Starting phenix.real_space_refine on Tue Jul 29 17:02:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tdw_41175/07_2025/8tdw_41175_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tdw_41175/07_2025/8tdw_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tdw_41175/07_2025/8tdw_41175.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tdw_41175/07_2025/8tdw_41175.map" model { file = "/net/cci-nas-00/data/ceres_data/8tdw_41175/07_2025/8tdw_41175_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tdw_41175/07_2025/8tdw_41175_neut.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 8, 'ASP:plan': 15, 'TYR:plan': 6, 'ASN:plan1': 7, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 11, 'ARG:plan': 10} 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: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 8, 'TRP:plan': 2, 'ASP:plan': 13, 'PHE:plan': 5, 'GLU:plan': 10, 'ARG:plan': 8} 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: {'GLN:plan1': 20, 'ASP:plan': 35, 'TYR:plan': 22, 'ASN:plan1': 19, 'TRP:plan': 5, 'HIS:plan': 16, 'PHE:plan': 20, 'GLU:plan': 32, 'ARG:plan': 25} 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: {'GLN:plan1': 19, 'ASP:plan': 32, 'TYR:plan': 20, 'ASN:plan1': 16, 'TRP:plan': 5, 'HIS:plan': 16, 'PHE:plan': 19, 'GLU:plan': 29, 'ARG:plan': 24} 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: 8.22, per 1000 atoms: 0.72 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: 3.08 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.45 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: 3.27 Time building geometry restraints manager: 3.58 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 1.50e-02 4.44e+03 6.28e+00 bond pdb=" CA GLY A 219 " pdb=" C GLY A 219 " ideal model delta sigma weight residual 1.515 1.505 0.009 6.20e-03 2.60e+04 2.30e+00 bond pdb=" O4' C J 7 " pdb=" C1' C J 7 " ideal model delta sigma weight residual 1.412 1.393 0.019 1.50e-02 4.44e+03 1.57e+00 bond pdb=" CG GLN A 271 " pdb=" CD GLN A 271 " ideal model delta sigma weight residual 1.516 1.486 0.030 2.50e-02 1.60e+03 1.45e+00 bond pdb=" C4' C J 10 " pdb=" O4' C J 10 " ideal model delta sigma weight residual 1.454 1.436 0.018 1.50e-02 4.44e+03 1.44e+00 ... (remaining 11503 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 15523 1.64 - 3.27: 257 3.27 - 4.91: 42 4.91 - 6.54: 11 6.54 - 8.18: 2 Bond angle restraints: 15835 Sorted by residual: angle pdb=" CA TYR B 315 " pdb=" CB TYR B 315 " pdb=" CG TYR B 315 " ideal model delta sigma weight residual 113.90 120.20 -6.30 1.80e+00 3.09e-01 1.23e+01 angle pdb=" C ASP B 314 " pdb=" N TYR B 315 " pdb=" CA TYR B 315 " ideal model delta sigma weight residual 121.14 115.13 6.01 1.75e+00 3.27e-01 1.18e+01 angle pdb=" C3' A K 9 " pdb=" O3' A K 9 " pdb=" P C K 10 " ideal model delta sigma weight residual 120.20 125.02 -4.82 1.50e+00 4.44e-01 1.03e+01 angle pdb=" CA TYR A 315 " pdb=" CB TYR A 315 " pdb=" CG TYR A 315 " ideal model delta sigma weight residual 113.90 119.53 -5.63 1.80e+00 3.09e-01 9.79e+00 angle pdb=" C4' C J 7 " pdb=" C3' C J 7 " pdb=" C2' C J 7 " ideal model delta sigma weight residual 102.60 105.71 -3.11 1.00e+00 1.00e+00 9.65e+00 ... (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: 1297 0.042 - 0.084: 476 0.084 - 0.125: 166 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: 0.570 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.340 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4809 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= 0.210 Angle : 0.563 8.176 15835 Z= 0.315 Chirality : 0.046 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.008 0.002 TRP B 285 HIS 0.009 0.002 HIS A 162 PHE 0.012 0.002 PHE B 213 TYR 0.031 0.002 TYR B 315 ARG 0.007 0.001 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.15507 ( 663) hydrogen bonds : angle 6.45357 ( 1845) covalent geometry : bond 0.00473 (11508) covalent geometry : angle 0.56278 (15835) *********************** 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 : 1.303 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: 0.2522 time to fit residues: 53.0735 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 : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 20.0000 chunk 137 optimal weight: 40.0000 chunk 76 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 93 optimal weight: 50.0000 chunk 73 optimal weight: 0.9990 chunk 142 optimal weight: 9.9990 chunk 55 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS A 375 GLN B 210 HIS B 358 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.261856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.177702 restraints weight = 12053.960| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.93 r_work: 0.3671 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11508 Z= 0.232 Angle : 0.588 9.217 15835 Z= 0.312 Chirality : 0.047 0.217 1952 Planarity : 0.004 0.039 2129 Dihedral : 13.246 177.804 2075 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 1.95 % Allowed : 9.93 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.20), residues: 1808 helix: 1.13 (0.18), residues: 857 sheet: -0.40 (0.59), residues: 88 loop : -1.12 (0.22), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 285 HIS 0.009 0.002 HIS A 162 PHE 0.012 0.002 PHE B 221 TYR 0.030 0.002 TYR B 315 ARG 0.005 0.001 ARG B 164 Details of bonding type rmsd hydrogen bonds : bond 0.03808 ( 663) hydrogen bonds : angle 4.74007 ( 1845) covalent geometry : bond 0.00535 (11508) covalent geometry : angle 0.58777 (15835) *********************** 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 150 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 1.142 Fit side-chains REVERT: A 230 LYS cc_start: 0.8992 (mttt) cc_final: 0.8509 (mttm) REVERT: A 235 GLN cc_start: 0.8597 (mt0) cc_final: 0.8335 (mt0) REVERT: A 239 MET cc_start: 0.8794 (mtp) cc_final: 0.8266 (mtp) REVERT: A 271 GLN cc_start: 0.8578 (mt0) cc_final: 0.8293 (mt0) REVERT: A 329 PHE cc_start: 0.8547 (t80) cc_final: 0.8193 (t80) REVERT: A 348 ARG cc_start: 0.7169 (mtm180) cc_final: 0.6701 (mtp85) REVERT: A 371 ARG cc_start: 0.7643 (ptm-80) cc_final: 0.7037 (ttp-170) REVERT: A 417 GLU cc_start: 0.7992 (tt0) cc_final: 0.7787 (tt0) REVERT: A 429 GLU cc_start: 0.7803 (tt0) cc_final: 0.7449 (mt-10) REVERT: A 437 LYS cc_start: 0.8583 (mtmt) cc_final: 0.7975 (mmtm) REVERT: B 255 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7473 (mt-10) REVERT: B 339 ARG cc_start: 0.7369 (mtp85) cc_final: 0.7057 (ptm160) REVERT: B 421 LYS cc_start: 0.8900 (mtmt) cc_final: 0.8248 (mptt) REVERT: B 435 ASP cc_start: 0.7811 (t0) cc_final: 0.7326 (t0) outliers start: 11 outliers final: 9 residues processed: 145 average time/residue: 0.2368 time to fit residues: 48.5392 Evaluate side-chains 135 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 182 LEU Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 417 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 85 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 73 optimal weight: 0.0770 chunk 127 optimal weight: 20.0000 chunk 98 optimal weight: 0.0870 chunk 109 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 166 optimal weight: 7.9990 chunk 101 optimal weight: 50.0000 chunk 74 optimal weight: 1.9990 overall best weight: 0.8322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 HIS A 303 ASN B 119 ASN B 125 HIS B 210 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.264418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.183575 restraints weight = 12216.739| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.42 r_work: 0.3749 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11508 Z= 0.126 Angle : 0.500 9.704 15835 Z= 0.266 Chirality : 0.045 0.199 1952 Planarity : 0.003 0.040 2129 Dihedral : 12.884 179.094 2075 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.48 % Allowed : 10.28 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.21), residues: 1808 helix: 1.51 (0.19), residues: 850 sheet: -0.23 (0.59), residues: 88 loop : -0.93 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 285 HIS 0.011 0.001 HIS B 210 PHE 0.013 0.001 PHE B 221 TYR 0.025 0.001 TYR A 315 ARG 0.004 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.03060 ( 663) hydrogen bonds : angle 4.23419 ( 1845) covalent geometry : bond 0.00283 (11508) covalent geometry : angle 0.49977 (15835) *********************** 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 150 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 1.202 Fit side-chains REVERT: A 119 ASN cc_start: 0.7757 (t0) cc_final: 0.7472 (m-40) REVERT: A 120 ASP cc_start: 0.8319 (t0) cc_final: 0.8061 (t0) REVERT: A 230 LYS cc_start: 0.9049 (mttt) cc_final: 0.8665 (mtpp) REVERT: A 235 GLN cc_start: 0.8609 (mt0) cc_final: 0.8407 (mt0) REVERT: A 239 MET cc_start: 0.8900 (mtp) cc_final: 0.8513 (mtp) REVERT: A 240 MET cc_start: 0.8903 (tpp) cc_final: 0.8621 (tpp) REVERT: A 271 GLN cc_start: 0.8581 (mt0) cc_final: 0.8230 (mt0) REVERT: A 329 PHE cc_start: 0.8547 (t80) cc_final: 0.8289 (t80) REVERT: A 348 ARG cc_start: 0.7251 (mtm180) cc_final: 0.6810 (mtp85) REVERT: A 371 ARG cc_start: 0.7670 (ptm-80) cc_final: 0.7012 (ttp-170) REVERT: A 429 GLU cc_start: 0.8090 (tt0) cc_final: 0.7698 (mt-10) REVERT: A 437 LYS cc_start: 0.8669 (mtmt) cc_final: 0.8035 (mmtm) REVERT: B 188 GLU cc_start: 0.8117 (pm20) cc_final: 0.7739 (pm20) REVERT: B 339 ARG cc_start: 0.7499 (mtp85) cc_final: 0.7018 (ptm160) REVERT: B 372 ARG cc_start: 0.8008 (mmt-90) cc_final: 0.6726 (mmm-85) REVERT: B 383 ASP cc_start: 0.8282 (m-30) cc_final: 0.8014 (m-30) REVERT: B 421 LYS cc_start: 0.8883 (mtmt) cc_final: 0.8256 (mptt) REVERT: B 435 ASP cc_start: 0.7834 (t0) cc_final: 0.7312 (t0) outliers start: 14 outliers final: 10 residues processed: 144 average time/residue: 0.2338 time to fit residues: 47.9647 Evaluate side-chains 139 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 325 ILE 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 288 LYS Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 391 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 80 optimal weight: 0.0670 chunk 158 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 104 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 HIS A 326 GLN B 125 HIS B 210 HIS ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.264084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.185197 restraints weight = 12148.550| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 3.72 r_work: 0.3686 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11508 Z= 0.153 Angle : 0.504 9.851 15835 Z= 0.268 Chirality : 0.045 0.209 1952 Planarity : 0.003 0.038 2129 Dihedral : 12.821 179.033 2075 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.66 % Allowed : 11.17 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.21), residues: 1808 helix: 1.54 (0.19), residues: 853 sheet: 0.21 (0.66), residues: 73 loop : -0.87 (0.22), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 285 HIS 0.009 0.001 HIS B 376 PHE 0.019 0.002 PHE B 329 TYR 0.026 0.001 TYR B 315 ARG 0.007 0.000 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.03072 ( 663) hydrogen bonds : angle 4.12723 ( 1845) covalent geometry : bond 0.00352 (11508) covalent geometry : angle 0.50366 (15835) *********************** 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 144 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 1.162 Fit side-chains REVERT: A 120 ASP cc_start: 0.8145 (t0) cc_final: 0.7596 (t0) REVERT: A 230 LYS cc_start: 0.9024 (mttt) cc_final: 0.8645 (mtpp) REVERT: A 239 MET cc_start: 0.8881 (mtp) cc_final: 0.8484 (mtp) REVERT: A 271 GLN cc_start: 0.8555 (mt0) cc_final: 0.8229 (mt0) REVERT: A 329 PHE cc_start: 0.8506 (t80) cc_final: 0.8210 (t80) REVERT: A 348 ARG cc_start: 0.7216 (mtm180) cc_final: 0.6776 (mtp85) REVERT: A 371 ARG cc_start: 0.7622 (ptm-80) cc_final: 0.6983 (ttp-170) REVERT: A 429 GLU cc_start: 0.7945 (tt0) cc_final: 0.7592 (mt-10) REVERT: A 437 LYS cc_start: 0.8628 (mtmt) cc_final: 0.7972 (mmtm) REVERT: B 188 GLU cc_start: 0.8010 (pm20) cc_final: 0.7664 (pm20) REVERT: B 339 ARG cc_start: 0.7424 (mtp85) cc_final: 0.6937 (ptm160) REVERT: B 372 ARG cc_start: 0.7931 (mmt-90) cc_final: 0.6684 (mmm-85) REVERT: B 383 ASP cc_start: 0.8203 (m-30) cc_final: 0.7900 (m-30) REVERT: B 421 LYS cc_start: 0.8872 (mtmt) cc_final: 0.8244 (mptt) REVERT: B 435 ASP cc_start: 0.7807 (t0) cc_final: 0.7289 (t0) outliers start: 15 outliers final: 13 residues processed: 138 average time/residue: 0.2360 time to fit residues: 46.5326 Evaluate side-chains 138 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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 325 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 94 optimal weight: 40.0000 chunk 12 optimal weight: 0.7980 chunk 143 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 86 optimal weight: 0.0980 chunk 139 optimal weight: 40.0000 chunk 109 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 105 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 HIS A 180 HIS B 210 HIS ** B 271 GLN ** 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 = 0.4738 r_free = 0.4738 target = 0.263421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.181833 restraints weight = 12133.664| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.44 r_work: 0.3728 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11508 Z= 0.175 Angle : 0.514 9.972 15835 Z= 0.273 Chirality : 0.045 0.210 1952 Planarity : 0.003 0.038 2129 Dihedral : 12.824 179.065 2075 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.66 % Allowed : 12.41 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.21), residues: 1808 helix: 1.53 (0.18), residues: 854 sheet: 0.23 (0.66), residues: 73 loop : -0.90 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 285 HIS 0.010 0.002 HIS B 376 PHE 0.014 0.002 PHE B 267 TYR 0.027 0.002 TYR B 315 ARG 0.006 0.001 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.03146 ( 663) hydrogen bonds : angle 4.10598 ( 1845) covalent geometry : bond 0.00405 (11508) covalent geometry : angle 0.51411 (15835) *********************** 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 138 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 1.143 Fit side-chains REVERT: A 120 ASP cc_start: 0.8300 (t0) cc_final: 0.7775 (t0) REVERT: A 230 LYS cc_start: 0.9049 (mttt) cc_final: 0.8666 (mtpp) REVERT: A 239 MET cc_start: 0.8873 (mtp) cc_final: 0.8448 (mtp) REVERT: A 271 GLN cc_start: 0.8660 (mt0) cc_final: 0.8362 (mt0) REVERT: A 329 PHE cc_start: 0.8504 (t80) cc_final: 0.8197 (t80) REVERT: A 348 ARG cc_start: 0.7300 (mtm180) cc_final: 0.6868 (mtp85) REVERT: A 371 ARG cc_start: 0.7726 (ptm-80) cc_final: 0.7027 (ttp-170) REVERT: A 429 GLU cc_start: 0.8141 (tt0) cc_final: 0.7750 (mt-10) REVERT: A 437 LYS cc_start: 0.8722 (mtmt) cc_final: 0.8110 (mmtm) REVERT: B 188 GLU cc_start: 0.8105 (pm20) cc_final: 0.7750 (pm20) REVERT: B 339 ARG cc_start: 0.7488 (mtp85) cc_final: 0.6997 (ptm160) REVERT: B 372 ARG cc_start: 0.7668 (mmt-90) cc_final: 0.6709 (mmm-85) REVERT: B 421 LYS cc_start: 0.8959 (mtmt) cc_final: 0.8328 (mptt) REVERT: B 435 ASP cc_start: 0.7860 (t0) cc_final: 0.7329 (t70) outliers start: 15 outliers final: 12 residues processed: 133 average time/residue: 0.2371 time to fit residues: 45.0341 Evaluate side-chains 134 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 325 ILE 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 105 optimal weight: 20.0000 chunk 51 optimal weight: 0.5980 chunk 151 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 159 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 160 optimal weight: 5.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN A 180 HIS B 210 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.262564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.182240 restraints weight = 12296.935| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 2.46 r_work: 0.3686 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 11508 Z= 0.205 Angle : 0.535 9.783 15835 Z= 0.284 Chirality : 0.046 0.216 1952 Planarity : 0.004 0.038 2129 Dihedral : 12.851 179.504 2075 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.37 % Allowed : 13.30 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.20), residues: 1808 helix: 1.46 (0.18), residues: 854 sheet: 0.26 (0.65), residues: 73 loop : -0.94 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 285 HIS 0.011 0.002 HIS B 376 PHE 0.016 0.002 PHE A 316 TYR 0.027 0.002 TYR B 315 ARG 0.006 0.001 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.03304 ( 663) hydrogen bonds : angle 4.15584 ( 1845) covalent geometry : bond 0.00479 (11508) covalent geometry : angle 0.53478 (15835) *********************** 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 140 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 1.270 Fit side-chains REVERT: A 150 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9198 (mm) REVERT: A 230 LYS cc_start: 0.8999 (mttt) cc_final: 0.8633 (mtpp) REVERT: A 239 MET cc_start: 0.8850 (mtp) cc_final: 0.8344 (mtp) REVERT: A 271 GLN cc_start: 0.8586 (mt0) cc_final: 0.8333 (mt0) REVERT: A 329 PHE cc_start: 0.8473 (t80) cc_final: 0.8136 (t80) REVERT: A 348 ARG cc_start: 0.7279 (mtm180) cc_final: 0.6818 (mtp85) REVERT: A 371 ARG cc_start: 0.7615 (ptm-80) cc_final: 0.6920 (ptt-90) REVERT: A 429 GLU cc_start: 0.7944 (tt0) cc_final: 0.7603 (mt-10) REVERT: A 437 LYS cc_start: 0.8704 (mtmt) cc_final: 0.8152 (mmtm) REVERT: B 188 GLU cc_start: 0.8030 (pm20) cc_final: 0.7690 (pm20) REVERT: B 339 ARG cc_start: 0.7354 (mtp85) cc_final: 0.7062 (ptm160) REVERT: B 383 ASP cc_start: 0.8220 (m-30) cc_final: 0.7888 (m-30) REVERT: B 421 LYS cc_start: 0.8911 (mtmt) cc_final: 0.8363 (mttp) REVERT: B 435 ASP cc_start: 0.7847 (t0) cc_final: 0.7351 (t70) outliers start: 19 outliers final: 15 residues processed: 135 average time/residue: 0.2421 time to fit residues: 46.5896 Evaluate side-chains 135 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 325 ILE 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 288 LYS 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 70 optimal weight: 0.7980 chunk 166 optimal weight: 10.0000 chunk 12 optimal weight: 0.6980 chunk 177 optimal weight: 50.0000 chunk 167 optimal weight: 9.9990 chunk 129 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 124 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 143 optimal weight: 20.0000 chunk 14 optimal weight: 0.5980 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 HIS 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 = 0.261133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.176103 restraints weight = 12315.551| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.21 r_work: 0.3688 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 11508 Z= 0.263 Angle : 0.581 9.730 15835 Z= 0.309 Chirality : 0.047 0.224 1952 Planarity : 0.004 0.038 2129 Dihedral : 12.924 179.540 2075 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 3.19 % Allowed : 13.83 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.20), residues: 1808 helix: 1.29 (0.18), residues: 850 sheet: 0.19 (0.65), residues: 73 loop : -1.03 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 285 HIS 0.012 0.002 HIS B 376 PHE 0.037 0.002 PHE B 329 TYR 0.030 0.002 TYR B 315 ARG 0.006 0.001 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.03658 ( 663) hydrogen bonds : angle 4.31722 ( 1845) covalent geometry : bond 0.00613 (11508) covalent geometry : angle 0.58061 (15835) *********************** 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 139 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 1.218 Fit side-chains REVERT: A 150 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9241 (mm) REVERT: A 230 LYS cc_start: 0.9090 (mttt) cc_final: 0.8716 (mtpp) REVERT: A 239 MET cc_start: 0.8860 (mtp) cc_final: 0.8366 (mtp) REVERT: A 271 GLN cc_start: 0.8653 (mt0) cc_final: 0.8397 (mt0) REVERT: A 329 PHE cc_start: 0.8558 (t80) cc_final: 0.8217 (t80) REVERT: A 348 ARG cc_start: 0.7593 (mtm180) cc_final: 0.7176 (mtp85) REVERT: A 371 ARG cc_start: 0.7761 (ptm-80) cc_final: 0.7108 (ttp-170) REVERT: A 429 GLU cc_start: 0.8211 (tt0) cc_final: 0.7811 (mt-10) REVERT: A 437 LYS cc_start: 0.8731 (mtmt) cc_final: 0.8216 (mmtm) REVERT: B 339 ARG cc_start: 0.7389 (mtp85) cc_final: 0.7134 (ptm160) REVERT: B 383 ASP cc_start: 0.8448 (m-30) cc_final: 0.8116 (m-30) REVERT: B 421 LYS cc_start: 0.8994 (mtmt) cc_final: 0.8416 (mttp) REVERT: B 435 ASP cc_start: 0.7940 (t0) cc_final: 0.7412 (t70) outliers start: 18 outliers final: 16 residues processed: 134 average time/residue: 0.3215 time to fit residues: 62.1262 Evaluate side-chains 137 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 2.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 325 ILE 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 256 GLN Chi-restraints excluded: chain B residue 288 LYS 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 139 optimal weight: 40.0000 chunk 32 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 chunk 135 optimal weight: 30.0000 chunk 152 optimal weight: 20.0000 chunk 95 optimal weight: 30.0000 chunk 33 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 45 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 overall best weight: 2.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 HIS ** A 206 HIS ** 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 = 0.4738 r_free = 0.4738 target = 0.261348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.173277 restraints weight = 12209.936| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.55 r_work: 0.3701 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 11508 Z= 0.311 Angle : 0.623 9.610 15835 Z= 0.331 Chirality : 0.048 0.230 1952 Planarity : 0.004 0.042 2129 Dihedral : 13.013 178.465 2075 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.20), residues: 1808 helix: 1.06 (0.18), residues: 846 sheet: 0.14 (0.64), residues: 71 loop : -1.17 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 313 HIS 0.013 0.002 HIS B 376 PHE 0.031 0.003 PHE B 329 TYR 0.031 0.002 TYR B 315 ARG 0.006 0.001 ARG B 164 Details of bonding type rmsd hydrogen bonds : bond 0.03954 ( 663) hydrogen bonds : angle 4.50721 ( 1845) covalent geometry : bond 0.00725 (11508) covalent geometry : angle 0.62295 (15835) *********************** 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 136 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 2.791 Fit side-chains REVERT: A 149 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8225 (tt0) REVERT: A 150 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9200 (mm) REVERT: A 230 LYS cc_start: 0.9025 (mttt) cc_final: 0.8649 (mtpp) REVERT: A 239 MET cc_start: 0.8778 (mtp) cc_final: 0.8245 (mtp) REVERT: A 271 GLN cc_start: 0.8619 (mt0) cc_final: 0.8362 (mt0) REVERT: A 329 PHE cc_start: 0.8527 (t80) cc_final: 0.8148 (t80) REVERT: A 348 ARG cc_start: 0.7480 (mtm180) cc_final: 0.7222 (mtp85) REVERT: A 371 ARG cc_start: 0.7656 (ptm-80) cc_final: 0.7080 (ttp-170) REVERT: A 429 GLU cc_start: 0.7932 (tt0) cc_final: 0.7571 (mt-10) REVERT: A 437 LYS cc_start: 0.8696 (mtmt) cc_final: 0.8148 (mmtm) REVERT: B 339 ARG cc_start: 0.7283 (mtp85) cc_final: 0.7002 (ptm160) REVERT: B 383 ASP cc_start: 0.8316 (m-30) cc_final: 0.7982 (m-30) REVERT: B 421 LYS cc_start: 0.8958 (mtmt) cc_final: 0.8339 (mttp) REVERT: B 435 ASP cc_start: 0.7885 (t0) cc_final: 0.7423 (t70) outliers start: 19 outliers final: 16 residues processed: 131 average time/residue: 0.4575 time to fit residues: 88.5162 Evaluate side-chains 134 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 4.397 ------------------------------------------------------------------------------- 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 210 HIS Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 325 ILE 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 256 GLN Chi-restraints excluded: chain B residue 288 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 124 optimal weight: 20.0000 chunk 107 optimal weight: 30.0000 chunk 81 optimal weight: 10.0000 chunk 144 optimal weight: 20.0000 chunk 64 optimal weight: 0.3980 chunk 133 optimal weight: 30.0000 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 136 optimal weight: 50.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 HIS B 210 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.263580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.181258 restraints weight = 12248.559| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.41 r_work: 0.3731 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3587 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11508 Z= 0.138 Angle : 0.504 9.777 15835 Z= 0.268 Chirality : 0.045 0.201 1952 Planarity : 0.003 0.042 2129 Dihedral : 12.873 179.633 2075 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.30 % Allowed : 15.07 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.20), residues: 1808 helix: 1.44 (0.18), residues: 856 sheet: 0.11 (0.64), residues: 73 loop : -1.01 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 285 HIS 0.010 0.001 HIS B 376 PHE 0.031 0.002 PHE B 329 TYR 0.023 0.001 TYR A 315 ARG 0.006 0.000 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.02969 ( 663) hydrogen bonds : angle 4.10494 ( 1845) covalent geometry : bond 0.00317 (11508) covalent geometry : angle 0.50372 (15835) *********************** 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 139 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 1.115 Fit side-chains REVERT: A 230 LYS cc_start: 0.9096 (mttt) cc_final: 0.8700 (mtpp) REVERT: A 239 MET cc_start: 0.8880 (mtp) cc_final: 0.8508 (mtp) REVERT: A 271 GLN cc_start: 0.8600 (mt0) cc_final: 0.8266 (mt0) REVERT: A 329 PHE cc_start: 0.8528 (t80) cc_final: 0.8236 (t80) REVERT: A 348 ARG cc_start: 0.7362 (mtm180) cc_final: 0.6928 (mtp85) REVERT: A 371 ARG cc_start: 0.7728 (ptm-80) cc_final: 0.7062 (ttp-170) REVERT: A 429 GLU cc_start: 0.8215 (tt0) cc_final: 0.7840 (mt-10) REVERT: A 437 LYS cc_start: 0.8699 (mtmt) cc_final: 0.8104 (mmtm) REVERT: B 188 GLU cc_start: 0.8099 (pm20) cc_final: 0.7679 (pm20) REVERT: B 339 ARG cc_start: 0.7473 (mtp85) cc_final: 0.7174 (ptm160) REVERT: B 383 ASP cc_start: 0.8378 (m-30) cc_final: 0.8039 (m-30) REVERT: B 421 LYS cc_start: 0.8964 (mtmt) cc_final: 0.8407 (mttp) REVERT: B 435 ASP cc_start: 0.7902 (t0) cc_final: 0.7367 (t70) outliers start: 13 outliers final: 11 residues processed: 135 average time/residue: 0.2581 time to fit residues: 50.3618 Evaluate side-chains 133 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 325 ILE 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 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 53 optimal weight: 1.9990 chunk 133 optimal weight: 30.0000 chunk 181 optimal weight: 0.0980 chunk 96 optimal weight: 20.0000 chunk 75 optimal weight: 0.0870 chunk 122 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 160 optimal weight: 40.0000 chunk 163 optimal weight: 7.9990 chunk 165 optimal weight: 7.9990 overall best weight: 0.5160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 HIS 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 = 0.4758 r_free = 0.4758 target = 0.265748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.183479 restraints weight = 12235.686| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 2.16 r_work: 0.3783 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11508 Z= 0.101 Angle : 0.473 9.228 15835 Z= 0.251 Chirality : 0.044 0.194 1952 Planarity : 0.003 0.042 2129 Dihedral : 12.818 178.347 2075 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.13 % Allowed : 15.25 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.21), residues: 1808 helix: 1.72 (0.19), residues: 862 sheet: 0.32 (0.65), residues: 73 loop : -0.88 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 285 HIS 0.016 0.001 HIS B 210 PHE 0.040 0.001 PHE B 329 TYR 0.021 0.001 TYR A 315 ARG 0.005 0.000 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.02619 ( 663) hydrogen bonds : angle 3.87257 ( 1845) covalent geometry : bond 0.00222 (11508) covalent geometry : angle 0.47338 (15835) ********************** 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 145 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 1.150 Fit side-chains REVERT: A 230 LYS cc_start: 0.9059 (mttt) cc_final: 0.8677 (mtpp) REVERT: A 239 MET cc_start: 0.8903 (mtp) cc_final: 0.8584 (mtp) REVERT: A 240 MET cc_start: 0.8874 (tpp) cc_final: 0.8587 (tpp) REVERT: A 271 GLN cc_start: 0.8531 (mt0) cc_final: 0.8154 (mt0) REVERT: A 329 PHE cc_start: 0.8456 (t80) cc_final: 0.8192 (t80) REVERT: A 348 ARG cc_start: 0.7316 (mtm180) cc_final: 0.6897 (mtp85) REVERT: A 371 ARG cc_start: 0.7694 (ptm-80) cc_final: 0.7072 (ttp-170) REVERT: A 429 GLU cc_start: 0.8155 (tt0) cc_final: 0.7791 (mt-10) REVERT: A 437 LYS cc_start: 0.8600 (mtmt) cc_final: 0.7983 (mmtm) REVERT: B 188 GLU cc_start: 0.8055 (pm20) cc_final: 0.7761 (pm20) REVERT: B 339 ARG cc_start: 0.7434 (mtp85) cc_final: 0.7148 (ptm160) REVERT: B 383 ASP cc_start: 0.8186 (m-30) cc_final: 0.7851 (m-30) REVERT: B 407 TYR cc_start: 0.8904 (m-80) cc_final: 0.8672 (m-80) REVERT: B 421 LYS cc_start: 0.8905 (mtmt) cc_final: 0.8285 (mptt) REVERT: B 435 ASP cc_start: 0.7875 (t0) cc_final: 0.7326 (t70) outliers start: 12 outliers final: 11 residues processed: 140 average time/residue: 0.2474 time to fit residues: 49.2098 Evaluate side-chains 139 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 325 ILE 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 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 164 optimal weight: 30.0000 chunk 31 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 97 optimal weight: 7.9990 chunk 177 optimal weight: 30.0000 chunk 149 optimal weight: 20.0000 chunk 172 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 175 optimal weight: 0.0000 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 HIS B 210 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.265583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.191897 restraints weight = 12203.842| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 3.55 r_work: 0.3704 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11508 Z= 0.102 Angle : 0.482 10.409 15835 Z= 0.251 Chirality : 0.044 0.269 1952 Planarity : 0.003 0.042 2129 Dihedral : 12.812 178.177 2075 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.13 % Allowed : 16.31 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.21), residues: 1808 helix: 1.83 (0.19), residues: 860 sheet: 0.39 (0.65), residues: 73 loop : -0.80 (0.22), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 285 HIS 0.010 0.001 HIS B 210 PHE 0.049 0.002 PHE B 329 TYR 0.022 0.001 TYR A 315 ARG 0.005 0.000 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.02564 ( 663) hydrogen bonds : angle 3.78624 ( 1845) covalent geometry : bond 0.00226 (11508) covalent geometry : angle 0.48226 (15835) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8892.01 seconds wall clock time: 158 minutes 14.88 seconds (9494.88 seconds total)