Starting phenix.real_space_refine on Mon Aug 5 20:11:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qxo_18734/08_2024/8qxo_18734_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qxo_18734/08_2024/8qxo_18734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qxo_18734/08_2024/8qxo_18734.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qxo_18734/08_2024/8qxo_18734.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qxo_18734/08_2024/8qxo_18734_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qxo_18734/08_2024/8qxo_18734_neut.cif" } resolution = 3.43 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= 0.006 sd= 0.139 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: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 24 5.49 5 Mg 2 5.21 5 S 76 5.16 5 C 9076 2.51 5 N 2479 2.21 5 O 2630 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 127": "OE1" <-> "OE2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A GLU 496": "OE1" <-> "OE2" Residue "C GLU 270": "OE1" <-> "OE2" Residue "D GLU 234": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 14291 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3412 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 17, 'TRANS': 399} Chain breaks: 2 Chain: "B" Number of atoms: 3704 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 457, 3698 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 20, 'TRANS': 436} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Conformer: "B" Number of residues, atoms: 457, 3698 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 20, 'TRANS': 436} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 bond proxies already assigned to first conformer: 3778 Chain: "C" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3318 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 17, 'TRANS': 398} Chain breaks: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 45 Chain: "D" Number of atoms: 3607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3607 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 20, 'TRANS': 436} Chain breaks: 1 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 70 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' FE': 1, ' MG': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 121 Unusual residues: {' FE': 1, 'DCP': 1, 'DTP': 2, 'GTP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 93 Unusual residues: {' FE': 1, 'DCP': 1, 'GTP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 9.54, per 1000 atoms: 0.67 Number of scatterers: 14291 At special positions: 0 Unit cell: (117.72, 95.92, 106.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 S 76 16.00 P 24 15.00 Mg 2 11.99 O 2630 8.00 N 2479 7.00 C 9076 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 - 3.50 Amino acid : False - 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: 5.91 Conformation dependent library (CDL) restraints added in 2.9 seconds 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3276 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 16 sheets defined 60.5% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 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 removed outlier: 3.637A pdb=" N ILE A 147 " --> pdb=" O LEU A 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 144 through 147' Processing helix chain 'A' and resid 150 through 156 removed outlier: 3.646A pdb=" N TYR A 154 " --> pdb=" O GLY A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 186 removed outlier: 4.022A pdb=" N HIS A 167 " --> pdb=" O ASN A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 190 removed outlier: 3.777A pdb=" N GLN A 190 " --> pdb=" O PRO A 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 187 through 190' Processing helix chain 'A' and resid 192 through 205 Processing helix chain 'A' and resid 215 through 226 removed outlier: 5.357A pdb=" N ILE A 222 " --> pdb=" O ASP A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 232 through 247 Processing helix chain 'A' and resid 249 through 257 removed outlier: 4.585A pdb=" N VAL A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.794A pdb=" N CYS A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 295 Processing helix chain 'A' and resid 309 through 324 removed outlier: 3.534A pdb=" N TRP A 313 " --> pdb=" O ASP A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 337 removed outlier: 3.839A 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 394 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 415 through 420 Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 424 through 433 removed outlier: 4.066A 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 Processing helix chain 'A' and resid 469 through 473 removed outlier: 3.905A pdb=" N TYR A 473 " --> pdb=" O ARG A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 482 removed outlier: 4.243A pdb=" N LYS A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 558 through 577 removed outlier: 3.760A pdb=" N GLN A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR A 568 " --> pdb=" O ALA A 564 " (cutoff:3.500A) 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 removed outlier: 3.529A pdb=" N ILE B 147 " --> pdb=" O LEU B 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 144 through 147' Processing helix chain 'B' and resid 150 through 156 removed outlier: 3.593A pdb=" N TYR B 154 " --> pdb=" O GLY B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 186 removed outlier: 4.168A pdb=" N HIS B 167 " --> pdb=" O ASN B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 205 removed outlier: 3.636A pdb=" N CYS B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 220 removed outlier: 4.342A pdb=" N ASP B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 226 removed outlier: 4.047A pdb=" N LEU B 224 " --> pdb=" O ARG B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 249 removed outlier: 3.748A pdb=" N GLY B 249 " --> pdb=" O ILE B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 257 Processing helix chain 'B' and resid 260 through 271 removed outlier: 4.140A pdb=" N CYS B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 300 removed outlier: 5.486A pdb=" N PHE B 296 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE B 300 " --> pdb=" O LEU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 324 removed outlier: 3.963A pdb=" N TRP B 313 " --> pdb=" O ASP B 309 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY B 324 " --> pdb=" O CYS B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 337 removed outlier: 4.179A pdb=" N PHE B 334 " --> pdb=" O ASP B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 373 Processing helix chain 'B' and resid 376 through 394 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 415 through 421 removed outlier: 4.054A pdb=" N LYS B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 433 removed outlier: 3.887A 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 Processing helix chain 'B' and resid 469 through 473 Processing helix chain 'B' and resid 474 through 483 removed outlier: 4.539A pdb=" N LYS B 478 " --> pdb=" O GLU B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 518 Processing helix chain 'B' and resid 558 through 576 Processing helix chain 'C' and resid 129 through 137 Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 144 through 147 Processing helix chain 'C' and resid 150 through 156 removed outlier: 3.629A pdb=" N GLY C 153 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR C 154 " --> pdb=" O GLY C 151 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR C 155 " --> pdb=" O GLY C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 186 removed outlier: 4.102A pdb=" N HIS C 167 " --> pdb=" O ASN C 163 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 190 removed outlier: 3.751A pdb=" N GLN C 190 " --> pdb=" O PRO C 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 187 through 190' Processing helix chain 'C' and resid 192 through 205 Processing helix chain 'C' and resid 214 through 221 removed outlier: 3.843A pdb=" N ASP C 218 " --> pdb=" O SER C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 232 through 248 Processing helix chain 'C' and resid 250 through 257 Processing helix chain 'C' and resid 260 through 273 removed outlier: 3.934A pdb=" N CYS C 266 " --> pdb=" O GLU C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 295 Processing helix chain 'C' and resid 296 through 300 removed outlier: 3.894A pdb=" N GLU C 299 " --> pdb=" O PHE C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 324 Processing helix chain 'C' and resid 330 through 337 removed outlier: 3.706A pdb=" N PHE C 334 " --> pdb=" O ASP C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 354 No H-bonds generated for 'chain 'C' and resid 352 through 354' Processing helix chain 'C' and resid 355 through 373 Processing helix chain 'C' and resid 376 through 393 Processing helix chain 'C' and resid 402 through 404 No H-bonds generated for 'chain 'C' and resid 402 through 404' Processing helix chain 'C' and resid 411 through 414 Processing helix chain 'C' and resid 415 through 421 removed outlier: 3.528A pdb=" N TYR C 419 " --> pdb=" O ASP C 415 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS C 421 " --> pdb=" O GLU C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 432 removed outlier: 4.077A pdb=" N LEU C 428 " --> pdb=" O ASP C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 437 No H-bonds generated for 'chain 'C' and resid 435 through 437' Processing helix chain 'C' and resid 438 through 450 Processing helix chain 'C' and resid 469 through 473 Processing helix chain 'C' and resid 474 through 483 removed outlier: 4.255A pdb=" N LYS C 478 " --> pdb=" O GLU C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 576 Processing helix chain 'D' and resid 129 through 137 removed outlier: 3.545A pdb=" N ASP D 137 " --> pdb=" O VAL D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 144 through 147 Processing helix chain 'D' and resid 163 through 186 removed outlier: 4.097A pdb=" N HIS D 167 " --> pdb=" O ASN D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 190 removed outlier: 3.654A pdb=" N GLN D 190 " --> pdb=" O PRO D 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 187 through 190' Processing helix chain 'D' and resid 192 through 205 Processing helix chain 'D' and resid 214 through 220 removed outlier: 4.342A pdb=" N ASP D 218 " --> pdb=" O SER D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 226 removed outlier: 3.825A pdb=" N LEU D 224 " --> pdb=" O ARG D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 249 removed outlier: 3.659A pdb=" N GLY D 236 " --> pdb=" O THR D 232 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY D 249 " --> pdb=" O ILE D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 257 Processing helix chain 'D' and resid 260 through 273 removed outlier: 4.025A pdb=" N CYS D 266 " --> pdb=" O GLU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 300 removed outlier: 6.043A pdb=" N PHE D 296 " --> pdb=" O ASN D 293 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR D 298 " --> pdb=" O SER D 295 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU D 299 " --> pdb=" O PHE D 296 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE D 300 " --> pdb=" O LEU D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 324 removed outlier: 3.799A pdb=" N TRP D 313 " --> pdb=" O ASP D 309 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY D 324 " --> pdb=" O CYS D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 337 removed outlier: 4.278A pdb=" N PHE D 334 " --> pdb=" O ASP D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 373 Processing helix chain 'D' and resid 376 through 393 Processing helix chain 'D' and resid 402 through 404 No H-bonds generated for 'chain 'D' and resid 402 through 404' Processing helix chain 'D' and resid 409 through 414 removed outlier: 3.922A pdb=" N ILE D 413 " --> pdb=" O SER D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 421 removed outlier: 4.025A pdb=" N LYS D 421 " --> pdb=" O GLU D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 432 removed outlier: 4.269A pdb=" N LEU D 428 " --> pdb=" O ASP D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 437 No H-bonds generated for 'chain 'D' and resid 435 through 437' Processing helix chain 'D' and resid 438 through 450 Processing helix chain 'D' and resid 474 through 483 removed outlier: 4.316A pdb=" N LYS D 478 " --> pdb=" O GLU D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 496 No H-bonds generated for 'chain 'D' and resid 494 through 496' Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 558 through 575 Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 120 removed outlier: 3.509A pdb=" N LYS A 116 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 343 removed outlier: 3.562A pdb=" N ARG A 348 " --> pdb=" O CYS A 341 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 398 through 400 Processing sheet with id=AA4, first strand: chain 'A' and resid 455 through 459 removed outlier: 3.793A pdb=" N LYS A 455 " --> pdb=" O CYS A 554 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N CYS A 554 " --> pdb=" O LYS A 455 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL A 552 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N GLU A 459 " --> pdb=" O ILE A 550 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ILE A 550 " --> pdb=" O GLU A 459 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 549 " --> pdb=" O ILE A 503 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 503 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG A 551 " --> pdb=" O ASP A 501 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 116 through 119 removed outlier: 3.620A pdb=" N LYS B 116 " --> pdb=" O LEU B 128 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 339 through 342 removed outlier: 3.527A pdb=" N ARG B 348 " --> pdb=" O CYS B 341 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N TYR B 521 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ALA B 351 " --> pdb=" O TYR B 521 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N CYS B 522 " --> pdb=" O ARG B 528 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ARG B 528 " --> pdb=" O CYS B 522 " (cutoff:3.500A) 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 459 removed outlier: 7.307A pdb=" N VAL B 552 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLU B 459 " --> pdb=" O ILE B 550 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE B 550 " --> pdb=" O GLU B 459 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU B 547 " --> pdb=" O MET B 505 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET B 505 " --> pdb=" O GLU B 547 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 116 through 118 removed outlier: 3.587A pdb=" N LYS C 116 " --> pdb=" O LEU C 128 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 339 through 342 Processing sheet with id=AB2, first strand: chain 'C' and resid 399 through 400 Processing sheet with id=AB3, first strand: chain 'C' and resid 456 through 459 removed outlier: 7.382A pdb=" N VAL C 552 " --> pdb=" O VAL C 457 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N GLU C 459 " --> pdb=" O ILE C 550 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE C 550 " --> pdb=" O GLU C 459 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 116 through 119 removed outlier: 4.191A pdb=" N LYS D 116 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 128 " --> pdb=" O LYS D 116 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 338 through 343 removed outlier: 3.529A pdb=" N ARG D 339 " --> pdb=" O CYS D 350 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG D 348 " --> pdb=" O CYS D 341 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N TYR D 521 " --> pdb=" O ILE D 349 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA D 351 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 399 through 400 Processing sheet with id=AB7, first strand: chain 'D' and resid 455 through 456 673 hydrogen bonds defined for protein. 1872 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: 4.05 Time building geometry restraints manager: 6.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4646 1.35 - 1.46: 3403 1.46 - 1.58: 6429 1.58 - 1.70: 38 1.70 - 1.82: 114 Bond restraints: 14630 Sorted by residual: bond pdb=" C4' DCP B 704 " pdb=" O4' DCP B 704 " ideal model delta sigma weight residual 1.444 1.411 0.033 1.00e-02 1.00e+04 1.09e+01 bond pdb=" O1A DCP B 704 " pdb=" PA DCP B 704 " ideal model delta sigma weight residual 1.477 1.509 -0.032 1.00e-02 1.00e+04 1.06e+01 bond pdb=" O1A DCP D 704 " pdb=" PA DCP D 704 " ideal model delta sigma weight residual 1.477 1.509 -0.032 1.00e-02 1.00e+04 1.06e+01 bond pdb=" C4 DCP D 704 " pdb=" C5 DCP D 704 " ideal model delta sigma weight residual 1.426 1.389 0.037 1.20e-02 6.94e+03 9.37e+00 bond pdb=" O1B DCP D 704 " pdb=" PB DCP D 704 " ideal model delta sigma weight residual 1.477 1.511 -0.034 1.10e-02 8.26e+03 9.30e+00 ... (remaining 14625 not shown) Histogram of bond angle deviations from ideal: 99.87 - 107.88: 626 107.88 - 115.88: 8842 115.88 - 123.89: 10030 123.89 - 131.89: 310 131.89 - 139.90: 31 Bond angle restraints: 19839 Sorted by residual: angle pdb=" PB DCP B 704 " pdb=" O3B DCP B 704 " pdb=" PG DCP B 704 " ideal model delta sigma weight residual 139.87 117.66 22.21 1.00e+00 1.00e+00 4.93e+02 angle pdb=" PB DCP D 704 " pdb=" O3B DCP D 704 " pdb=" PG DCP D 704 " ideal model delta sigma weight residual 139.87 120.50 19.37 1.00e+00 1.00e+00 3.75e+02 angle pdb=" PA DCP B 704 " pdb=" O3A DCP B 704 " pdb=" PB DCP B 704 " ideal model delta sigma weight residual 136.83 119.97 16.86 1.00e+00 1.00e+00 2.84e+02 angle pdb=" PA DCP D 704 " pdb=" O3A DCP D 704 " pdb=" PB DCP D 704 " ideal model delta sigma weight residual 136.83 123.46 13.37 1.00e+00 1.00e+00 1.79e+02 angle pdb=" O2G DCP B 704 " pdb=" PG DCP B 704 " pdb=" O3B DCP B 704 " ideal model delta sigma weight residual 104.48 110.28 -5.80 1.14e+00 7.76e-01 2.61e+01 ... (remaining 19834 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.02: 8499 34.02 - 68.04: 250 68.04 - 102.06: 28 102.06 - 136.08: 3 136.08 - 170.10: 1 Dihedral angle restraints: 8781 sinusoidal: 3678 harmonic: 5103 Sorted by residual: dihedral pdb=" O3A GTP B 702 " pdb=" O3B GTP B 702 " pdb=" PB GTP B 702 " pdb=" PG GTP B 702 " ideal model delta sinusoidal sigma weight residual 303.79 133.69 170.10 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C4' GTP A 701 " pdb=" C5' GTP A 701 " pdb=" O5' GTP A 701 " pdb=" PA GTP A 701 " ideal model delta sinusoidal sigma weight residual 260.87 137.39 123.49 1 2.00e+01 2.50e-03 3.72e+01 dihedral pdb=" C4' GTP D 701 " pdb=" C5' GTP D 701 " pdb=" O5' GTP D 701 " pdb=" PA GTP D 701 " ideal model delta sinusoidal sigma weight residual 260.87 143.18 117.69 1 2.00e+01 2.50e-03 3.52e+01 ... (remaining 8778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1719 0.049 - 0.098: 290 0.098 - 0.146: 104 0.146 - 0.195: 4 0.195 - 0.244: 4 Chirality restraints: 2121 Sorted by residual: chirality pdb=" C3' DTP B 701 " pdb=" C2' DTP B 701 " pdb=" C4' DTP B 701 " pdb=" O3' DTP B 701 " both_signs ideal model delta sigma weight residual False -2.68 -2.92 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" C3' DTP B 705 " pdb=" C2' DTP B 705 " pdb=" C4' DTP B 705 " pdb=" O3' DTP B 705 " both_signs ideal model delta sigma weight residual False -2.68 -2.91 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" C4' DTP B 705 " pdb=" C3' DTP B 705 " pdb=" C5' DTP B 705 " pdb=" O4' DTP B 705 " both_signs ideal model delta sigma weight residual False -2.50 -2.73 0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 2118 not shown) Planarity restraints: 2525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DCP B 704 " -0.353 2.00e-02 2.50e+03 2.21e-01 1.10e+03 pdb=" C2 DCP B 704 " 0.026 2.00e-02 2.50e+03 pdb=" C4 DCP B 704 " -0.087 2.00e-02 2.50e+03 pdb=" C5 DCP B 704 " 0.068 2.00e-02 2.50e+03 pdb=" C6 DCP B 704 " 0.289 2.00e-02 2.50e+03 pdb=" N1 DCP B 704 " 0.051 2.00e-02 2.50e+03 pdb=" N3 DCP B 704 " -0.325 2.00e-02 2.50e+03 pdb=" N4 DCP B 704 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DCP B 704 " 0.332 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DCP D 704 " -0.016 2.00e-02 2.50e+03 7.27e-02 1.19e+02 pdb=" C2 DCP D 704 " -0.016 2.00e-02 2.50e+03 pdb=" C4 DCP D 704 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DCP D 704 " 0.113 2.00e-02 2.50e+03 pdb=" C6 DCP D 704 " -0.017 2.00e-02 2.50e+03 pdb=" N1 DCP D 704 " -0.068 2.00e-02 2.50e+03 pdb=" N3 DCP D 704 " -0.120 2.00e-02 2.50e+03 pdb=" N4 DCP D 704 " 0.002 2.00e-02 2.50e+03 pdb=" O2 DCP D 704 " 0.123 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS D 129 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO D 130 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 130 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 130 " 0.025 5.00e-02 4.00e+02 ... (remaining 2522 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 65 2.39 - 3.02: 8446 3.02 - 3.64: 21287 3.64 - 4.27: 30083 4.27 - 4.90: 51022 Nonbonded interactions: 110903 Sorted by model distance: nonbonded pdb=" O3B GTP A 701 " pdb="MG MG A 703 " model vdw 1.759 2.170 nonbonded pdb=" O2A GTP A 701 " pdb="MG MG A 703 " model vdw 1.802 2.170 nonbonded pdb="MG MG C 802 " pdb=" O2A GTP D 701 " model vdw 1.933 2.170 nonbonded pdb=" OD1 ASP A 311 " pdb="FE FE A 702 " model vdw 1.990 2.260 nonbonded pdb="MG MG C 802 " pdb=" O3B GTP D 701 " model vdw 2.005 2.170 ... (remaining 110898 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 114 through 227 or (resid 228 and (name N or name CA or na \ me C or name O or name CB )) or resid 229 or (resid 230 and (name N or name CA o \ r name C or name O or name CB )) or resid 231 through 261 or (resid 262 and (nam \ e N or name CA or name C or name O or name CB )) or resid 263 through 275 or (re \ sid 276 and (name N or name CA or name C or name O or name CB )) or resid 285 th \ rough 287 or (resid 288 and (name N or name CA or name C or name O or name CB )) \ or resid 289 through 291 or (resid 292 and (name N or name CA or name C or name \ O or name CB )) or resid 293 through 303 or (resid 304 through 305 and (name N \ or name CA or name C or name O or name CB )) or resid 306 through 325 or (resid \ 326 and (name N or name CA or name C or name O or name CB )) or resid 327 throug \ h 341 or (resid 342 and (name N or name CA or name C or name O or name CB )) or \ resid 343 or (resid 344 through 345 and (name N or name CA or name C or name O o \ r name CB )) or resid 346 through 397 or (resid 398 and (name N or name CA or na \ me C or name O or name CB )) or resid 399 through 434 or (resid 435 and (name N \ or name CA or name C or name O or name CB )) or resid 436 or resid 438 through 4 \ 64 or (resid 465 and (name N or name CA or name C or name O or name CB )) or res \ id 466 or (resid 467 and (name N or name CA or name C or name O or name CB )) or \ resid 468 or (resid 469 and (name N or name CA or name C or name O or name CB ) \ ) or resid 470 or (resid 471 and (name N or name CA or name C or name O or name \ CB )) or resid 472 through 473 or (resid 474 and (name N or name CA or name C or \ name O or name CB )) or resid 475 through 477 or (resid 478 and (name N or name \ CA or name C or name O or name CB )) or resid 479 through 485 or (resid 486 thr \ ough 490 and (name N or name CA or name C or name O or name CB )) or resid 491 o \ r (resid 492 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 93 or (resid 494 through 496 and (name N or name CA or name C or name O or name \ CB )) or resid 497 through 558 or (resid 559 through 560 and (name N or name CA \ or name C or name O or name CB )) or resid 561 through 577)) selection = (chain 'B' and (resid 114 through 227 or (resid 228 and (name N or name CA or na \ me C or name O or name CB )) or resid 229 or (resid 230 and (name N or name CA o \ r name C or name O or name CB )) or resid 231 through 261 or (resid 262 and (nam \ e N or name CA or name C or name O or name CB )) or resid 263 through 275 or (re \ sid 276 and (name N or name CA or name C or name O or name CB )) or resid 285 th \ rough 287 or (resid 288 and (name N or name CA or name C or name O or name CB )) \ or resid 289 through 291 or (resid 292 and (name N or name CA or name C or name \ O or name CB )) or resid 293 through 303 or (resid 304 through 305 and (name N \ or name CA or name C or name O or name CB )) or resid 306 through 325 or (resid \ 326 and (name N or name CA or name C or name O or name CB )) or resid 327 throug \ h 341 or (resid 342 and (name N or name CA or name C or name O or name CB )) or \ resid 343 or (resid 344 through 345 and (name N or name CA or name C or name O o \ r name CB )) or resid 346 through 397 or (resid 398 and (name N or name CA or na \ me C or name O or name CB )) or resid 399 through 434 or (resid 435 and (name N \ or name CA or name C or name O or name CB )) or resid 436 or resid 438 through 4 \ 64 or (resid 465 and (name N or name CA or name C or name O or name CB )) or res \ id 466 through 468 or (resid 469 and (name N or name CA or name C or name O or n \ ame CB )) or resid 470 or (resid 471 and (name N or name CA or name C or name O \ or name CB )) or resid 472 through 473 or (resid 474 and (name N or name CA or n \ ame C or name O or name CB )) or resid 475 through 477 or (resid 478 and (name N \ or name CA or name C or name O or name CB )) or resid 479 through 485 or (resid \ 486 through 490 and (name N or name CA or name C or name O or name CB )) or res \ id 491 or (resid 492 and (name N or name CA or name C or name O or name CB )) or \ resid 493 through 506 or resid 547 through 577)) selection = (chain 'C' and (resid 114 through 227 or (resid 228 and (name N or name CA or na \ me C or name O or name CB )) or resid 229 through 275 or (resid 284 and (name N \ or name CA or name C or name O or name CB )) or resid 285 through 303 or (resid \ 304 through 305 and (name N or name CA or name C or name O or name CB )) or resi \ d 306 through 436 or resid 438 through 466 or (resid 467 and (name N or name CA \ or name C or name O or name CB )) or resid 468 or (resid 469 and (name N or name \ CA or name C or name O or name CB )) or resid 470 or (resid 471 and (name N or \ name CA or name C or name O or name CB )) or resid 472 through 473 or (resid 474 \ and (name N or name CA or name C or name O or name CB )) or resid 475 through 5 \ 77)) selection = (chain 'D' and (resid 114 through 276 or resid 285 through 325 or (resid 326 and \ (name N or name CA or name C or name O or name CB )) or resid 327 through 436 o \ r resid 438 through 486 or (resid 487 through 490 and (name N or name CA or name \ C or name O or name CB )) or resid 491 through 506 or resid 547 through 577)) } 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=0.34 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 41.450 Find NCS groups from input model: 0.760 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: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14630 Z= 0.180 Angle : 0.634 22.210 19839 Z= 0.406 Chirality : 0.043 0.244 2121 Planarity : 0.006 0.221 2525 Dihedral : 16.427 170.101 5505 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.95 % Favored : 96.93 % Rotamer: Outliers : 0.13 % Allowed : 9.31 % Favored : 90.56 % 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: 0.60 (0.21), residues: 1728 helix: 1.31 (0.19), residues: 879 sheet: 1.45 (0.60), residues: 79 loop : -0.78 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 285 HIS 0.006 0.001 HIS B 233 PHE 0.011 0.001 PHE B 316 TYR 0.022 0.001 TYR A 315 ARG 0.009 0.000 ARG D 528 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 383 time to evaluate : 1.511 Fit side-chains REVERT: A 367 ASN cc_start: 0.7164 (m-40) cc_final: 0.6800 (m-40) REVERT: A 433 SER cc_start: 0.8513 (t) cc_final: 0.8254 (t) REVERT: A 455 LYS cc_start: 0.5482 (tppt) cc_final: 0.5193 (tttp) REVERT: B 235 GLN cc_start: 0.8008 (mt0) cc_final: 0.7501 (tt0) REVERT: B 285 TRP cc_start: 0.6454 (t60) cc_final: 0.5743 (t60) REVERT: B 396 TYR cc_start: 0.7681 (m-80) cc_final: 0.7196 (m-80) REVERT: B 469 LYS cc_start: 0.7504 (mttt) cc_final: 0.6827 (mmmt) REVERT: B 505 MET cc_start: 0.7500 (ttp) cc_final: 0.7252 (ttm) REVERT: B 547 GLU cc_start: 0.7215 (pm20) cc_final: 0.4814 (tp30) REVERT: C 155 TYR cc_start: 0.8069 (m-80) cc_final: 0.7654 (m-80) REVERT: C 348 ARG cc_start: 0.7056 (mmt90) cc_final: 0.6358 (ttt-90) REVERT: D 120 ASP cc_start: 0.6834 (m-30) cc_final: 0.6561 (m-30) REVERT: D 133 VAL cc_start: 0.7074 (t) cc_final: 0.6862 (t) REVERT: D 239 MET cc_start: 0.8051 (mtm) cc_final: 0.7676 (mtp) REVERT: D 371 ARG cc_start: 0.8070 (ttp-110) cc_final: 0.7715 (ttp80) REVERT: D 506 ASP cc_start: 0.8737 (p0) cc_final: 0.8294 (p0) REVERT: D 528 ARG cc_start: 0.6990 (mtm110) cc_final: 0.6568 (ttm-80) REVERT: D 539 GLN cc_start: 0.7014 (mt0) cc_final: 0.6606 (mt0) outliers start: 1 outliers final: 0 residues processed: 383 average time/residue: 0.3188 time to fit residues: 168.7107 Evaluate side-chains 189 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 0.0010 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 52 optimal weight: 0.2980 chunk 81 optimal weight: 0.0270 chunk 100 optimal weight: 4.9990 chunk 156 optimal weight: 0.9980 overall best weight: 0.6646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 517 HIS B 539 GLN C 367 ASN C 447 GLN C 548 GLN D 321 HIS D 571 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14630 Z= 0.223 Angle : 0.611 7.970 19839 Z= 0.313 Chirality : 0.047 0.257 2121 Planarity : 0.004 0.064 2525 Dihedral : 10.812 164.725 2095 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.47 % Favored : 96.41 % Rotamer: Outliers : 2.09 % Allowed : 14.83 % Favored : 83.07 % 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: 0.75 (0.21), residues: 1728 helix: 1.42 (0.18), residues: 862 sheet: 2.05 (0.58), residues: 84 loop : -0.72 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 285 HIS 0.007 0.001 HIS B 233 PHE 0.020 0.002 PHE D 141 TYR 0.031 0.002 TYR B 315 ARG 0.009 0.001 ARG D 470 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 201 time to evaluate : 1.651 Fit side-chains REVERT: A 254 MET cc_start: 0.6880 (ttm) cc_final: 0.6610 (ttm) REVERT: A 303 ASN cc_start: 0.5727 (OUTLIER) cc_final: 0.5356 (m-40) REVERT: A 367 ASN cc_start: 0.7325 (m-40) cc_final: 0.6991 (m-40) REVERT: A 416 MET cc_start: 0.5207 (pmm) cc_final: 0.4710 (mmt) REVERT: A 435 ASP cc_start: 0.6860 (m-30) cc_final: 0.6508 (m-30) REVERT: A 455 LYS cc_start: 0.5394 (tppt) cc_final: 0.4976 (tttp) REVERT: B 254 MET cc_start: 0.7535 (ttm) cc_final: 0.7295 (ttp) REVERT: B 396 TYR cc_start: 0.7737 (m-80) cc_final: 0.7177 (m-80) REVERT: B 469 LYS cc_start: 0.7334 (mttt) cc_final: 0.6537 (mmmt) REVERT: B 505 MET cc_start: 0.7541 (ttp) cc_final: 0.7187 (ttm) REVERT: B 547 GLU cc_start: 0.7437 (pm20) cc_final: 0.5508 (tp30) REVERT: C 287 TYR cc_start: 0.7429 (m-80) cc_final: 0.7118 (m-80) REVERT: C 374 TYR cc_start: 0.7198 (m-80) cc_final: 0.5858 (m-80) REVERT: C 385 MET cc_start: 0.7562 (mtp) cc_final: 0.7305 (mtp) REVERT: D 239 MET cc_start: 0.8468 (mtm) cc_final: 0.8126 (mtp) REVERT: D 371 ARG cc_start: 0.8190 (ttp-110) cc_final: 0.7942 (ttp80) REVERT: D 383 ASP cc_start: 0.7618 (OUTLIER) cc_final: 0.7101 (m-30) REVERT: D 470 ARG cc_start: 0.7407 (tpt90) cc_final: 0.7009 (tpt170) REVERT: D 506 ASP cc_start: 0.8321 (p0) cc_final: 0.7883 (p0) REVERT: D 528 ARG cc_start: 0.7156 (mtm110) cc_final: 0.6796 (ttm-80) REVERT: D 539 GLN cc_start: 0.7488 (mt0) cc_final: 0.6839 (mt0) REVERT: D 547 GLU cc_start: 0.8011 (pm20) cc_final: 0.7807 (pt0) outliers start: 30 outliers final: 17 residues processed: 220 average time/residue: 0.3109 time to fit residues: 95.2169 Evaluate side-chains 184 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 165 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 406 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 169 optimal weight: 0.0170 chunk 139 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 HIS B 210 HIS D 125 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14630 Z= 0.193 Angle : 0.548 6.144 19839 Z= 0.278 Chirality : 0.045 0.151 2121 Planarity : 0.004 0.050 2525 Dihedral : 10.331 161.176 2095 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.36 % Favored : 96.58 % Rotamer: Outliers : 1.96 % Allowed : 16.05 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.81 (0.21), residues: 1728 helix: 1.45 (0.18), residues: 877 sheet: 2.13 (0.52), residues: 104 loop : -0.80 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 313 HIS 0.008 0.001 HIS B 233 PHE 0.019 0.001 PHE D 141 TYR 0.024 0.001 TYR B 315 ARG 0.006 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 180 time to evaluate : 1.781 Fit side-chains REVERT: A 303 ASN cc_start: 0.5564 (OUTLIER) cc_final: 0.5208 (m110) REVERT: A 367 ASN cc_start: 0.7398 (m-40) cc_final: 0.7033 (m-40) REVERT: A 416 MET cc_start: 0.5432 (pmm) cc_final: 0.4803 (mmp) REVERT: A 435 ASP cc_start: 0.7067 (m-30) cc_final: 0.6842 (t0) REVERT: A 455 LYS cc_start: 0.5416 (tppt) cc_final: 0.5015 (tttp) REVERT: B 207 ASP cc_start: 0.8479 (p0) cc_final: 0.8259 (p0) REVERT: B 327 ASN cc_start: 0.6622 (p0) cc_final: 0.6354 (t0) REVERT: B 396 TYR cc_start: 0.7677 (m-80) cc_final: 0.7184 (m-80) REVERT: B 405 LYS cc_start: 0.7077 (mttp) cc_final: 0.6728 (ttpt) REVERT: B 438 LEU cc_start: 0.8037 (mt) cc_final: 0.7770 (mt) REVERT: B 469 LYS cc_start: 0.7398 (mttt) cc_final: 0.6563 (mmmt) REVERT: B 505 MET cc_start: 0.7568 (ttp) cc_final: 0.7246 (ttm) REVERT: B 547 GLU cc_start: 0.7797 (pm20) cc_final: 0.6391 (tp30) REVERT: C 287 TYR cc_start: 0.7625 (m-80) cc_final: 0.7326 (m-80) REVERT: C 374 TYR cc_start: 0.7389 (m-80) cc_final: 0.6120 (m-80) REVERT: C 385 MET cc_start: 0.7652 (mtp) cc_final: 0.7357 (mtp) REVERT: C 555 LYS cc_start: 0.7229 (mmmm) cc_final: 0.6646 (mmtp) REVERT: D 239 MET cc_start: 0.8446 (mtm) cc_final: 0.8152 (mtp) REVERT: D 371 ARG cc_start: 0.8023 (ttp-110) cc_final: 0.7804 (ttp80) REVERT: D 506 ASP cc_start: 0.8338 (p0) cc_final: 0.7817 (p0) REVERT: D 528 ARG cc_start: 0.7416 (mtm110) cc_final: 0.7004 (ttm-80) REVERT: D 539 GLN cc_start: 0.7636 (mt0) cc_final: 0.7416 (mt0) REVERT: D 547 GLU cc_start: 0.8035 (pm20) cc_final: 0.7833 (pt0) REVERT: D 571 GLN cc_start: 0.7429 (tp40) cc_final: 0.7201 (tp40) outliers start: 28 outliers final: 18 residues processed: 201 average time/residue: 0.2948 time to fit residues: 84.2048 Evaluate side-chains 189 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 170 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain D residue 406 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 74 optimal weight: 0.4980 chunk 105 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14630 Z= 0.266 Angle : 0.596 7.271 19839 Z= 0.303 Chirality : 0.047 0.161 2121 Planarity : 0.004 0.049 2525 Dihedral : 10.348 157.930 2095 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.97 % Allowed : 16.59 % Favored : 80.45 % 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: 0.70 (0.21), residues: 1728 helix: 1.39 (0.18), residues: 868 sheet: 1.94 (0.50), residues: 114 loop : -0.90 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 313 HIS 0.008 0.001 HIS B 233 PHE 0.026 0.002 PHE D 141 TYR 0.028 0.002 TYR B 315 ARG 0.004 0.001 ARG A 164 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 172 time to evaluate : 1.905 Fit side-chains revert: symmetry clash REVERT: A 303 ASN cc_start: 0.5686 (OUTLIER) cc_final: 0.5428 (m110) REVERT: A 367 ASN cc_start: 0.7635 (m-40) cc_final: 0.7388 (m-40) REVERT: A 385 MET cc_start: 0.7371 (ttp) cc_final: 0.6969 (ptm) REVERT: A 416 MET cc_start: 0.5611 (pmm) cc_final: 0.5013 (mmp) REVERT: A 433 SER cc_start: 0.8420 (OUTLIER) cc_final: 0.7618 (p) REVERT: A 455 LYS cc_start: 0.5395 (tppt) cc_final: 0.4822 (tttp) REVERT: B 142 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.6264 (mp10) REVERT: B 396 TYR cc_start: 0.7588 (m-80) cc_final: 0.7278 (m-80) REVERT: B 405 LYS cc_start: 0.7337 (mttp) cc_final: 0.6742 (ttpt) REVERT: B 469 LYS cc_start: 0.7223 (mttt) cc_final: 0.6924 (mmtt) REVERT: B 505 MET cc_start: 0.7334 (ttp) cc_final: 0.7101 (ttm) REVERT: C 254 MET cc_start: 0.7255 (mtm) cc_final: 0.6919 (mtm) REVERT: C 287 TYR cc_start: 0.7701 (m-80) cc_final: 0.7464 (m-80) REVERT: C 336 LYS cc_start: 0.6394 (tttt) cc_final: 0.6137 (tttt) REVERT: C 385 MET cc_start: 0.7671 (mtp) cc_final: 0.7196 (mtt) REVERT: C 548 GLN cc_start: 0.6733 (tt0) cc_final: 0.6493 (tt0) REVERT: C 555 LYS cc_start: 0.7568 (mmmm) cc_final: 0.7089 (mmtp) REVERT: D 239 MET cc_start: 0.8359 (mtm) cc_final: 0.8135 (mtp) REVERT: D 326 GLN cc_start: 0.7286 (mm-40) cc_final: 0.6697 (mt0) REVERT: D 506 ASP cc_start: 0.8600 (p0) cc_final: 0.8019 (p0) REVERT: D 528 ARG cc_start: 0.7478 (mtm110) cc_final: 0.7162 (ttm-80) REVERT: D 539 GLN cc_start: 0.7825 (mt0) cc_final: 0.7608 (mt0) outliers start: 43 outliers final: 23 residues processed: 206 average time/residue: 0.3214 time to fit residues: 91.7606 Evaluate side-chains 175 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 149 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 573 CYS Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 406 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 123 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN A 271 GLN ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 GLN C 370 HIS D 571 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.5557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 14630 Z= 0.443 Angle : 0.724 8.102 19839 Z= 0.369 Chirality : 0.051 0.202 2121 Planarity : 0.005 0.056 2525 Dihedral : 11.038 154.295 2095 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.64 % Allowed : 17.46 % Favored : 78.89 % 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: 0.12 (0.20), residues: 1728 helix: 0.99 (0.18), residues: 853 sheet: 1.90 (0.52), residues: 110 loop : -1.27 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 313 HIS 0.008 0.002 HIS B 233 PHE 0.027 0.003 PHE B 157 TYR 0.034 0.003 TYR B 315 ARG 0.007 0.001 ARG B 470 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 152 time to evaluate : 1.707 Fit side-chains revert: symmetry clash REVERT: A 235 GLN cc_start: 0.8249 (tm-30) cc_final: 0.7978 (tm-30) REVERT: A 346 GLU cc_start: 0.3432 (OUTLIER) cc_final: 0.2937 (pm20) REVERT: A 371 ARG cc_start: 0.6341 (ttp80) cc_final: 0.5852 (ttm110) REVERT: A 416 MET cc_start: 0.5596 (pmm) cc_final: 0.4957 (mmp) REVERT: A 437 LYS cc_start: 0.8100 (mtpt) cc_final: 0.7518 (mmtt) REVERT: A 455 LYS cc_start: 0.5648 (tppt) cc_final: 0.4903 (tttp) REVERT: B 134 ARG cc_start: 0.7472 (ttm-80) cc_final: 0.7243 (ttm-80) REVERT: B 142 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.6225 (mp10) REVERT: B 448 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7938 (mt) REVERT: B 469 LYS cc_start: 0.7431 (mttt) cc_final: 0.6625 (mmmt) REVERT: C 195 ASP cc_start: 0.6931 (OUTLIER) cc_final: 0.6705 (m-30) REVERT: C 385 MET cc_start: 0.7716 (mtp) cc_final: 0.7241 (mtt) REVERT: C 555 LYS cc_start: 0.7810 (mmmm) cc_final: 0.7422 (mmtp) REVERT: D 326 GLN cc_start: 0.7405 (mm-40) cc_final: 0.6775 (mt0) REVERT: D 470 ARG cc_start: 0.7619 (tpt90) cc_final: 0.6860 (tpt170) REVERT: D 506 ASP cc_start: 0.8769 (p0) cc_final: 0.8074 (p0) REVERT: D 547 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7194 (pm20) outliers start: 53 outliers final: 34 residues processed: 193 average time/residue: 0.3365 time to fit residues: 89.2796 Evaluate side-chains 178 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 139 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 573 CYS Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 180 HIS Chi-restraints excluded: chain C residue 194 ARG Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 370 HIS Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 511 GLU Chi-restraints excluded: chain D residue 547 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 97 optimal weight: 0.0970 chunk 41 optimal weight: 2.9990 chunk 166 optimal weight: 0.0270 chunk 138 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 160 optimal weight: 0.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN A 271 GLN A 367 ASN A 548 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.5530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14630 Z= 0.169 Angle : 0.545 7.682 19839 Z= 0.276 Chirality : 0.045 0.161 2121 Planarity : 0.004 0.050 2525 Dihedral : 10.413 153.764 2095 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.76 % Allowed : 18.88 % Favored : 78.35 % 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: 0.54 (0.21), residues: 1728 helix: 1.32 (0.18), residues: 872 sheet: 2.03 (0.51), residues: 114 loop : -1.11 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 285 HIS 0.015 0.001 HIS C 370 PHE 0.018 0.001 PHE D 334 TYR 0.021 0.001 TYR D 396 ARG 0.005 0.000 ARG A 348 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 149 time to evaluate : 1.601 Fit side-chains revert: symmetry clash REVERT: A 235 GLN cc_start: 0.8289 (tm-30) cc_final: 0.8024 (tm-30) REVERT: A 371 ARG cc_start: 0.6311 (ttp80) cc_final: 0.5917 (ttm170) REVERT: A 416 MET cc_start: 0.5629 (pmm) cc_final: 0.4964 (mmp) REVERT: A 437 LYS cc_start: 0.8023 (mtpt) cc_final: 0.7431 (mmtt) REVERT: A 442 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7302 (ttp80) REVERT: A 455 LYS cc_start: 0.5331 (tppt) cc_final: 0.4722 (tttp) REVERT: A 551 ARG cc_start: 0.5406 (mtm180) cc_final: 0.5014 (ptp-170) REVERT: B 142 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.6327 (mp10) REVERT: B 469 LYS cc_start: 0.7436 (mttt) cc_final: 0.6622 (mmmt) REVERT: B 470 ARG cc_start: 0.7376 (tpt90) cc_final: 0.7077 (tpp-160) REVERT: C 369 LEU cc_start: 0.7669 (tt) cc_final: 0.7236 (tp) REVERT: C 385 MET cc_start: 0.7521 (mtp) cc_final: 0.7105 (mtt) REVERT: C 503 ILE cc_start: 0.6200 (OUTLIER) cc_final: 0.5664 (tp) REVERT: C 548 GLN cc_start: 0.6841 (tt0) cc_final: 0.6612 (tt0) REVERT: C 555 LYS cc_start: 0.7780 (mmmm) cc_final: 0.7489 (mmtp) REVERT: D 271 GLN cc_start: 0.8114 (mt0) cc_final: 0.7887 (mt0) REVERT: D 326 GLN cc_start: 0.7314 (mm-40) cc_final: 0.6733 (mt0) REVERT: D 470 ARG cc_start: 0.7438 (tpt90) cc_final: 0.6846 (tpt170) REVERT: D 506 ASP cc_start: 0.8654 (p0) cc_final: 0.7996 (p0) REVERT: D 547 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7276 (pm20) outliers start: 40 outliers final: 22 residues processed: 181 average time/residue: 0.3527 time to fit residues: 87.1681 Evaluate side-chains 162 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 136 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 442 ARG Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 573 CYS Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 370 HIS Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 503 ILE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 406 LYS Chi-restraints excluded: chain D residue 547 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 0.0000 chunk 94 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 102 optimal weight: 0.2980 chunk 66 optimal weight: 2.9990 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN C 370 HIS D 125 HIS D 367 ASN D 571 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.5655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14630 Z= 0.221 Angle : 0.562 8.095 19839 Z= 0.283 Chirality : 0.046 0.168 2121 Planarity : 0.004 0.047 2525 Dihedral : 10.389 149.017 2095 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.56 % Allowed : 19.15 % Favored : 78.29 % 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: 0.64 (0.21), residues: 1728 helix: 1.43 (0.18), residues: 869 sheet: 2.06 (0.51), residues: 110 loop : -1.07 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 285 HIS 0.007 0.001 HIS B 233 PHE 0.014 0.001 PHE A 267 TYR 0.024 0.002 TYR D 315 ARG 0.006 0.000 ARG A 348 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 140 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 371 ARG cc_start: 0.6404 (ttp80) cc_final: 0.5878 (ttm170) REVERT: A 416 MET cc_start: 0.5623 (pmm) cc_final: 0.5012 (mmp) REVERT: A 437 LYS cc_start: 0.8061 (mtpt) cc_final: 0.7483 (mmtt) REVERT: A 442 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7263 (ttp80) REVERT: A 455 LYS cc_start: 0.5351 (tppt) cc_final: 0.4600 (tttp) REVERT: A 551 ARG cc_start: 0.5476 (mtm180) cc_final: 0.5169 (ptp-170) REVERT: B 142 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.6193 (mp10) REVERT: B 469 LYS cc_start: 0.7440 (mttt) cc_final: 0.6615 (mmmt) REVERT: B 470 ARG cc_start: 0.7398 (tpt90) cc_final: 0.6986 (tpp-160) REVERT: C 385 MET cc_start: 0.7680 (mtp) cc_final: 0.7172 (mtt) REVERT: C 503 ILE cc_start: 0.6192 (OUTLIER) cc_final: 0.5643 (tp) REVERT: C 555 LYS cc_start: 0.7761 (mmmm) cc_final: 0.7462 (mmtp) REVERT: D 149 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8171 (tt0) REVERT: D 326 GLN cc_start: 0.7010 (mm-40) cc_final: 0.6699 (mt0) REVERT: D 497 ASP cc_start: 0.6957 (m-30) cc_final: 0.6116 (t0) REVERT: D 506 ASP cc_start: 0.8420 (p0) cc_final: 0.7770 (p0) REVERT: D 547 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7338 (pm20) outliers start: 37 outliers final: 26 residues processed: 167 average time/residue: 0.3369 time to fit residues: 77.6659 Evaluate side-chains 163 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 132 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 442 ARG Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 573 CYS Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain C residue 194 ARG Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 370 HIS Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 503 ILE Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 149 GLN Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 406 LYS Chi-restraints excluded: chain D residue 547 GLU Chi-restraints excluded: chain D residue 570 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 81 optimal weight: 0.2980 chunk 15 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN C 370 HIS ** C 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 HIS D 271 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.5721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14630 Z= 0.188 Angle : 0.539 7.316 19839 Z= 0.272 Chirality : 0.045 0.161 2121 Planarity : 0.004 0.048 2525 Dihedral : 10.192 145.151 2095 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.56 % Allowed : 19.15 % Favored : 78.29 % 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: 0.69 (0.21), residues: 1728 helix: 1.48 (0.18), residues: 870 sheet: 2.12 (0.54), residues: 90 loop : -0.97 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 285 HIS 0.016 0.001 HIS C 370 PHE 0.013 0.001 PHE D 267 TYR 0.023 0.001 TYR D 315 ARG 0.006 0.000 ARG A 348 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 137 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 371 ARG cc_start: 0.6551 (ttp80) cc_final: 0.5956 (ttm170) REVERT: A 416 MET cc_start: 0.5536 (pmm) cc_final: 0.5004 (mmp) REVERT: A 442 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7288 (ttp80) REVERT: A 455 LYS cc_start: 0.5279 (tppt) cc_final: 0.4590 (tttp) REVERT: A 551 ARG cc_start: 0.5397 (mtm180) cc_final: 0.5162 (ptp-170) REVERT: B 142 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.6310 (mp10) REVERT: B 469 LYS cc_start: 0.7420 (mttt) cc_final: 0.7176 (mmtt) REVERT: B 470 ARG cc_start: 0.7343 (tpt90) cc_final: 0.6956 (tpp-160) REVERT: C 371 ARG cc_start: 0.6699 (ptp-170) cc_final: 0.6389 (ptp-110) REVERT: C 385 MET cc_start: 0.7675 (mtp) cc_final: 0.7171 (mtt) REVERT: C 416 MET cc_start: 0.5612 (mmm) cc_final: 0.4861 (mmm) REVERT: C 503 ILE cc_start: 0.6350 (OUTLIER) cc_final: 0.5731 (tp) REVERT: C 555 LYS cc_start: 0.7634 (mmmm) cc_final: 0.7379 (mmtp) REVERT: D 120 ASP cc_start: 0.7872 (t0) cc_final: 0.7429 (t0) REVERT: D 149 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8160 (tt0) REVERT: D 271 GLN cc_start: 0.8286 (mt0) cc_final: 0.7951 (mt0) REVERT: D 326 GLN cc_start: 0.6918 (mm-40) cc_final: 0.6661 (mt0) REVERT: D 470 ARG cc_start: 0.7565 (tpt90) cc_final: 0.7030 (tpp-160) REVERT: D 497 ASP cc_start: 0.6956 (m-30) cc_final: 0.6132 (t0) REVERT: D 506 ASP cc_start: 0.8411 (p0) cc_final: 0.7775 (p0) REVERT: D 547 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7353 (pm20) outliers start: 37 outliers final: 24 residues processed: 167 average time/residue: 0.3334 time to fit residues: 77.0885 Evaluate side-chains 162 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 133 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 442 ARG Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 573 CYS Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 503 ILE Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 149 GLN Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 406 LYS Chi-restraints excluded: chain D residue 547 GLU Chi-restraints excluded: chain D residue 570 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 153 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 chunk 163 optimal weight: 5.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN C 370 HIS ** C 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 HIS D 375 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.5968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14630 Z= 0.340 Angle : 0.629 7.611 19839 Z= 0.319 Chirality : 0.048 0.176 2121 Planarity : 0.005 0.047 2525 Dihedral : 10.457 137.177 2095 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.86 % Favored : 95.08 % Rotamer: Outliers : 2.56 % Allowed : 19.49 % Favored : 77.95 % 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: 0.44 (0.21), residues: 1728 helix: 1.22 (0.18), residues: 874 sheet: 1.82 (0.50), residues: 110 loop : -1.09 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 313 HIS 0.008 0.002 HIS B 233 PHE 0.019 0.002 PHE B 157 TYR 0.029 0.002 TYR B 315 ARG 0.006 0.001 ARG A 348 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 141 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 371 ARG cc_start: 0.6647 (ttp80) cc_final: 0.5860 (ttm170) REVERT: A 416 MET cc_start: 0.5615 (pmm) cc_final: 0.5112 (mmp) REVERT: A 437 LYS cc_start: 0.8070 (mtpt) cc_final: 0.7496 (mmtt) REVERT: A 442 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7286 (ttp80) REVERT: A 455 LYS cc_start: 0.5403 (tppt) cc_final: 0.4581 (tttp) REVERT: A 551 ARG cc_start: 0.5465 (mtm180) cc_final: 0.5132 (ptp-170) REVERT: B 142 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.6274 (mp10) REVERT: B 469 LYS cc_start: 0.7521 (mttt) cc_final: 0.7280 (mmtt) REVERT: C 362 MET cc_start: 0.6083 (tmm) cc_final: 0.5601 (ttt) REVERT: C 385 MET cc_start: 0.7838 (mtp) cc_final: 0.7323 (mtt) REVERT: C 503 ILE cc_start: 0.6150 (OUTLIER) cc_final: 0.5669 (tp) REVERT: C 555 LYS cc_start: 0.7728 (mmmm) cc_final: 0.7420 (mmtp) REVERT: D 149 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8151 (tt0) REVERT: D 271 GLN cc_start: 0.8296 (mt0) cc_final: 0.8039 (mt0) REVERT: D 326 GLN cc_start: 0.6997 (mm-40) cc_final: 0.6702 (mt0) REVERT: D 470 ARG cc_start: 0.7673 (tpt90) cc_final: 0.6940 (tpt170) REVERT: D 497 ASP cc_start: 0.6929 (m-30) cc_final: 0.6093 (t0) REVERT: D 506 ASP cc_start: 0.8726 (p0) cc_final: 0.8069 (p0) REVERT: D 528 ARG cc_start: 0.7559 (mtm110) cc_final: 0.7236 (ttt-90) REVERT: D 547 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7157 (pm20) outliers start: 37 outliers final: 28 residues processed: 169 average time/residue: 0.3288 time to fit residues: 77.0390 Evaluate side-chains 170 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 137 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 442 ARG Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 573 CYS Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 503 ILE Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 149 GLN Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 406 LYS Chi-restraints excluded: chain D residue 547 GLU Chi-restraints excluded: chain D residue 570 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 0.0980 chunk 77 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 171 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 108 optimal weight: 0.0970 chunk 145 optimal weight: 3.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 HIS C 548 GLN D 125 HIS D 571 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.5956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14630 Z= 0.178 Angle : 0.539 8.438 19839 Z= 0.272 Chirality : 0.045 0.158 2121 Planarity : 0.004 0.048 2525 Dihedral : 10.020 135.776 2095 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.36 % Allowed : 19.76 % Favored : 77.88 % 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: 0.64 (0.21), residues: 1728 helix: 1.46 (0.18), residues: 870 sheet: 2.06 (0.53), residues: 90 loop : -1.02 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 285 HIS 0.006 0.001 HIS B 233 PHE 0.011 0.001 PHE D 141 TYR 0.022 0.001 TYR B 315 ARG 0.007 0.000 ARG A 348 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 135 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 371 ARG cc_start: 0.6763 (ttp80) cc_final: 0.5921 (ttm170) REVERT: A 416 MET cc_start: 0.5362 (pmm) cc_final: 0.5019 (mmp) REVERT: A 437 LYS cc_start: 0.8020 (mtpt) cc_final: 0.7448 (mmtt) REVERT: A 442 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7298 (ttp80) REVERT: A 455 LYS cc_start: 0.5236 (tppt) cc_final: 0.4504 (tttp) REVERT: B 142 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.6360 (mp10) REVERT: B 469 LYS cc_start: 0.7450 (mttt) cc_final: 0.7237 (mmtt) REVERT: C 385 MET cc_start: 0.7695 (mtp) cc_final: 0.7227 (mtp) REVERT: C 416 MET cc_start: 0.5574 (mmm) cc_final: 0.4943 (mmm) REVERT: C 503 ILE cc_start: 0.6340 (OUTLIER) cc_final: 0.5809 (tp) REVERT: C 555 LYS cc_start: 0.7666 (mmmm) cc_final: 0.7387 (mmtp) REVERT: D 149 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8206 (tt0) REVERT: D 271 GLN cc_start: 0.8263 (mt0) cc_final: 0.7889 (mt0) REVERT: D 326 GLN cc_start: 0.6818 (mm-40) cc_final: 0.6596 (mt0) REVERT: D 470 ARG cc_start: 0.7415 (tpt90) cc_final: 0.6691 (tpt170) REVERT: D 497 ASP cc_start: 0.6914 (m-30) cc_final: 0.6085 (t0) REVERT: D 506 ASP cc_start: 0.8676 (p0) cc_final: 0.8024 (p0) REVERT: D 528 ARG cc_start: 0.7492 (mtm110) cc_final: 0.7252 (ttt-90) REVERT: D 547 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7177 (pm20) outliers start: 34 outliers final: 25 residues processed: 165 average time/residue: 0.3278 time to fit residues: 75.4570 Evaluate side-chains 159 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 129 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 442 ARG Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 573 CYS Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 503 ILE Chi-restraints excluded: chain C residue 548 GLN Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 149 GLN Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 406 LYS Chi-restraints excluded: chain D residue 547 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 37 optimal weight: 0.0980 chunk 136 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 140 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 119 optimal weight: 0.1980 chunk 7 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 HIS C 548 GLN D 125 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.167989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.139930 restraints weight = 23651.282| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.10 r_work: 0.3375 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.5989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14630 Z= 0.171 Angle : 0.538 8.830 19839 Z= 0.269 Chirality : 0.045 0.160 2121 Planarity : 0.004 0.047 2525 Dihedral : 9.786 135.085 2095 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.49 % Allowed : 19.82 % Favored : 77.68 % 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: 0.77 (0.21), residues: 1728 helix: 1.55 (0.18), residues: 870 sheet: 2.12 (0.53), residues: 90 loop : -0.92 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 285 HIS 0.006 0.001 HIS B 233 PHE 0.014 0.001 PHE A 267 TYR 0.021 0.001 TYR D 315 ARG 0.007 0.000 ARG A 348 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2941.49 seconds wall clock time: 53 minutes 48.10 seconds (3228.10 seconds total)