Starting phenix.real_space_refine on Mon Jan 20 01:34:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qxm_18732/01_2025/8qxm_18732.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qxm_18732/01_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_18732/01_2025/8qxm_18732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qxm_18732/01_2025/8qxm_18732.map" model { file = "/net/cci-nas-00/data/ceres_data/8qxm_18732/01_2025/8qxm_18732.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qxm_18732/01_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 9.49, per 1000 atoms: 0.65 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: 4.45 Conformation dependent library (CDL) restraints added in 1.7 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: 1.60 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: 4.49 Time building geometry restraints manager: 5.09 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: 3.880 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.220 Process input model: 35.670 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.060 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:13.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.510 ------------------------------------------------------------------------------- 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 15002 Z= 0.171 Angle : 0.626 19.365 20356 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 *********************** 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 : 1.602 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: 1.4030 time to fit residues: 299.8059 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 : 1.675 ------------------------------------------------------------------------------- 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 = 0.131887 restraints weight = 16138.140| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.28 r_work: 0.3137 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 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 15002 Z= 0.230 Angle : 0.585 8.943 20356 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 *********************** 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 : 1.678 Fit side-chains REVERT: A 193 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6828 (mm-30) REVERT: A 426 ILE cc_start: 0.8338 (mm) cc_final: 0.8075 (tp) REVERT: B 185 LYS cc_start: 0.7745 (mtpt) cc_final: 0.7254 (mtmt) REVERT: B 501 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7496 (t70) REVERT: B 509 MET cc_start: 0.8392 (mmm) cc_final: 0.8150 (mmm) REVERT: B 549 LEU cc_start: 0.8326 (mp) cc_final: 0.8092 (mt) REVERT: B 568 TYR cc_start: 0.8554 (m-80) cc_final: 0.8352 (m-80) REVERT: D 347 LEU cc_start: 0.8738 (mm) cc_final: 0.8436 (mt) REVERT: D 501 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7569 (m-30) REVERT: D 505 MET cc_start: 0.8503 (mmt) cc_final: 0.8285 (mmm) outliers start: 17 outliers final: 9 residues processed: 194 average time/residue: 1.3534 time to fit residues: 287.8403 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 : 1.722 ------------------------------------------------------------------------------- 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: 0.6980 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: 0.3980 chunk 21 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.158846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.132759 restraints weight = 16256.971| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.25 r_work: 0.3212 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15002 Z= 0.175 Angle : 0.534 8.179 20356 Z= 0.279 Chirality : 0.045 0.178 2171 Planarity : 0.004 0.054 2581 Dihedral : 13.518 147.859 2192 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.65 % Allowed : 9.84 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.21), residues: 1760 helix: 1.31 (0.19), residues: 863 sheet: 0.78 (0.49), residues: 121 loop : -0.53 (0.22), residues: 776 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 0.013 0.001 PHE A 267 TYR 0.033 0.001 TYR B 315 ARG 0.005 0.000 ARG D 576 *********************** 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 197 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 1.704 Fit side-chains REVERT: A 193 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6839 (mm-30) REVERT: A 426 ILE cc_start: 0.8364 (mm) cc_final: 0.8046 (tp) REVERT: A 551 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7311 (mtt180) REVERT: A 571 GLN cc_start: 0.6373 (OUTLIER) cc_final: 0.5816 (tp-100) REVERT: B 185 LYS cc_start: 0.7716 (mtpt) cc_final: 0.7203 (mtmt) REVERT: B 474 GLU cc_start: 0.6515 (OUTLIER) cc_final: 0.5780 (pm20) REVERT: B 501 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7431 (t70) REVERT: B 549 LEU cc_start: 0.8543 (mp) cc_final: 0.8278 (mt) REVERT: D 127 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7194 (tm-30) REVERT: D 347 LEU cc_start: 0.8669 (mm) cc_final: 0.8366 (mt) REVERT: D 501 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7436 (m-30) outliers start: 25 outliers final: 11 residues processed: 188 average time/residue: 1.3201 time to fit residues: 273.0091 Evaluate side-chains 181 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 1.613 ------------------------------------------------------------------------------- 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 229 VAL Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain A residue 571 GLN 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 474 GLU 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: 0.9980 chunk 36 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 B 536 GLN ** C 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.156035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.129702 restraints weight = 16107.157| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.29 r_work: 0.3124 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15002 Z= 0.287 Angle : 0.606 10.340 20356 Z= 0.316 Chirality : 0.047 0.207 2171 Planarity : 0.005 0.054 2581 Dihedral : 13.647 155.410 2192 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.92 % Allowed : 11.89 % 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: 0.43 (0.20), residues: 1760 helix: 1.10 (0.18), residues: 867 sheet: 0.37 (0.46), residues: 136 loop : -0.63 (0.22), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 572 HIS 0.007 0.002 HIS A 233 PHE 0.014 0.002 PHE B 363 TYR 0.031 0.002 TYR B 315 ARG 0.005 0.001 ARG D 576 *********************** 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 193 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 1.727 Fit side-chains REVERT: A 193 GLU cc_start: 0.7292 (mm-30) cc_final: 0.7040 (mm-30) REVERT: A 426 ILE cc_start: 0.8498 (mm) cc_final: 0.8136 (tp) REVERT: A 551 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7700 (mtt180) REVERT: A 571 GLN cc_start: 0.6402 (OUTLIER) cc_final: 0.5808 (tp-100) REVERT: B 185 LYS cc_start: 0.8056 (mtpt) cc_final: 0.7510 (mtmt) REVERT: B 355 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7942 (mt-10) REVERT: B 501 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7650 (t70) REVERT: C 240 MET cc_start: 0.8935 (tpt) cc_final: 0.8599 (tpt) REVERT: C 305 ARG cc_start: 0.6547 (ttp-110) cc_final: 0.6012 (tmt170) REVERT: C 576 ARG cc_start: 0.6634 (OUTLIER) cc_final: 0.5859 (mtt-85) REVERT: D 501 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7514 (m-30) outliers start: 29 outliers final: 14 residues processed: 183 average time/residue: 1.3449 time to fit residues: 271.0571 Evaluate side-chains 178 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 1.707 ------------------------------------------------------------------------------- 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 A residue 551 ARG Chi-restraints excluded: chain A residue 571 GLN 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 355 GLU 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 576 ARG Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 395 ASP 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: 0.6980 chunk 48 optimal weight: 1.9990 chunk 167 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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** ** C 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.154887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.128572 restraints weight = 16332.534| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.29 r_work: 0.3110 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15002 Z= 0.310 Angle : 0.623 11.006 20356 Z= 0.325 Chirality : 0.048 0.209 2171 Planarity : 0.005 0.054 2581 Dihedral : 13.630 159.924 2192 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.97 % Allowed : 12.15 % Favored : 84.87 % 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: 0.31 (0.20), residues: 1760 helix: 1.03 (0.18), residues: 864 sheet: 0.43 (0.47), residues: 131 loop : -0.74 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 572 HIS 0.007 0.002 HIS A 233 PHE 0.014 0.002 PHE B 363 TYR 0.029 0.002 TYR B 315 ARG 0.008 0.001 ARG D 576 *********************** 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 205 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 160 time to evaluate : 1.664 Fit side-chains revert: symmetry clash REVERT: A 193 GLU cc_start: 0.7263 (mm-30) cc_final: 0.7013 (mm-30) REVERT: A 208 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8832 (mp) REVERT: A 426 ILE cc_start: 0.8487 (mm) cc_final: 0.8126 (tp) REVERT: B 185 LYS cc_start: 0.8082 (mtpt) cc_final: 0.7498 (mtmt) REVERT: B 250 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8073 (mm) REVERT: B 355 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7929 (mt-10) REVERT: B 501 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7607 (t70) REVERT: C 184 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6577 (tt0) REVERT: C 240 MET cc_start: 0.8956 (tpt) cc_final: 0.8710 (tpt) REVERT: C 305 ARG cc_start: 0.6575 (ttp-110) cc_final: 0.6073 (tmt170) REVERT: C 499 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8379 (mm) REVERT: C 576 ARG cc_start: 0.6669 (OUTLIER) cc_final: 0.5886 (mtt-85) REVERT: D 501 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7419 (m-30) REVERT: D 509 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.7616 (mtm) outliers start: 45 outliers final: 17 residues processed: 188 average time/residue: 1.3599 time to fit residues: 281.4108 Evaluate side-chains 182 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 2.001 ------------------------------------------------------------------------------- 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 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 293 ASN Chi-restraints excluded: chain B residue 355 GLU 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 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 356 VAL 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: 0.0870 chunk 3 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 chunk 161 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.7762 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.157280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.131202 restraints weight = 16355.465| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.28 r_work: 0.3186 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15002 Z= 0.189 Angle : 0.547 11.377 20356 Z= 0.284 Chirality : 0.045 0.183 2171 Planarity : 0.004 0.046 2581 Dihedral : 12.900 154.499 2192 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.85 % Allowed : 14.27 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.21), residues: 1760 helix: 1.21 (0.18), residues: 866 sheet: 0.50 (0.48), residues: 131 loop : -0.57 (0.23), residues: 763 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 *********************** 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: 28 poor density : 163 time to evaluate : 1.785 Fit side-chains revert: symmetry clash REVERT: A 193 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6895 (mm-30) REVERT: A 426 ILE cc_start: 0.8454 (mm) cc_final: 0.8089 (tp) REVERT: A 494 LYS cc_start: 0.6919 (mppt) cc_final: 0.6529 (mppt) REVERT: B 185 LYS cc_start: 0.7885 (mtpt) cc_final: 0.7330 (mtmt) REVERT: B 355 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7864 (mt-10) REVERT: B 501 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7584 (t70) REVERT: C 240 MET cc_start: 0.8896 (tpt) cc_final: 0.8636 (tpt) REVERT: C 330 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.7464 (t0) REVERT: C 576 ARG cc_start: 0.6496 (OUTLIER) cc_final: 0.5703 (mtt-85) REVERT: D 250 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8037 (mm) REVERT: D 509 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.7455 (mtm) outliers start: 28 outliers final: 14 residues processed: 182 average time/residue: 1.3639 time to fit residues: 274.2426 Evaluate side-chains 178 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 1.682 ------------------------------------------------------------------------------- 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 293 ASN Chi-restraints excluded: chain B residue 355 GLU 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 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 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: 0.2980 chunk 79 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 36 optimal weight: 8.9990 chunk 154 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 78 optimal weight: 0.4980 chunk 121 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.156677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.130614 restraints weight = 16332.493| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.27 r_work: 0.3173 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15002 Z= 0.215 Angle : 0.568 12.479 20356 Z= 0.295 Chirality : 0.046 0.193 2171 Planarity : 0.004 0.044 2581 Dihedral : 12.812 156.962 2192 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.58 % Allowed : 14.27 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.20), residues: 1760 helix: 1.23 (0.18), residues: 863 sheet: 0.60 (0.49), residues: 131 loop : -0.70 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 572 HIS 0.007 0.001 HIS A 233 PHE 0.013 0.002 PHE D 165 TYR 0.027 0.002 TYR B 315 ARG 0.005 0.000 ARG B 576 *********************** 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 198 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 159 time to evaluate : 1.635 Fit side-chains revert: symmetry clash REVERT: A 193 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6955 (mm-30) REVERT: A 208 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8783 (mp) REVERT: A 426 ILE cc_start: 0.8467 (mm) cc_final: 0.8095 (tp) REVERT: A 494 LYS cc_start: 0.6987 (mppt) cc_final: 0.6616 (mppt) REVERT: A 551 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7181 (mtt180) REVERT: B 185 LYS cc_start: 0.7904 (mtpt) cc_final: 0.7336 (mtmt) REVERT: B 250 ILE cc_start: 0.8264 (OUTLIER) cc_final: 0.8056 (mm) REVERT: B 355 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7891 (mt-10) REVERT: B 501 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7605 (t70) REVERT: C 240 MET cc_start: 0.8901 (tpt) cc_final: 0.8631 (tpt) REVERT: C 330 ASP cc_start: 0.7746 (OUTLIER) cc_final: 0.7506 (t0) REVERT: C 576 ARG cc_start: 0.6479 (OUTLIER) cc_final: 0.5727 (mtt-85) REVERT: D 250 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8092 (mm) REVERT: D 501 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7532 (m-30) REVERT: D 509 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.7622 (mtm) outliers start: 39 outliers final: 19 residues processed: 186 average time/residue: 1.3129 time to fit residues: 269.3905 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 : 1.964 ------------------------------------------------------------------------------- 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 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 259 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 549 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 149 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 116 optimal weight: 0.0670 chunk 157 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3690 r_free = 0.3690 target = 0.156007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.129949 restraints weight = 16281.564| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.28 r_work: 0.3164 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15002 Z= 0.242 Angle : 0.584 13.403 20356 Z= 0.303 Chirality : 0.046 0.194 2171 Planarity : 0.005 0.045 2581 Dihedral : 12.845 159.231 2192 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.31 % Allowed : 14.66 % Favored : 83.03 % 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: 0.46 (0.20), residues: 1760 helix: 1.18 (0.18), residues: 863 sheet: 0.55 (0.49), residues: 131 loop : -0.72 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 572 HIS 0.007 0.001 HIS A 233 PHE 0.013 0.002 PHE D 165 TYR 0.027 0.002 TYR B 315 ARG 0.004 0.000 ARG B 576 *********************** 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 189 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 1.719 Fit side-chains revert: symmetry clash REVERT: A 193 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6958 (mm-30) REVERT: A 208 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8796 (mp) REVERT: A 426 ILE cc_start: 0.8468 (mm) cc_final: 0.8088 (tp) REVERT: A 494 LYS cc_start: 0.7004 (mppt) cc_final: 0.6667 (mppt) REVERT: A 551 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7144 (mtt180) REVERT: B 185 LYS cc_start: 0.7953 (mtpt) cc_final: 0.7374 (mtmt) REVERT: B 250 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.8051 (mm) REVERT: B 355 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: B 501 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7605 (t70) REVERT: C 240 MET cc_start: 0.8888 (tpt) cc_final: 0.8619 (tpt) REVERT: C 330 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7478 (t0) REVERT: C 576 ARG cc_start: 0.6495 (OUTLIER) cc_final: 0.5737 (mtt-85) REVERT: D 250 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8081 (mm) REVERT: D 501 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7527 (m-30) REVERT: D 509 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.7682 (mtm) outliers start: 35 outliers final: 19 residues processed: 179 average time/residue: 1.2936 time to fit residues: 255.7802 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 : 1.805 ------------------------------------------------------------------------------- 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 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 259 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 549 LEU 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 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: 0.8980 chunk 58 optimal weight: 0.6980 chunk 50 optimal weight: 0.0070 chunk 135 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 166 optimal weight: 0.0060 chunk 124 optimal weight: 0.0170 chunk 10 optimal weight: 0.3980 chunk 49 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 overall best weight: 0.2052 ------------------------------------------------------------------------------- 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 D 548 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.161542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.136754 restraints weight = 16152.900| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.22 r_work: 0.3242 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15002 Z= 0.125 Angle : 0.510 13.384 20356 Z= 0.261 Chirality : 0.043 0.167 2171 Planarity : 0.004 0.041 2581 Dihedral : 11.694 150.120 2192 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.52 % Allowed : 15.65 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.91 (0.21), residues: 1760 helix: 1.50 (0.19), residues: 859 sheet: 0.72 (0.49), residues: 131 loop : -0.39 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 285 HIS 0.005 0.001 HIS A 233 PHE 0.012 0.001 PHE D 165 TYR 0.023 0.001 TYR B 315 ARG 0.003 0.000 ARG C 134 *********************** 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 194 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 1.699 Fit side-chains REVERT: A 426 ILE cc_start: 0.8405 (mm) cc_final: 0.8054 (tp) REVERT: A 494 LYS cc_start: 0.7014 (mppt) cc_final: 0.6748 (mppt) REVERT: B 185 LYS cc_start: 0.7768 (mtpt) cc_final: 0.7245 (mtmt) REVERT: B 355 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7709 (mt-10) REVERT: B 501 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7501 (t70) REVERT: C 369 LEU cc_start: 0.8134 (mt) cc_final: 0.7748 (mt) REVERT: C 576 ARG cc_start: 0.6310 (OUTLIER) cc_final: 0.5582 (mtt-85) REVERT: D 250 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.7969 (mm) REVERT: D 501 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7406 (m-30) REVERT: D 509 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.7495 (mtm) outliers start: 23 outliers final: 12 residues processed: 185 average time/residue: 1.2430 time to fit residues: 255.1890 Evaluate side-chains 182 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 355 GLU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 48 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 167 optimal weight: 0.8980 chunk 160 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 0.0770 chunk 154 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN C 210 HIS C 548 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.158958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.133525 restraints weight = 16266.100| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.23 r_work: 0.3183 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15002 Z= 0.183 Angle : 0.550 14.214 20356 Z= 0.284 Chirality : 0.045 0.182 2171 Planarity : 0.004 0.041 2581 Dihedral : 11.937 155.050 2192 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.52 % Allowed : 16.31 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.21), residues: 1760 helix: 1.37 (0.18), residues: 869 sheet: 0.88 (0.49), residues: 126 loop : -0.49 (0.22), residues: 765 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 0.005 0.000 ARG A 371 ********************** 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 186 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 1.644 Fit side-chains REVERT: A 426 ILE cc_start: 0.8440 (mm) cc_final: 0.8099 (tp) REVERT: A 494 LYS cc_start: 0.7044 (mppt) cc_final: 0.6736 (mppt) REVERT: A 576 ARG cc_start: 0.6006 (ttt-90) cc_final: 0.5713 (ttt-90) REVERT: B 185 LYS cc_start: 0.7833 (mtpt) cc_final: 0.7275 (mtmt) REVERT: B 355 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7806 (mt-10) REVERT: B 501 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7554 (t70) REVERT: C 369 LEU cc_start: 0.8174 (mt) cc_final: 0.7773 (mt) REVERT: C 552 VAL cc_start: 0.7026 (t) cc_final: 0.6808 (p) REVERT: C 576 ARG cc_start: 0.6417 (OUTLIER) cc_final: 0.5739 (mtt-85) REVERT: D 250 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8045 (mm) REVERT: D 501 ASP cc_start: 0.7961 (OUTLIER) cc_final: 0.7512 (m-30) REVERT: D 509 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.7581 (mtm) outliers start: 23 outliers final: 13 residues processed: 178 average time/residue: 1.2448 time to fit residues: 245.4212 Evaluate side-chains 178 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 355 GLU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 561 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 130 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 82 optimal weight: 0.3980 chunk 35 optimal weight: 0.2980 chunk 120 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 215 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.155440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.129162 restraints weight = 16438.784| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.26 r_work: 0.3136 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15002 Z= 0.210 Angle : 0.569 14.461 20356 Z= 0.294 Chirality : 0.045 0.191 2171 Planarity : 0.004 0.042 2581 Dihedral : 12.195 158.483 2192 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.52 % Allowed : 16.64 % Favored : 81.84 % 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: 0.67 (0.20), residues: 1760 helix: 1.27 (0.18), residues: 869 sheet: 0.90 (0.49), residues: 126 loop : -0.56 (0.22), residues: 765 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 0.002 PHE D 165 TYR 0.028 0.002 TYR B 315 ARG 0.006 0.000 ARG A 371 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8872.36 seconds wall clock time: 159 minutes 22.38 seconds (9562.38 seconds total)