 50 residues processed: 325 average time/residue: 0.1911 time to fit residues: 103.0883 Evaluate side-chains 304 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 252 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 153 LEU 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 278 VAL 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 266 VAL Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 416 TYR 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 350 ILE Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 454 GLN 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 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 405 ILE Chi-restraints excluded: chain F residue 455 VAL 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 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 478 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 287 optimal weight: 2.9990 chunk 233 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 281 optimal weight: 8.9990 chunk 78 optimal weight: 8.9990 chunk 59 optimal weight: 0.8980 chunk 337 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 190 optimal weight: 9.9990 chunk 191 optimal weight: 5.9990 chunk 336 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN D 293 ASN ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 HIS ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 454 GLN ** G 138 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.107737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.091495 restraints weight = 201366.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.092926 restraints weight = 144279.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.093763 restraints weight = 114113.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.094577 restraints weight = 97640.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.094981 restraints weight = 86723.566| |-----------------------------------------------------------------------------| r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6404 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 33064 Z= 0.147 Angle : 0.635 16.061 45256 Z= 0.329 Chirality : 0.042 0.174 4968 Planarity : 0.005 0.076 5236 Dihedral : 17.620 163.947 5860 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.78 % Favored : 93.94 % Rotamer: Outliers : 2.91 % Allowed : 14.80 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.14), residues: 3532 helix: 0.48 (0.15), residues: 1210 sheet: -1.59 (0.21), residues: 592 loop : -1.19 (0.15), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 114 TYR 0.019 0.001 TYR D 56 PHE 0.028 0.002 PHE A 17 TRP 0.030 0.002 TRP G 33 HIS 0.009 0.001 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00329 (33064) covalent geometry : angle 0.63492 (45256) hydrogen bonds : bond 0.04638 ( 1021) hydrogen bonds : angle 5.44606 ( 2798) *********************** 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 372 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 279 time to evaluate : 1.150 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: A 210 TYR cc_start: 0.7204 (t80) cc_final: 0.6916 (t80) REVERT: A 268 LEU cc_start: 0.7416 (mm) cc_final: 0.7176 (mm) REVERT: B 118 VAL cc_start: 0.7381 (t) cc_final: 0.7137 (t) REVERT: B 303 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.7011 (ttm) REVERT: C 122 MET cc_start: 0.7454 (tmm) cc_final: 0.6935 (tmm) REVERT: C 388 ASP cc_start: 0.7410 (OUTLIER) cc_final: 0.6929 (p0) REVERT: C 395 MET cc_start: 0.5955 (OUTLIER) cc_final: 0.5405 (tmm) REVERT: C 410 PHE cc_start: 0.6366 (m-10) cc_final: 0.5983 (m-80) REVERT: D 137 ASP cc_start: 0.7038 (OUTLIER) cc_final: 0.6492 (t0) REVERT: D 398 LYS cc_start: 0.6678 (pttt) cc_final: 0.6449 (pttm) REVERT: E 287 MET cc_start: 0.5174 (tmm) cc_final: 0.4809 (tmm) REVERT: F 81 VAL cc_start: 0.7612 (m) cc_final: 0.7198 (p) REVERT: F 353 TYR cc_start: 0.6546 (OUTLIER) cc_final: 0.5948 (m-10) REVERT: G 133 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8834 (pt0) REVERT: G 309 MET cc_start: 0.5998 (tmm) cc_final: 0.5795 (tmm) REVERT: G 391 PHE cc_start: 0.8059 (p90) cc_final: 0.7836 (p90) REVERT: G 393 LEU cc_start: 0.8709 (mt) cc_final: 0.8472 (tp) REVERT: H 86 TRP cc_start: 0.6852 (t60) cc_final: 0.5876 (t60) REVERT: H 243 ARG cc_start: 0.5379 (mtp180) cc_final: 0.4014 (ptp90) REVERT: H 262 TYR cc_start: 0.7868 (t80) cc_final: 0.7571 (t80) REVERT: H 303 MET cc_start: 0.4170 (ttm) cc_final: 0.3934 (ttm) REVERT: H 435 MET cc_start: 0.5024 (tmm) cc_final: 0.4730 (tmm) REVERT: H 504 LYS cc_start: 0.7281 (mtmt) cc_final: 0.6817 (mtmm) outliers start: 93 outliers final: 57 residues processed: 341 average time/residue: 0.1828 time to fit residues: 103.9309 Evaluate side-chains 323 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 261 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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 282 VAL 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 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 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 208 VAL 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 395 MET Chi-restraints excluded: chain C residue 416 TYR 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 350 ILE 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 87 GLN Chi-restraints excluded: chain E residue 97 LEU 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 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 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 423 VAL Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain G residue 34 CYS Chi-restraints excluded: chain G residue 56 ASP 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 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 478 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 232 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 247 optimal weight: 20.0000 chunk 52 optimal weight: 30.0000 chunk 346 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 chunk 111 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 163 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 354 optimal weight: 10.0000 overall best weight: 3.0786 ------------------------------------------------------------------------------- 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 ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 HIS ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN ** 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 302 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.106336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.090192 restraints weight = 202557.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.091638 restraints weight = 145933.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.092643 restraints weight = 115561.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.093240 restraints weight = 97916.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.093808 restraints weight = 87392.706| |-----------------------------------------------------------------------------| r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 33064 Z= 0.157 Angle : 0.643 11.076 45256 Z= 0.336 Chirality : 0.043 0.195 4968 Planarity : 0.005 0.064 5236 Dihedral : 17.664 165.806 5860 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.20 % Favored : 93.49 % Rotamer: Outliers : 3.07 % Allowed : 15.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.14), residues: 3532 helix: 0.36 (0.15), residues: 1230 sheet: -1.67 (0.21), residues: 588 loop : -1.23 (0.15), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 114 TYR 0.021 0.002 TYR D 56 PHE 0.046 0.002 PHE F 121 TRP 0.017 0.002 TRP D 231 HIS 0.008 0.001 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00352 (33064) covalent geometry : angle 0.64350 (45256) hydrogen bonds : bond 0.04654 ( 1021) hydrogen bonds : angle 5.46672 ( 2798) *********************** 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 382 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 284 time to evaluate : 0.940 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: A 210 TYR cc_start: 0.7259 (t80) cc_final: 0.6954 (t80) REVERT: A 268 LEU cc_start: 0.7493 (mm) cc_final: 0.7117 (mm) REVERT: B 118 VAL cc_start: 0.7340 (t) cc_final: 0.7070 (t) REVERT: B 303 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.7003 (ttm) REVERT: C 14 ASP cc_start: 0.6712 (t0) cc_final: 0.6292 (m-30) REVERT: C 122 MET cc_start: 0.7322 (tmm) cc_final: 0.6835 (tmm) REVERT: C 204 THR cc_start: 0.7468 (t) cc_final: 0.7115 (t) REVERT: C 395 MET cc_start: 0.5964 (OUTLIER) cc_final: 0.5452 (tmm) REVERT: D 137 ASP cc_start: 0.7112 (OUTLIER) cc_final: 0.6545 (t0) REVERT: D 398 LYS cc_start: 0.6147 (pttt) cc_final: 0.5745 (pttp) REVERT: E 287 MET cc_start: 0.5343 (OUTLIER) cc_final: 0.4975 (tmt) REVERT: F 81 VAL cc_start: 0.7497 (m) cc_final: 0.7057 (p) REVERT: F 353 TYR cc_start: 0.6560 (OUTLIER) cc_final: 0.5970 (m-10) REVERT: G 133 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8775 (pt0) REVERT: G 192 TRP cc_start: 0.6220 (p-90) cc_final: 0.4306 (t60) REVERT: G 287 MET cc_start: -0.0795 (tpt) cc_final: -0.1024 (tpt) REVERT: G 393 LEU cc_start: 0.8586 (mt) cc_final: 0.8353 (tp) REVERT: H 86 TRP cc_start: 0.7024 (t60) cc_final: 0.6026 (t60) REVERT: H 106 TYR cc_start: 0.4308 (m-80) cc_final: 0.3851 (m-80) REVERT: H 243 ARG cc_start: 0.5601 (mtp180) cc_final: 0.4154 (ptp90) REVERT: H 262 TYR cc_start: 0.7819 (t80) cc_final: 0.7382 (t80) outliers start: 98 outliers final: 70 residues processed: 343 average time/residue: 0.1686 time to fit residues: 95.6478 Evaluate side-chains 331 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 256 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 282 VAL 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 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 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 112 ILE 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 395 MET Chi-restraints excluded: chain C residue 416 TYR 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 350 ILE 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 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 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 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 117 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 353 TYR 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 455 VAL Chi-restraints excluded: chain F residue 459 ILE 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 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 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 478 VAL Chi-restraints excluded: chain H residue 484 ASP Chi-restraints excluded: chain H residue 501 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 136 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 197 optimal weight: 6.9990 chunk 194 optimal weight: 0.9990 chunk 201 optimal weight: 10.0000 chunk 143 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 146 optimal weight: 0.9990 chunk 321 optimal weight: 6.9990 chunk 308 optimal weight: 9.9990 chunk 270 optimal weight: 8.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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** ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 ASN ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 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 209 GLN ** 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 = 0.4438 r_free = 0.4438 target = 0.105945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.089774 restraints weight = 203288.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.091217 restraints weight = 146422.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.092204 restraints weight = 115550.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.092809 restraints weight = 97739.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.093367 restraints weight = 87407.385| |-----------------------------------------------------------------------------| r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33064 Z= 0.154 Angle : 0.643 12.369 45256 Z= 0.334 Chirality : 0.043 0.227 4968 Planarity : 0.005 0.065 5236 Dihedral : 17.705 167.112 5860 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.40 % Favored : 93.37 % Rotamer: Outliers : 3.00 % Allowed : 16.86 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.14), residues: 3532 helix: 0.50 (0.15), residues: 1204 sheet: -1.83 (0.20), residues: 600 loop : -1.23 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 114 TYR 0.023 0.001 TYR H 346 PHE 0.021 0.002 PHE C 410 TRP 0.015 0.002 TRP G 33 HIS 0.009 0.001 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00346 (33064) covalent geometry : angle 0.64302 (45256) hydrogen bonds : bond 0.04551 ( 1021) hydrogen bonds : angle 5.46448 ( 2798) *********************** 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 364 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 268 time to evaluate : 1.220 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: A 210 TYR cc_start: 0.7159 (t80) cc_final: 0.6850 (t80) REVERT: A 268 LEU cc_start: 0.7459 (mm) cc_final: 0.7173 (mm) REVERT: B 118 VAL cc_start: 0.7257 (t) cc_final: 0.6986 (t) REVERT: B 303 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.7108 (ttm) REVERT: B 435 MET cc_start: 0.0563 (mmt) cc_final: -0.0109 (ptt) REVERT: C 122 MET cc_start: 0.7292 (tmm) cc_final: 0.6777 (tmm) REVERT: C 388 ASP cc_start: 0.7305 (OUTLIER) cc_final: 0.6845 (p0) REVERT: C 395 MET cc_start: 0.5948 (OUTLIER) cc_final: 0.5512 (tmm) REVERT: D 137 ASP cc_start: 0.7108 (OUTLIER) cc_final: 0.6546 (t0) REVERT: D 398 LYS cc_start: 0.6101 (pttt) cc_final: 0.5692 (pttp) REVERT: E 287 MET cc_start: 0.5555 (OUTLIER) cc_final: 0.5181 (tmt) REVERT: F 81 VAL cc_start: 0.7350 (m) cc_final: 0.6966 (p) REVERT: F 353 TYR cc_start: 0.6563 (OUTLIER) cc_final: 0.5985 (m-10) REVERT: G 133 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8792 (pt0) REVERT: G 287 MET cc_start: -0.0983 (tpt) cc_final: -0.1302 (tpt) REVERT: G 391 PHE cc_start: 0.8183 (p90) cc_final: 0.7945 (p90) REVERT: G 393 LEU cc_start: 0.8610 (mt) cc_final: 0.8378 (tp) REVERT: H 86 TRP cc_start: 0.6988 (t60) cc_final: 0.6331 (t60) REVERT: H 243 ARG cc_start: 0.5885 (mtp180) cc_final: 0.4467 (ptp90) REVERT: H 489 ILE cc_start: 0.6363 (tp) cc_final: 0.6139 (tp) outliers start: 96 outliers final: 76 residues processed: 330 average time/residue: 0.1872 time to fit residues: 101.3306 Evaluate side-chains 332 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 250 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 282 VAL 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 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 B residue 468 ASN Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 112 ILE 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 395 MET 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 334 GLU Chi-restraints excluded: chain D residue 350 ILE 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 87 GLN Chi-restraints excluded: chain E residue 97 LEU 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 308 THR 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 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 117 LEU Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 281 LEU 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 423 VAL Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 459 ILE 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 110 ILE 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 223 ILE Chi-restraints excluded: chain H residue 274 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 484 ASP Chi-restraints excluded: chain H residue 501 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 242 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 141 optimal weight: 7.9990 chunk 190 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 199 optimal weight: 20.0000 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 HIS ** E 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 358 HIS ** E 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 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 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 302 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.107229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.091013 restraints weight = 201719.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.092481 restraints weight = 144339.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.093349 restraints weight = 113873.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 72)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.094186 restraints weight = 97164.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.094591 restraints weight = 85849.310| |-----------------------------------------------------------------------------| r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 33064 Z= 0.127 Angle : 0.632 15.287 45256 Z= 0.324 Chirality : 0.042 0.242 4968 Planarity : 0.004 0.065 5236 Dihedral : 17.675 168.978 5860 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.23 % Favored : 93.54 % Rotamer: Outliers : 2.60 % Allowed : 17.77 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.14), residues: 3532 helix: 0.56 (0.15), residues: 1222 sheet: -1.50 (0.21), residues: 554 loop : -1.22 (0.15), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 114 TYR 0.021 0.001 TYR H 346 PHE 0.044 0.002 PHE F 121 TRP 0.039 0.002 TRP A 175 HIS 0.008 0.001 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00284 (33064) covalent geometry : angle 0.63224 (45256) hydrogen bonds : bond 0.04201 ( 1021) hydrogen bonds : angle 5.28058 ( 2798) *********************** 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 343 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 260 time to evaluate : 0.864 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: A 210 TYR cc_start: 0.7131 (t80) cc_final: 0.6844 (t80) REVERT: A 268 LEU cc_start: 0.7389 (mm) cc_final: 0.7141 (mm) REVERT: B 25 ASP cc_start: 0.6950 (m-30) cc_final: 0.6691 (m-30) REVERT: B 118 VAL cc_start: 0.7244 (t) cc_final: 0.6952 (t) REVERT: B 303 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.6950 (ttm) REVERT: B 435 MET cc_start: 0.0528 (mmt) cc_final: -0.0066 (ptt) REVERT: C 14 ASP cc_start: 0.6766 (t0) cc_final: 0.6247 (m-30) REVERT: C 122 MET cc_start: 0.7302 (tmm) cc_final: 0.6833 (tmm) REVERT: C 217 PHE cc_start: 0.4917 (OUTLIER) cc_final: 0.3757 (m-10) REVERT: C 388 ASP cc_start: 0.7316 (OUTLIER) cc_final: 0.6801 (p0) REVERT: C 395 MET cc_start: 0.5929 (OUTLIER) cc_final: 0.5532 (tmm) REVERT: D 137 ASP cc_start: 0.6890 (OUTLIER) cc_final: 0.6360 (t0) REVERT: D 398 LYS cc_start: 0.6272 (pttt) cc_final: 0.5922 (pttp) REVERT: E 122 MET cc_start: 0.8059 (mmm) cc_final: 0.7565 (mmm) REVERT: E 287 MET cc_start: 0.5598 (OUTLIER) cc_final: 0.5187 (tmm) REVERT: F 353 TYR cc_start: 0.6314 (OUTLIER) cc_final: 0.5872 (m-10) REVERT: G 287 MET cc_start: -0.1363 (tpt) cc_final: -0.1579 (tpt) REVERT: H 86 TRP cc_start: 0.7020 (t60) cc_final: 0.6375 (t60) REVERT: H 161 MET cc_start: 0.1867 (mpp) cc_final: 0.1155 (ttt) REVERT: H 243 ARG cc_start: 0.5902 (mtp180) cc_final: 0.4586 (ptp90) REVERT: H 435 MET cc_start: 0.4371 (tmm) cc_final: -0.0101 (mtt) REVERT: H 489 ILE cc_start: 0.6814 (tp) cc_final: 0.6595 (tp) outliers start: 83 outliers final: 64 residues processed: 314 average time/residue: 0.1607 time to fit residues: 83.2118 Evaluate side-chains 320 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 249 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 282 VAL 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 74 MET 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 112 ILE 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 395 MET 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 137 ASP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 244 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 350 ILE 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 97 LEU 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 308 THR 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 117 LEU Chi-restraints excluded: chain F residue 219 ILE 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 423 VAL Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain G residue 34 CYS Chi-restraints excluded: chain G residue 67 TYR Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 340 HIS Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 411 TYR Chi-restraints excluded: chain H residue 426 VAL Chi-restraints excluded: chain H residue 484 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 4 optimal weight: 0.0870 chunk 36 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 51 optimal weight: 20.0000 chunk 274 optimal weight: 20.0000 chunk 359 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 175 optimal weight: 0.0980 chunk 213 optimal weight: 0.5980 chunk 303 optimal weight: 20.0000 chunk 304 optimal weight: 7.9990 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS ** A 267 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** D 322 ASN E 9 HIS ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 358 HIS ** E 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN G 226 HIS ** G 340 HIS ** 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 468 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.108944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.092889 restraints weight = 199260.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.094332 restraints weight = 142215.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.095364 restraints weight = 111699.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.095954 restraints weight = 94111.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.096474 restraints weight = 84160.094| |-----------------------------------------------------------------------------| r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6346 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33064 Z= 0.117 Angle : 0.629 13.907 45256 Z= 0.320 Chirality : 0.042 0.236 4968 Planarity : 0.004 0.065 5236 Dihedral : 17.651 170.827 5860 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.78 % Favored : 94.00 % Rotamer: Outliers : 2.22 % Allowed : 18.40 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.14), residues: 3532 helix: 0.61 (0.15), residues: 1222 sheet: -1.57 (0.21), residues: 560 loop : -1.14 (0.15), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 295 TYR 0.027 0.001 TYR D 321 PHE 0.030 0.001 PHE A 17 TRP 0.032 0.002 TRP A 175 HIS 0.008 0.001 HIS H 251 Details of bonding type rmsd covalent geometry : bond 0.00256 (33064) covalent geometry : angle 0.62882 (45256) hydrogen bonds : bond 0.04031 ( 1021) hydrogen bonds : angle 5.17536 ( 2798) *********************** 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 352 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 281 time to evaluate : 0.849 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: A 210 TYR cc_start: 0.7184 (t80) cc_final: 0.6908 (t80) REVERT: A 268 LEU cc_start: 0.7372 (mm) cc_final: 0.7127 (mm) REVERT: B 7 ILE cc_start: 0.8333 (pt) cc_final: 0.7823 (mp) REVERT: B 25 ASP cc_start: 0.7046 (m-30) cc_final: 0.6819 (m-30) REVERT: B 72 ARG cc_start: 0.7160 (mpt180) cc_final: 0.6960 (mmt180) REVERT: B 118 VAL cc_start: 0.7188 (t) cc_final: 0.6909 (t) REVERT: B 303 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.6877 (ttm) REVERT: B 435 MET cc_start: 0.0562 (mmt) cc_final: -0.0081 (ptt) REVERT: C 14 ASP cc_start: 0.6614 (t0) cc_final: 0.6232 (m-30) REVERT: C 122 MET cc_start: 0.7284 (tmm) cc_final: 0.6791 (tmm) REVERT: C 217 PHE cc_start: 0.4509 (OUTLIER) cc_final: 0.3528 (m-10) REVERT: C 388 ASP cc_start: 0.7188 (OUTLIER) cc_final: 0.6645 (p0) REVERT: C 391 PHE cc_start: 0.8301 (p90) cc_final: 0.8099 (p90) REVERT: C 395 MET cc_start: 0.5940 (OUTLIER) cc_final: 0.5571 (tmm) REVERT: D 137 ASP cc_start: 0.6936 (OUTLIER) cc_final: 0.6490 (t0) REVERT: D 398 LYS cc_start: 0.6479 (pttt) cc_final: 0.6202 (pttm) REVERT: E 287 MET cc_start: 0.5512 (OUTLIER) cc_final: 0.5147 (tmm) REVERT: F 371 ASP cc_start: 0.8043 (t0) cc_final: 0.7457 (p0) REVERT: G 393 LEU cc_start: 0.8583 (mt) cc_final: 0.8359 (mp) REVERT: H 36 LEU cc_start: 0.7015 (tt) cc_final: 0.6777 (mm) REVERT: H 86 TRP cc_start: 0.6987 (t60) cc_final: 0.6371 (t60) REVERT: H 435 MET cc_start: 0.4384 (tmm) cc_final: -0.0078 (mtt) REVERT: H 489 ILE cc_start: 0.6752 (tp) cc_final: 0.6499 (tp) outliers start: 71 outliers final: 53 residues processed: 324 average time/residue: 0.1701 time to fit residues: 89.9852 Evaluate side-chains 314 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 255 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 282 VAL 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 303 MET Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 468 ASN Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain C residue 16 ASP 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 395 MET 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 244 ASP Chi-restraints excluded: chain D residue 279 CYS Chi-restraints excluded: chain D residue 299 CYS Chi-restraints excluded: chain D residue 350 ILE 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 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 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 117 LEU Chi-restraints excluded: chain F residue 299 CYS Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain G residue 67 TYR Chi-restraints excluded: chain G residue 144 VAL 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 340 HIS Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 411 TYR Chi-restraints excluded: chain H residue 426 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 301 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 201 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 202 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 239 optimal weight: 0.8980 chunk 122 optimal weight: 20.0000 chunk 111 optimal weight: 3.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- 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 16 HIS ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN E 358 HIS F 61 GLN F 111 HIS ** 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 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.105354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.089556 restraints weight = 204016.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.090889 restraints weight = 146063.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.091759 restraints weight = 114866.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.092429 restraints weight = 97511.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.092962 restraints weight = 86675.601| |-----------------------------------------------------------------------------| r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 moved from start: 0.5060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 33064 Z= 0.166 Angle : 0.681 14.633 45256 Z= 0.350 Chirality : 0.044 0.278 4968 Planarity : 0.005 0.065 5236 Dihedral : 17.696 171.176 5860 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.05 % Favored : 92.72 % Rotamer: Outliers : 2.10 % Allowed : 18.68 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.14), residues: 3532 helix: 0.60 (0.15), residues: 1200 sheet: -1.51 (0.21), residues: 564 loop : -1.18 (0.15), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 263 TYR 0.039 0.002 TYR H 106 PHE 0.022 0.002 PHE F 78 TRP 0.025 0.002 TRP A 175 HIS 0.007 0.001 HIS F 59 Details of bonding type rmsd covalent geometry : bond 0.00371 (33064) covalent geometry : angle 0.68128 (45256) hydrogen bonds : bond 0.04509 ( 1021) hydrogen bonds : angle 5.41812 ( 2798) ********************** 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 322 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 255 time to evaluate : 1.003 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: A 106 ASP cc_start: 0.8302 (p0) cc_final: 0.8094 (p0) REVERT: A 210 TYR cc_start: 0.7199 (t80) cc_final: 0.6872 (t80) REVERT: A 268 LEU cc_start: 0.7556 (mm) cc_final: 0.7281 (mm) REVERT: B 118 VAL cc_start: 0.7303 (t) cc_final: 0.7060 (t) REVERT: B 303 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7133 (ttm) REVERT: B 435 MET cc_start: 0.0927 (mmt) cc_final: 0.0218 (ptt) REVERT: B 503 PHE cc_start: 0.6510 (m-10) cc_final: 0.6186 (m-80) REVERT: C 122 MET cc_start: 0.7374 (tmm) cc_final: 0.6842 (tmm) REVERT: C 217 PHE cc_start: 0.5073 (OUTLIER) cc_final: 0.3656 (m-10) REVERT: C 388 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.7033 (p0) REVERT: C 395 MET cc_start: 0.6087 (OUTLIER) cc_final: 0.5767 (tmm) REVERT: D 74 MET cc_start: 0.5655 (tpt) cc_final: 0.5191 (tpt) REVERT: D 398 LYS cc_start: 0.6111 (pttt) cc_final: 0.5361 (pttt) REVERT: E 287 MET cc_start: 0.5759 (OUTLIER) cc_final: 0.5459 (tmm) REVERT: F 405 ILE cc_start: 0.6476 (OUTLIER) cc_final: 0.6043 (mm) REVERT: G 133 GLU cc_start: 0.9165 (mt-10) cc_final: 0.8801 (pt0) REVERT: G 393 LEU cc_start: 0.8703 (mt) cc_final: 0.8440 (pt) REVERT: H 86 TRP cc_start: 0.7035 (t60) cc_final: 0.6403 (t60) REVERT: H 435 MET cc_start: 0.4375 (tmm) cc_final: -0.0053 (mtt) outliers start: 67 outliers final: 55 residues processed: 300 average time/residue: 0.1686 time to fit residues: 82.7753 Evaluate side-chains 309 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 248 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 295 LEU 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 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 C residue 16 ASP 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 395 MET 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 279 CYS Chi-restraints excluded: chain D residue 299 CYS Chi-restraints excluded: chain D residue 350 ILE 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 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 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 299 CYS Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain G residue 67 TYR Chi-restraints excluded: chain G residue 110 ILE 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 1 MET Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 411 TYR Chi-restraints excluded: chain H residue 426 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 339 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 299 optimal weight: 2.9990 chunk 149 optimal weight: 0.0970 chunk 62 optimal weight: 4.9990 chunk 354 optimal weight: 10.0000 chunk 358 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 184 optimal weight: 0.3980 chunk 76 optimal weight: 6.9990 overall best weight: 2.6984 ------------------------------------------------------------------------------- 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 314 GLN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 HIS ** 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 209 GLN ** 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 = 0.4436 r_free = 0.4436 target = 0.105752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.089778 restraints weight = 203210.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.091195 restraints weight = 145219.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.092052 restraints weight = 114420.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.092833 restraints weight = 97591.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.093227 restraints weight = 86433.860| |-----------------------------------------------------------------------------| r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33064 Z= 0.145 Angle : 0.666 13.743 45256 Z= 0.339 Chirality : 0.043 0.271 4968 Planarity : 0.005 0.065 5236 Dihedral : 17.745 174.190 5860 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.31 % Favored : 93.49 % Rotamer: Outliers : 2.10 % Allowed : 18.90 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.14), residues: 3532 helix: 0.64 (0.15), residues: 1198 sheet: -1.46 (0.22), residues: 530 loop : -1.21 (0.15), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 407 TYR 0.036 0.001 TYR H 106 PHE 0.030 0.002 PHE C 17 TRP 0.027 0.002 TRP A 175 HIS 0.007 0.001 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00326 (33064) covalent geometry : angle 0.66623 (45256) hydrogen bonds : bond 0.04238 ( 1021) hydrogen bonds : angle 5.36181 ( 2798) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6007.79 seconds wall clock time: 104 minutes 58.42 seconds (6298.42 seconds total)