Starting phenix.real_space_refine on Wed Aug 5 19:54:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tdw_41175/08_2026/8tdw_41175_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tdw_41175/08_2026/8tdw_41175.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tdw_41175/08_2026/8tdw_41175_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tdw_41175/08_2026/8tdw_41175_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tdw_41175/08_2026/8tdw_41175.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tdw_41175/08_2026/8tdw_41175.map" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.069 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 2 7.16 5 P 12 5.49 5 S 29 5.16 5 C 6978 2.51 5 N 2135 2.21 5 O 2203 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11359 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3346 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 140} Link IDs: {'PTRANS': 23, 'TRANS': 446} Chain breaks: 2 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 513 Unresolved non-hydrogen angles: 650 Unresolved non-hydrogen dihedrals: 428 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLU:plan': 11, 'ASP:plan': 15, 'ARG:plan': 10, 'ASN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 6, 'GLN:plan1': 8, 'PHE:plan': 4, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 286 Chain: "B" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3371 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 133} Link IDs: {'PTRANS': 23, 'TRANS': 447} Chain breaks: 2 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 502 Unresolved non-hydrogen angles: 639 Unresolved non-hydrogen dihedrals: 424 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'HIS:plan': 3, 'ASN:plan1': 8, 'ASP:plan': 13, 'GLU:plan': 10, 'ARG:plan': 8, 'PHE:plan': 5, 'TYR:plan': 7, 'GLN:plan1': 7, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 283 Chain: "E" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 2261 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 407} Link IDs: {'PTRANS': 22, 'TRANS': 435} Chain breaks: 1 Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 1567 Unresolved non-hydrogen angles: 2002 Unresolved non-hydrogen dihedrals: 1327 Unresolved non-hydrogen chiralities: 119 Planarities with less than four sites: {'ASN:plan1': 19, 'ASP:plan': 35, 'HIS:plan': 16, 'GLU:plan': 32, 'ARG:plan': 25, 'GLN:plan1': 20, 'PHE:plan': 20, 'TYR:plan': 22, 'TRP:plan': 5} Unresolved non-hydrogen planarities: 894 Chain: "F" Number of atoms: 2128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 2128 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 382} Link IDs: {'PTRANS': 21, 'TRANS': 409} Chain breaks: 2 Unresolved chain link angles: 21 Unresolved non-hydrogen bonds: 1472 Unresolved non-hydrogen angles: 1882 Unresolved non-hydrogen dihedrals: 1248 Unresolved non-hydrogen chiralities: 114 Planarities with less than four sites: {'ASN:plan1': 16, 'ASP:plan': 32, 'HIS:plan': 16, 'GLU:plan': 29, 'ARG:plan': 24, 'GLN:plan1': 19, 'PHE:plan': 19, 'TYR:plan': 20, 'TRP:plan': 5} Unresolved non-hydrogen planarities: 835 Chain: "J" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pyr': 1} Link IDs: {'rna2p': 4, 'rna3p': 1} Chain: "K" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 125 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pyr': 1} Link IDs: {'rna2p': 5} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.19, per 1000 atoms: 0.28 Number of scatterers: 11359 At special positions: 0 Unit cell: (109.154, 115.152, 129.546, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 S 29 16.00 P 12 15.00 O 2203 8.00 N 2135 7.00 C 6978 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: 1.08 Conformation dependent library (CDL) restraints added in 608.9 milliseconds 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3436 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 15 sheets defined 58.7% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 150 through 156 removed outlier: 3.790A pdb=" N TYR A 154 " --> pdb=" O GLY A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 186 removed outlier: 3.820A pdb=" N HIS A 167 " --> pdb=" O ASN A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 205 Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 220 through 226 removed outlier: 3.677A pdb=" N LEU A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 248 Processing helix chain 'A' and resid 249 through 257 removed outlier: 4.437A pdb=" N VAL A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 274 removed outlier: 4.733A pdb=" N CYS A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 300 removed outlier: 5.969A pdb=" N PHE A 296 " --> pdb=" O ASN A 293 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR A 298 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE A 300 " --> pdb=" O LEU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 324 Processing helix chain 'A' and resid 330 through 338 removed outlier: 3.690A pdb=" N PHE A 334 " --> pdb=" O ASP A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 373 Processing helix chain 'A' and resid 376 through 393 removed outlier: 3.674A pdb=" N ILE A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 410 through 414 removed outlier: 3.815A pdb=" N ILE A 413 " --> pdb=" O SER A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 424 through 432 removed outlier: 4.053A pdb=" N LEU A 428 " --> pdb=" O ASP A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 438 through 450 removed outlier: 3.548A pdb=" N ILE A 448 " --> pdb=" O ILE A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 removed outlier: 4.769A pdb=" N GLU A 474 " --> pdb=" O GLU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.675A pdb=" N GLU A 479 " --> pdb=" O SER A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 536 removed outlier: 4.269A pdb=" N ASN A 535 " --> pdb=" O ILE A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 574 Processing helix chain 'A' and resid 583 through 588 Processing helix chain 'B' and resid 129 through 137 Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 144 through 147 Processing helix chain 'B' and resid 150 through 154 removed outlier: 3.754A pdb=" N TYR B 154 " --> pdb=" O GLY B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 186 removed outlier: 3.718A pdb=" N HIS B 167 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 206 Processing helix chain 'B' and resid 214 through 220 removed outlier: 4.237A pdb=" N ASP B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 Processing helix chain 'B' and resid 232 through 248 Processing helix chain 'B' and resid 249 through 258 removed outlier: 4.352A pdb=" N VAL B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 274 removed outlier: 4.251A pdb=" N CYS B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 300 removed outlier: 6.059A pdb=" N PHE B 296 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE B 300 " --> pdb=" O LEU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 324 removed outlier: 3.501A pdb=" N TRP B 313 " --> pdb=" O ASP B 309 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 336 Processing helix chain 'B' and resid 352 through 354 No H-bonds generated for 'chain 'B' and resid 352 through 354' Processing helix chain 'B' and resid 355 through 373 Processing helix chain 'B' and resid 378 through 393 Processing helix chain 'B' and resid 402 through 404 No H-bonds generated for 'chain 'B' and resid 402 through 404' Processing helix chain 'B' and resid 410 through 414 removed outlier: 4.146A pdb=" N ILE B 413 " --> pdb=" O SER B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 421 removed outlier: 3.988A pdb=" N LYS B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 432 removed outlier: 4.108A pdb=" N LEU B 428 " --> pdb=" O ASP B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 437 No H-bonds generated for 'chain 'B' and resid 435 through 437' Processing helix chain 'B' and resid 438 through 450 removed outlier: 3.865A pdb=" N ILE B 448 " --> pdb=" O ILE B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 481 removed outlier: 4.348A pdb=" N LYS B 478 " --> pdb=" O GLU B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 498 removed outlier: 3.552A pdb=" N PHE B 498 " --> pdb=" O ALA B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 576 Processing helix chain 'B' and resid 583 through 588 removed outlier: 3.525A pdb=" N ILE B 587 " --> pdb=" O GLY B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 600 removed outlier: 3.676A pdb=" N ASN B 599 " --> pdb=" O LYS B 595 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP B 600 " --> pdb=" O LYS B 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 595 through 600' Processing helix chain 'E' and resid 129 through 137 removed outlier: 3.984A pdb=" N ASP E 137 " --> pdb=" O VAL E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 146 removed outlier: 3.998A pdb=" N ARG E 145 " --> pdb=" O PHE E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 154 Processing helix chain 'E' and resid 163 through 186 removed outlier: 3.636A pdb=" N HIS E 167 " --> pdb=" O ASN E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 190 Processing helix chain 'E' and resid 192 through 204 removed outlier: 3.511A pdb=" N VAL E 196 " --> pdb=" O SER E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 220 removed outlier: 3.764A pdb=" N ASP E 218 " --> pdb=" O SER E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 226 removed outlier: 3.896A pdb=" N ARG E 226 " --> pdb=" O ILE E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 249 removed outlier: 3.587A pdb=" N GLY E 236 " --> pdb=" O THR E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 257 Processing helix chain 'E' and resid 260 through 274 removed outlier: 4.423A pdb=" N CYS E 266 " --> pdb=" O GLU E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 324 Processing helix chain 'E' and resid 330 through 337 Processing helix chain 'E' and resid 355 through 373 Processing helix chain 'E' and resid 377 through 393 Processing helix chain 'E' and resid 394 through 396 No H-bonds generated for 'chain 'E' and resid 394 through 396' Processing helix chain 'E' and resid 402 through 404 No H-bonds generated for 'chain 'E' and resid 402 through 404' Processing helix chain 'E' and resid 411 through 414 removed outlier: 3.897A pdb=" N ASP E 414 " --> pdb=" O THR E 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 411 through 414' Processing helix chain 'E' and resid 415 through 420 Processing helix chain 'E' and resid 424 through 432 Processing helix chain 'E' and resid 438 through 450 removed outlier: 3.675A pdb=" N ILE E 444 " --> pdb=" O ASP E 440 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR E 450 " --> pdb=" O LYS E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 482 removed outlier: 3.622A pdb=" N TYR E 473 " --> pdb=" O LYS E 469 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU E 474 " --> pdb=" O ARG E 470 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER E 475 " --> pdb=" O GLU E 471 " (cutoff:3.500A) Proline residue: E 477 - end of helix Processing helix chain 'E' and resid 558 through 576 Processing helix chain 'E' and resid 583 through 588 Processing helix chain 'E' and resid 591 through 594 Processing helix chain 'E' and resid 595 through 600 removed outlier: 4.317A pdb=" N ASN E 599 " --> pdb=" O LYS E 595 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 137 Processing helix chain 'F' and resid 138 through 144 Processing helix chain 'F' and resid 145 through 147 No H-bonds generated for 'chain 'F' and resid 145 through 147' Processing helix chain 'F' and resid 152 through 157 removed outlier: 3.701A pdb=" N VAL F 156 " --> pdb=" O GLY F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 186 Processing helix chain 'F' and resid 187 through 190 Processing helix chain 'F' and resid 192 through 205 removed outlier: 3.783A pdb=" N VAL F 196 " --> pdb=" O SER F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 214 through 221 removed outlier: 3.704A pdb=" N ASP F 218 " --> pdb=" O SER F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 226 Processing helix chain 'F' and resid 232 through 249 removed outlier: 3.918A pdb=" N GLY F 236 " --> pdb=" O THR F 232 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY F 249 " --> pdb=" O ILE F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 256 Processing helix chain 'F' and resid 260 through 272 Processing helix chain 'F' and resid 311 through 324 Processing helix chain 'F' and resid 330 through 337 Processing helix chain 'F' and resid 355 through 376 removed outlier: 3.731A pdb=" N HIS F 376 " --> pdb=" O ARG F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 393 Processing helix chain 'F' and resid 394 through 397 removed outlier: 4.165A pdb=" N ILE F 397 " --> pdb=" O ASP F 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 394 through 397' Processing helix chain 'F' and resid 401 through 405 removed outlier: 3.691A pdb=" N LYS F 405 " --> pdb=" O ALA F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 412 removed outlier: 3.757A pdb=" N ALA F 412 " --> pdb=" O ILE F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 421 removed outlier: 3.651A pdb=" N LYS F 421 " --> pdb=" O GLU F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 433 removed outlier: 4.908A pdb=" N LEU F 431 " --> pdb=" O PHE F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 437 No H-bonds generated for 'chain 'F' and resid 435 through 437' Processing helix chain 'F' and resid 438 through 450 removed outlier: 3.814A pdb=" N LEU F 445 " --> pdb=" O ALA F 441 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE F 448 " --> pdb=" O ILE F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 482 Processing helix chain 'F' and resid 558 through 577 Processing helix chain 'F' and resid 583 through 588 Processing helix chain 'F' and resid 590 through 595 removed outlier: 4.361A pdb=" N LYS F 595 " --> pdb=" O ILE F 591 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA2, first strand: chain 'A' and resid 339 through 343 removed outlier: 7.803A pdb=" N TYR A 521 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA A 351 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 399 through 400 Processing sheet with id=AA4, first strand: chain 'A' and resid 455 through 460 removed outlier: 6.018A pdb=" N TYR A 456 " --> pdb=" O CYS A 554 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N CYS A 554 " --> pdb=" O TYR A 456 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY A 458 " --> pdb=" O VAL A 552 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 117 through 120 Processing sheet with id=AA6, first strand: chain 'B' and resid 339 through 342 Processing sheet with id=AA7, first strand: chain 'B' and resid 399 through 400 Processing sheet with id=AA8, first strand: chain 'B' and resid 455 through 460 removed outlier: 6.520A pdb=" N VAL B 552 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLU B 459 " --> pdb=" O ILE B 550 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE B 550 " --> pdb=" O GLU B 459 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 341 through 343 Processing sheet with id=AB1, first strand: chain 'E' and resid 398 through 400 Processing sheet with id=AB2, first strand: chain 'E' and resid 455 through 456 Processing sheet with id=AB3, first strand: chain 'E' and resid 501 through 504 Processing sheet with id=AB4, first strand: chain 'F' and resid 338 through 343 Processing sheet with id=AB5, first strand: chain 'F' and resid 455 through 458 removed outlier: 6.744A pdb=" N VAL F 552 " --> pdb=" O VAL F 457 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 502 through 503 removed outlier: 3.868A pdb=" N LEU F 549 " --> pdb=" O ILE F 503 " (cutoff:3.500A) 663 hydrogen bonds defined for protein. 1845 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: 1.88 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4127 1.34 - 1.46: 2160 1.46 - 1.58: 5155 1.58 - 1.70: 21 1.70 - 1.81: 45 Bond restraints: 11508 Sorted by residual: bond pdb=" O3' G J 9 " pdb=" P C J 10 " ideal model delta sigma weight residual 1.607 1.569 0.038 1.20e-02 6.94e+03 9.82e+00 bond pdb=" N9 A K 9 " pdb=" C4 A K 9 " ideal model delta sigma weight residual 1.374 1.363 0.011 6.00e-03 2.78e+04 3.47e+00 bond pdb=" C4' C J 10 " pdb=" O4' C J 10 " ideal model delta sigma weight residual 1.454 1.436 0.018 1.00e-02 1.00e+04 3.25e+00 bond pdb=" C5 G K 8 " pdb=" C4 G K 8 " ideal model delta sigma weight residual 1.379 1.367 0.012 7.00e-03 2.04e+04 2.97e+00 bond pdb=" C8 G J 8 " pdb=" N7 G J 8 " ideal model delta sigma weight residual 1.305 1.296 0.009 6.00e-03 2.78e+04 2.41e+00 ... (remaining 11503 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 15512 1.64 - 3.27: 265 3.27 - 4.91: 43 4.91 - 6.54: 13 6.54 - 8.18: 2 Bond angle restraints: 15835 Sorted by residual: angle pdb=" O5' G J 8 " pdb=" C5' G J 8 " pdb=" C4' G J 8 " ideal model delta sigma weight residual 109.40 114.48 -5.08 8.00e-01 1.56e+00 4.03e+01 angle pdb=" C1' C K 11 " pdb=" N1 C K 11 " pdb=" C2 C K 11 " ideal model delta sigma weight residual 118.80 124.14 -5.34 1.10e+00 8.26e-01 2.35e+01 angle pdb=" N1 C K 11 " pdb=" C2 C K 11 " pdb=" O2 C K 11 " ideal model delta sigma weight residual 118.90 121.72 -2.82 6.00e-01 2.78e+00 2.21e+01 angle pdb=" C3' A K 9 " pdb=" O3' A K 9 " pdb=" P C K 10 " ideal model delta sigma weight residual 119.70 125.02 -5.32 1.20e+00 6.94e-01 1.96e+01 angle pdb=" O2 C K 11 " pdb=" C2 C K 11 " pdb=" N3 C K 11 " ideal model delta sigma weight residual 121.90 118.92 2.98 7.00e-01 2.04e+00 1.81e+01 ... (remaining 15830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 6715 35.78 - 71.56: 72 71.56 - 107.33: 16 107.33 - 143.11: 3 143.11 - 178.89: 4 Dihedral angle restraints: 6810 sinusoidal: 1523 harmonic: 5287 Sorted by residual: dihedral pdb=" O4' C K 11 " pdb=" C1' C K 11 " pdb=" N1 C K 11 " pdb=" C2 C K 11 " ideal model delta sinusoidal sigma weight residual 200.00 57.53 142.47 1 1.50e+01 4.44e-03 7.65e+01 dihedral pdb=" O4' C J 10 " pdb=" C1' C J 10 " pdb=" N1 C J 10 " pdb=" C2 C J 10 " ideal model delta sinusoidal sigma weight residual 232.00 62.23 169.77 1 1.70e+01 3.46e-03 6.59e+01 dihedral pdb=" O4' C K 7 " pdb=" C1' C K 7 " pdb=" N1 C K 7 " pdb=" C2 C K 7 " ideal model delta sinusoidal sigma weight residual 232.00 62.68 169.32 1 1.70e+01 3.46e-03 6.59e+01 ... (remaining 6807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1290 0.042 - 0.084: 479 0.084 - 0.125: 170 0.125 - 0.167: 9 0.167 - 0.209: 4 Chirality restraints: 1952 Sorted by residual: chirality pdb=" C3' A K 9 " pdb=" C4' A K 9 " pdb=" O3' A K 9 " pdb=" C2' A K 9 " both_signs ideal model delta sigma weight residual False -2.74 -2.54 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA TYR B 315 " pdb=" N TYR B 315 " pdb=" C TYR B 315 " pdb=" CB TYR B 315 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C3' C J 10 " pdb=" C4' C J 10 " pdb=" O3' C J 10 " pdb=" C2' C J 10 " both_signs ideal model delta sigma weight residual False -2.74 -2.55 -0.20 2.00e-01 2.50e+01 9.73e-01 ... (remaining 1949 not shown) Planarity restraints: 2129 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 368 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C SER A 368 " 0.055 2.00e-02 2.50e+03 pdb=" O SER A 368 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU A 369 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 360 " 0.015 2.00e-02 2.50e+03 3.09e-02 9.57e+00 pdb=" C TYR A 360 " -0.054 2.00e-02 2.50e+03 pdb=" O TYR A 360 " 0.020 2.00e-02 2.50e+03 pdb=" N ASP A 361 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 366 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.29e+00 pdb=" C ARG A 366 " -0.050 2.00e-02 2.50e+03 pdb=" O ARG A 366 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN A 367 " 0.017 2.00e-02 2.50e+03 ... (remaining 2126 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1836 2.75 - 3.29: 10962 3.29 - 3.83: 18434 3.83 - 4.36: 19678 4.36 - 4.90: 33905 Nonbonded interactions: 84815 Sorted by model distance: nonbonded pdb=" O TYR B 155 " pdb=" NH2 ARG B 451 " model vdw 2.217 3.120 nonbonded pdb=" NE1 TRP A 285 " pdb=" O ARG A 290 " model vdw 2.227 3.120 nonbonded pdb=" NH2 ARG B 194 " pdb=" OD1 ASP B 264 " model vdw 2.231 3.120 nonbonded pdb=" O GLU B 292 " pdb=" OG SER B 295 " model vdw 2.233 3.040 nonbonded pdb=" NH2 ARG B 143 " pdb=" O HIS B 210 " model vdw 2.240 3.120 ... (remaining 84810 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 115 through 123 and (name N or name CA or name C or name \ O or name CB )) or resid 124 or (resid 125 through 150 and (name N or name CA or \ name C or name O or name CB )) or resid 151 through 153 or (resid 154 through 1 \ 58 and (name N or name CA or name C or name O or name CB )) or (resid 159 throug \ h 169 and (name N or name CA or name C or name O or name CB )) or resid 170 or ( \ resid 171 and (name N or name CA or name C or name O or name CB )) or resid 172 \ or (resid 173 through 175 and (name N or name CA or name C or name O or name CB \ )) or resid 176 or (resid 177 through 182 and (name N or name CA or name C or na \ me O or name CB )) or (resid 183 through 202 and (name N or name CA or name C or \ name O or name CB )) or resid 203 or (resid 204 through 208 and (name N or name \ CA or name C or name O or name CB )) or resid 209 or (resid 210 and (name N or \ name CA or name C or name O or name CB )) or resid 211 or (resid 212 through 218 \ and (name N or name CA or name C or name O or name CB )) or resid 219 or (resid \ 220 through 235 and (name N or name CA or name C or name O or name CB )) or res \ id 236 or (resid 237 through 248 and (name N or name CA or name C or name O or n \ ame CB )) or resid 249 or (resid 250 through 257 and (name N or name CA or name \ C or name O or name CB )) or resid 258 or (resid 259 through 273 and (name N or \ name CA or name C or name O or name CB )) or resid 274 or (resid 275 through 288 \ and (name N or name CA or name C or name O or name CB )) or resid 289 or (resid \ 290 through 295 and (name N or name CA or name C or name O or name CB )) or (re \ sid 310 through 323 and (name N or name CA or name C or name O or name CB )) or \ resid 324 or (resid 325 through 356 and (name N or name CA or name C or name O o \ r name CB )) or resid 357 or (resid 358 through 378 and (name N or name CA or na \ me C or name O or name CB )) or resid 379 or (resid 380 through 400 and (name N \ or name CA or name C or name O or name CB )) or (resid 401 through 457 and (name \ N or name CA or name C or name O or name CB )) or resid 458 through 504 or resi \ d 548 through 602)) selection = (chain 'B' and ((resid 115 through 123 and (name N or name CA or name C or name \ O or name CB )) or resid 124 or (resid 125 through 150 and (name N or name CA or \ name C or name O or name CB )) or resid 151 through 153 or (resid 154 through 1 \ 58 and (name N or name CA or name C or name O or name CB )) or (resid 159 throug \ h 169 and (name N or name CA or name C or name O or name CB )) or resid 170 or ( \ resid 171 and (name N or name CA or name C or name O or name CB )) or resid 172 \ or (resid 173 through 175 and (name N or name CA or name C or name O or name CB \ )) or resid 176 or (resid 177 through 182 and (name N or name CA or name C or na \ me O or name CB )) or resid 183 or (resid 184 through 202 and (name N or name CA \ or name C or name O or name CB )) or resid 203 or (resid 204 through 208 and (n \ ame N or name CA or name C or name O or name CB )) or resid 209 or (resid 210 an \ d (name N or name CA or name C or name O or name CB )) or resid 211 or (resid 21 \ 2 through 218 and (name N or name CA or name C or name O or name CB )) or resid \ 219 or (resid 220 through 235 and (name N or name CA or name C or name O or name \ CB )) or resid 236 or (resid 237 through 248 and (name N or name CA or name C o \ r name O or name CB )) or resid 249 or (resid 250 through 257 and (name N or nam \ e CA or name C or name O or name CB )) or resid 258 or (resid 259 through 273 an \ d (name N or name CA or name C or name O or name CB )) or resid 274 or (resid 27 \ 5 through 288 and (name N or name CA or name C or name O or name CB )) or resid \ 289 or (resid 290 through 295 and (name N or name CA or name C or name O or name \ CB )) or (resid 310 through 323 and (name N or name CA or name C or name O or n \ ame CB )) or resid 324 or (resid 325 through 356 and (name N or name CA or name \ C or name O or name CB )) or resid 357 or (resid 358 through 378 and (name N or \ name CA or name C or name O or name CB )) or resid 379 or (resid 380 through 400 \ and (name N or name CA or name C or name O or name CB )) or (resid 401 through \ 457 and (name N or name CA or name C or name O or name CB )) or resid 458 throug \ h 504 or resid 548 through 602)) selection = (chain 'E' and (resid 115 through 295 or resid 310 through 504 or resid 548 thro \ ugh 602)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.430 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5030 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11508 Z= 0.222 Angle : 0.570 8.176 15835 Z= 0.359 Chirality : 0.047 0.209 1952 Planarity : 0.004 0.040 2129 Dihedral : 14.081 178.887 3374 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.21), residues: 1808 helix: 1.07 (0.19), residues: 858 sheet: -0.57 (0.58), residues: 90 loop : -1.16 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 164 TYR 0.031 0.002 TYR B 315 PHE 0.012 0.002 PHE B 213 TRP 0.008 0.002 TRP B 285 HIS 0.009 0.002 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.22 (11508) covalent geometry : angle 0.56966 / 0.36 (15835) hydrogen bonds : bond 0.15507 / 10.42 ( 663) hydrogen bonds : angle 6.45357 / 4.69 ( 1845) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.408 Fit side-chains REVERT: A 180 HIS cc_start: 0.6012 (t-90) cc_final: 0.5803 (t-170) REVERT: A 227 PRO cc_start: 0.8597 (Cg_endo) cc_final: 0.8364 (Cg_exo) REVERT: A 230 LYS cc_start: 0.8627 (mttt) cc_final: 0.8143 (mttm) REVERT: A 239 MET cc_start: 0.7565 (mtp) cc_final: 0.7073 (mtp) REVERT: A 271 GLN cc_start: 0.7825 (mt0) cc_final: 0.7434 (mt0) REVERT: A 329 PHE cc_start: 0.8122 (t80) cc_final: 0.7722 (t80) REVERT: A 348 ARG cc_start: 0.6135 (mtm180) cc_final: 0.5665 (mtp85) REVERT: A 371 ARG cc_start: 0.6908 (ptm-80) cc_final: 0.6210 (ttp80) REVERT: A 417 GLU cc_start: 0.7473 (tt0) cc_final: 0.6934 (tt0) REVERT: A 429 GLU cc_start: 0.6438 (tt0) cc_final: 0.5919 (mt-10) REVERT: B 164 ARG cc_start: 0.7382 (mmt180) cc_final: 0.7114 (mmt180) REVERT: B 240 MET cc_start: 0.8088 (tpp) cc_final: 0.7504 (tpp) REVERT: B 255 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6892 (mt-10) REVERT: B 271 GLN cc_start: 0.7126 (mt0) cc_final: 0.6886 (mt0) REVERT: B 331 TYR cc_start: 0.6763 (p90) cc_final: 0.6546 (p90) REVERT: B 339 ARG cc_start: 0.6890 (mtp85) cc_final: 0.6440 (ptm160) REVERT: B 421 LYS cc_start: 0.8079 (mtmt) cc_final: 0.6945 (mptt) REVERT: B 435 ASP cc_start: 0.7384 (t0) cc_final: 0.6802 (t0) REVERT: B 437 LYS cc_start: 0.7656 (mtmt) cc_final: 0.7395 (mttm) REVERT: B 439 LYS cc_start: 0.6834 (tttt) cc_final: 0.6541 (tttm) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.1166 time to fit residues: 24.7786 Evaluate side-chains 129 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 4.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 HIS A 367 ASN A 375 GLN B 210 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.262022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.178170 restraints weight = 12209.640| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.47 r_work: 0.3714 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.0749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 11508 Z= 0.202 Angle : 0.572 10.641 15835 Z= 0.309 Chirality : 0.048 0.370 1952 Planarity : 0.004 0.040 2129 Dihedral : 13.378 179.920 2075 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.24 % Allowed : 9.93 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.21), residues: 1808 helix: 1.17 (0.18), residues: 856 sheet: -0.43 (0.59), residues: 88 loop : -1.05 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 164 TYR 0.028 0.002 TYR B 315 PHE 0.015 0.002 PHE B 221 TRP 0.009 0.002 TRP B 285 HIS 0.008 0.001 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 (11508) covalent geometry : angle 0.57230 / 0.31 (15835) hydrogen bonds : bond 0.03973 / 2.72 ( 663) hydrogen bonds : angle 4.93297 / 3.56 ( 1845) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 135 time to evaluate : 0.422 Fit side-chains REVERT: A 180 HIS cc_start: 0.7526 (t-90) cc_final: 0.7316 (t-170) REVERT: A 230 LYS cc_start: 0.9048 (mttt) cc_final: 0.8588 (mttm) REVERT: A 239 MET cc_start: 0.8913 (mtp) cc_final: 0.8518 (mtp) REVERT: A 271 GLN cc_start: 0.8627 (mt0) cc_final: 0.8364 (mt0) REVERT: A 329 PHE cc_start: 0.8574 (t80) cc_final: 0.8274 (t80) REVERT: A 348 ARG cc_start: 0.7459 (mtm180) cc_final: 0.7037 (mtp85) REVERT: A 371 ARG cc_start: 0.7749 (ptm-80) cc_final: 0.7185 (ttp-170) REVERT: A 417 GLU cc_start: 0.8279 (tt0) cc_final: 0.8035 (tt0) REVERT: A 429 GLU cc_start: 0.8045 (tt0) cc_final: 0.7671 (mt-10) REVERT: A 437 LYS cc_start: 0.8557 (mtmt) cc_final: 0.7836 (mmtm) REVERT: B 164 ARG cc_start: 0.8834 (mmt180) cc_final: 0.8552 (mtp85) REVERT: B 339 ARG cc_start: 0.7534 (mtp85) cc_final: 0.7063 (ptm160) REVERT: B 421 LYS cc_start: 0.8954 (mtmt) cc_final: 0.8338 (mptt) REVERT: B 435 ASP cc_start: 0.7881 (t0) cc_final: 0.7378 (t0) outliers start: 7 outliers final: 7 residues processed: 139 average time/residue: 0.1151 time to fit residues: 22.8820 Evaluate side-chains 133 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 368 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 38 optimal weight: 5.9990 chunk 143 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 127 optimal weight: 20.0000 chunk 86 optimal weight: 10.0000 chunk 157 optimal weight: 30.0000 chunk 21 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 170 optimal weight: 9.9990 chunk 173 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN B 210 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.259632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.171827 restraints weight = 12339.083| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 2.49 r_work: 0.3687 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.073 11508 Z= 0.389 Angle : 0.712 10.309 15835 Z= 0.382 Chirality : 0.053 0.406 1952 Planarity : 0.005 0.054 2129 Dihedral : 13.383 179.581 2075 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.25 % Favored : 92.70 % Rotamer: Outliers : 3.55 % Allowed : 11.70 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.20), residues: 1808 helix: 0.66 (0.18), residues: 847 sheet: -0.54 (0.57), residues: 88 loop : -1.37 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 164 TYR 0.036 0.003 TYR B 315 PHE 0.017 0.003 PHE B 213 TRP 0.015 0.003 TRP A 313 HIS 0.015 0.003 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00905 / 0.39 (11508) covalent geometry : angle 0.71172 / 0.38 (15835) hydrogen bonds : bond 0.04722 / 3.26 ( 663) hydrogen bonds : angle 5.04156 / 3.68 ( 1845) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.399 Fit side-chains REVERT: A 120 ASP cc_start: 0.8426 (t70) cc_final: 0.8183 (t70) REVERT: A 150 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9231 (mt) REVERT: A 230 LYS cc_start: 0.9081 (mttt) cc_final: 0.8620 (mttm) REVERT: A 239 MET cc_start: 0.8812 (mtp) cc_final: 0.8246 (mtp) REVERT: A 348 ARG cc_start: 0.7609 (mtm180) cc_final: 0.7184 (mtp85) REVERT: A 371 ARG cc_start: 0.7852 (ptm-80) cc_final: 0.7270 (ttp-170) REVERT: A 429 GLU cc_start: 0.8142 (tt0) cc_final: 0.7755 (mt-10) REVERT: A 437 LYS cc_start: 0.8663 (mtmt) cc_final: 0.8050 (mmtm) REVERT: B 190 GLN cc_start: 0.7574 (mt0) cc_final: 0.7354 (mm-40) REVERT: B 239 MET cc_start: 0.8575 (mtp) cc_final: 0.8331 (mtp) REVERT: B 339 ARG cc_start: 0.7321 (mtp85) cc_final: 0.7055 (ptm160) REVERT: B 362 MET cc_start: 0.6678 (OUTLIER) cc_final: 0.6452 (ttm) REVERT: B 372 ARG cc_start: 0.8012 (mmt-90) cc_final: 0.6746 (mmm-85) REVERT: B 383 ASP cc_start: 0.8586 (m-30) cc_final: 0.8284 (m-30) REVERT: B 421 LYS cc_start: 0.9037 (mtmt) cc_final: 0.8427 (mttt) REVERT: B 435 ASP cc_start: 0.7961 (t0) cc_final: 0.7449 (t0) REVERT: B 439 LYS cc_start: 0.8330 (tttt) cc_final: 0.8090 (tttm) outliers start: 20 outliers final: 16 residues processed: 138 average time/residue: 0.0981 time to fit residues: 19.3587 Evaluate side-chains 138 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 417 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 70 optimal weight: 0.8980 chunk 153 optimal weight: 5.9990 chunk 152 optimal weight: 20.0000 chunk 120 optimal weight: 30.0000 chunk 94 optimal weight: 30.0000 chunk 86 optimal weight: 10.0000 chunk 178 optimal weight: 8.9990 chunk 62 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 102 optimal weight: 30.0000 chunk 44 optimal weight: 20.0000 overall best weight: 3.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 HIS ** A 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN B 125 HIS B 210 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.259062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.171833 restraints weight = 12295.525| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.50 r_work: 0.3691 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.075 11508 Z= 0.388 Angle : 0.699 10.210 15835 Z= 0.376 Chirality : 0.052 0.408 1952 Planarity : 0.005 0.053 2129 Dihedral : 13.379 178.809 2075 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.41 % Favored : 92.53 % Rotamer: Outliers : 4.08 % Allowed : 12.41 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.20), residues: 1808 helix: 0.44 (0.18), residues: 845 sheet: -0.62 (0.56), residues: 86 loop : -1.47 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 164 TYR 0.030 0.003 TYR B 315 PHE 0.016 0.003 PHE A 329 TRP 0.014 0.003 TRP B 285 HIS 0.014 0.002 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00902 / 0.39 (11508) covalent geometry : angle 0.69937 / 0.38 (15835) hydrogen bonds : bond 0.04545 / 3.13 ( 663) hydrogen bonds : angle 5.04694 / 3.69 ( 1845) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.396 Fit side-chains REVERT: A 230 LYS cc_start: 0.9004 (mttt) cc_final: 0.8550 (mttm) REVERT: A 239 MET cc_start: 0.8759 (mtp) cc_final: 0.8184 (mtp) REVERT: A 326 GLN cc_start: 0.8417 (tt0) cc_final: 0.8193 (tt0) REVERT: A 329 PHE cc_start: 0.8622 (t80) cc_final: 0.8324 (t80) REVERT: A 371 ARG cc_start: 0.7722 (ptm-80) cc_final: 0.7217 (ttp-170) REVERT: A 429 GLU cc_start: 0.7853 (tt0) cc_final: 0.7497 (mt-10) REVERT: A 437 LYS cc_start: 0.8682 (mtmt) cc_final: 0.8170 (mmtm) REVERT: B 239 MET cc_start: 0.8501 (mtp) cc_final: 0.8212 (mtp) REVERT: B 339 ARG cc_start: 0.7303 (mtp85) cc_final: 0.7034 (ptm160) REVERT: B 362 MET cc_start: 0.6560 (OUTLIER) cc_final: 0.6359 (ttm) REVERT: B 372 ARG cc_start: 0.7943 (mmt-90) cc_final: 0.6689 (mmm-85) REVERT: B 383 ASP cc_start: 0.8397 (m-30) cc_final: 0.8191 (m-30) REVERT: B 421 LYS cc_start: 0.8938 (mtmt) cc_final: 0.8309 (mttt) REVERT: B 435 ASP cc_start: 0.7919 (t0) cc_final: 0.7471 (t70) REVERT: B 439 LYS cc_start: 0.8383 (tttt) cc_final: 0.8165 (tttm) outliers start: 23 outliers final: 16 residues processed: 138 average time/residue: 0.1077 time to fit residues: 21.1486 Evaluate side-chains 140 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 417 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 103 optimal weight: 20.0000 chunk 75 optimal weight: 0.7980 chunk 81 optimal weight: 8.9990 chunk 74 optimal weight: 0.6980 chunk 173 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 107 optimal weight: 50.0000 chunk 87 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 HIS B 210 HIS B 358 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.263489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.182479 restraints weight = 12184.146| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.91 r_work: 0.3724 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11508 Z= 0.124 Angle : 0.510 10.409 15835 Z= 0.276 Chirality : 0.045 0.375 1952 Planarity : 0.004 0.046 2129 Dihedral : 13.170 179.665 2075 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.37 % Allowed : 13.83 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.20), residues: 1808 helix: 1.10 (0.18), residues: 850 sheet: -0.19 (0.65), residues: 73 loop : -1.14 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 220 TYR 0.025 0.001 TYR A 315 PHE 0.020 0.002 PHE B 221 TRP 0.012 0.001 TRP B 285 HIS 0.008 0.001 HIS B 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (11508) covalent geometry : angle 0.50964 / 0.28 (15835) hydrogen bonds : bond 0.03126 / 2.12 ( 663) hydrogen bonds : angle 4.45477 / 3.24 ( 1845) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.242 Fit side-chains REVERT: A 120 ASP cc_start: 0.8181 (t70) cc_final: 0.7860 (t70) REVERT: A 149 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8238 (tt0) REVERT: A 150 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9172 (mm) REVERT: A 230 LYS cc_start: 0.9007 (mttt) cc_final: 0.8463 (mtpp) REVERT: A 239 MET cc_start: 0.8833 (mtp) cc_final: 0.8454 (mtp) REVERT: A 271 GLN cc_start: 0.8464 (mt0) cc_final: 0.8163 (mt0) REVERT: A 329 PHE cc_start: 0.8521 (t80) cc_final: 0.8306 (t80) REVERT: A 348 ARG cc_start: 0.7182 (mtm180) cc_final: 0.6752 (mtp85) REVERT: A 371 ARG cc_start: 0.7634 (ptm-80) cc_final: 0.7063 (ttp-170) REVERT: A 429 GLU cc_start: 0.7805 (tt0) cc_final: 0.7465 (mt-10) REVERT: A 437 LYS cc_start: 0.8679 (mtmt) cc_final: 0.8082 (mmtm) REVERT: B 210 HIS cc_start: 0.8461 (OUTLIER) cc_final: 0.7903 (t70) REVERT: B 239 MET cc_start: 0.8472 (mtp) cc_final: 0.8179 (mtp) REVERT: B 339 ARG cc_start: 0.7333 (mtp85) cc_final: 0.7014 (ptm160) REVERT: B 372 ARG cc_start: 0.7621 (mmt-90) cc_final: 0.6718 (mmm-85) REVERT: B 421 LYS cc_start: 0.8817 (mtmt) cc_final: 0.8170 (mptt) REVERT: B 435 ASP cc_start: 0.7818 (t0) cc_final: 0.7328 (t0) outliers start: 19 outliers final: 11 residues processed: 141 average time/residue: 0.0922 time to fit residues: 18.7512 Evaluate side-chains 134 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 417 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 88 optimal weight: 20.0000 chunk 0 optimal weight: 3.9990 chunk 171 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 147 optimal weight: 20.0000 chunk 120 optimal weight: 30.0000 chunk 108 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 178 optimal weight: 9.9990 chunk 164 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 HIS A 206 HIS ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN B 125 HIS B 210 HIS B 271 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.258406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.189216 restraints weight = 12324.860| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 4.53 r_work: 0.3734 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.133 11508 Z= 0.452 Angle : 0.753 9.760 15835 Z= 0.403 Chirality : 0.054 0.415 1952 Planarity : 0.005 0.081 2129 Dihedral : 13.376 179.548 2075 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.30 % Favored : 91.65 % Rotamer: Outliers : 4.43 % Allowed : 14.18 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.20), residues: 1808 helix: 0.43 (0.18), residues: 852 sheet: -0.31 (0.64), residues: 71 loop : -1.48 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 164 TYR 0.034 0.003 TYR B 315 PHE 0.025 0.003 PHE B 329 TRP 0.019 0.004 TRP A 313 HIS 0.016 0.003 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.01060 / 0.45 (11508) covalent geometry : angle 0.75275 / 0.40 (15835) hydrogen bonds : bond 0.04806 / 3.32 ( 663) hydrogen bonds : angle 5.02413 / 3.68 ( 1845) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.331 Fit side-chains REVERT: A 149 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8376 (tt0) REVERT: A 150 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9149 (mt) REVERT: A 206 HIS cc_start: 0.8128 (OUTLIER) cc_final: 0.7177 (p90) REVERT: A 230 LYS cc_start: 0.9102 (mttt) cc_final: 0.8632 (mttm) REVERT: A 239 MET cc_start: 0.8786 (mtp) cc_final: 0.8245 (mtp) REVERT: A 371 ARG cc_start: 0.7829 (ptm-80) cc_final: 0.7175 (ttp-170) REVERT: A 429 GLU cc_start: 0.8110 (tt0) cc_final: 0.7711 (mt-10) REVERT: A 437 LYS cc_start: 0.8747 (mtmt) cc_final: 0.8212 (mmtm) REVERT: B 339 ARG cc_start: 0.7348 (mtp85) cc_final: 0.7063 (ptm160) REVERT: B 372 ARG cc_start: 0.8099 (mmt-90) cc_final: 0.6819 (mmm-85) REVERT: B 383 ASP cc_start: 0.8591 (m-30) cc_final: 0.8248 (m-30) REVERT: B 435 ASP cc_start: 0.8048 (t0) cc_final: 0.7582 (t70) REVERT: B 439 LYS cc_start: 0.8330 (tttt) cc_final: 0.8108 (tttm) outliers start: 25 outliers final: 18 residues processed: 137 average time/residue: 0.0871 time to fit residues: 17.4349 Evaluate side-chains 139 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 186 GLN Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 417 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 166 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 165 optimal weight: 6.9990 chunk 155 optimal weight: 0.0270 chunk 32 optimal weight: 1.9990 chunk 44 optimal weight: 30.0000 chunk 115 optimal weight: 20.0000 chunk 117 optimal weight: 50.0000 chunk 157 optimal weight: 30.0000 chunk 40 optimal weight: 20.0000 chunk 164 optimal weight: 7.9990 overall best weight: 3.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 HIS A 206 HIS A 210 HIS ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.259664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.171619 restraints weight = 12317.223| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.77 r_work: 0.3703 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 11508 Z= 0.348 Angle : 0.669 9.044 15835 Z= 0.360 Chirality : 0.051 0.404 1952 Planarity : 0.005 0.063 2129 Dihedral : 13.374 178.262 2075 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 4.43 % Allowed : 15.78 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.20), residues: 1808 helix: 0.43 (0.18), residues: 855 sheet: -0.38 (0.64), residues: 71 loop : -1.52 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 290 TYR 0.028 0.002 TYR B 315 PHE 0.018 0.003 PHE B 213 TRP 0.013 0.003 TRP B 285 HIS 0.023 0.003 HIS B 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00811 / 0.35 (11508) covalent geometry : angle 0.66876 / 0.36 (15835) hydrogen bonds : bond 0.04278 / 2.95 ( 663) hydrogen bonds : angle 4.92249 / 3.60 ( 1845) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.269 Fit side-chains REVERT: A 149 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8318 (tt0) REVERT: A 150 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9160 (mm) REVERT: A 230 LYS cc_start: 0.9061 (mttt) cc_final: 0.8579 (mttm) REVERT: A 239 MET cc_start: 0.8752 (mtp) cc_final: 0.8219 (mtp) REVERT: A 329 PHE cc_start: 0.8533 (t80) cc_final: 0.8130 (t80) REVERT: A 371 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7172 (ttp-170) REVERT: A 429 GLU cc_start: 0.7876 (tt0) cc_final: 0.7505 (mt-10) REVERT: A 437 LYS cc_start: 0.8700 (mtmt) cc_final: 0.8160 (mmtm) REVERT: B 270 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7167 (tt0) REVERT: B 339 ARG cc_start: 0.7247 (mtp85) cc_final: 0.6967 (ptm160) REVERT: B 372 ARG cc_start: 0.7761 (mmt-90) cc_final: 0.6786 (mmm-85) REVERT: B 383 ASP cc_start: 0.8513 (m-30) cc_final: 0.8200 (m-30) REVERT: B 435 ASP cc_start: 0.7906 (t0) cc_final: 0.7408 (t70) outliers start: 25 outliers final: 18 residues processed: 137 average time/residue: 0.0867 time to fit residues: 17.0922 Evaluate side-chains 141 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 371 ARG Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 186 GLN Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 417 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 128 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 92 optimal weight: 40.0000 chunk 135 optimal weight: 30.0000 chunk 171 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 37 optimal weight: 30.0000 chunk 48 optimal weight: 0.9980 chunk 154 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 152 optimal weight: 20.0000 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 HIS ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.261195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.174885 restraints weight = 12170.115| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.65 r_work: 0.3693 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11508 Z= 0.260 Angle : 0.598 7.612 15835 Z= 0.323 Chirality : 0.048 0.392 1952 Planarity : 0.004 0.052 2129 Dihedral : 13.260 178.565 2075 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.55 % Allowed : 16.31 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.20), residues: 1808 helix: 0.67 (0.18), residues: 855 sheet: -0.32 (0.64), residues: 71 loop : -1.39 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 164 TYR 0.026 0.002 TYR B 315 PHE 0.040 0.002 PHE B 329 TRP 0.014 0.002 TRP B 285 HIS 0.016 0.002 HIS B 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00605 / 0.26 (11508) covalent geometry : angle 0.59839 / 0.32 (15835) hydrogen bonds : bond 0.03789 / 2.61 ( 663) hydrogen bonds : angle 4.70448 / 3.44 ( 1845) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.368 Fit side-chains REVERT: A 149 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8274 (tt0) REVERT: A 150 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9182 (mm) REVERT: A 230 LYS cc_start: 0.9067 (mttt) cc_final: 0.8468 (mtpp) REVERT: A 239 MET cc_start: 0.8790 (mtp) cc_final: 0.8263 (mtp) REVERT: A 329 PHE cc_start: 0.8514 (t80) cc_final: 0.8158 (t80) REVERT: A 348 ARG cc_start: 0.7451 (mtm180) cc_final: 0.7170 (mtp85) REVERT: A 371 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.7097 (ttp-170) REVERT: A 429 GLU cc_start: 0.7855 (tt0) cc_final: 0.7486 (mt-10) REVERT: A 437 LYS cc_start: 0.8705 (mtmt) cc_final: 0.8125 (mmtm) REVERT: B 270 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.6958 (tt0) REVERT: B 339 ARG cc_start: 0.7228 (mtp85) cc_final: 0.6977 (ptm160) REVERT: B 372 ARG cc_start: 0.7737 (mmt-90) cc_final: 0.6693 (mmm-85) REVERT: B 383 ASP cc_start: 0.8482 (m-30) cc_final: 0.8188 (m-30) REVERT: B 435 ASP cc_start: 0.7877 (t0) cc_final: 0.7373 (t70) outliers start: 20 outliers final: 14 residues processed: 136 average time/residue: 0.1035 time to fit residues: 20.2438 Evaluate side-chains 139 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 371 ARG Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 417 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 113 optimal weight: 0.0970 chunk 158 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 171 optimal weight: 6.9990 chunk 163 optimal weight: 30.0000 chunk 71 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 119 optimal weight: 8.9990 chunk 125 optimal weight: 8.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 HIS ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.258617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.171780 restraints weight = 12147.968| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.71 r_work: 0.3684 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.115 11508 Z= 0.394 Angle : 0.712 8.757 15835 Z= 0.381 Chirality : 0.052 0.409 1952 Planarity : 0.005 0.054 2129 Dihedral : 13.270 179.143 2075 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.63 % Favored : 91.32 % Rotamer: Outliers : 4.08 % Allowed : 16.13 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.20), residues: 1808 helix: 0.34 (0.18), residues: 853 sheet: -0.65 (0.63), residues: 72 loop : -1.57 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 164 TYR 0.031 0.003 TYR B 315 PHE 0.042 0.003 PHE B 329 TRP 0.014 0.003 TRP A 313 HIS 0.014 0.002 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00922 / 0.39 (11508) covalent geometry : angle 0.71182 / 0.38 (15835) hydrogen bonds : bond 0.04567 / 3.16 ( 663) hydrogen bonds : angle 5.02527 / 3.69 ( 1845) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.413 Fit side-chains REVERT: A 149 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8350 (tt0) REVERT: A 150 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9125 (mm) REVERT: A 230 LYS cc_start: 0.9066 (mttt) cc_final: 0.8598 (mttm) REVERT: A 239 MET cc_start: 0.8756 (mtp) cc_final: 0.8230 (mtp) REVERT: A 329 PHE cc_start: 0.8553 (t80) cc_final: 0.8077 (t80) REVERT: A 348 ARG cc_start: 0.7470 (mtm180) cc_final: 0.7160 (mtp85) REVERT: A 429 GLU cc_start: 0.7918 (tt0) cc_final: 0.7554 (mt-10) REVERT: A 437 LYS cc_start: 0.8718 (mtmt) cc_final: 0.8171 (mmtm) REVERT: B 239 MET cc_start: 0.8539 (mtp) cc_final: 0.8250 (mtp) REVERT: B 270 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7160 (tt0) REVERT: B 339 ARG cc_start: 0.7262 (mtp85) cc_final: 0.7003 (ptm160) REVERT: B 372 ARG cc_start: 0.7828 (mmt-90) cc_final: 0.6911 (mmm-85) REVERT: B 383 ASP cc_start: 0.8521 (m-30) cc_final: 0.8156 (m-30) REVERT: B 435 ASP cc_start: 0.7993 (t0) cc_final: 0.7512 (t70) REVERT: B 439 LYS cc_start: 0.8355 (tttt) cc_final: 0.8095 (tttm) outliers start: 23 outliers final: 18 residues processed: 134 average time/residue: 0.1118 time to fit residues: 21.4420 Evaluate side-chains 138 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 417 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 108 optimal weight: 30.0000 chunk 115 optimal weight: 20.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 HIS ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 HIS B 271 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.262672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.180627 restraints weight = 12171.680| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.57 r_work: 0.3710 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11508 Z= 0.138 Angle : 0.525 7.315 15835 Z= 0.284 Chirality : 0.045 0.371 1952 Planarity : 0.004 0.054 2129 Dihedral : 13.083 179.976 2075 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.19 % Allowed : 16.84 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.20), residues: 1808 helix: 1.07 (0.18), residues: 841 sheet: -0.72 (0.67), residues: 61 loop : -1.23 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 220 TYR 0.026 0.002 TYR A 315 PHE 0.042 0.002 PHE B 329 TRP 0.016 0.002 TRP B 285 HIS 0.012 0.002 HIS B 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (11508) covalent geometry : angle 0.52501 / 0.28 (15835) hydrogen bonds : bond 0.03163 / 2.15 ( 663) hydrogen bonds : angle 4.44892 / 3.24 ( 1845) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.352 Fit side-chains REVERT: A 149 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8296 (tt0) REVERT: A 150 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9193 (mm) REVERT: A 230 LYS cc_start: 0.9129 (mttt) cc_final: 0.8558 (mtpp) REVERT: A 239 MET cc_start: 0.8879 (mtp) cc_final: 0.8496 (mtp) REVERT: A 240 MET cc_start: 0.8940 (tpp) cc_final: 0.8617 (tpp) REVERT: A 329 PHE cc_start: 0.8542 (t80) cc_final: 0.8146 (t80) REVERT: A 348 ARG cc_start: 0.7351 (mtm180) cc_final: 0.6932 (mtp85) REVERT: A 371 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7157 (ttp-170) REVERT: A 429 GLU cc_start: 0.8153 (tt0) cc_final: 0.7760 (mt-10) REVERT: A 437 LYS cc_start: 0.8737 (mtmt) cc_final: 0.8142 (mmtm) REVERT: B 239 MET cc_start: 0.8520 (mtp) cc_final: 0.8209 (mtp) REVERT: B 339 ARG cc_start: 0.7355 (mtp85) cc_final: 0.7065 (ptm160) REVERT: B 383 ASP cc_start: 0.8588 (m-30) cc_final: 0.8374 (m-30) REVERT: B 435 ASP cc_start: 0.7915 (t0) cc_final: 0.7387 (t70) outliers start: 18 outliers final: 12 residues processed: 136 average time/residue: 0.1000 time to fit residues: 19.7194 Evaluate side-chains 135 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 371 ARG Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 417 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 22 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 7 optimal weight: 0.5980 chunk 151 optimal weight: 30.0000 chunk 37 optimal weight: 20.0000 chunk 92 optimal weight: 40.0000 chunk 28 optimal weight: 3.9990 chunk 99 optimal weight: 30.0000 chunk 174 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 HIS ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 HIS ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.260561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.178934 restraints weight = 12228.381| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 3.75 r_work: 0.3687 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 11508 Z= 0.301 Angle : 0.626 7.754 15835 Z= 0.337 Chirality : 0.049 0.393 1952 Planarity : 0.004 0.051 2129 Dihedral : 13.132 178.416 2075 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.58 % Favored : 92.37 % Rotamer: Outliers : 3.19 % Allowed : 17.20 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.20), residues: 1808 helix: 0.84 (0.18), residues: 847 sheet: -0.45 (0.64), residues: 72 loop : -1.33 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 164 TYR 0.028 0.002 TYR B 315 PHE 0.042 0.003 PHE B 329 TRP 0.012 0.002 TRP B 285 HIS 0.016 0.002 HIS B 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00704 / 0.30 (11508) covalent geometry : angle 0.62646 / 0.34 (15835) hydrogen bonds : bond 0.03936 / 2.71 ( 663) hydrogen bonds : angle 4.64331 / 3.40 ( 1845) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3607.76 seconds wall clock time: 61 minutes 50.35 seconds (3710.35 seconds total)