Starting phenix.real_space_refine on Sun Aug 24 02:13:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rwa_24712/08_2025/7rwa_24712.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rwa_24712/08_2025/7rwa_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7rwa_24712/08_2025/7rwa_24712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rwa_24712/08_2025/7rwa_24712.map" model { file = "/net/cci-nas-00/data/ceres_data/7rwa_24712/08_2025/7rwa_24712.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rwa_24712/08_2025/7rwa_24712.cif" } 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-2.0-5787/lib/python3.9/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: 5.08, per 1000 atoms: 0.31 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: 1.82 Conformation dependent library (CDL) restraints added in 803.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.75 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: 2.96 Time building geometry restraints manager: 2.31 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: 0.05 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: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.420 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 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 aren 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 covalent geometry : bond 0.00278 (16144) covalent geometry : angle 0.88643 (22506) hydrogen bonds : bond 0.17051 ( 1528) hydrogen bonds : angle 7.17457 ( 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 : 0.067 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0123 time to fit residues: 0.3510 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 : 0.115 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 : 0.104 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0129 time to fit residues: 0.2926 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 : 0.057 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 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0096 time to fit residues: 0.3215 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 : 0.027 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0049 time to fit residues: 0.0730 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: 0.0510 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=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... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- 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: 0.6646 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 aren 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 covalent geometry : bond 0.00147 (16144) covalent geometry : angle 0.45222 (22506) hydrogen bonds : bond 0.03606 ( 1528) hydrogen bonds : angle 4.53012 ( 4590) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 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 : 0.103 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0155 time to fit residues: 0.4309 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 : 0.068 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: 0.0120 time to fit residues: 0.2849 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 : 0.059 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 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0065 time to fit residues: 0.2127 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 : 0.019 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0038 time to fit residues: 0.0701 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 : 0.031 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: 0.0204 time to fit residues: 0.0256 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 119 optimal weight: 1.9990 chunk 283 optimal weight: 40.0000 chunk 216 optimal weight: 0.9980 chunk 164 optimal weight: 10.0000 chunk 257 optimal weight: 30.0000 chunk 48 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 247 optimal weight: 6.9990 chunk 151 optimal weight: 0.0030 chunk 253 optimal weight: 10.0000 chunk 239 optimal weight: 8.9990 overall best weight: 2.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.041646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.032204 restraints weight = 56264.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.032201 restraints weight = 58579.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.032201 restraints weight = 58666.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.032201 restraints weight = 58666.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.032201 restraints weight = 58666.573| |-----------------------------------------------------------------------------| r_work (final): 0.3104 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.049231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.039092 restraints weight = 35193.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.039546 restraints weight = 29242.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.039895 restraints weight = 25117.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.040158 restraints weight = 22179.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.040252 restraints weight = 20186.526| |-----------------------------------------------------------------------------| r_work (final): 0.3036 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.038449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.033434 restraints weight = 62773.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.032834 restraints weight = 85205.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.032824 restraints weight = 106301.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.032762 restraints weight = 107632.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.032762 restraints weight = 124434.683| |-----------------------------------------------------------------------------| r_work (final): 0.2687 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.041234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.035464 restraints weight = 9749.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.035953 restraints weight = 7773.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.036318 restraints weight = 6467.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.036638 restraints weight = 5583.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.036810 restraints weight = 4929.926| |-----------------------------------------------------------------------------| r_work (final): 0.2809 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.063892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.060200 restraints weight = 523.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.061238 restraints weight = 281.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.061903 restraints weight = 175.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.062375 restraints weight = 118.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.062797 restraints weight = 85.237| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5906 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16144 Z= 0.144 Angle : 0.541 7.367 22506 Z= 0.341 Chirality : 0.045 0.197 3138 Planarity : 0.004 0.046 3236 Dihedral : 4.642 25.915 3232 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.73 % 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 aren not related in a simple way. whole: 0.27 (0.15), residues: 3212 helix: 1.27 (0.12), residues: 1916 sheet: 0.19 (0.27), residues: 328 loop : -2.08 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 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 covalent geometry : bond 0.00200 (16144) covalent geometry : angle 0.54135 (22506) hydrogen bonds : bond 0.03698 ( 1528) hydrogen bonds : angle 4.55529 ( 4590) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 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: 0.0143 time to fit residues: 0.4248 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 : 0.080 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 : 0.069 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0081 time to fit residues: 0.1841 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 : 0.068 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0096 time to fit residues: 0.3208 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 : 0.027 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0048 time to fit residues: 0.0709 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 : 0.019 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 : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0030 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 : 0.002 ------------------------------------------------------------------------------- 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: 0.0370 chunk 314 optimal weight: 20.0000 chunk 255 optimal weight: 40.0000 chunk 57 optimal weight: 20.0000 chunk 286 optimal weight: 20.0000 chunk 238 optimal weight: 40.0000 chunk 142 optimal weight: 30.0000 chunk 275 optimal weight: 3.9990 chunk 167 optimal weight: 50.0000 chunk 129 optimal weight: 0.0270 chunk 288 optimal weight: 10.0000 overall best weight: 6.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.041285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.031615 restraints weight = 58546.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.031601 restraints weight = 60004.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.031601 restraints weight = 60429.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.031601 restraints weight = 60429.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.031601 restraints weight = 60429.859| |-----------------------------------------------------------------------------| r_work (final): 0.2695 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.048669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.038790 restraints weight = 36782.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.039213 restraints weight = 30817.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.039551 restraints weight = 26725.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.039801 restraints weight = 23858.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.040015 restraints weight = 21723.842| |-----------------------------------------------------------------------------| r_work (final): 0.3034 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.043445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.036431 restraints weight = 29699.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.036517 restraints weight = 28189.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.036628 restraints weight = 27222.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.036632 restraints weight = 26401.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.036632 restraints weight = 26353.558| |-----------------------------------------------------------------------------| r_work (final): 0.2967 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.041233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.035426 restraints weight = 9914.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.035926 restraints weight = 7872.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.036308 restraints weight = 6534.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 15)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.036572 restraints weight = 5612.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.036839 restraints weight = 5007.564| |-----------------------------------------------------------------------------| r_work (final): 0.2810 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.067613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.063250 restraints weight = 459.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.064066 restraints weight = 272.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.064842 restraints weight = 192.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.065331 restraints weight = 140.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.065821 restraints weight = 110.628| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16144 Z= 0.144 Angle : 0.541 7.383 22506 Z= 0.341 Chirality : 0.045 0.196 3138 Planarity : 0.004 0.046 3236 Dihedral : 4.642 25.914 3232 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.73 % 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 aren not related in a simple way. whole: 0.27 (0.15), residues: 3212 helix: 1.27 (0.12), residues: 1916 sheet: 0.19 (0.27), residues: 328 loop : -2.09 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 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 covalent geometry : bond 0.00199 (16144) covalent geometry : angle 0.54130 (22506) hydrogen bonds : bond 0.03698 ( 1528) hydrogen bonds : angle 4.55534 ( 4590) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 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: 0.0127 time to fit residues: 0.4020 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 : 0.098 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 : 0.091 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0121 time to fit residues: 0.2825 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 : 0.060 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: 0.0100 time to fit residues: 0.3343 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: 0.0049 time to fit residues: 0.0726 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 0 residues out of total 5 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0027 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 : 0.002 ------------------------------------------------------------------------------- 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: 50.0000 chunk 67 optimal weight: 50.0000 chunk 277 optimal weight: 4.9990 chunk 271 optimal weight: 5.9990 chunk 18 optimal weight: 40.0000 chunk 86 optimal weight: 50.0000 chunk 184 optimal weight: 5.9990 chunk 283 optimal weight: 40.0000 chunk 108 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.041285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.031675 restraints weight = 56907.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.031675 restraints weight = 58504.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.031675 restraints weight = 58507.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.031675 restraints weight = 58510.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.031675 restraints weight = 58510.759| |-----------------------------------------------------------------------------| r_work (final): 0.2698 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.048669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.038846 restraints weight = 35819.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.039253 restraints weight = 30308.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.039504 restraints weight = 26300.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.039834 restraints weight = 23596.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.039959 restraints weight = 21531.086| |-----------------------------------------------------------------------------| r_work (final): 0.3032 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.038449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.033598 restraints weight = 65920.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.032148 restraints weight = 108467.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.032137 restraints weight = 133893.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.031753 restraints weight = 141763.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.031753 restraints weight = 160062.392| |-----------------------------------------------------------------------------| r_work (final): 0.2641 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.041233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.035388 restraints weight = 10074.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.035885 restraints weight = 7986.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.036270 restraints weight = 6636.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.036582 restraints weight = 5700.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.036833 restraints weight = 5034.451| |-----------------------------------------------------------------------------| r_work (final): 0.2810 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.067613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.063142 restraints weight = 496.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.064153 restraints weight = 279.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.064872 restraints weight = 190.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.065347 restraints weight = 139.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.065827 restraints weight = 110.047| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16144 Z= 0.144 Angle : 0.541 7.383 22506 Z= 0.341 Chirality : 0.045 0.196 3138 Planarity : 0.004 0.046 3236 Dihedral : 4.642 25.914 3232 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.73 % 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 aren not related in a simple way. whole: 0.27 (0.15), residues: 3212 helix: 1.27 (0.12), residues: 1916 sheet: 0.19 (0.27), residues: 328 loop : -2.09 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 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 covalent geometry : bond 0.00199 (16144) covalent geometry : angle 0.54130 (22506) hydrogen bonds : bond 0.03698 ( 1528) hydrogen bonds : angle 4.55534 ( 4590) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 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 : 0.088 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0126 time to fit residues: 0.3547 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 : 0.060 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0124 time to fit residues: 0.2627 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 : 0.079 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0102 time to fit residues: 0.3400 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 : 0.049 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: 0.0042 time to fit residues: 0.0591 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 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: 0.0044 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: 50.0000 chunk 109 optimal weight: 50.0000 chunk 228 optimal weight: 4.9990 chunk 246 optimal weight: 50.0000 chunk 79 optimal weight: 0.0040 chunk 199 optimal weight: 0.4980 chunk 187 optimal weight: 6.9990 chunk 158 optimal weight: 0.1980 chunk 145 optimal weight: 20.0000 chunk 313 optimal weight: 3.9990 chunk 181 optimal weight: 50.0000 overall best weight: 1.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.041285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.031668 restraints weight = 57174.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.031668 restraints weight = 58693.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.031668 restraints weight = 58693.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.031668 restraints weight = 58693.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.031668 restraints weight = 58693.357| |-----------------------------------------------------------------------------| r_work (final): 0.2698 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.048669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.038852 restraints weight = 35594.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.039294 restraints weight = 30156.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.039534 restraints weight = 26137.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.039812 restraints weight = 23543.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.040034 restraints weight = 21577.232| |-----------------------------------------------------------------------------| r_work (final): 0.3035 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.043445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.036449 restraints weight = 29418.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.036538 restraints weight = 28015.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.036634 restraints weight = 27080.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.036637 restraints weight = 26347.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.036637 restraints weight = 26312.779| |-----------------------------------------------------------------------------| r_work (final): 0.2967 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.041233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.035376 restraints weight = 10102.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.035885 restraints weight = 8012.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.036229 restraints weight = 6641.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.036567 restraints weight = 5754.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.036816 restraints weight = 5066.102| |-----------------------------------------------------------------------------| r_work (final): 0.2809 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.067613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.063362 restraints weight = 436.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.064309 restraints weight = 259.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.064996 restraints weight = 179.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.065547 restraints weight = 131.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.065927 restraints weight = 101.164| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16144 Z= 0.144 Angle : 0.541 7.383 22506 Z= 0.341 Chirality : 0.045 0.196 3138 Planarity : 0.004 0.046 3236 Dihedral : 4.642 25.914 3232 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.73 % 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 aren not related in a simple way. whole: 0.27 (0.15), residues: 3212 helix: 1.27 (0.12), residues: 1916 sheet: 0.19 (0.27), residues: 328 loop : -2.09 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 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 covalent geometry : bond 0.00199 (16144) covalent geometry : angle 0.54130 (22506) hydrogen bonds : bond 0.03698 ( 1528) hydrogen bonds : angle 4.55534 ( 4590) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 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 : 0.093 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0114 time to fit residues: 0.3222 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 : 0.100 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 : 0.086 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0112 time to fit residues: 0.2815 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 : 0.073 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 : 0.068 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0093 time to fit residues: 0.3168 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 : 0.073 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: 0.0053 time to fit residues: 0.0709 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: 0.0042 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 : 0.002 ------------------------------------------------------------------------------- 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: 30.0000 chunk 187 optimal weight: 6.9990 chunk 280 optimal weight: 0.0970 chunk 67 optimal weight: 50.0000 chunk 104 optimal weight: 40.0000 chunk 14 optimal weight: 6.9990 chunk 244 optimal weight: 20.0000 chunk 265 optimal weight: 20.0000 chunk 274 optimal weight: 30.0000 chunk 299 optimal weight: 0.0170 chunk 315 optimal weight: 0.2980 overall best weight: 2.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.041285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.031627 restraints weight = 58406.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.031627 restraints weight = 59612.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.031627 restraints weight = 59613.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.031627 restraints weight = 59613.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.031627 restraints weight = 59613.503| |-----------------------------------------------------------------------------| r_work (final): 0.2696 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.048669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.038831 restraints weight = 36030.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.039260 restraints weight = 30287.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.039489 restraints weight = 26314.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.039833 restraints weight = 23588.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.040025 restraints weight = 21522.773| |-----------------------------------------------------------------------------| r_work (final): 0.3035 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.038449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.033407 restraints weight = 64215.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.032853 restraints weight = 84743.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.032845 restraints weight = 104120.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.032237 restraints weight = 106041.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.031986 restraints weight = 128932.107| |-----------------------------------------------------------------------------| r_work (final): 0.2653 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.041233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.035374 restraints weight = 10133.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.035872 restraints weight = 8027.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.036266 restraints weight = 6671.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.036551 restraints weight = 5723.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.036815 restraints weight = 5073.688| |-----------------------------------------------------------------------------| r_work (final): 0.2809 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.067613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.062954 restraints weight = 526.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.063865 restraints weight = 301.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.064696 restraints weight = 208.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.065223 restraints weight = 150.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.065691 restraints weight = 116.663| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16144 Z= 0.144 Angle : 0.541 7.383 22506 Z= 0.341 Chirality : 0.045 0.196 3138 Planarity : 0.004 0.046 3236 Dihedral : 4.642 25.914 3232 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.73 % 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 aren not related in a simple way. whole: 0.27 (0.15), residues: 3212 helix: 1.27 (0.12), residues: 1916 sheet: 0.19 (0.27), residues: 328 loop : -2.09 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 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 covalent geometry : bond 0.00199 (16144) covalent geometry : angle 0.54130 (22506) hydrogen bonds : bond 0.03698 ( 1528) hydrogen bonds : angle 4.55534 ( 4590) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 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 : 0.088 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0119 time to fit residues: 0.3475 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 : 0.075 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 : 0.055 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0089 time to fit residues: 0.2047 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 : 0.075 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0083 time to fit residues: 0.2760 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 : 0.045 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 : 0.016 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0032 time to fit residues: 0.0481 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 : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0026 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 : 0.002 ------------------------------------------------------------------------------- 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: 20.0000 chunk 138 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 300 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 50 optimal weight: 20.0000 chunk 290 optimal weight: 20.0000 chunk 252 optimal weight: 100.0000 chunk 25 optimal weight: 10.0000 chunk 165 optimal weight: 30.0000 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.041285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.031614 restraints weight = 58597.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.031614 restraints weight = 60040.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.031614 restraints weight = 60040.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.031614 restraints weight = 60040.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.031614 restraints weight = 60040.698| |-----------------------------------------------------------------------------| r_work (final): 0.2696 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.048669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.038867 restraints weight = 35509.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.039183 restraints weight = 29871.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.039583 restraints weight = 26278.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.039763 restraints weight = 23526.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.040016 restraints weight = 21700.596| |-----------------------------------------------------------------------------| r_work (final): 0.3035 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.043445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.036415 restraints weight = 29897.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.036514 restraints weight = 28374.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.036514 restraints weight = 27344.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.036514 restraints weight = 27344.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.036514 restraints weight = 27344.519| |-----------------------------------------------------------------------------| r_work (final): 0.2962 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.041233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.035462 restraints weight = 9713.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.035899 restraints weight = 7763.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.036296 restraints weight = 6550.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.036571 restraints weight = 5628.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.036830 restraints weight = 5009.099| |-----------------------------------------------------------------------------| r_work (final): 0.2810 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.067613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.063361 restraints weight = 435.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.064310 restraints weight = 259.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.064989 restraints weight = 178.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.065510 restraints weight = 131.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.065943 restraints weight = 101.795| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16144 Z= 0.144 Angle : 0.541 7.383 22506 Z= 0.341 Chirality : 0.045 0.196 3138 Planarity : 0.004 0.046 3236 Dihedral : 4.642 25.914 3232 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.73 % 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 aren not related in a simple way. whole: 0.27 (0.15), residues: 3212 helix: 1.27 (0.12), residues: 1916 sheet: 0.19 (0.27), residues: 328 loop : -2.09 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 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 covalent geometry : bond 0.00199 (16144) covalent geometry : angle 0.54130 (22506) hydrogen bonds : bond 0.03698 ( 1528) hydrogen bonds : angle 4.55534 ( 4590) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 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: 0.0144 time to fit residues: 0.4266 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 : 0.115 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 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0124 time to fit residues: 0.2922 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 : 0.052 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0092 time to fit residues: 0.3194 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 : 0.077 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: 0.0049 time to fit residues: 0.0767 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 : 0.035 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 : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0054 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 165 optimal weight: 30.0000 chunk 260 optimal weight: 40.0000 chunk 211 optimal weight: 10.0000 chunk 267 optimal weight: 5.9990 chunk 177 optimal weight: 30.0000 chunk 241 optimal weight: 20.0000 chunk 240 optimal weight: 9.9990 chunk 223 optimal weight: 6.9990 chunk 230 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.041285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.031648 restraints weight = 57776.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.031631 restraints weight = 59123.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.031631 restraints weight = 59624.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.031631 restraints weight = 59624.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.031631 restraints weight = 59624.958| |-----------------------------------------------------------------------------| r_work (final): 0.2697 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.048669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.038860 restraints weight = 35744.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.039179 restraints weight = 29969.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.039591 restraints weight = 26290.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.039829 restraints weight = 23532.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.039962 restraints weight = 21544.164| |-----------------------------------------------------------------------------| r_work (final): 0.3033 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.038449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.033408 restraints weight = 63506.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.032872 restraints weight = 84849.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.032521 restraints weight = 104189.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.032516 restraints weight = 123060.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.032509 restraints weight = 124897.316| |-----------------------------------------------------------------------------| r_work (final): 0.2674 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.041233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.035368 restraints weight = 10159.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.035768 restraints weight = 8044.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.036209 restraints weight = 6841.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.036497 restraints weight = 5832.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.036758 restraints weight = 5163.316| |-----------------------------------------------------------------------------| r_work (final): 0.2807 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.067613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.063129 restraints weight = 488.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.064071 restraints weight = 285.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.064810 restraints weight = 195.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.065228 restraints weight = 143.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.065740 restraints weight = 114.759| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16144 Z= 0.144 Angle : 0.541 7.383 22506 Z= 0.341 Chirality : 0.045 0.196 3138 Planarity : 0.004 0.046 3236 Dihedral : 4.642 25.914 3232 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.73 % 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 aren not related in a simple way. whole: 0.27 (0.15), residues: 3212 helix: 1.27 (0.12), residues: 1916 sheet: 0.19 (0.27), residues: 328 loop : -2.09 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 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 covalent geometry : bond 0.00199 (16144) covalent geometry : angle 0.54130 (22506) hydrogen bonds : bond 0.03698 ( 1528) hydrogen bonds : angle 4.55534 ( 4590) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 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 : 0.132 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0097 time to fit residues: 0.3177 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 : 0.121 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: 0.0138 time to fit residues: 0.3439 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 : 0.073 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0098 time to fit residues: 0.3306 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 : 0.068 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: 0.0048 time to fit residues: 0.0723 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 0 residues out of total 5 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0027 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 794, in minimization_ncs weight = real_space_weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 394, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 126, in refine minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 424, in __init__ minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 456, in compute_functional_and_gradients t,g = self.target_and_grads_object.target_and_gradients( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 242, in target_and_gradients t_restraints, g_restraints = restraints_target_and_grads( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 110, in restraints_target_and_grads ef = restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.4784 > 50: distance: 6 - 7: 7.943 distance: 6 - 9: 3.901 distance: 7 - 8: 5.502 distance: 7 - 10: 10.059 distance: 10 - 11: 5.152 distance: 11 - 12: 4.012 distance: 11 - 14: 9.044 distance: 12 - 13: 9.271 distance: 12 - 15: 8.671 distance: 15 - 16: 5.408 distance: 16 - 17: 4.349 distance: 16 - 19: 4.625 distance: 17 - 18: 8.016 distance: 20 - 21: 4.973 distance: 21 - 22: 27.843 distance: 21 - 24: 6.931 distance: 22 - 23: 53.478 distance: 22 - 25: 31.216 distance: 26 - 27: 9.368 distance: 26 - 29: 4.445 distance: 27 - 28: 13.018 distance: 27 - 30: 5.892 distance: 30 - 31: 5.051 distance: 31 - 32: 4.448 distance: 31 - 34: 5.754 distance: 32 - 33: 5.899 distance: 32 - 35: 3.980 distance: 35 - 36: 6.429 distance: 36 - 37: 9.769 distance: 36 - 39: 6.735 distance: 37 - 38: 11.170 distance: 37 - 40: 7.090 distance: 40 - 41: 5.588 distance: 41 - 42: 4.940 distance: 41 - 44: 5.953 distance: 42 - 43: 4.012 distance: 42 - 45: 3.511