Starting phenix.real_space_refine on Fri Jul 3 21:02:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rwa_24712/07_2026/7rwa_24712.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rwa_24712/07_2026/7rwa_24712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rwa_24712/07_2026/7rwa_24712.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rwa_24712/07_2026/7rwa_24712.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rwa_24712/07_2026/7rwa_24712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rwa_24712/07_2026/7rwa_24712.map" } resolution = 4.7 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= 0.002 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 9654 2.51 5 N 3252 2.21 5 O 3252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16158 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 2978 Classifications: {'peptide': 600} Incomplete info: {'truncation_to_alanine': 526} Link IDs: {'PTRANS': 22, 'TRANS': 577} Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 1845 Unresolved non-hydrogen angles: 2366 Unresolved non-hydrogen dihedrals: 1508 Unresolved non-hydrogen chiralities: 193 Planarities with less than four sites: {'ARG:plan': 33, 'PHE:plan': 20, 'ASP:plan': 29, 'ASN:plan1': 29, 'GLU:plan': 39, 'TYR:plan': 22, 'HIS:plan': 14, 'GLN:plan1': 22, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 963 Chain: "B" Number of atoms: 2471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 2471 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 447} Link IDs: {'PTRANS': 24, 'TRANS': 471} Unresolved chain link angles: 24 Unresolved non-hydrogen bonds: 1523 Unresolved non-hydrogen angles: 1953 Unresolved non-hydrogen dihedrals: 1222 Unresolved non-hydrogen chiralities: 165 Planarities with less than four sites: {'ASN:plan1': 25, 'PHE:plan': 12, 'ASP:plan': 35, 'GLU:plan': 40, 'ARG:plan': 23, 'TYR:plan': 16, 'HIS:plan': 6, 'GLN:plan1': 19, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 772 Chain: "M" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 1875 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 339} Link IDs: {'PTRANS': 17, 'TRANS': 361} Chain breaks: 3 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1259 Unresolved non-hydrogen angles: 1596 Unresolved non-hydrogen dihedrals: 1066 Unresolved non-hydrogen chiralities: 107 Planarities with less than four sites: {'PHE:plan': 19, 'TYR:plan': 14, 'ASN:plan1': 20, 'HIS:plan': 6, 'GLU:plan': 23, 'ARG:plan': 27, 'ASP:plan': 15, 'GLN:plan1': 11, 'TRP:plan': 5} Unresolved non-hydrogen planarities: 663 Chain: "S" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 707 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 131} Link IDs: {'TRANS': 141} Unresolved non-hydrogen bonds: 517 Unresolved non-hydrogen angles: 665 Unresolved non-hydrogen dihedrals: 430 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'ARG:plan': 8, 'PHE:plan': 11, 'GLN:plan1': 6, 'ASN:plan1': 10, 'TRP:plan': 1, 'TYR:plan': 8, 'ASP:plan': 8, 'GLU:plan': 12, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 317 Chain: "Y" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Restraints were copied for chains: a, b, m, s, y Time building chain proxies: 4.85, per 1000 atoms: 0.30 Number of scatterers: 16158 At special positions: 0 Unit cell: (199.815, 158.235, 103.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 3252 8.00 N 3252 7.00 C 9654 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 1.1 seconds 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6272 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 20 sheets defined 62.4% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 Processing helix chain 'A' and resid 25 through 45 removed outlier: 3.755A pdb=" N GLU A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 69 Processing helix chain 'A' and resid 76 through 84 removed outlier: 4.241A pdb=" N LEU A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 101 Processing helix chain 'A' and resid 106 through 121 removed outlier: 3.863A pdb=" N ALA A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 138 removed outlier: 3.829A pdb=" N MET A 128 " --> pdb=" O ASN A 124 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 138 " --> pdb=" O CYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 146 removed outlier: 3.511A pdb=" N ALA A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 156 Processing helix chain 'A' and resid 161 through 179 Processing helix chain 'A' and resid 188 through 193 removed outlier: 3.672A pdb=" N VAL A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 198 removed outlier: 3.692A pdb=" N ASN A 197 " --> pdb=" O HIS A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 218 Processing helix chain 'A' and resid 219 through 223 removed outlier: 3.517A pdb=" N PHE A 222 " --> pdb=" O PRO A 219 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS A 223 " --> pdb=" O GLU A 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 219 through 223' Processing helix chain 'A' and resid 224 through 238 removed outlier: 4.740A pdb=" N LEU A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 254 through 266 removed outlier: 3.694A pdb=" N SER A 258 " --> pdb=" O ALA A 254 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 293 removed outlier: 3.521A pdb=" N GLU A 293 " --> pdb=" O ASN A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 321 removed outlier: 4.318A pdb=" N SER A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 339 removed outlier: 3.883A pdb=" N GLN A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 357 Processing helix chain 'A' and resid 359 through 369 removed outlier: 4.316A pdb=" N GLU A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ALA A 365 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 380 Processing helix chain 'A' and resid 383 through 396 removed outlier: 3.653A pdb=" N GLN A 387 " --> pdb=" O VAL A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 415 Processing helix chain 'A' and resid 419 through 435 Processing helix chain 'A' and resid 438 through 453 Processing helix chain 'A' and resid 460 through 473 removed outlier: 3.562A pdb=" N ASP A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 488 removed outlier: 4.579A pdb=" N TYR A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN A 488 " --> pdb=" O PHE A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 512 removed outlier: 6.620A pdb=" N ASN A 509 " --> pdb=" O GLY A 505 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU A 510 " --> pdb=" O GLU A 506 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A 511 " --> pdb=" O PHE A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 517 Processing helix chain 'A' and resid 518 through 530 Processing helix chain 'A' and resid 534 through 552 Processing helix chain 'A' and resid 555 through 563 Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 573 through 590 Processing helix chain 'A' and resid 593 through 599 removed outlier: 3.544A pdb=" N LEU A 599 " --> pdb=" O LEU A 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 96 Processing helix chain 'B' and resid 99 through 113 removed outlier: 3.584A pdb=" N CYS B 112 " --> pdb=" O ARG B 108 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 removed outlier: 4.534A pdb=" N GLU B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) Proline residue: B 125 - end of helix removed outlier: 4.250A pdb=" N LYS B 128 " --> pdb=" O GLU B 124 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS B 129 " --> pdb=" O PRO B 125 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 150 removed outlier: 3.638A pdb=" N ASP B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 168 Processing helix chain 'B' and resid 173 through 188 Processing helix chain 'B' and resid 200 through 214 Processing helix chain 'B' and resid 215 through 226 Processing helix chain 'B' and resid 227 through 229 No H-bonds generated for 'chain 'B' and resid 227 through 229' Processing helix chain 'B' and resid 233 through 245 removed outlier: 3.771A pdb=" N ALA B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 266 Processing helix chain 'B' and resid 275 through 291 removed outlier: 3.695A pdb=" N MET B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA B 285 " --> pdb=" O LEU B 281 " (cutoff:3.500A) Proline residue: B 286 - end of helix removed outlier: 3.563A pdb=" N LEU B 291 " --> pdb=" O PRO B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 294 No H-bonds generated for 'chain 'B' and resid 292 through 294' Processing helix chain 'B' and resid 295 through 313 Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 350 through 363 removed outlier: 3.786A pdb=" N THR B 363 " --> pdb=" O LYS B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 384 Processing helix chain 'B' and resid 384 through 400 Processing helix chain 'B' and resid 403 through 421 Processing helix chain 'B' and resid 427 through 435 removed outlier: 4.273A pdb=" N THR B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 455 Processing helix chain 'B' and resid 461 through 470 Processing helix chain 'B' and resid 477 through 495 Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 499 through 514 Processing helix chain 'B' and resid 516 through 531 Processing helix chain 'B' and resid 533 through 541 removed outlier: 3.628A pdb=" N GLU B 539 " --> pdb=" O VAL B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 564 Processing helix chain 'B' and resid 569 through 575 removed outlier: 4.124A pdb=" N VAL B 573 " --> pdb=" O SER B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 581 Processing helix chain 'M' and resid 25 through 37 removed outlier: 3.889A pdb=" N VAL M 29 " --> pdb=" O GLY M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 94 removed outlier: 3.913A pdb=" N VAL M 78 " --> pdb=" O ASN M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 103 Processing helix chain 'M' and resid 104 through 115 Processing helix chain 'M' and resid 414 through 416 No H-bonds generated for 'chain 'M' and resid 414 through 416' Processing helix chain 'S' and resid 24 through 41 removed outlier: 3.719A pdb=" N VAL S 41 " --> pdb=" O ALA S 37 " (cutoff:3.500A) Processing helix chain 'S' and resid 76 through 96 removed outlier: 3.540A pdb=" N PHE S 95 " --> pdb=" O LEU S 91 " (cutoff:3.500A) Processing helix chain 'S' and resid 99 through 106 removed outlier: 3.535A pdb=" N LEU S 103 " --> pdb=" O CYS S 99 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 117 Processing helix chain 'S' and resid 127 through 141 removed outlier: 3.899A pdb=" N LEU S 141 " --> pdb=" O MET S 137 " (cutoff:3.500A) Processing helix chain 'a' and resid 11 through 22 Processing helix chain 'a' and resid 25 through 45 removed outlier: 3.755A pdb=" N GLU a 29 " --> pdb=" O SER a 25 " (cutoff:3.500A) Processing helix chain 'a' and resid 52 through 69 Processing helix chain 'a' and resid 76 through 84 removed outlier: 4.242A pdb=" N LEU a 82 " --> pdb=" O GLU a 78 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU a 83 " --> pdb=" O ALA a 79 " (cutoff:3.500A) Processing helix chain 'a' and resid 87 through 101 Processing helix chain 'a' and resid 106 through 121 removed outlier: 3.862A pdb=" N ALA a 121 " --> pdb=" O LYS a 117 " (cutoff:3.500A) Processing helix chain 'a' and resid 124 through 138 removed outlier: 3.829A pdb=" N MET a 128 " --> pdb=" O ASN a 124 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL a 138 " --> pdb=" O CYS a 134 " (cutoff:3.500A) Processing helix chain 'a' and resid 140 through 146 removed outlier: 3.511A pdb=" N ALA a 144 " --> pdb=" O SER a 140 " (cutoff:3.500A) Processing helix chain 'a' and resid 149 through 156 Processing helix chain 'a' and resid 161 through 179 Processing helix chain 'a' and resid 188 through 193 removed outlier: 3.672A pdb=" N VAL a 192 " --> pdb=" O TRP a 188 " (cutoff:3.500A) Processing helix chain 'a' and resid 194 through 198 removed outlier: 3.691A pdb=" N ASN a 197 " --> pdb=" O HIS a 194 " (cutoff:3.500A) Processing helix chain 'a' and resid 200 through 218 Processing helix chain 'a' and resid 219 through 223 removed outlier: 3.516A pdb=" N PHE a 222 " --> pdb=" O PRO a 219 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS a 223 " --> pdb=" O GLU a 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 219 through 223' Processing helix chain 'a' and resid 224 through 238 removed outlier: 4.740A pdb=" N LEU a 228 " --> pdb=" O THR a 224 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR a 238 " --> pdb=" O SER a 234 " (cutoff:3.500A) Processing helix chain 'a' and resid 244 through 246 No H-bonds generated for 'chain 'a' and resid 244 through 246' Processing helix chain 'a' and resid 254 through 266 removed outlier: 3.694A pdb=" N SER a 258 " --> pdb=" O ALA a 254 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN a 266 " --> pdb=" O LEU a 262 " (cutoff:3.500A) Processing helix chain 'a' and resid 273 through 293 removed outlier: 3.520A pdb=" N GLU a 293 " --> pdb=" O ASN a 289 " (cutoff:3.500A) Processing helix chain 'a' and resid 299 through 321 removed outlier: 4.318A pdb=" N SER a 303 " --> pdb=" O LYS a 299 " (cutoff:3.500A) Processing helix chain 'a' and resid 323 through 339 removed outlier: 3.884A pdb=" N GLN a 339 " --> pdb=" O GLY a 335 " (cutoff:3.500A) Processing helix chain 'a' and resid 342 through 357 Processing helix chain 'a' and resid 359 through 369 removed outlier: 4.315A pdb=" N GLU a 364 " --> pdb=" O GLU a 360 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ALA a 365 " --> pdb=" O PHE a 361 " (cutoff:3.500A) Processing helix chain 'a' and resid 369 through 380 Processing helix chain 'a' and resid 383 through 396 removed outlier: 3.654A pdb=" N GLN a 387 " --> pdb=" O VAL a 383 " (cutoff:3.500A) Processing helix chain 'a' and resid 398 through 415 Processing helix chain 'a' and resid 419 through 435 Processing helix chain 'a' and resid 438 through 453 Processing helix chain 'a' and resid 460 through 473 removed outlier: 3.561A pdb=" N ASP a 473 " --> pdb=" O VAL a 469 " (cutoff:3.500A) Processing helix chain 'a' and resid 474 through 488 removed outlier: 4.579A pdb=" N TYR a 478 " --> pdb=" O ASP a 474 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN a 488 " --> pdb=" O PHE a 484 " (cutoff:3.500A) Processing helix chain 'a' and resid 493 through 512 removed outlier: 6.619A pdb=" N ASN a 509 " --> pdb=" O GLY a 505 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU a 510 " --> pdb=" O GLU a 506 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE a 511 " --> pdb=" O PHE a 507 " (cutoff:3.500A) Processing helix chain 'a' and resid 514 through 517 Processing helix chain 'a' and resid 518 through 530 Processing helix chain 'a' and resid 534 through 552 Processing helix chain 'a' and resid 555 through 563 Processing helix chain 'a' and resid 565 through 570 Processing helix chain 'a' and resid 573 through 590 Processing helix chain 'a' and resid 593 through 599 removed outlier: 3.544A pdb=" N LEU a 599 " --> pdb=" O LEU a 595 " (cutoff:3.500A) Processing helix chain 'b' and resid 88 through 96 Processing helix chain 'b' and resid 99 through 113 removed outlier: 3.584A pdb=" N CYS b 112 " --> pdb=" O ARG b 108 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE b 113 " --> pdb=" O THR b 109 " (cutoff:3.500A) Processing helix chain 'b' and resid 117 through 131 removed outlier: 4.534A pdb=" N GLU b 124 " --> pdb=" O GLU b 120 " (cutoff:3.500A) Proline residue: b 125 - end of helix removed outlier: 4.249A pdb=" N LYS b 128 " --> pdb=" O GLU b 124 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS b 129 " --> pdb=" O PRO b 125 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS b 131 " --> pdb=" O ARG b 127 " (cutoff:3.500A) Processing helix chain 'b' and resid 134 through 150 removed outlier: 3.638A pdb=" N ASP b 150 " --> pdb=" O ALA b 146 " (cutoff:3.500A) Processing helix chain 'b' and resid 155 through 168 Processing helix chain 'b' and resid 173 through 188 Processing helix chain 'b' and resid 200 through 214 Processing helix chain 'b' and resid 215 through 226 Processing helix chain 'b' and resid 227 through 229 No H-bonds generated for 'chain 'b' and resid 227 through 229' Processing helix chain 'b' and resid 233 through 245 removed outlier: 3.771A pdb=" N ALA b 237 " --> pdb=" O ASP b 233 " (cutoff:3.500A) Processing helix chain 'b' and resid 252 through 266 Processing helix chain 'b' and resid 275 through 291 removed outlier: 3.695A pdb=" N MET b 279 " --> pdb=" O ASP b 275 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA b 285 " --> pdb=" O LEU b 281 " (cutoff:3.500A) Proline residue: b 286 - end of helix removed outlier: 3.563A pdb=" N LEU b 291 " --> pdb=" O PRO b 287 " (cutoff:3.500A) Processing helix chain 'b' and resid 292 through 294 No H-bonds generated for 'chain 'b' and resid 292 through 294' Processing helix chain 'b' and resid 295 through 313 Processing helix chain 'b' and resid 331 through 346 Processing helix chain 'b' and resid 350 through 363 removed outlier: 3.787A pdb=" N THR b 363 " --> pdb=" O LYS b 359 " (cutoff:3.500A) Processing helix chain 'b' and resid 366 through 384 Processing helix chain 'b' and resid 384 through 400 Processing helix chain 'b' and resid 403 through 421 Processing helix chain 'b' and resid 427 through 435 removed outlier: 4.273A pdb=" N THR b 431 " --> pdb=" O SER b 427 " (cutoff:3.500A) Processing helix chain 'b' and resid 441 through 455 Processing helix chain 'b' and resid 461 through 470 Processing helix chain 'b' and resid 477 through 495 Processing helix chain 'b' and resid 496 through 498 No H-bonds generated for 'chain 'b' and resid 496 through 498' Processing helix chain 'b' and resid 499 through 514 Processing helix chain 'b' and resid 516 through 531 Processing helix chain 'b' and resid 533 through 541 removed outlier: 3.629A pdb=" N GLU b 539 " --> pdb=" O VAL b 535 " (cutoff:3.500A) Processing helix chain 'b' and resid 556 through 564 Processing helix chain 'b' and resid 569 through 575 removed outlier: 4.123A pdb=" N VAL b 573 " --> pdb=" O SER b 569 " (cutoff:3.500A) Processing helix chain 'b' and resid 577 through 581 Processing helix chain 'm' and resid 25 through 37 removed outlier: 3.890A pdb=" N VAL m 29 " --> pdb=" O GLY m 25 " (cutoff:3.500A) Processing helix chain 'm' and resid 74 through 94 removed outlier: 3.911A pdb=" N VAL m 78 " --> pdb=" O ASN m 74 " (cutoff:3.500A) Processing helix chain 'm' and resid 97 through 103 Processing helix chain 'm' and resid 104 through 115 Processing helix chain 'm' and resid 414 through 416 No H-bonds generated for 'chain 'm' and resid 414 through 416' Processing helix chain 's' and resid 24 through 41 removed outlier: 3.719A pdb=" N VAL s 41 " --> pdb=" O ALA s 37 " (cutoff:3.500A) Processing helix chain 's' and resid 76 through 96 removed outlier: 3.540A pdb=" N PHE s 95 " --> pdb=" O LEU s 91 " (cutoff:3.500A) Processing helix chain 's' and resid 99 through 106 removed outlier: 3.535A pdb=" N LEU s 103 " --> pdb=" O CYS s 99 " (cutoff:3.500A) Processing helix chain 's' and resid 106 through 117 Processing helix chain 's' and resid 127 through 141 removed outlier: 3.899A pdb=" N LEU s 141 " --> pdb=" O MET s 137 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 248 through 249 Processing sheet with id=AA2, first strand: chain 'M' and resid 14 through 19 removed outlier: 7.117A pdb=" N ILE M 7 " --> pdb=" O LEU M 15 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N SER M 17 " --> pdb=" O LEU M 5 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU M 5 " --> pdb=" O SER M 17 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLY M 4 " --> pdb=" O VAL M 68 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL M 68 " --> pdb=" O GLY M 4 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL M 58 " --> pdb=" O LEU M 65 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR M 69 " --> pdb=" O SER M 54 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER M 54 " --> pdb=" O THR M 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 116 through 117 Processing sheet with id=AA4, first strand: chain 'M' and resid 245 through 248 removed outlier: 3.587A pdb=" N ASP M 245 " --> pdb=" O ARG M 278 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N MET M 275 " --> pdb=" O VAL M 200 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL M 200 " --> pdb=" O MET M 275 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU M 178 " --> pdb=" O ARG M 199 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN M 171 " --> pdb=" O ILE M 419 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N TRP M 421 " --> pdb=" O ASN M 171 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU M 173 " --> pdb=" O TRP M 421 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ARG M 423 " --> pdb=" O LEU M 173 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU M 175 " --> pdb=" O ARG M 423 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE M 425 " --> pdb=" O LEU M 175 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VAL M 177 " --> pdb=" O ILE M 425 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ARG M 427 " --> pdb=" O VAL M 177 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLU M 179 " --> pdb=" O ARG M 427 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY M 429 " --> pdb=" O GLU M 179 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL M 181 " --> pdb=" O GLY M 429 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N TYR M 431 " --> pdb=" O VAL M 181 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU M 183 " --> pdb=" O TYR M 431 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N THR M 433 " --> pdb=" O LEU M 183 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N MET M 185 " --> pdb=" O THR M 433 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ARG M 427 " --> pdb=" O VAL M 392 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL M 392 " --> pdb=" O ARG M 427 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLY M 429 " --> pdb=" O PHE M 390 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N PHE M 390 " --> pdb=" O GLY M 429 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N TYR M 431 " --> pdb=" O MET M 388 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER M 387 " --> pdb=" O ARG M 323 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLU M 391 " --> pdb=" O LYS M 319 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LYS M 319 " --> pdb=" O GLU M 391 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL M 322 " --> pdb=" O TRP M 353 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP M 353 " --> pdb=" O VAL M 322 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE M 324 " --> pdb=" O ILE M 351 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE M 351 " --> pdb=" O ILE M 324 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 270 through 272 removed outlier: 3.535A pdb=" N LEU M 178 " --> pdb=" O ARG M 199 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN M 171 " --> pdb=" O ILE M 419 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N TRP M 421 " --> pdb=" O ASN M 171 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU M 173 " --> pdb=" O TRP M 421 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ARG M 423 " --> pdb=" O LEU M 173 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU M 175 " --> pdb=" O ARG M 423 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE M 425 " --> pdb=" O LEU M 175 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VAL M 177 " --> pdb=" O ILE M 425 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ARG M 427 " --> pdb=" O VAL M 177 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLU M 179 " --> pdb=" O ARG M 427 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY M 429 " --> pdb=" O GLU M 179 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL M 181 " --> pdb=" O GLY M 429 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N TYR M 431 " --> pdb=" O VAL M 181 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU M 183 " --> pdb=" O TYR M 431 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N THR M 433 " --> pdb=" O LEU M 183 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N MET M 185 " --> pdb=" O THR M 433 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 263 through 265 removed outlier: 4.239A pdb=" N ILE M 263 " --> pdb=" O PHE M 214 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 287 through 290 Processing sheet with id=AA8, first strand: chain 'M' and resid 287 through 290 removed outlier: 3.525A pdb=" N VAL M 303 " --> pdb=" O ALA M 368 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 14 through 19 removed outlier: 7.760A pdb=" N THR S 14 " --> pdb=" O ASN S 9 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ASN S 9 " --> pdb=" O THR S 14 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU S 16 " --> pdb=" O ILE S 7 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE S 7 " --> pdb=" O LEU S 16 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS S 56 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL S 50 " --> pdb=" O ILE S 57 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 118 through 119 Processing sheet with id=AB2, first strand: chain 'a' and resid 248 through 249 Processing sheet with id=AB3, first strand: chain 'm' and resid 14 through 19 removed outlier: 7.117A pdb=" N ILE m 7 " --> pdb=" O LEU m 15 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N SER m 17 " --> pdb=" O LEU m 5 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU m 5 " --> pdb=" O SER m 17 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY m 4 " --> pdb=" O VAL m 68 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL m 68 " --> pdb=" O GLY m 4 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL m 58 " --> pdb=" O LEU m 65 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR m 69 " --> pdb=" O SER m 54 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER m 54 " --> pdb=" O THR m 69 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'm' and resid 116 through 117 Processing sheet with id=AB5, first strand: chain 'm' and resid 245 through 248 removed outlier: 3.587A pdb=" N ASP m 245 " --> pdb=" O ARG m 278 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N MET m 275 " --> pdb=" O VAL m 200 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL m 200 " --> pdb=" O MET m 275 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU m 178 " --> pdb=" O ARG m 199 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN m 171 " --> pdb=" O ILE m 419 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N TRP m 421 " --> pdb=" O ASN m 171 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU m 173 " --> pdb=" O TRP m 421 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ARG m 423 " --> pdb=" O LEU m 173 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU m 175 " --> pdb=" O ARG m 423 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE m 425 " --> pdb=" O LEU m 175 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VAL m 177 " --> pdb=" O ILE m 425 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ARG m 427 " --> pdb=" O VAL m 177 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLU m 179 " --> pdb=" O ARG m 427 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY m 429 " --> pdb=" O GLU m 179 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL m 181 " --> pdb=" O GLY m 429 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N TYR m 431 " --> pdb=" O VAL m 181 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU m 183 " --> pdb=" O TYR m 431 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N THR m 433 " --> pdb=" O LEU m 183 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N MET m 185 " --> pdb=" O THR m 433 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ARG m 427 " --> pdb=" O VAL m 392 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL m 392 " --> pdb=" O ARG m 427 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLY m 429 " --> pdb=" O PHE m 390 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N PHE m 390 " --> pdb=" O GLY m 429 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR m 431 " --> pdb=" O MET m 388 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER m 387 " --> pdb=" O ARG m 323 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLU m 391 " --> pdb=" O LYS m 319 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LYS m 319 " --> pdb=" O GLU m 391 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL m 322 " --> pdb=" O TRP m 353 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TRP m 353 " --> pdb=" O VAL m 322 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE m 324 " --> pdb=" O ILE m 351 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE m 351 " --> pdb=" O ILE m 324 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'm' and resid 270 through 272 removed outlier: 3.535A pdb=" N LEU m 178 " --> pdb=" O ARG m 199 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN m 171 " --> pdb=" O ILE m 419 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N TRP m 421 " --> pdb=" O ASN m 171 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU m 173 " --> pdb=" O TRP m 421 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ARG m 423 " --> pdb=" O LEU m 173 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU m 175 " --> pdb=" O ARG m 423 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE m 425 " --> pdb=" O LEU m 175 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VAL m 177 " --> pdb=" O ILE m 425 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ARG m 427 " --> pdb=" O VAL m 177 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLU m 179 " --> pdb=" O ARG m 427 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY m 429 " --> pdb=" O GLU m 179 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL m 181 " --> pdb=" O GLY m 429 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N TYR m 431 " --> pdb=" O VAL m 181 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU m 183 " --> pdb=" O TYR m 431 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N THR m 433 " --> pdb=" O LEU m 183 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N MET m 185 " --> pdb=" O THR m 433 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'm' and resid 263 through 265 removed outlier: 4.239A pdb=" N ILE m 263 " --> pdb=" O PHE m 214 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'm' and resid 287 through 290 Processing sheet with id=AB9, first strand: chain 'm' and resid 287 through 290 removed outlier: 3.525A pdb=" N VAL m 303 " --> pdb=" O ALA m 368 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 's' and resid 14 through 19 removed outlier: 7.759A pdb=" N THR s 14 " --> pdb=" O ASN s 9 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ASN s 9 " --> pdb=" O THR s 14 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU s 16 " --> pdb=" O ILE s 7 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE s 7 " --> pdb=" O LEU s 16 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS s 56 " --> pdb=" O VAL s 71 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL s 50 " --> pdb=" O ILE s 57 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 's' and resid 118 through 119 1562 hydrogen bonds defined for protein. 4590 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.27 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 3250 1.29 - 1.36: 3228 1.36 - 1.42: 22 1.42 - 1.49: 3248 1.49 - 1.55: 6396 Bond restraints: 16144 Sorted by residual: bond pdb=" C VAL a 535 " pdb=" N PRO a 536 " ideal model delta sigma weight residual 1.335 1.368 -0.033 1.28e-02 6.10e+03 6.76e+00 bond pdb=" C VAL A 535 " pdb=" N PRO A 536 " ideal model delta sigma weight residual 1.335 1.368 -0.033 1.28e-02 6.10e+03 6.74e+00 bond pdb=" C THR b 245 " pdb=" N PRO b 246 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.08e-02 8.57e+03 3.91e+00 bond pdb=" C THR B 245 " pdb=" N PRO B 246 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.08e-02 8.57e+03 3.91e+00 bond pdb=" C GLU b 124 " pdb=" N PRO b 125 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.36e-02 5.41e+03 3.67e+00 ... (remaining 16139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 21728 2.06 - 4.12: 686 4.12 - 6.18: 64 6.18 - 8.24: 15 8.24 - 10.30: 13 Bond angle restraints: 22506 Sorted by residual: angle pdb=" C GLU a 323 " pdb=" N PRO a 324 " pdb=" CA PRO a 324 " ideal model delta sigma weight residual 118.85 127.24 -8.39 1.09e+00 8.42e-01 5.92e+01 angle pdb=" C GLU A 323 " pdb=" N PRO A 324 " pdb=" CA PRO A 324 " ideal model delta sigma weight residual 118.85 127.08 -8.23 1.09e+00 8.42e-01 5.70e+01 angle pdb=" OE1 GLN Y 351 " pdb=" CD GLN Y 351 " pdb=" NE2 GLN Y 351 " ideal model delta sigma weight residual 122.60 115.68 6.92 1.00e+00 1.00e+00 4.78e+01 angle pdb=" OE1 GLN y 351 " pdb=" CD GLN y 351 " pdb=" NE2 GLN y 351 " ideal model delta sigma weight residual 122.60 115.73 6.87 1.00e+00 1.00e+00 4.73e+01 angle pdb=" N ASP a 321 " pdb=" CA ASP a 321 " pdb=" C ASP a 321 " ideal model delta sigma weight residual 111.74 120.45 -8.71 1.35e+00 5.49e-01 4.17e+01 ... (remaining 22501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.50: 8849 6.50 - 13.00: 557 13.00 - 19.51: 96 19.51 - 26.01: 22 26.01 - 32.51: 6 Dihedral angle restraints: 9530 sinusoidal: 28 harmonic: 9502 Sorted by residual: dihedral pdb=" CA SER B 274 " pdb=" C SER B 274 " pdb=" N ASP B 275 " pdb=" CA ASP B 275 " ideal model delta harmonic sigma weight residual -180.00 -149.88 -30.12 0 5.00e+00 4.00e-02 3.63e+01 dihedral pdb=" CA SER b 274 " pdb=" C SER b 274 " pdb=" N ASP b 275 " pdb=" CA ASP b 275 " ideal model delta harmonic sigma weight residual -180.00 -149.91 -30.09 0 5.00e+00 4.00e-02 3.62e+01 dihedral pdb=" CA SER a 458 " pdb=" C SER a 458 " pdb=" N GLU a 459 " pdb=" CA GLU a 459 " ideal model delta harmonic sigma weight residual 180.00 154.18 25.82 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 9527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2440 0.056 - 0.112: 630 0.112 - 0.169: 60 0.169 - 0.225: 6 0.225 - 0.281: 2 Chirality restraints: 3138 Sorted by residual: chirality pdb=" CA ASP A 321 " pdb=" N ASP A 321 " pdb=" C ASP A 321 " pdb=" CB ASP A 321 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA ASP a 321 " pdb=" N ASP a 321 " pdb=" C ASP a 321 " pdb=" CB ASP a 321 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA GLU a 423 " pdb=" N GLU a 423 " pdb=" C GLU a 423 " pdb=" CB GLU a 423 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.99e-01 ... (remaining 3135 not shown) Planarity restraints: 3236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN a 401 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.73e+00 pdb=" C ASN a 401 " -0.038 2.00e-02 2.50e+03 pdb=" O ASN a 401 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA a 402 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 401 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.59e+00 pdb=" C ASN A 401 " 0.037 2.00e-02 2.50e+03 pdb=" O ASN A 401 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA A 402 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE a 420 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.26e+00 pdb=" C ILE a 420 " 0.031 2.00e-02 2.50e+03 pdb=" O ILE a 420 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG a 421 " -0.010 2.00e-02 2.50e+03 ... (remaining 3233 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4064 2.79 - 3.32: 16056 3.32 - 3.84: 24955 3.84 - 4.37: 22143 4.37 - 4.90: 38483 Nonbonded interactions: 105701 Sorted by model distance: nonbonded pdb=" O THR M 299 " pdb=" N LEU M 372 " model vdw 2.260 3.120 nonbonded pdb=" O THR m 299 " pdb=" N LEU m 372 " model vdw 2.260 3.120 nonbonded pdb=" O SER b 274 " pdb=" N TYR b 276 " model vdw 2.350 3.120 nonbonded pdb=" O SER B 274 " pdb=" N TYR B 276 " model vdw 2.351 3.120 nonbonded pdb=" O SER A 419 " pdb=" N GLU A 422 " model vdw 2.353 3.120 ... (remaining 105696 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'S' selection = chain 's' } ncs_group { reference = chain 'Y' selection = chain 'y' } Set up NCS constraints Number of NCS constrained groups: 5 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'a' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'b' } pdb_interpretation.ncs_group { reference = chain 'M' selection = chain 'm' } pdb_interpretation.ncs_group { reference = chain 'S' selection = chain 's' } pdb_interpretation.ncs_group { reference = chain 'Y' selection = chain 'y' } Set refine NCS operators NCS operators will be refined. 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: 2.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 17.400 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 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 : 0.003 0.038 16144 Z= 0.201 Angle : 0.886 10.299 22506 Z= 0.619 Chirality : 0.047 0.281 3138 Planarity : 0.002 0.022 3236 Dihedral : 5.837 32.509 3258 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.79 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.15), residues: 3212 helix: 0.74 (0.12), residues: 1822 sheet: 0.33 (0.28), residues: 340 loop : -1.63 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG Y 352 TYR 0.004 0.000 TYR y 350 PHE 0.000 0.000 PHE A 16 TRP 0.000 0.000 TRP A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.20 (16144) covalent geometry : angle 0.88643 / 0.62 (22506) hydrogen bonds : bond 0.17051 / 13.04 ( 1528) hydrogen bonds : angle 7.17457 / 5.61 ( 4590) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.087 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0106 time to fit residues: 0.2950 Evaluate side-chains 10 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.086 Evaluate side-chains 7 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.093 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0117 time to fit residues: 0.2854 Evaluate side-chains 7 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.106 Evaluate side-chains 13 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.072 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0096 time to fit residues: 0.3266 Evaluate side-chains 13 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.043 Evaluate side-chains 4 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.017 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0041 time to fit residues: 0.0556 Evaluate side-chains 4 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.028 Evaluate side-chains 1 residues out of total 5 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0532 time to fit residues: 0.0578 Evaluate side-chains 0 residues out of total 5 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 197 optimal weight: 0.0070 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 0.0570 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.1980 chunk 298 optimal weight: 0.0170 overall best weight: 1.6556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.042136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.032611 restraints weight = 58267.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.032611 restraints weight = 59675.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.032611 restraints weight = 59675.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.032611 restraints weight = 59675.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.032611 restraints weight = 59675.488| |-----------------------------------------------------------------------------| r_work (final): 0.2730 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.048874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.038983 restraints weight = 35969.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.039411 restraints weight = 30340.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.039735 restraints weight = 26470.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.039932 restraints weight = 23684.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.040167 restraints weight = 21807.984| |-----------------------------------------------------------------------------| r_work (final): 0.3039 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.038948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.034329 restraints weight = 62588.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.033708 restraints weight = 89530.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.033677 restraints weight = 110905.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.033355 restraints weight = 120883.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.033355 restraints weight = 150362.502| |-----------------------------------------------------------------------------| r_work (final): 0.2714 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.041539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.035852 restraints weight = 10087.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.036356 restraints weight = 7869.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.036714 restraints weight = 6456.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.037073 restraints weight = 5558.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.037294 restraints weight = 4844.788| |-----------------------------------------------------------------------------| r_work (final): 0.2823 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.062324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.057251 restraints weight = 483.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.058212 restraints weight = 320.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.059032 restraints weight = 237.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.059632 restraints weight = 176.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.059738 restraints weight = 138.077| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.014 16144 Z= 0.109 Angle : 0.452 7.219 22506 Z= 0.280 Chirality : 0.042 0.138 3138 Planarity : 0.002 0.012 3236 Dihedral : 4.575 28.343 3232 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.92 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.15), residues: 3212 helix: 1.84 (0.12), residues: 1906 sheet: 0.47 (0.28), residues: 332 loop : -1.59 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Y 352 TYR 0.007 0.000 TYR Y 350 PHE 0.000 0.000 PHE A 16 TRP 0.000 0.000 TRP A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00147 / 0.11 (16144) covalent geometry : angle 0.45222 / 0.28 (22506) hydrogen bonds : bond 0.03606 / 2.76 ( 1528) hydrogen bonds : angle 4.53012 / 3.54 ( 4590) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.072 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0128 time to fit residues: 0.3936 Evaluate side-chains 10 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.118 Evaluate side-chains 7 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.093 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0118 time to fit residues: 0.2695 Evaluate side-chains 7 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.056 Evaluate side-chains 13 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.092 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0089 time to fit residues: 0.2899 Evaluate side-chains 13 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.075 Evaluate side-chains 4 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.029 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0047 time to fit residues: 0.0731 Evaluate side-chains 4 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.017 Evaluate side-chains 1 residues out of total 5 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0118 time to fit residues: 0.0147 Evaluate side-chains 1 residues out of total 5 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 119 optimal weight: 1.9990 chunk 283 optimal weight: 4.9990 chunk 216 optimal weight: 6.9990 chunk 164 optimal weight: 0.7980 chunk 257 optimal weight: 30.0000 chunk 48 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 chunk 247 optimal weight: 6.9990 chunk 151 optimal weight: 20.0000 chunk 253 optimal weight: 10.0000 chunk 239 optimal weight: 8.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.043364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.033978 restraints weight = 41281.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.033501 restraints weight = 53526.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.033142 restraints weight = 64842.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.032893 restraints weight = 75327.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.032662 restraints weight = 83782.064| |-----------------------------------------------------------------------------| r_work (final): 0.2776 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.045518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.034524 restraints weight = 42381.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.034524 restraints weight = 40554.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.034524 restraints weight = 40554.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.034524 restraints weight = 40554.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.034524 restraints weight = 40554.688| |-----------------------------------------------------------------------------| r_work (final): 0.2720 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.037027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.032092 restraints weight = 62934.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.031524 restraints weight = 84745.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.031012 restraints weight = 108993.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.030814 restraints weight = 131199.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.030814 restraints weight = 145723.356| |-----------------------------------------------------------------------------| r_work (final): 0.2634 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.038701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.033566 restraints weight = 10157.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.034007 restraints weight = 8184.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.034351 restraints weight = 6851.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.034652 restraints weight = 5905.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.034652 restraints weight = 5156.890| |-----------------------------------------------------------------------------| r_work (final): 0.2750 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.071581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.056714 restraints weight = 445.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.056714 restraints weight = 441.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.056714 restraints weight = 441.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.056714 restraints weight = 441.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.056714 restraints weight = 441.072| |-----------------------------------------------------------------------------| r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5587 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 16144 Z= 0.147 Angle : 0.459 7.072 22506 Z= 0.289 Chirality : 0.042 0.207 3138 Planarity : 0.002 0.019 3236 Dihedral : 4.299 24.139 3232 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.73 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 40.00 % Favored : 60.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.15), residues: 3212 helix: 2.30 (0.12), residues: 1896 sheet: 0.11 (0.27), residues: 360 loop : -1.50 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.004 ARG y 352 TYR 0.002 0.000 TYR y 350 PHE 0.000 0.000 PHE A 16 TRP 0.000 0.000 TRP A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.15 (16144) covalent geometry : angle 0.45929 / 0.29 (22506) hydrogen bonds : bond 0.03601 / 2.75 ( 1528) hydrogen bonds : angle 4.29957 / 3.36 ( 4590) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.119 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0139 time to fit residues: 0.4367 Evaluate side-chains 10 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.113 Evaluate side-chains 7 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.093 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0120 time to fit residues: 0.2889 Evaluate side-chains 7 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.096 Evaluate side-chains 13 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.080 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0093 time to fit residues: 0.3250 Evaluate side-chains 13 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.072 Evaluate side-chains 4 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.034 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0047 time to fit residues: 0.0784 Evaluate side-chains 4 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.027 Evaluate side-chains 0 residues out of total 5 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0038 Evaluate side-chains 0 residues out of total 5 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 126 optimal weight: 20.0000 chunk 314 optimal weight: 20.0000 chunk 255 optimal weight: 3.9990 chunk 57 optimal weight: 20.0000 chunk 286 optimal weight: 30.0000 chunk 238 optimal weight: 0.9980 chunk 142 optimal weight: 20.0000 chunk 275 optimal weight: 9.9990 chunk 167 optimal weight: 0.1980 chunk 129 optimal weight: 0.2980 chunk 288 optimal weight: 10.0000 overall best weight: 3.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.039660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.030154 restraints weight = 58592.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.030154 restraints weight = 61396.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.030154 restraints weight = 61396.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.030154 restraints weight = 61396.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.030154 restraints weight = 61396.993| |-----------------------------------------------------------------------------| r_work (final): 0.2655 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.045405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.034581 restraints weight = 41885.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.034581 restraints weight = 40127.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.034581 restraints weight = 40127.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.034581 restraints weight = 40127.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.034581 restraints weight = 40127.771| |-----------------------------------------------------------------------------| r_work (final): 0.3160 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.041463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.034379 restraints weight = 29692.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.034512 restraints weight = 28300.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.034587 restraints weight = 26897.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.034706 restraints weight = 25981.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.034721 restraints weight = 25245.280| |-----------------------------------------------------------------------------| r_work (final): 0.2918 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.038143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.033169 restraints weight = 10449.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.033518 restraints weight = 8564.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.033836 restraints weight = 7382.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.034125 restraints weight = 6458.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.034305 restraints weight = 5709.835| |-----------------------------------------------------------------------------| r_work (final): 0.2729 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.069001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.059871 restraints weight = 427.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.061442 restraints weight = 340.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.061442 restraints weight = 281.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.061452 restraints weight = 281.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.061451 restraints weight = 281.246| |-----------------------------------------------------------------------------| r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4992 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.027 16144 Z= 0.099 Angle : 0.401 6.621 22506 Z= 0.248 Chirality : 0.041 0.134 3138 Planarity : 0.002 0.012 3236 Dihedral : 3.955 23.977 3232 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 0.81 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.48 % Favored : 95.21 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.15), residues: 3212 helix: 2.51 (0.12), residues: 1928 sheet: 0.40 (0.27), residues: 350 loop : -1.40 (0.21), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Y 352 TYR 0.004 0.000 TYR Y 350 PHE 0.000 0.000 PHE A 16 TRP 0.000 0.000 TRP A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00137 / 0.10 (16144) covalent geometry : angle 0.40089 / 0.25 (22506) hydrogen bonds : bond 0.03020 / 2.30 ( 1528) hydrogen bonds : angle 3.84095 / 3.00 ( 4590) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.112 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0138 time to fit residues: 0.4213 Evaluate side-chains 10 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.112 Evaluate side-chains 7 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.094 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0119 time to fit residues: 0.2893 Evaluate side-chains 7 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.088 Evaluate side-chains 13 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.072 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0093 time to fit residues: 0.3181 Evaluate side-chains 13 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.054 Evaluate side-chains 4 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.025 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0043 time to fit residues: 0.0666 Evaluate side-chains 4 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.028 Evaluate side-chains 1 residues out of total 5 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0505 time to fit residues: 0.0553 Evaluate side-chains 0 residues out of total 5 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 227 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 277 optimal weight: 20.0000 chunk 271 optimal weight: 20.0000 chunk 18 optimal weight: 30.0000 chunk 86 optimal weight: 20.0000 chunk 184 optimal weight: 0.0270 chunk 283 optimal weight: 0.0980 chunk 108 optimal weight: 0.9990 chunk 248 optimal weight: 20.0000 chunk 117 optimal weight: 20.0000 overall best weight: 3.4244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.040763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.030604 restraints weight = 41178.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.030604 restraints weight = 45990.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.030604 restraints weight = 45990.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.030604 restraints weight = 45990.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.030604 restraints weight = 45990.299| |-----------------------------------------------------------------------------| r_work (final): 0.2694 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.044486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.033926 restraints weight = 41109.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.033926 restraints weight = 39754.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.033926 restraints weight = 39754.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.033926 restraints weight = 39754.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.033926 restraints weight = 39754.591| |-----------------------------------------------------------------------------| r_work (final): 0.2705 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.037305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.033525 restraints weight = 59749.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.033167 restraints weight = 82819.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.033136 restraints weight = 107795.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.033096 restraints weight = 107484.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.033096 restraints weight = 104536.650| |-----------------------------------------------------------------------------| r_work (final): 0.3170 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.037592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.032572 restraints weight = 10847.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.032934 restraints weight = 8844.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.033164 restraints weight = 7551.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.033489 restraints weight = 6757.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.033720 restraints weight = 5995.444| |-----------------------------------------------------------------------------| r_work (final): 0.2704 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.062842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.055752 restraints weight = 528.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.056833 restraints weight = 392.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.057582 restraints weight = 314.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.058169 restraints weight = 266.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.058638 restraints weight = 232.692| |-----------------------------------------------------------------------------| r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5382 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 16144 Z= 0.117 Angle : 0.405 6.341 22506 Z= 0.255 Chirality : 0.041 0.133 3138 Planarity : 0.002 0.016 3236 Dihedral : 3.907 27.351 3232 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.92 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.16), residues: 3212 helix: 2.73 (0.12), residues: 1926 sheet: 0.87 (0.29), residues: 310 loop : -1.31 (0.21), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG Y 352 TYR 0.006 0.000 TYR y 350 PHE 0.000 0.000 PHE A 16 TRP 0.000 0.000 TRP A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00160 / 0.12 (16144) covalent geometry : angle 0.40522 / 0.26 (22506) hydrogen bonds : bond 0.03044 / 2.33 ( 1528) hydrogen bonds : angle 3.79747 / 2.98 ( 4590) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.110 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0133 time to fit residues: 0.4049 Evaluate side-chains 10 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.106 Evaluate side-chains 7 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.101 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0119 time to fit residues: 0.2626 Evaluate side-chains 7 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.097 Evaluate side-chains 13 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.072 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0104 time to fit residues: 0.3358 Evaluate side-chains 13 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.072 Evaluate side-chains 4 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.030 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0046 time to fit residues: 0.0708 Evaluate side-chains 4 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.017 Evaluate side-chains 1 residues out of total 5 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0499 time to fit residues: 0.0548 Evaluate side-chains 0 residues out of total 5 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 10 optimal weight: 9.9990 chunk 109 optimal weight: 50.0000 chunk 228 optimal weight: 0.0470 chunk 246 optimal weight: 20.0000 chunk 79 optimal weight: 8.9990 chunk 199 optimal weight: 40.0000 chunk 187 optimal weight: 10.0000 chunk 158 optimal weight: 20.0000 chunk 145 optimal weight: 30.0000 chunk 313 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 overall best weight: 5.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.036078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.032058 restraints weight = 105880.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.032104 restraints weight = 101507.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.032130 restraints weight = 98065.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.032170 restraints weight = 96496.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.032170 restraints weight = 93949.021| |-----------------------------------------------------------------------------| r_work (final): 0.2990 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.044215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.035142 restraints weight = 36979.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.035628 restraints weight = 29483.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 15)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.035888 restraints weight = 24644.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.036230 restraints weight = 21669.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.036351 restraints weight = 19448.491| |-----------------------------------------------------------------------------| r_work (final): 0.2921 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.035731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.032042 restraints weight = 61134.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.031752 restraints weight = 76262.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.031709 restraints weight = 89333.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.031686 restraints weight = 91453.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.031686 restraints weight = 91457.921| |-----------------------------------------------------------------------------| r_work (final): 0.3146 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.035514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.031161 restraints weight = 11027.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.031523 restraints weight = 8797.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.031923 restraints weight = 7416.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.032187 restraints weight = 6292.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.032340 restraints weight = 5522.362| |-----------------------------------------------------------------------------| r_work (final): 0.2665 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.054727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.051076 restraints weight = 478.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.051775 restraints weight = 314.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.052297 restraints weight = 238.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.052804 restraints weight = 185.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.053124 restraints weight = 146.372| |-----------------------------------------------------------------------------| r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.4974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16144 Z= 0.153 Angle : 0.447 6.179 22506 Z= 0.288 Chirality : 0.041 0.132 3138 Planarity : 0.002 0.014 3236 Dihedral : 4.433 31.750 3232 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.92 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.15), residues: 3212 helix: 2.32 (0.12), residues: 1920 sheet: 0.39 (0.28), residues: 342 loop : -1.24 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG y 352 TYR 0.020 0.001 TYR y 350 PHE 0.000 0.000 PHE A 16 TRP 0.000 0.000 TRP A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.15 (16144) covalent geometry : angle 0.44746 / 0.29 (22506) hydrogen bonds : bond 0.03674 / 2.81 ( 1528) hydrogen bonds : angle 4.35192 / 3.41 ( 4590) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.114 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0115 time to fit residues: 0.3656 Evaluate side-chains 10 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.118 Evaluate side-chains 7 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.097 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0121 time to fit residues: 0.2969 Evaluate side-chains 7 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.092 Evaluate side-chains 13 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.069 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0094 time to fit residues: 0.3214 Evaluate side-chains 13 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.069 Evaluate side-chains 4 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.029 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0047 time to fit residues: 0.0696 Evaluate side-chains 4 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.027 Evaluate side-chains 1 residues out of total 5 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0182 time to fit residues: 0.0227 Evaluate side-chains 1 residues out of total 5 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 314 optimal weight: 20.0000 chunk 187 optimal weight: 5.9990 chunk 280 optimal weight: 20.0000 chunk 67 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 244 optimal weight: 0.6980 chunk 265 optimal weight: 30.0000 chunk 274 optimal weight: 0.9980 chunk 299 optimal weight: 50.0000 chunk 315 optimal weight: 0.6980 overall best weight: 2.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.036570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.032325 restraints weight = 107402.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.032368 restraints weight = 102813.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.032369 restraints weight = 99777.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.032369 restraints weight = 99739.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.032369 restraints weight = 99739.471| |-----------------------------------------------------------------------------| r_work (final): 0.2945 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.044654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.035359 restraints weight = 37120.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.035841 restraints weight = 29310.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.036194 restraints weight = 24644.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.036384 restraints weight = 21522.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.036668 restraints weight = 19393.628| |-----------------------------------------------------------------------------| r_work (final): 0.2929 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.035800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.031772 restraints weight = 64146.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.031780 restraints weight = 62358.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.031780 restraints weight = 61735.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.031780 restraints weight = 61735.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.031780 restraints weight = 61735.717| |-----------------------------------------------------------------------------| r_work (final): 0.3045 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.035890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.031321 restraints weight = 11010.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.031765 restraints weight = 8859.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.032185 restraints weight = 7414.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.032452 restraints weight = 6297.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.032614 restraints weight = 5500.550| |-----------------------------------------------------------------------------| r_work (final): 0.2689 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.068872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.063704 restraints weight = 517.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.065570 restraints weight = 294.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.066605 restraints weight = 191.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.067217 restraints weight = 133.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.067698 restraints weight = 97.947| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.5087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.017 16144 Z= 0.097 Angle : 0.378 6.377 22506 Z= 0.237 Chirality : 0.040 0.134 3138 Planarity : 0.002 0.008 3236 Dihedral : 3.870 26.650 3232 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.92 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.16), residues: 3212 helix: 2.67 (0.12), residues: 1942 sheet: 0.70 (0.29), residues: 316 loop : -1.23 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.002 ARG Y 352 TYR 0.005 0.000 TYR y 350 PHE 0.000 0.000 PHE A 16 TRP 0.000 0.000 TRP A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00131 / 0.10 (16144) covalent geometry : angle 0.37801 / 0.24 (22506) hydrogen bonds : bond 0.03051 / 2.33 ( 1528) hydrogen bonds : angle 3.85803 / 3.03 ( 4590) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.114 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0181 time to fit residues: 0.5067 Evaluate side-chains 10 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.084 Evaluate side-chains 7 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.090 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0116 time to fit residues: 0.2805 Evaluate side-chains 7 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.092 Evaluate side-chains 13 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.069 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0096 time to fit residues: 0.3243 Evaluate side-chains 13 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.070 Evaluate side-chains 4 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.028 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0047 time to fit residues: 0.0720 Evaluate side-chains 4 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.029 Evaluate side-chains 1 residues out of total 5 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0190 time to fit residues: 0.0235 Evaluate side-chains 1 residues out of total 5 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 147 optimal weight: 30.0000 chunk 222 optimal weight: 7.9990 chunk 138 optimal weight: 0.0670 chunk 40 optimal weight: 5.9990 chunk 300 optimal weight: 0.0030 chunk 13 optimal weight: 40.0000 chunk 50 optimal weight: 30.0000 chunk 290 optimal weight: 40.0000 chunk 252 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 165 optimal weight: 7.9990 overall best weight: 3.0134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.036624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.032389 restraints weight = 106439.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.032426 restraints weight = 102422.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.032426 restraints weight = 99990.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.032426 restraints weight = 99990.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.032426 restraints weight = 99990.541| |-----------------------------------------------------------------------------| r_work (final): 0.2976 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.044503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.035330 restraints weight = 36612.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.035792 restraints weight = 29149.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.036165 restraints weight = 24527.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.036356 restraints weight = 21359.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.036627 restraints weight = 19365.674| |-----------------------------------------------------------------------------| r_work (final): 0.2932 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.036244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.032012 restraints weight = 63908.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.032036 restraints weight = 62132.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.032088 restraints weight = 61033.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 15)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.032088 restraints weight = 58732.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.032088 restraints weight = 58739.514| |-----------------------------------------------------------------------------| r_work (final): 0.3151 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.035575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.031210 restraints weight = 10624.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.031585 restraints weight = 8605.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.031964 restraints weight = 7292.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.032236 restraints weight = 6238.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.032469 restraints weight = 5466.387| |-----------------------------------------------------------------------------| r_work (final): 0.2684 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.060068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.055928 restraints weight = 483.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.056936 restraints weight = 316.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.057522 restraints weight = 231.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.058014 restraints weight = 180.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.058345 restraints weight = 142.667| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.5340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.017 16144 Z= 0.101 Angle : 0.372 6.433 22506 Z= 0.234 Chirality : 0.040 0.132 3138 Planarity : 0.002 0.011 3236 Dihedral : 3.786 25.527 3232 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.35 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.16), residues: 3212 helix: 2.89 (0.12), residues: 1934 sheet: 0.77 (0.29), residues: 314 loop : -1.10 (0.22), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG Y 352 TYR 0.004 0.000 TYR y 350 PHE 0.000 0.000 PHE A 16 TRP 0.000 0.000 TRP A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00135 / 0.10 (16144) covalent geometry : angle 0.37217 / 0.23 (22506) hydrogen bonds : bond 0.02977 / 2.27 ( 1528) hydrogen bonds : angle 3.77102 / 2.95 ( 4590) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.113 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0131 time to fit residues: 0.3549 Evaluate side-chains 10 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.074 Evaluate side-chains 7 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.088 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0114 time to fit residues: 0.2737 Evaluate side-chains 7 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.093 Evaluate side-chains 13 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.071 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0095 time to fit residues: 0.3175 Evaluate side-chains 13 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.074 Evaluate side-chains 4 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.028 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0046 time to fit residues: 0.0718 Evaluate side-chains 4 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.027 Evaluate side-chains 1 residues out of total 5 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0233 time to fit residues: 0.0278 Evaluate side-chains 1 residues out of total 5 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 165 optimal weight: 5.9990 chunk 260 optimal weight: 7.9990 chunk 211 optimal weight: 8.9990 chunk 267 optimal weight: 20.0000 chunk 177 optimal weight: 0.0980 chunk 241 optimal weight: 0.9990 chunk 240 optimal weight: 0.2980 chunk 223 optimal weight: 1.9990 chunk 230 optimal weight: 20.0000 chunk 44 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.037422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.030779 restraints weight = 77002.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.030814 restraints weight = 75023.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.030848 restraints weight = 73308.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.030879 restraints weight = 71942.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.030898 restraints weight = 70861.643| |-----------------------------------------------------------------------------| r_work (final): 0.2757 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.043848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.032709 restraints weight = 41589.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.032726 restraints weight = 40884.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.032759 restraints weight = 40502.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.032760 restraints weight = 39913.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 12)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.032760 restraints weight = 39882.961| |-----------------------------------------------------------------------------| r_work (final): 0.2700 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.036641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.032389 restraints weight = 62392.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.032389 restraints weight = 62366.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.032389 restraints weight = 62365.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.032389 restraints weight = 62365.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.032389 restraints weight = 62365.939| |-----------------------------------------------------------------------------| r_work (final): 0.3169 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.036425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.031637 restraints weight = 11155.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.032177 restraints weight = 8712.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.032467 restraints weight = 7078.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.032867 restraints weight = 6121.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.033126 restraints weight = 5273.944| |-----------------------------------------------------------------------------| r_work (final): 0.2710 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.062170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.057127 restraints weight = 499.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.058532 restraints weight = 302.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.059382 restraints weight = 212.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.059954 restraints weight = 156.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.060433 restraints weight = 119.313| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6106 moved from start: 0.5388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.014 16144 Z= 0.072 Angle : 0.342 4.682 22506 Z= 0.211 Chirality : 0.040 0.131 3138 Planarity : 0.001 0.008 3236 Dihedral : 3.402 19.741 3232 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.17 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.49 (0.16), residues: 3212 helix: 3.07 (0.12), residues: 1946 sheet: 0.63 (0.30), residues: 292 loop : -1.14 (0.21), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Y 352 TYR 0.002 0.000 TYR Y 350 PHE 0.000 0.000 PHE A 16 TRP 0.000 0.000 TRP A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00096 / 0.07 (16144) covalent geometry : angle 0.34208 / 0.21 (22506) hydrogen bonds : bond 0.02603 / 1.99 ( 1528) hydrogen bonds : angle 3.41776 / 2.68 ( 4590) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.110 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0134 time to fit residues: 0.4030 Evaluate side-chains 10 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.112 Evaluate side-chains 7 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.093 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0114 time to fit residues: 0.2650 Evaluate side-chains 7 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.096 Evaluate side-chains 13 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.075 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0094 time to fit residues: 0.3232 Evaluate side-chains 13 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.070 Evaluate side-chains 4 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.027 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0044 time to fit residues: 0.0687 Evaluate side-chains 4 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.029 Evaluate side-chains 1 residues out of total 5 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0202 time to fit residues: 0.0249 Evaluate side-chains 1 residues out of total 5 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 212 optimal weight: 1.9990 chunk 186 optimal weight: 50.0000 chunk 39 optimal weight: 30.0000 chunk 115 optimal weight: 20.0000 chunk 154 optimal weight: 20.0000 chunk 100 optimal weight: 7.9990 chunk 22 optimal weight: 30.0000 chunk 231 optimal weight: 0.0970 chunk 53 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 30.0000 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.040735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.032705 restraints weight = 49891.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.032479 restraints weight = 58829.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.032295 restraints weight = 66989.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.032220 restraints weight = 73525.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.032220 restraints weight = 76808.494| |-----------------------------------------------------------------------------| r_work (final): 0.2906 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.044191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.035165 restraints weight = 36214.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.035644 restraints weight = 28653.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.035902 restraints weight = 23950.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.036245 restraints weight = 21035.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.036457 restraints weight = 18857.006| |-----------------------------------------------------------------------------| r_work (final): 0.2930 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.035892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.031688 restraints weight = 62755.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.031703 restraints weight = 61278.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.031703 restraints weight = 60762.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.031703 restraints weight = 60762.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.031703 restraints weight = 60762.555| |-----------------------------------------------------------------------------| r_work (final): 0.3152 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.035380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.031124 restraints weight = 11051.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.031535 restraints weight = 8819.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.031995 restraints weight = 7318.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.032232 restraints weight = 6028.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.032517 restraints weight = 5267.906| |-----------------------------------------------------------------------------| r_work (final): 0.2678 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.063567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.056641 restraints weight = 415.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.057979 restraints weight = 303.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.058911 restraints weight = 240.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.059481 restraints weight = 199.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.060010 restraints weight = 168.810| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.5792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 16144 Z= 0.124 Angle : 0.377 4.477 22506 Z= 0.244 Chirality : 0.040 0.131 3138 Planarity : 0.002 0.009 3236 Dihedral : 3.695 23.348 3232 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.10 % Favored : 93.77 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.16), residues: 3212 helix: 2.90 (0.12), residues: 1942 sheet: 0.85 (0.29), residues: 314 loop : -0.98 (0.22), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.002 ARG Y 352 TYR 0.005 0.000 TYR y 350 PHE 0.000 0.000 PHE A 16 TRP 0.000 0.000 TRP A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00167 / 0.12 (16144) covalent geometry : angle 0.37657 / 0.24 (22506) hydrogen bonds : bond 0.03101 / 2.37 ( 1528) hydrogen bonds : angle 3.82254 / 2.99 ( 4590) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6424 Ramachandran restraints generated. 3212 Oldfield, 0 Emsley, 3212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.118 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0099 time to fit residues: 0.3492 Evaluate side-chains 10 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.112 Evaluate side-chains 7 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.096 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0120 time to fit residues: 0.2873 Evaluate side-chains 7 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.095 Evaluate side-chains 13 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.076 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0096 time to fit residues: 0.3240 Evaluate side-chains 13 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.070 Evaluate side-chains 4 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.028 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0046 time to fit residues: 0.0716 Evaluate side-chains 4 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.056 Evaluate side-chains 1 residues out of total 5 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0216 time to fit residues: 0.0267 Evaluate side-chains 1 residues out of total 5 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 263 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 265 optimal weight: 40.0000 chunk 96 optimal weight: 6.9990 chunk 306 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 226 optimal weight: 0.8980 chunk 214 optimal weight: 0.0270 chunk 157 optimal weight: 10.0000 chunk 184 optimal weight: 20.0000 chunk 211 optimal weight: 5.9990 overall best weight: 3.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.037042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.029411 restraints weight = 107092.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.029392 restraints weight = 109666.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.029392 restraints weight = 111143.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.029392 restraints weight = 111143.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.029392 restraints weight = 111143.516| |-----------------------------------------------------------------------------| r_work (final): 0.2635 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.043912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.034962 restraints weight = 36539.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.035451 restraints weight = 28712.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.035770 restraints weight = 23835.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.036038 restraints weight = 20902.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.036294 restraints weight = 18722.672| |-----------------------------------------------------------------------------| r_work (final): 0.2779 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.036857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.032653 restraints weight = 63243.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.032719 restraints weight = 61248.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.032759 restraints weight = 58744.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.032794 restraints weight = 57132.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.032846 restraints weight = 55651.157| |-----------------------------------------------------------------------------| r_work (final): 0.3137 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.035200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.030905 restraints weight = 11402.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.031336 restraints weight = 8965.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.031639 restraints weight = 7410.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.032090 restraints weight = 6434.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.032378 restraints weight = 5462.785| |-----------------------------------------------------------------------------| r_work (final): 0.2678 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.059867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.051275 restraints weight = 466.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.053081 restraints weight = 328.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.054277 restraints weight = 257.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.055122 restraints weight = 214.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.055698 restraints weight = 184.221| |-----------------------------------------------------------------------------| r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5784 moved from start: 0.6109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.013 16144 Z= 0.107 Angle : 0.361 4.668 22506 Z= 0.231 Chirality : 0.040 0.131 3138 Planarity : 0.002 0.009 3236 Dihedral : 3.639 23.023 3232 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.67 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.16), residues: 3212 helix: 2.91 (0.12), residues: 1942 sheet: 0.75 (0.29), residues: 314 loop : -1.03 (0.22), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG y 352 TYR 0.005 0.000 TYR y 350 PHE 0.000 0.000 PHE A 16 TRP 0.000 0.000 TRP A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00143 / 0.11 (16144) covalent geometry : angle 0.36064 / 0.23 (22506) hydrogen bonds : bond 0.02963 / 2.26 ( 1528) hydrogen bonds : angle 3.74497 / 2.94 ( 4590) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1785.87 seconds wall clock time: 31 minutes 11.92 seconds (1871.92 seconds total)