Starting phenix.real_space_refine on Fri Jun 13 02:35:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qxm_18732/06_2025/8qxm_18732.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qxm_18732/06_2025/8qxm_18732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qxm_18732/06_2025/8qxm_18732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qxm_18732/06_2025/8qxm_18732.map" model { file = "/net/cci-nas-00/data/ceres_data/8qxm_18732/06_2025/8qxm_18732.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qxm_18732/06_2025/8qxm_18732.cif" } resolution = 2.94 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= 0.004 sd= 0.121 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 30 5.49 5 Mg 10 5.21 5 S 78 5.16 5 C 9293 2.51 5 N 2538 2.21 5 O 2705 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14658 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3556 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 18, 'TRANS': 416} Chain breaks: 3 Chain: "B" Number of atoms: 3698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3698 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 436} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 3462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3462 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 18, 'TRANS': 415} Chain breaks: 3 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: 3624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3624 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 20, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 63 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' FE': 1, ' MG': 2, 'DTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 126 Unusual residues: {' FE': 1, ' MG': 3, 'DCP': 1, 'DTP': 1, 'GTP': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {' FE': 1, ' MG': 3, 'DTP': 1, 'GTP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 93 Unusual residues: {' FE': 1, ' MG': 2, 'DCP': 1, 'DTP': 1, 'GTP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 10.94, per 1000 atoms: 0.75 Number of scatterers: 14658 At special positions: 0 Unit cell: (118.8, 93.96, 105.84, 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 78 16.00 P 30 15.00 Mg 10 11.99 O 2705 8.00 N 2538 7.00 C 9293 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 341 " - pdb=" SG CYS A 350 " distance=2.03 Simple disulfide: pdb=" SG CYS B 341 " - pdb=" SG CYS B 350 " distance=2.03 Simple disulfide: pdb=" SG CYS C 341 " - pdb=" SG CYS C 350 " distance=2.03 Simple disulfide: pdb=" SG CYS D 341 " - pdb=" SG CYS D 350 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.41 Conformation dependent library (CDL) restraints added in 3.3 seconds 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3348 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 17 sheets defined 61.2% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 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: 3.588A 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 151 through 156 Processing helix chain 'A' and resid 163 through 186 removed outlier: 4.036A pdb=" N HIS A 167 " --> pdb=" O ASN A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 190 removed outlier: 3.992A 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 removed outlier: 3.829A pdb=" N VAL A 196 " --> pdb=" O SER A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 226 removed outlier: 4.194A pdb=" N ASP A 218 " --> pdb=" O SER A 214 " (cutoff:3.500A) removed outlier: 4.986A 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 249 removed outlier: 3.505A pdb=" N GLY A 249 " --> pdb=" O ILE A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 257 Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 291 through 295 removed outlier: 3.564A pdb=" N SER A 295 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 300 removed outlier: 3.699A pdb=" N GLU A 299 " --> pdb=" O PHE A 296 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE A 300 " --> pdb=" O LEU A 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 296 through 300' Processing helix chain 'A' and resid 309 through 324 Processing helix chain 'A' and resid 330 through 338 removed outlier: 3.559A 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 removed outlier: 3.648A pdb=" N ASN A 380 " --> pdb=" O HIS A 376 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 411 through 414 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 432 removed outlier: 4.113A 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 474 removed outlier: 4.684A pdb=" N GLU A 474 " --> pdb=" O GLU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.657A pdb=" N GLU A 479 " --> pdb=" O SER A 475 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 576 removed outlier: 3.910A pdb=" N VAL A 570 " --> pdb=" O ARG A 566 " (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: 3.568A 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 Processing helix chain 'B' and resid 163 through 186 removed outlier: 4.047A pdb=" N HIS B 167 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 190 removed outlier: 3.912A pdb=" N GLN B 190 " --> pdb=" O PRO B 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 187 through 190' Processing helix chain 'B' and resid 192 through 205 removed outlier: 3.505A pdb=" N VAL B 196 " --> pdb=" O SER B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 226 removed outlier: 4.227A pdb=" N ASP B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ILE B 222 " --> pdb=" O ASP B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 232 through 249 Processing helix chain 'B' and resid 250 through 257 Processing helix chain 'B' and resid 260 through 271 removed outlier: 4.234A pdb=" N CYS B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 299 removed outlier: 5.194A pdb=" N PHE B 296 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU B 299 " --> pdb=" O PHE B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 324 removed outlier: 3.986A pdb=" N TRP B 313 " --> pdb=" O ASP B 309 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY B 324 " --> pdb=" O CYS B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 337 removed outlier: 3.757A 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 410 through 414 removed outlier: 4.246A pdb=" N ILE B 413 " --> pdb=" O SER B 410 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP B 414 " --> pdb=" O THR B 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 410 through 414' Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 421 through 423 No H-bonds generated for 'chain 'B' and resid 421 through 423' Processing helix chain 'B' and resid 424 through 432 removed outlier: 4.111A 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 474 removed outlier: 4.475A pdb=" N GLU B 474 " --> pdb=" O GLU B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 482 Processing helix chain 'B' and resid 513 through 518 removed outlier: 3.659A pdb=" N VAL B 518 " --> pdb=" O ILE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 537 removed outlier: 3.518A pdb=" N VAL B 537 " --> pdb=" O LYS B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 577 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 removed outlier: 3.625A pdb=" N ILE C 147 " --> pdb=" O LEU C 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 144 through 147' Processing helix chain 'C' and resid 150 through 156 removed outlier: 3.588A pdb=" N GLY C 153 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR C 154 " --> pdb=" O GLY C 151 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR C 155 " --> pdb=" O GLY C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 186 removed outlier: 4.034A pdb=" N HIS C 167 " --> pdb=" O ASN C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 190 removed outlier: 3.719A 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 removed outlier: 3.555A pdb=" N VAL C 196 " --> pdb=" O SER C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 226 removed outlier: 4.193A pdb=" N ASP C 218 " --> pdb=" O SER C 214 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ILE C 222 " --> pdb=" O ASP C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix 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: 3.718A pdb=" N CYS C 266 " --> pdb=" O GLU C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 300 removed outlier: 3.580A pdb=" N LYS C 294 " --> pdb=" O PRO C 291 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER C 295 " --> pdb=" O GLU C 292 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N PHE C 296 " --> pdb=" O ASN C 293 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU C 299 " --> pdb=" O PHE C 296 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE C 300 " --> pdb=" O LEU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 324 Processing helix chain 'C' and resid 330 through 337 Processing helix chain 'C' and resid 357 through 373 removed outlier: 3.623A pdb=" N ASP C 361 " --> pdb=" O GLY C 357 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET C 362 " --> pdb=" O ASN C 358 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N PHE C 363 " --> pdb=" O LEU C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 394 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 420 Processing helix chain 'C' and resid 421 through 423 No H-bonds generated for 'chain 'C' and resid 421 through 423' Processing helix chain 'C' and resid 424 through 432 removed outlier: 3.976A 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 removed outlier: 3.537A pdb=" N ILE C 448 " --> pdb=" O ILE C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 483 removed outlier: 4.199A pdb=" N LYS C 478 " --> pdb=" O GLU C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 496 No H-bonds generated for 'chain 'C' and resid 494 through 496' Processing helix chain 'C' and resid 558 through 577 removed outlier: 3.680A pdb=" N VAL C 570 " --> pdb=" O ARG C 566 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN C 571 " --> pdb=" O GLN C 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 137 Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 144 through 147 removed outlier: 3.560A pdb=" N ILE D 147 " --> pdb=" O LEU D 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 144 through 147' Processing helix chain 'D' and resid 150 through 156 removed outlier: 3.578A pdb=" N TYR D 155 " --> pdb=" O GLY D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 186 removed outlier: 4.021A pdb=" N HIS D 167 " --> pdb=" O ASN D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 190 Processing helix chain 'D' and resid 192 through 205 Processing helix chain 'D' and resid 214 through 226 removed outlier: 3.934A pdb=" N ASP D 218 " --> pdb=" O SER D 214 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ILE D 222 " --> pdb=" O ASP D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 232 through 249 Processing helix chain 'D' and resid 249 through 257 removed outlier: 4.533A pdb=" N VAL D 253 " --> pdb=" O GLY D 249 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR D 257 " --> pdb=" O VAL D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 273 removed outlier: 4.000A pdb=" N CYS D 266 " --> pdb=" O GLU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 299 removed outlier: 3.544A pdb=" N LYS D 294 " --> pdb=" O PRO D 291 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N PHE D 296 " --> pdb=" O ASN D 293 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU D 299 " --> pdb=" O PHE D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 324 removed outlier: 3.873A pdb=" N TRP D 313 " --> pdb=" O ASP D 309 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA D 317 " --> pdb=" O TRP D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 337 removed outlier: 3.870A 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 394 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 411 through 414 Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 421 through 423 No H-bonds generated for 'chain 'D' and resid 421 through 423' Processing helix chain 'D' and resid 424 through 432 removed outlier: 4.018A 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 451 Processing helix chain 'D' and resid 469 through 474 removed outlier: 3.707A pdb=" N TYR D 473 " --> pdb=" O ARG D 470 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N GLU D 474 " --> pdb=" O GLU D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 483 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 533 through 537 Processing helix chain 'D' and resid 558 through 576 Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 120 Processing sheet with id=AA2, first strand: chain 'A' and resid 339 through 343 removed outlier: 7.878A pdb=" N TYR A 521 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ALA A 351 " --> pdb=" O TYR A 521 " (cutoff:3.500A) removed outlier: 10.521A pdb=" N PHE A 520 " --> pdb=" O ASN A 527 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N ASN A 527 " --> pdb=" O PHE A 520 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS A 522 " --> pdb=" O ALA A 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 399 through 400 Processing sheet with id=AA4, first strand: chain 'A' and resid 455 through 460 removed outlier: 6.022A pdb=" N TYR A 456 " --> pdb=" O CYS A 554 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N CYS A 554 " --> pdb=" O TYR A 456 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 550 " --> pdb=" O THR A 460 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 504 through 505 Processing sheet with id=AA6, first strand: chain 'B' and resid 116 through 119 removed outlier: 3.561A pdb=" N LYS B 116 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 128 " --> pdb=" O LYS B 116 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 339 through 340 removed outlier: 8.345A pdb=" N TYR B 521 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA B 351 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 399 through 400 Processing sheet with id=AA9, first strand: chain 'B' and resid 455 through 460 removed outlier: 6.786A pdb=" N VAL B 552 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU B 459 " --> pdb=" O ILE B 550 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE B 550 " --> pdb=" O GLU B 459 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 116 through 119 Processing sheet with id=AB2, first strand: chain 'C' and resid 338 through 342 removed outlier: 8.103A pdb=" N TYR C 521 " --> pdb=" O ILE C 349 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ALA C 351 " --> pdb=" O TYR C 521 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 399 through 400 Processing sheet with id=AB4, first strand: chain 'C' and resid 455 through 459 removed outlier: 3.643A pdb=" N LYS C 455 " --> pdb=" O CYS C 554 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL C 552 " --> pdb=" O VAL C 457 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLU C 459 " --> pdb=" O ILE C 550 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ILE C 550 " --> pdb=" O GLU C 459 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 116 through 119 Processing sheet with id=AB6, first strand: chain 'D' and resid 338 through 343 removed outlier: 8.385A pdb=" N TYR D 521 " --> pdb=" O ILE D 349 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA D 351 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 399 through 400 Processing sheet with id=AB8, first strand: chain 'D' and resid 455 through 459 removed outlier: 5.666A pdb=" N TYR D 456 " --> pdb=" O CYS D 554 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N CYS D 554 " --> pdb=" O TYR D 456 " (cutoff:3.500A) 689 hydrogen bonds defined for protein. 1899 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: 4.81 Time building geometry restraints manager: 5.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4748 1.34 - 1.46: 3455 1.46 - 1.58: 6636 1.58 - 1.70: 47 1.70 - 1.82: 116 Bond restraints: 15002 Sorted by residual: bond pdb=" O1A DCP B 707 " pdb=" PA DCP B 707 " ideal model delta sigma weight residual 1.477 1.509 -0.032 1.00e-02 1.00e+04 1.05e+01 bond pdb=" O1A DCP D 706 " pdb=" PA DCP D 706 " ideal model delta sigma weight residual 1.477 1.509 -0.032 1.00e-02 1.00e+04 1.04e+01 bond pdb=" C4 DCP B 707 " pdb=" C5 DCP B 707 " ideal model delta sigma weight residual 1.426 1.388 0.038 1.20e-02 6.94e+03 1.02e+01 bond pdb=" C4 DCP D 706 " pdb=" C5 DCP D 706 " ideal model delta sigma weight residual 1.426 1.389 0.037 1.20e-02 6.94e+03 9.57e+00 bond pdb=" C4' DCP B 707 " pdb=" O4' DCP B 707 " ideal model delta sigma weight residual 1.444 1.414 0.030 1.00e-02 1.00e+04 8.94e+00 ... (remaining 14997 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.87: 20303 3.87 - 7.75: 49 7.75 - 11.62: 0 11.62 - 15.49: 2 15.49 - 19.36: 2 Bond angle restraints: 20356 Sorted by residual: angle pdb=" PB DCP B 707 " pdb=" O3B DCP B 707 " pdb=" PG DCP B 707 " ideal model delta sigma weight residual 139.87 120.51 19.36 1.00e+00 1.00e+00 3.75e+02 angle pdb=" PB DCP D 706 " pdb=" O3B DCP D 706 " pdb=" PG DCP D 706 " ideal model delta sigma weight residual 139.87 120.70 19.17 1.00e+00 1.00e+00 3.67e+02 angle pdb=" PA DCP D 706 " pdb=" O3A DCP D 706 " pdb=" PB DCP D 706 " ideal model delta sigma weight residual 136.83 121.59 15.24 1.00e+00 1.00e+00 2.32e+02 angle pdb=" PA DCP B 707 " pdb=" O3A DCP B 707 " pdb=" PB DCP B 707 " ideal model delta sigma weight residual 136.83 121.63 15.20 1.00e+00 1.00e+00 2.31e+02 angle pdb=" O3B DCP B 707 " pdb=" PG DCP B 707 " pdb=" O3G DCP B 707 " ideal model delta sigma weight residual 104.48 110.03 -5.55 1.14e+00 7.76e-01 2.39e+01 ... (remaining 20351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.75: 8508 28.75 - 57.51: 411 57.51 - 86.26: 91 86.26 - 115.01: 9 115.01 - 143.76: 3 Dihedral angle restraints: 9022 sinusoidal: 3812 harmonic: 5210 Sorted by residual: dihedral pdb=" CB CYS D 341 " pdb=" SG CYS D 341 " pdb=" SG CYS D 350 " pdb=" CB CYS D 350 " ideal model delta sinusoidal sigma weight residual -86.00 -167.83 81.83 1 1.00e+01 1.00e-02 8.24e+01 dihedral pdb=" O3A GTP B 701 " pdb=" O3B GTP B 701 " pdb=" PB GTP B 701 " pdb=" PG GTP B 701 " ideal model delta sinusoidal sigma weight residual 303.79 160.03 143.76 1 2.00e+01 2.50e-03 4.34e+01 dihedral pdb=" O3A GTP C 702 " pdb=" O3B GTP C 702 " pdb=" PB GTP C 702 " pdb=" PG GTP C 702 " ideal model delta sinusoidal sigma weight residual 303.79 164.19 139.60 1 2.00e+01 2.50e-03 4.23e+01 ... (remaining 9019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1719 0.049 - 0.098: 339 0.098 - 0.146: 98 0.146 - 0.195: 7 0.195 - 0.244: 8 Chirality restraints: 2171 Sorted by residual: chirality pdb=" C3' DTP C 701 " pdb=" C2' DTP C 701 " pdb=" C4' DTP C 701 " pdb=" O3' DTP C 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 A 804 " pdb=" C2' DTP A 804 " pdb=" C4' DTP A 804 " pdb=" O3' DTP A 804 " both_signs ideal model delta sigma weight residual False -2.68 -2.92 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" C3' DTP D 701 " pdb=" C2' DTP D 701 " pdb=" C4' DTP D 701 " pdb=" O3' DTP D 701 " both_signs ideal model delta sigma weight residual False -2.68 -2.91 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 2168 not shown) Planarity restraints: 2581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DCP B 707 " 0.247 2.00e-02 2.50e+03 1.38e-01 4.27e+02 pdb=" C2 DCP B 707 " -0.031 2.00e-02 2.50e+03 pdb=" C4 DCP B 707 " 0.060 2.00e-02 2.50e+03 pdb=" C5 DCP B 707 " 0.015 2.00e-02 2.50e+03 pdb=" C6 DCP B 707 " -0.208 2.00e-02 2.50e+03 pdb=" N1 DCP B 707 " -0.080 2.00e-02 2.50e+03 pdb=" N3 DCP B 707 " 0.165 2.00e-02 2.50e+03 pdb=" N4 DCP B 707 " -0.000 2.00e-02 2.50e+03 pdb=" O2 DCP B 707 " -0.167 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DCP D 706 " -0.220 2.00e-02 2.50e+03 1.35e-01 4.12e+02 pdb=" C2 DCP D 706 " 0.026 2.00e-02 2.50e+03 pdb=" C4 DCP D 706 " -0.049 2.00e-02 2.50e+03 pdb=" C5 DCP D 706 " 0.074 2.00e-02 2.50e+03 pdb=" C6 DCP D 706 " 0.097 2.00e-02 2.50e+03 pdb=" N1 DCP D 706 " 0.100 2.00e-02 2.50e+03 pdb=" N3 DCP D 706 " -0.226 2.00e-02 2.50e+03 pdb=" N4 DCP D 706 " 0.005 2.00e-02 2.50e+03 pdb=" O2 DCP D 706 " 0.192 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN C 461 " -0.038 5.00e-02 4.00e+02 5.80e-02 5.38e+00 pdb=" N PRO C 462 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 462 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 462 " -0.032 5.00e-02 4.00e+02 ... (remaining 2578 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 50 2.43 - 3.05: 9119 3.05 - 3.66: 20411 3.66 - 4.28: 32274 4.28 - 4.90: 55301 Nonbonded interactions: 117155 Sorted by model distance: nonbonded pdb=" O1B DTP A 804 " pdb="MG MG C 706 " model vdw 1.812 2.170 nonbonded pdb=" O1G DTP A 804 " pdb="MG MG C 706 " model vdw 1.844 2.170 nonbonded pdb=" OD2 ASP A 207 " pdb="FE FE A 801 " model vdw 1.951 2.260 nonbonded pdb=" OD2 ASP A 319 " pdb=" OH TYR A 374 " model vdw 1.951 3.040 nonbonded pdb="MG MG A 803 " pdb=" O1B GTP B 701 " model vdw 1.968 2.170 ... (remaining 117150 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 115 through 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 437 and (nam \ e N or name CA or name C or name O or name CB )) or resid 438 through 464 or (re \ sid 465 and (name N or name CA or name C or name O or name CB )) or resid 466 or \ (resid 467 and (name N or name CA or name C or name O or name CB )) or resid 46 \ 8 or (resid 469 and (name N or name CA or name C or name O or name CB )) or resi \ d 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 o \ r name CB )) or resid 475 through 477 or (resid 478 and (name N or name CA or na \ me C or name O or name CB )) or resid 479 through 483 or (resid 484 and (name N \ or name CA or name C or name O or name CB )) or resid 485 or (resid 486 through \ 490 and (name N or name CA or name C or name O or name CB )) or resid 491 or (re \ sid 492 and (name N or name CA or name C or name O or name CB )) or resid 493 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 na \ me C or name O or name CB )) or resid 561 through 578)) selection = (chain 'B' and (resid 115 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 437 and (nam \ e N or name CA or name C or name O or name CB )) or resid 438 through 464 or (re \ sid 465 and (name N or name CA or name C or name O or name CB )) or resid 466 or \ (resid 467 and (name N or name CA or name C or name O or name CB )) or resid 46 \ 8 or (resid 469 and (name N or name CA or name C or name O or name CB )) or resi \ d 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 o \ r name CB )) or resid 475 through 477 or (resid 478 and (name N or name CA or na \ me C or name O or name CB )) or resid 479 through 483 or (resid 484 and (name N \ or name CA or name C or name O or name CB )) or resid 485 through 486 or (resid \ 487 through 490 and (name N or name CA or name C or name O or name CB )) or resi \ d 491 through 506 or resid 515 through 530 or resid 546 through 578)) selection = (chain 'C' and (resid 115 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 466 or (resid 467 and (name N or name CA or name C or name O or na \ me CB )) or resid 468 or (resid 469 and (name N or name CA or name C or name O o \ r 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 o \ r name C or name O or name CB )) or resid 475 through 483 or (resid 484 and (nam \ e N or name CA or name C or name O or name CB )) or resid 485 through 578)) selection = (chain 'D' and (resid 115 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 464 o \ r (resid 465 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 66 through 486 or (resid 487 through 490 and (name N or name CA or name C or nam \ e O or name CB )) or resid 491 through 506 or resid 515 through 530 or resid 546 \ through 578)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.950 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: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 41.200 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: 0.000 Load rotamer database and sin/cos tables:15.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 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 15006 Z= 0.154 Angle : 0.626 19.365 20364 Z= 0.406 Chirality : 0.045 0.244 2171 Planarity : 0.005 0.138 2581 Dihedral : 17.600 143.762 5662 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.21), residues: 1760 helix: 0.58 (0.19), residues: 875 sheet: 0.75 (0.51), residues: 124 loop : -0.64 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 285 HIS 0.006 0.001 HIS C 129 PHE 0.021 0.001 PHE A 267 TYR 0.019 0.001 TYR B 568 ARG 0.005 0.000 ARG A 576 Details of bonding type rmsd hydrogen bonds : bond 0.18369 ( 689) hydrogen bonds : angle 6.35650 ( 1899) SS BOND : bond 0.00144 ( 4) SS BOND : angle 1.49720 ( 8) covalent geometry : bond 0.00265 (15002) covalent geometry : angle 0.62551 (20356) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 1.781 Fit side-chains REVERT: B 509 MET cc_start: 0.8122 (mmm) cc_final: 0.7899 (mmm) REVERT: D 505 MET cc_start: 0.7976 (mmt) cc_final: 0.7687 (mmm) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 1.6467 time to fit residues: 353.6632 Evaluate side-chains 163 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 159 optimal weight: 0.0970 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 271 GLN A 461 GLN B 306 ASN C 129 HIS C 210 HIS D 243 HIS D 548 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.157824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.131888 restraints weight = 16138.140| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.28 r_work: 0.3137 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15006 Z= 0.153 Angle : 0.586 8.943 20364 Z= 0.307 Chirality : 0.046 0.188 2171 Planarity : 0.005 0.063 2581 Dihedral : 14.586 149.806 2192 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.12 % Allowed : 7.07 % Favored : 91.81 % 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: 0.47 (0.21), residues: 1760 helix: 1.02 (0.19), residues: 866 sheet: 0.77 (0.49), residues: 124 loop : -0.52 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 572 HIS 0.007 0.002 HIS A 233 PHE 0.020 0.002 PHE A 267 TYR 0.037 0.002 TYR B 315 ARG 0.005 0.001 ARG A 576 Details of bonding type rmsd hydrogen bonds : bond 0.05978 ( 689) hydrogen bonds : angle 4.68861 ( 1899) SS BOND : bond 0.00161 ( 4) SS BOND : angle 1.70569 ( 8) covalent geometry : bond 0.00347 (15002) covalent geometry : angle 0.58489 (20356) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 184 time to evaluate : 1.638 Fit side-chains REVERT: A 193 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6828 (mm-30) REVERT: A 426 ILE cc_start: 0.8338 (mm) cc_final: 0.8074 (tp) REVERT: B 185 LYS cc_start: 0.7747 (mtpt) cc_final: 0.7257 (mtmt) REVERT: B 501 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7486 (t70) REVERT: B 509 MET cc_start: 0.8390 (mmm) cc_final: 0.8149 (mmm) REVERT: B 549 LEU cc_start: 0.8327 (mp) cc_final: 0.8094 (mt) REVERT: D 347 LEU cc_start: 0.8739 (mm) cc_final: 0.8437 (mt) REVERT: D 501 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7543 (m-30) REVERT: D 505 MET cc_start: 0.8505 (mmt) cc_final: 0.8287 (mmm) outliers start: 17 outliers final: 9 residues processed: 194 average time/residue: 1.2613 time to fit residues: 269.8270 Evaluate side-chains 168 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 157 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 501 ASP Chi-restraints excluded: chain D residue 549 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 110 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 293 ASN ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.155779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.129648 restraints weight = 16312.502| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.27 r_work: 0.3147 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15006 Z= 0.169 Angle : 0.599 8.947 20364 Z= 0.313 Chirality : 0.047 0.200 2171 Planarity : 0.005 0.059 2581 Dihedral : 14.039 154.448 2192 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.98 % Allowed : 10.17 % Favored : 87.85 % 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 (0.20), residues: 1760 helix: 1.09 (0.19), residues: 865 sheet: 0.57 (0.48), residues: 126 loop : -0.62 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 572 HIS 0.008 0.002 HIS A 233 PHE 0.015 0.002 PHE A 267 TYR 0.034 0.002 TYR B 315 ARG 0.006 0.001 ARG D 576 Details of bonding type rmsd hydrogen bonds : bond 0.06203 ( 689) hydrogen bonds : angle 4.53225 ( 1899) SS BOND : bond 0.00208 ( 4) SS BOND : angle 1.71639 ( 8) covalent geometry : bond 0.00394 (15002) covalent geometry : angle 0.59800 (20356) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 1.769 Fit side-chains REVERT: A 193 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6934 (mm-30) REVERT: A 426 ILE cc_start: 0.8462 (mm) cc_final: 0.8107 (tp) REVERT: A 551 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7533 (mtt180) REVERT: B 185 LYS cc_start: 0.7937 (mtpt) cc_final: 0.7401 (mtmt) REVERT: B 501 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7479 (t70) REVERT: B 549 LEU cc_start: 0.8611 (mp) cc_final: 0.8410 (mt) REVERT: C 305 ARG cc_start: 0.6544 (ttp-110) cc_final: 0.6103 (tmt170) REVERT: C 567 GLN cc_start: 0.7685 (mm-40) cc_final: 0.7287 (mm-40) REVERT: D 127 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7372 (tm-30) REVERT: D 501 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7441 (m-30) REVERT: D 505 MET cc_start: 0.8553 (mmt) cc_final: 0.8279 (mmm) outliers start: 30 outliers final: 10 residues processed: 185 average time/residue: 1.3165 time to fit residues: 268.4874 Evaluate side-chains 172 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 501 ASP Chi-restraints excluded: chain D residue 549 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 169 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 165 optimal weight: 0.7980 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 190 GLN A 293 ASN ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 ASN C 548 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.155861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.129308 restraints weight = 16195.564| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.31 r_work: 0.3149 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15006 Z= 0.153 Angle : 0.574 9.997 20364 Z= 0.300 Chirality : 0.046 0.190 2171 Planarity : 0.005 0.054 2581 Dihedral : 13.535 154.016 2192 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.78 % Allowed : 12.02 % Favored : 86.20 % 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: 0.49 (0.20), residues: 1760 helix: 1.15 (0.19), residues: 863 sheet: 0.39 (0.47), residues: 136 loop : -0.60 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 572 HIS 0.007 0.001 HIS A 233 PHE 0.013 0.002 PHE D 165 TYR 0.030 0.002 TYR B 315 ARG 0.006 0.000 ARG D 576 Details of bonding type rmsd hydrogen bonds : bond 0.05691 ( 689) hydrogen bonds : angle 4.45669 ( 1899) SS BOND : bond 0.00142 ( 4) SS BOND : angle 2.17275 ( 8) covalent geometry : bond 0.00354 (15002) covalent geometry : angle 0.57240 (20356) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 1.681 Fit side-chains revert: symmetry clash REVERT: A 193 GLU cc_start: 0.7256 (mm-30) cc_final: 0.6979 (mm-30) REVERT: A 426 ILE cc_start: 0.8468 (mm) cc_final: 0.8108 (tp) REVERT: B 185 LYS cc_start: 0.7932 (mtpt) cc_final: 0.7377 (mtmt) REVERT: B 501 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7574 (t70) REVERT: C 305 ARG cc_start: 0.6593 (ttp-110) cc_final: 0.6075 (tmt170) REVERT: C 330 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7571 (t0) REVERT: C 576 ARG cc_start: 0.6659 (OUTLIER) cc_final: 0.5927 (mtt-85) REVERT: D 501 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7518 (m-30) REVERT: D 505 MET cc_start: 0.8528 (mmt) cc_final: 0.8292 (mmm) outliers start: 27 outliers final: 12 residues processed: 179 average time/residue: 1.2980 time to fit residues: 256.7313 Evaluate side-chains 172 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 576 ARG Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 501 ASP Chi-restraints excluded: chain D residue 549 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 173 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 HIS A 190 GLN A 293 ASN ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 GLN C 210 HIS C 447 GLN ** C 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.152333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.126552 restraints weight = 16336.345| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.20 r_work: 0.3096 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 15006 Z= 0.234 Angle : 0.676 11.536 20364 Z= 0.352 Chirality : 0.049 0.222 2171 Planarity : 0.006 0.057 2581 Dihedral : 14.043 162.248 2192 Min Nonbonded Distance : 1.678 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.91 % Allowed : 12.35 % Favored : 84.74 % 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: 1760 helix: 0.87 (0.18), residues: 866 sheet: 0.34 (0.47), residues: 131 loop : -0.85 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 572 HIS 0.008 0.002 HIS C 162 PHE 0.015 0.002 PHE B 363 TYR 0.030 0.002 TYR B 315 ARG 0.008 0.001 ARG D 576 Details of bonding type rmsd hydrogen bonds : bond 0.07368 ( 689) hydrogen bonds : angle 4.70581 ( 1899) SS BOND : bond 0.00320 ( 4) SS BOND : angle 3.80081 ( 8) covalent geometry : bond 0.00567 (15002) covalent geometry : angle 0.67142 (20356) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 157 time to evaluate : 1.582 Fit side-chains revert: symmetry clash REVERT: A 193 GLU cc_start: 0.7304 (mm-30) cc_final: 0.7085 (mm-30) REVERT: A 208 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8855 (mp) REVERT: A 426 ILE cc_start: 0.8504 (mm) cc_final: 0.8143 (tp) REVERT: A 551 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7712 (mtt180) REVERT: B 185 LYS cc_start: 0.8135 (mtpt) cc_final: 0.7569 (mtmt) REVERT: B 250 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.8087 (mm) REVERT: B 501 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7625 (t70) REVERT: C 184 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6639 (tt0) REVERT: C 305 ARG cc_start: 0.6618 (ttp-110) cc_final: 0.6124 (tmt170) REVERT: C 499 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8377 (mm) REVERT: C 576 ARG cc_start: 0.6714 (OUTLIER) cc_final: 0.5922 (mtt-85) REVERT: D 250 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8131 (mm) REVERT: D 346 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7333 (tp30) REVERT: D 501 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7671 (m-30) REVERT: D 505 MET cc_start: 0.8599 (mmt) cc_final: 0.8343 (mmm) REVERT: D 509 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.7685 (mtm) outliers start: 44 outliers final: 18 residues processed: 185 average time/residue: 1.2654 time to fit residues: 258.0370 Evaluate side-chains 181 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 576 ARG Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain D residue 501 ASP Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 549 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 95 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 156 optimal weight: 0.0670 chunk 168 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 160 optimal weight: 0.7980 chunk 161 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 293 ASN ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 548 GLN D 215 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.157453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.131842 restraints weight = 16344.437| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.27 r_work: 0.3176 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15006 Z= 0.123 Angle : 0.545 11.320 20364 Z= 0.284 Chirality : 0.045 0.180 2171 Planarity : 0.004 0.048 2581 Dihedral : 13.001 154.931 2192 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.05 % Allowed : 14.27 % Favored : 83.69 % 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: 0.52 (0.21), residues: 1760 helix: 1.17 (0.18), residues: 866 sheet: 0.49 (0.48), residues: 131 loop : -0.59 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 572 HIS 0.007 0.001 HIS A 233 PHE 0.014 0.001 PHE D 165 TYR 0.027 0.001 TYR B 315 ARG 0.007 0.000 ARG B 576 Details of bonding type rmsd hydrogen bonds : bond 0.04955 ( 689) hydrogen bonds : angle 4.34929 ( 1899) SS BOND : bond 0.00162 ( 4) SS BOND : angle 2.29333 ( 8) covalent geometry : bond 0.00269 (15002) covalent geometry : angle 0.54308 (20356) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 1.584 Fit side-chains revert: symmetry clash REVERT: A 193 GLU cc_start: 0.7107 (mm-30) cc_final: 0.6892 (mm-30) REVERT: A 208 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8787 (mp) REVERT: A 426 ILE cc_start: 0.8442 (mm) cc_final: 0.8095 (tp) REVERT: A 494 LYS cc_start: 0.6932 (mppt) cc_final: 0.6559 (mppt) REVERT: B 185 LYS cc_start: 0.7857 (mtpt) cc_final: 0.7309 (mtmt) REVERT: B 250 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.8029 (mm) REVERT: B 501 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7611 (t70) REVERT: C 499 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8300 (mm) REVERT: C 576 ARG cc_start: 0.6492 (OUTLIER) cc_final: 0.5697 (mtt-85) REVERT: D 250 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8060 (mm) REVERT: D 501 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7424 (m-30) REVERT: D 505 MET cc_start: 0.8508 (mmt) cc_final: 0.8232 (mmm) REVERT: D 509 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.7462 (mtm) outliers start: 31 outliers final: 14 residues processed: 180 average time/residue: 1.2594 time to fit residues: 250.3559 Evaluate side-chains 176 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 576 ARG Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 501 ASP Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 549 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 44 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 84 optimal weight: 0.0670 chunk 79 optimal weight: 0.3980 chunk 160 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 overall best weight: 0.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 293 ASN ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 548 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.158082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.133370 restraints weight = 16330.505| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.18 r_work: 0.3187 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15006 Z= 0.122 Angle : 0.546 12.133 20364 Z= 0.283 Chirality : 0.045 0.183 2171 Planarity : 0.004 0.044 2581 Dihedral : 12.491 155.172 2192 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.11 % Allowed : 14.66 % Favored : 83.22 % 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 (0.20), residues: 1760 helix: 1.25 (0.18), residues: 872 sheet: 0.80 (0.49), residues: 126 loop : -0.63 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 572 HIS 0.007 0.001 HIS A 233 PHE 0.014 0.001 PHE D 165 TYR 0.027 0.001 TYR B 315 ARG 0.004 0.000 ARG B 576 Details of bonding type rmsd hydrogen bonds : bond 0.04890 ( 689) hydrogen bonds : angle 4.27508 ( 1899) SS BOND : bond 0.00164 ( 4) SS BOND : angle 2.06255 ( 8) covalent geometry : bond 0.00269 (15002) covalent geometry : angle 0.54456 (20356) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 1.641 Fit side-chains REVERT: A 208 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8749 (mp) REVERT: A 426 ILE cc_start: 0.8436 (mm) cc_final: 0.8089 (tp) REVERT: A 494 LYS cc_start: 0.7014 (mppt) cc_final: 0.6660 (mppt) REVERT: A 571 GLN cc_start: 0.5831 (OUTLIER) cc_final: 0.5423 (tp-100) REVERT: B 185 LYS cc_start: 0.7803 (mtpt) cc_final: 0.7257 (mtmt) REVERT: B 501 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7561 (t70) REVERT: C 576 ARG cc_start: 0.6479 (OUTLIER) cc_final: 0.5705 (mtt-85) REVERT: D 501 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7547 (m-30) REVERT: D 505 MET cc_start: 0.8518 (mmt) cc_final: 0.8269 (mmm) REVERT: D 509 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.7521 (mtm) outliers start: 32 outliers final: 15 residues processed: 179 average time/residue: 1.2663 time to fit residues: 253.8137 Evaluate side-chains 172 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 576 ARG Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 501 ASP Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 549 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 149 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 293 ASN ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.152530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.126369 restraints weight = 16289.519| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.22 r_work: 0.3122 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15006 Z= 0.210 Angle : 0.651 13.656 20364 Z= 0.339 Chirality : 0.048 0.213 2171 Planarity : 0.005 0.052 2581 Dihedral : 13.303 164.530 2192 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.58 % Allowed : 14.93 % Favored : 82.50 % 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: 0.26 (0.20), residues: 1760 helix: 0.97 (0.18), residues: 869 sheet: 0.50 (0.48), residues: 131 loop : -0.79 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 572 HIS 0.008 0.002 HIS A 162 PHE 0.014 0.002 PHE B 363 TYR 0.027 0.002 TYR B 315 ARG 0.004 0.001 ARG B 576 Details of bonding type rmsd hydrogen bonds : bond 0.06804 ( 689) hydrogen bonds : angle 4.55461 ( 1899) SS BOND : bond 0.00250 ( 4) SS BOND : angle 2.47043 ( 8) covalent geometry : bond 0.00507 (15002) covalent geometry : angle 0.64941 (20356) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 1.518 Fit side-chains REVERT: A 208 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8855 (mp) REVERT: A 426 ILE cc_start: 0.8496 (mm) cc_final: 0.8127 (tp) REVERT: A 494 LYS cc_start: 0.6983 (mppt) cc_final: 0.6636 (mppt) REVERT: A 551 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7674 (mtt180) REVERT: A 576 ARG cc_start: 0.6011 (ttt-90) cc_final: 0.5722 (ttt-90) REVERT: B 185 LYS cc_start: 0.8092 (mtpt) cc_final: 0.7515 (mtmt) REVERT: B 501 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7641 (t70) REVERT: C 305 ARG cc_start: 0.6633 (ttp-110) cc_final: 0.6074 (ttt180) REVERT: C 369 LEU cc_start: 0.8167 (mt) cc_final: 0.7753 (mt) REVERT: C 470 ARG cc_start: 0.6334 (ptp-170) cc_final: 0.6094 (ptp-170) REVERT: C 576 ARG cc_start: 0.6522 (OUTLIER) cc_final: 0.5837 (mtt-85) REVERT: D 250 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8131 (mm) REVERT: D 501 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7486 (m-30) REVERT: D 505 MET cc_start: 0.8575 (mmt) cc_final: 0.8280 (mmm) REVERT: D 509 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.7696 (mtm) outliers start: 39 outliers final: 17 residues processed: 180 average time/residue: 1.3409 time to fit residues: 266.0008 Evaluate side-chains 174 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 576 ARG Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 501 ASP Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 549 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 35 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 50 optimal weight: 0.0970 chunk 135 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 166 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 293 ASN A 328 ASN C 548 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.157601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.132383 restraints weight = 16171.453| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.25 r_work: 0.3175 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15006 Z= 0.117 Angle : 0.547 13.664 20364 Z= 0.284 Chirality : 0.044 0.175 2171 Planarity : 0.004 0.046 2581 Dihedral : 12.436 158.037 2192 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.11 % Allowed : 15.52 % Favored : 82.36 % 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: 0.55 (0.21), residues: 1760 helix: 1.16 (0.18), residues: 877 sheet: 0.77 (0.49), residues: 126 loop : -0.61 (0.22), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 572 HIS 0.006 0.001 HIS A 233 PHE 0.014 0.001 PHE D 165 TYR 0.026 0.001 TYR B 315 ARG 0.003 0.000 ARG C 134 Details of bonding type rmsd hydrogen bonds : bond 0.04666 ( 689) hydrogen bonds : angle 4.29807 ( 1899) SS BOND : bond 0.00410 ( 4) SS BOND : angle 2.47637 ( 8) covalent geometry : bond 0.00254 (15002) covalent geometry : angle 0.54508 (20356) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 1.556 Fit side-chains REVERT: A 426 ILE cc_start: 0.8443 (mm) cc_final: 0.8089 (tp) REVERT: A 494 LYS cc_start: 0.6974 (mppt) cc_final: 0.6677 (mppt) REVERT: A 551 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7572 (mtt180) REVERT: A 576 ARG cc_start: 0.5940 (ttt-90) cc_final: 0.5617 (ttt-90) REVERT: B 185 LYS cc_start: 0.7882 (mtpt) cc_final: 0.7335 (mtmt) REVERT: B 501 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7590 (t70) REVERT: C 369 LEU cc_start: 0.8225 (mt) cc_final: 0.7795 (mt) REVERT: C 576 ARG cc_start: 0.6435 (OUTLIER) cc_final: 0.5668 (mtt-85) REVERT: D 250 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.8044 (mm) REVERT: D 505 MET cc_start: 0.8535 (mmt) cc_final: 0.8285 (mmm) REVERT: D 509 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.7585 (mtm) outliers start: 32 outliers final: 14 residues processed: 174 average time/residue: 1.2177 time to fit residues: 234.2834 Evaluate side-chains 169 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 576 ARG Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 549 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 48 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 167 optimal weight: 0.0870 chunk 160 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 0.0050 chunk 154 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 overall best weight: 0.4972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 293 ASN C 548 GLN D 548 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.158486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.132803 restraints weight = 16319.387| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.29 r_work: 0.3200 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15006 Z= 0.112 Angle : 0.546 14.346 20364 Z= 0.282 Chirality : 0.044 0.174 2171 Planarity : 0.004 0.044 2581 Dihedral : 12.170 157.487 2192 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.39 % Allowed : 16.18 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.21), residues: 1760 helix: 1.25 (0.18), residues: 877 sheet: 0.80 (0.47), residues: 136 loop : -0.56 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 572 HIS 0.006 0.001 HIS A 233 PHE 0.013 0.001 PHE D 165 TYR 0.026 0.001 TYR B 315 ARG 0.005 0.000 ARG A 372 Details of bonding type rmsd hydrogen bonds : bond 0.04476 ( 689) hydrogen bonds : angle 4.24057 ( 1899) SS BOND : bond 0.00159 ( 4) SS BOND : angle 2.22717 ( 8) covalent geometry : bond 0.00240 (15002) covalent geometry : angle 0.54429 (20356) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 1.516 Fit side-chains REVERT: A 208 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8769 (mp) REVERT: A 426 ILE cc_start: 0.8445 (mm) cc_final: 0.8072 (tp) REVERT: A 494 LYS cc_start: 0.7003 (mppt) cc_final: 0.6742 (mppt) REVERT: A 576 ARG cc_start: 0.5934 (ttt-90) cc_final: 0.5639 (ttt-90) REVERT: B 185 LYS cc_start: 0.7814 (mtpt) cc_final: 0.7271 (mtmt) REVERT: B 250 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7929 (mm) REVERT: B 501 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7552 (t70) REVERT: C 369 LEU cc_start: 0.8186 (mt) cc_final: 0.7786 (mt) REVERT: C 552 VAL cc_start: 0.6999 (t) cc_final: 0.6786 (p) REVERT: C 576 ARG cc_start: 0.6410 (OUTLIER) cc_final: 0.5680 (mtt-85) REVERT: D 250 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.8030 (mm) REVERT: D 346 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7393 (tp30) REVERT: D 505 MET cc_start: 0.8472 (mmt) cc_final: 0.8218 (mmm) REVERT: D 509 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.7542 (mtm) outliers start: 21 outliers final: 13 residues processed: 169 average time/residue: 1.2226 time to fit residues: 229.1968 Evaluate side-chains 173 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 576 ARG Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 549 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 130 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 28 optimal weight: 0.0570 chunk 174 optimal weight: 4.9990 overall best weight: 0.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 375 GLN C 548 GLN D 125 HIS D 215 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.156861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.131766 restraints weight = 16365.667| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.20 r_work: 0.3177 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15006 Z= 0.131 Angle : 0.563 14.475 20364 Z= 0.291 Chirality : 0.045 0.187 2171 Planarity : 0.004 0.045 2581 Dihedral : 12.237 160.237 2192 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.92 % Allowed : 15.72 % Favored : 82.36 % 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: 0.59 (0.21), residues: 1760 helix: 1.22 (0.18), residues: 875 sheet: 0.81 (0.49), residues: 132 loop : -0.63 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 572 HIS 0.007 0.001 HIS A 233 PHE 0.014 0.001 PHE D 165 TYR 0.027 0.001 TYR B 315 ARG 0.005 0.000 ARG A 371 Details of bonding type rmsd hydrogen bonds : bond 0.05051 ( 689) hydrogen bonds : angle 4.30347 ( 1899) SS BOND : bond 0.00167 ( 4) SS BOND : angle 2.39084 ( 8) covalent geometry : bond 0.00296 (15002) covalent geometry : angle 0.56117 (20356) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9604.48 seconds wall clock time: 167 minutes 7.76 seconds (10027.76 seconds total)