Starting phenix.real_space_refine on Sat Dec 28 20:42:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gw6_34303/12_2024/8gw6_34303_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gw6_34303/12_2024/8gw6_34303.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gw6_34303/12_2024/8gw6_34303.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gw6_34303/12_2024/8gw6_34303.map" model { file = "/net/cci-nas-00/data/ceres_data/8gw6_34303/12_2024/8gw6_34303_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gw6_34303/12_2024/8gw6_34303_trim.cif" } resolution = 3.3 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= 0.002 sd= 0.049 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: 5 Type Number sf(0) Gaussians S 45 5.16 5 Cl 3 4.86 5 C 6018 2.51 5 N 1380 2.21 5 O 1437 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8883 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2925 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 367, 2917 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 22, 'TRANS': 344} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 367, 2917 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 22, 'TRANS': 344} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 3011 Chain: "B" Number of atoms: 2925 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 367, 2917 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 22, 'TRANS': 344} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 367, 2917 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 22, 'TRANS': 344} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 3011 Chain: "C" Number of atoms: 2925 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 367, 2917 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 22, 'TRANS': 344} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 367, 2917 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 22, 'TRANS': 344} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 3011 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 71 Unusual residues: {' CL': 1, 'Y01': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {' CL': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.64, per 1000 atoms: 1.09 Number of scatterers: 8883 At special positions: 0 Unit cell: (105.4, 97.75, 78.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 3 17.00 S 45 16.00 O 1437 8.00 N 1380 7.00 C 6018 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.31 Conformation dependent library (CDL) restraints added in 2.1 seconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 0 sheets defined 70.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 189 through 192 removed outlier: 3.555A pdb=" N CYS A 192 " --> pdb=" O PRO A 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 189 through 192' Processing helix chain 'A' and resid 193 through 212 removed outlier: 3.536A pdb=" N GLN A 202 " --> pdb=" O GLY A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 259 removed outlier: 3.565A pdb=" N LEU A 226 " --> pdb=" O PRO A 222 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 241 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A 246 " --> pdb=" O THR A 242 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N GLU A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ALA A 253 " --> pdb=" O PHE A 249 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 267 removed outlier: 3.701A pdb=" N ASN A 265 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 280 Processing helix chain 'A' and resid 293 through 314 removed outlier: 4.412A pdb=" N TRP A 297 " --> pdb=" O HIS A 293 " (cutoff:3.500A) Proline residue: A 303 - end of helix removed outlier: 4.106A pdb=" N LYS A 310 " --> pdb=" O PHE A 306 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 334 removed outlier: 4.031A pdb=" N HIS A 332 " --> pdb=" O PRO A 329 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 333 " --> pdb=" O SER A 330 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER A 334 " --> pdb=" O SER A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 347 removed outlier: 4.463A pdb=" N PHE A 339 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE A 343 " --> pdb=" O PHE A 339 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 344 " --> pdb=" O VAL A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 371 Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'A' and resid 387 through 393 removed outlier: 3.671A pdb=" N MET A 392 " --> pdb=" O VAL A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 408 Processing helix chain 'A' and resid 412 through 431 removed outlier: 3.728A pdb=" N ARG A 416 " --> pdb=" O ASP A 412 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR A 417 " --> pdb=" O GLY A 413 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N CYS A 418 " --> pdb=" O CYS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 449 removed outlier: 4.292A pdb=" N TRP A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N SER A 447 " --> pdb=" O VAL A 443 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A 449 " --> pdb=" O TRP A 445 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 442 through 449' Processing helix chain 'A' and resid 449 through 466 removed outlier: 3.730A pdb=" N ALA A 455 " --> pdb=" O PRO A 451 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N SER A 456 " --> pdb=" O MET A 452 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS A 461 " --> pdb=" O VAL A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 499 removed outlier: 3.659A pdb=" N SER A 479 " --> pdb=" O ALA A 475 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE A 480 " --> pdb=" O LEU A 476 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 494 " --> pdb=" O PHE A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 511 removed outlier: 3.646A pdb=" N ILE A 510 " --> pdb=" O ASP A 507 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 511 " --> pdb=" O LEU A 508 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 507 through 511' Processing helix chain 'B' and resid 184 through 188 Processing helix chain 'B' and resid 189 through 192 removed outlier: 3.555A pdb=" N CYS B 192 " --> pdb=" O PRO B 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 189 through 192' Processing helix chain 'B' and resid 193 through 212 removed outlier: 3.535A pdb=" N GLN B 202 " --> pdb=" O GLY B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 259 removed outlier: 3.564A pdb=" N LEU B 226 " --> pdb=" O PRO B 222 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE B 241 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS B 246 " --> pdb=" O THR B 242 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N GLU B 252 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ALA B 253 " --> pdb=" O PHE B 249 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG B 256 " --> pdb=" O GLU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 267 removed outlier: 3.702A pdb=" N ASN B 265 " --> pdb=" O VAL B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 280 Processing helix chain 'B' and resid 293 through 314 removed outlier: 4.411A pdb=" N TRP B 297 " --> pdb=" O HIS B 293 " (cutoff:3.500A) Proline residue: B 303 - end of helix removed outlier: 4.106A pdb=" N LYS B 310 " --> pdb=" O PHE B 306 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE B 311 " --> pdb=" O LEU B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 334 removed outlier: 4.031A pdb=" N HIS B 332 " --> pdb=" O PRO B 329 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 333 " --> pdb=" O SER B 330 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER B 334 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 347 removed outlier: 4.464A pdb=" N PHE B 339 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE B 343 " --> pdb=" O PHE B 339 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 344 " --> pdb=" O VAL B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 371 Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'B' and resid 387 through 393 removed outlier: 3.671A pdb=" N MET B 392 " --> pdb=" O VAL B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 408 Processing helix chain 'B' and resid 412 through 431 removed outlier: 3.729A pdb=" N ARG B 416 " --> pdb=" O ASP B 412 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR B 417 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N CYS B 418 " --> pdb=" O CYS B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 449 removed outlier: 4.293A pdb=" N TRP B 446 " --> pdb=" O SER B 442 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N SER B 447 " --> pdb=" O VAL B 443 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR B 449 " --> pdb=" O TRP B 445 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 442 through 449' Processing helix chain 'B' and resid 449 through 466 removed outlier: 3.730A pdb=" N ALA B 455 " --> pdb=" O PRO B 451 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N SER B 456 " --> pdb=" O MET B 452 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 457 " --> pdb=" O THR B 453 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS B 461 " --> pdb=" O VAL B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 499 removed outlier: 3.659A pdb=" N SER B 479 " --> pdb=" O ALA B 475 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 494 " --> pdb=" O PHE B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 511 removed outlier: 3.646A pdb=" N ILE B 510 " --> pdb=" O ASP B 507 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 511 " --> pdb=" O LEU B 508 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 507 through 511' Processing helix chain 'C' and resid 184 through 188 Processing helix chain 'C' and resid 189 through 192 removed outlier: 3.556A pdb=" N CYS C 192 " --> pdb=" O PRO C 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 189 through 192' Processing helix chain 'C' and resid 193 through 212 removed outlier: 3.536A pdb=" N GLN C 202 " --> pdb=" O GLY C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 259 removed outlier: 3.565A pdb=" N LEU C 226 " --> pdb=" O PRO C 222 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE C 241 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS C 246 " --> pdb=" O THR C 242 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N GLU C 252 " --> pdb=" O ILE C 248 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ALA C 253 " --> pdb=" O PHE C 249 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG C 256 " --> pdb=" O GLU C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 267 removed outlier: 3.701A pdb=" N ASN C 265 " --> pdb=" O VAL C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 280 Processing helix chain 'C' and resid 293 through 314 removed outlier: 4.412A pdb=" N TRP C 297 " --> pdb=" O HIS C 293 " (cutoff:3.500A) Proline residue: C 303 - end of helix removed outlier: 4.106A pdb=" N LYS C 310 " --> pdb=" O PHE C 306 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE C 311 " --> pdb=" O LEU C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 334 removed outlier: 4.031A pdb=" N HIS C 332 " --> pdb=" O PRO C 329 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU C 333 " --> pdb=" O SER C 330 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER C 334 " --> pdb=" O SER C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 347 removed outlier: 4.464A pdb=" N PHE C 339 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE C 343 " --> pdb=" O PHE C 339 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU C 344 " --> pdb=" O VAL C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 371 Processing helix chain 'C' and resid 372 through 374 No H-bonds generated for 'chain 'C' and resid 372 through 374' Processing helix chain 'C' and resid 387 through 393 removed outlier: 3.672A pdb=" N MET C 392 " --> pdb=" O VAL C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 408 Processing helix chain 'C' and resid 412 through 431 removed outlier: 3.728A pdb=" N ARG C 416 " --> pdb=" O ASP C 412 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR C 417 " --> pdb=" O GLY C 413 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N CYS C 418 " --> pdb=" O CYS C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 449 removed outlier: 4.292A pdb=" N TRP C 446 " --> pdb=" O SER C 442 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N SER C 447 " --> pdb=" O VAL C 443 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR C 449 " --> pdb=" O TRP C 445 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 442 through 449' Processing helix chain 'C' and resid 449 through 466 removed outlier: 3.730A pdb=" N ALA C 455 " --> pdb=" O PRO C 451 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N SER C 456 " --> pdb=" O MET C 452 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C 457 " --> pdb=" O THR C 453 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS C 461 " --> pdb=" O VAL C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 499 removed outlier: 3.660A pdb=" N SER C 479 " --> pdb=" O ALA C 475 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE C 480 " --> pdb=" O LEU C 476 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU C 494 " --> pdb=" O PHE C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 511 removed outlier: 3.646A pdb=" N ILE C 510 " --> pdb=" O ASP C 507 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA C 511 " --> pdb=" O LEU C 508 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 507 through 511' 462 hydrogen bonds defined for protein. 1314 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: 2.31 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1561 1.33 - 1.45: 2541 1.45 - 1.57: 5036 1.57 - 1.69: 0 1.69 - 1.81: 63 Bond restraints: 9201 Sorted by residual: bond pdb=" CAT Y01 C 901 " pdb=" CBH Y01 C 901 " ideal model delta sigma weight residual 1.545 1.451 0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" CAT Y01 A 903 " pdb=" CBH Y01 A 903 " ideal model delta sigma weight residual 1.545 1.451 0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" CAT Y01 A 902 " pdb=" CBH Y01 A 902 " ideal model delta sigma weight residual 1.545 1.451 0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" CBD Y01 A 902 " pdb=" CBF Y01 A 902 " ideal model delta sigma weight residual 1.536 1.451 0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" CBD Y01 C 901 " pdb=" CBF Y01 C 901 " ideal model delta sigma weight residual 1.536 1.451 0.085 2.00e-02 2.50e+03 1.79e+01 ... (remaining 9196 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 12459 2.44 - 4.88: 114 4.88 - 7.32: 15 7.32 - 9.76: 6 9.76 - 12.20: 6 Bond angle restraints: 12600 Sorted by residual: angle pdb=" CAK Y01 A 902 " pdb=" CAI Y01 A 902 " pdb=" CAZ Y01 A 902 " ideal model delta sigma weight residual 124.96 112.76 12.20 3.00e+00 1.11e-01 1.65e+01 angle pdb=" CAK Y01 C 901 " pdb=" CAI Y01 C 901 " pdb=" CAZ Y01 C 901 " ideal model delta sigma weight residual 124.96 112.77 12.19 3.00e+00 1.11e-01 1.65e+01 angle pdb=" CAK Y01 A 903 " pdb=" CAI Y01 A 903 " pdb=" CAZ Y01 A 903 " ideal model delta sigma weight residual 124.96 112.78 12.18 3.00e+00 1.11e-01 1.65e+01 angle pdb=" OAG Y01 C 901 " pdb=" CAY Y01 C 901 " pdb=" OAW Y01 C 901 " ideal model delta sigma weight residual 123.38 113.43 9.95 3.00e+00 1.11e-01 1.10e+01 angle pdb=" OAG Y01 A 903 " pdb=" CAY Y01 A 903 " pdb=" OAW Y01 A 903 " ideal model delta sigma weight residual 123.38 113.49 9.89 3.00e+00 1.11e-01 1.09e+01 ... (remaining 12595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.02: 4729 13.02 - 26.04: 439 26.04 - 39.05: 154 39.05 - 52.07: 45 52.07 - 65.09: 27 Dihedral angle restraints: 5394 sinusoidal: 2139 harmonic: 3255 Sorted by residual: dihedral pdb=" CB LYS C 169 " pdb=" CG LYS C 169 " pdb=" CD LYS C 169 " pdb=" CE LYS C 169 " ideal model delta sinusoidal sigma weight residual 180.00 120.03 59.97 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB LYS A 169 " pdb=" CG LYS A 169 " pdb=" CD LYS A 169 " pdb=" CE LYS A 169 " ideal model delta sinusoidal sigma weight residual 180.00 120.04 59.96 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB LYS B 169 " pdb=" CG LYS B 169 " pdb=" CD LYS B 169 " pdb=" CE LYS B 169 " ideal model delta sinusoidal sigma weight residual 180.00 120.07 59.93 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 5391 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 1413 0.146 - 0.293: 9 0.293 - 0.439: 0 0.439 - 0.585: 0 0.585 - 0.731: 3 Chirality restraints: 1425 Sorted by residual: chirality pdb=" CBH Y01 A 902 " pdb=" CAT Y01 A 902 " pdb=" CAZ Y01 A 902 " pdb=" CBF Y01 A 902 " both_signs ideal model delta sigma weight residual False -2.85 -2.12 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" CBH Y01 A 903 " pdb=" CAT Y01 A 903 " pdb=" CAZ Y01 A 903 " pdb=" CBF Y01 A 903 " both_signs ideal model delta sigma weight residual False -2.85 -2.12 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" CBH Y01 C 901 " pdb=" CAT Y01 C 901 " pdb=" CAZ Y01 C 901 " pdb=" CBF Y01 C 901 " both_signs ideal model delta sigma weight residual False -2.85 -2.12 -0.73 2.00e-01 2.50e+01 1.33e+01 ... (remaining 1422 not shown) Planarity restraints: 1518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 376 " 0.058 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO C 377 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO C 377 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 377 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 376 " -0.058 5.00e-02 4.00e+02 8.64e-02 1.20e+01 pdb=" N PRO A 377 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO A 377 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 377 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 376 " -0.058 5.00e-02 4.00e+02 8.63e-02 1.19e+01 pdb=" N PRO B 377 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO B 377 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 377 " -0.047 5.00e-02 4.00e+02 ... (remaining 1515 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 3631 2.90 - 3.40: 8873 3.40 - 3.90: 13587 3.90 - 4.40: 15914 4.40 - 4.90: 26515 Nonbonded interactions: 68520 Sorted by model distance: nonbonded pdb=" O ASN B 216 " pdb=" OD1 ASN B 216 " model vdw 2.397 3.040 nonbonded pdb=" O ASN A 216 " pdb=" OD1 ASN A 216 " model vdw 2.397 3.040 nonbonded pdb=" O ASN C 216 " pdb=" OD1 ASN C 216 " model vdw 2.397 3.040 nonbonded pdb=" O THR B 378 " pdb=" OG1 THR B 378 " model vdw 2.446 3.040 nonbonded pdb=" O THR A 378 " pdb=" OG1 THR A 378 " model vdw 2.447 3.040 ... (remaining 68515 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 150 through 320 or resid 322 through 516)) selection = (chain 'B' and (resid 150 through 320 or resid 322 through 516)) selection = (chain 'C' and (resid 150 through 320 or resid 322 through 516)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 28.160 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 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 : 0.004 0.094 9201 Z= 0.246 Angle : 0.599 12.201 12600 Z= 0.249 Chirality : 0.052 0.731 1425 Planarity : 0.005 0.087 1518 Dihedral : 12.881 65.090 3288 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.65 % Allowed : 0.97 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.28), residues: 1098 helix: 1.23 (0.23), residues: 672 sheet: None (None), residues: 0 loop : -0.74 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 206 HIS 0.001 0.000 HIS C 496 PHE 0.011 0.001 PHE B 362 TYR 0.005 0.001 TYR C 312 ARG 0.002 0.000 ARG B 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 132 time to evaluate : 0.875 Fit side-chains REVERT: A 161 ARG cc_start: 0.7325 (ppt170) cc_final: 0.5940 (ppt170) REVERT: B 190 ILE cc_start: 0.7990 (tp) cc_final: 0.7709 (tp) REVERT: C 161 ARG cc_start: 0.7389 (ppt170) cc_final: 0.5941 (ppt170) REVERT: C 213 PRO cc_start: 0.7965 (Cg_exo) cc_final: 0.7686 (Cg_endo) outliers start: 3 outliers final: 0 residues processed: 132 average time/residue: 0.2244 time to fit residues: 40.7111 Evaluate side-chains 121 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 84 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 0.1980 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 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 225 ASN A 265 ASN ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN B 225 ASN ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9201 Z= 0.217 Angle : 0.658 12.456 12600 Z= 0.325 Chirality : 0.043 0.142 1425 Planarity : 0.005 0.065 1518 Dihedral : 8.770 59.366 1398 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.19 % Allowed : 7.23 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.26), residues: 1098 helix: 0.94 (0.21), residues: 684 sheet: None (None), residues: 0 loop : -0.70 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 206 HIS 0.004 0.001 HIS B 496 PHE 0.021 0.002 PHE C 441 TYR 0.019 0.002 TYR C 312 ARG 0.005 0.000 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.888 Fit side-chains REVERT: A 155 ARG cc_start: 0.7537 (mmm160) cc_final: 0.7222 (tpp-160) REVERT: A 161 ARG cc_start: 0.7481 (ppt170) cc_final: 0.6074 (ppt170) REVERT: A 375 ARG cc_start: 0.6807 (ttp-170) cc_final: 0.6466 (ptt90) REVERT: A 405 ASN cc_start: 0.8065 (t0) cc_final: 0.7802 (t0) REVERT: B 155 ARG cc_start: 0.7686 (mmm160) cc_final: 0.7302 (tpp-160) REVERT: B 375 ARG cc_start: 0.7076 (ttm110) cc_final: 0.6797 (ttp-110) REVERT: B 405 ASN cc_start: 0.7863 (t0) cc_final: 0.7646 (t0) REVERT: C 155 ARG cc_start: 0.7565 (mmm160) cc_final: 0.7333 (tpp-160) REVERT: C 375 ARG cc_start: 0.7032 (ttm170) cc_final: 0.6714 (ttp-110) REVERT: C 405 ASN cc_start: 0.7888 (t0) cc_final: 0.7645 (t0) REVERT: C 407 ILE cc_start: 0.7709 (OUTLIER) cc_final: 0.7368 (mp) outliers start: 11 outliers final: 6 residues processed: 130 average time/residue: 0.2375 time to fit residues: 42.0102 Evaluate side-chains 115 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 491 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN B 265 ASN ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 338 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9201 Z= 0.228 Angle : 0.616 9.523 12600 Z= 0.303 Chirality : 0.043 0.187 1425 Planarity : 0.005 0.063 1518 Dihedral : 8.753 59.846 1398 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.54 % Allowed : 11.54 % Favored : 87.92 % 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: 0.45 (0.26), residues: 1098 helix: 0.95 (0.21), residues: 648 sheet: None (None), residues: 0 loop : -0.58 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 229 HIS 0.003 0.001 HIS C 260 PHE 0.032 0.001 PHE C 362 TYR 0.018 0.002 TYR A 312 ARG 0.004 0.000 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 109 time to evaluate : 0.976 Fit side-chains REVERT: A 155 ARG cc_start: 0.7548 (mmm160) cc_final: 0.7209 (tpp-160) REVERT: A 161 ARG cc_start: 0.7554 (ppt170) cc_final: 0.6068 (ppt170) REVERT: A 375 ARG cc_start: 0.6894 (ttp-170) cc_final: 0.6500 (ptt90) REVERT: A 405 ASN cc_start: 0.8272 (t0) cc_final: 0.8009 (t0) REVERT: A 476 LEU cc_start: 0.8119 (mt) cc_final: 0.7904 (mt) REVERT: B 155 ARG cc_start: 0.7603 (mmm160) cc_final: 0.7319 (tpp-160) REVERT: B 375 ARG cc_start: 0.6992 (ttm170) cc_final: 0.6753 (ttp-110) REVERT: C 375 ARG cc_start: 0.7009 (ttm170) cc_final: 0.6645 (ttp-170) REVERT: C 407 ILE cc_start: 0.7642 (OUTLIER) cc_final: 0.7283 (mp) outliers start: 5 outliers final: 4 residues processed: 110 average time/residue: 0.2694 time to fit residues: 41.0548 Evaluate side-chains 108 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 443 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 ASN ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9201 Z= 0.220 Angle : 0.610 11.878 12600 Z= 0.296 Chirality : 0.042 0.174 1425 Planarity : 0.005 0.060 1518 Dihedral : 8.906 59.758 1398 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.19 % Allowed : 11.76 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.26), residues: 1098 helix: 0.83 (0.21), residues: 669 sheet: None (None), residues: 0 loop : -0.65 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 229 HIS 0.002 0.001 HIS C 260 PHE 0.018 0.001 PHE A 362 TYR 0.015 0.001 TYR A 312 ARG 0.004 0.000 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.912 Fit side-chains REVERT: A 161 ARG cc_start: 0.7558 (ppt170) cc_final: 0.6074 (ppt170) REVERT: A 375 ARG cc_start: 0.6919 (ttp-170) cc_final: 0.6498 (ptt90) REVERT: A 405 ASN cc_start: 0.8327 (t0) cc_final: 0.8035 (t0) REVERT: A 441 PHE cc_start: 0.7066 (t80) cc_final: 0.6760 (t80) REVERT: A 476 LEU cc_start: 0.8119 (mt) cc_final: 0.7915 (mt) REVERT: B 155 ARG cc_start: 0.7602 (mmm160) cc_final: 0.7134 (tpp-160) REVERT: B 306 PHE cc_start: 0.6769 (t80) cc_final: 0.6534 (t80) REVERT: B 375 ARG cc_start: 0.7023 (ttm170) cc_final: 0.6772 (ttp-110) REVERT: B 441 PHE cc_start: 0.6675 (t80) cc_final: 0.6428 (t80) REVERT: C 375 ARG cc_start: 0.7007 (ttm170) cc_final: 0.6611 (ttp-170) REVERT: C 441 PHE cc_start: 0.6792 (t80) cc_final: 0.6409 (t80) outliers start: 11 outliers final: 5 residues processed: 121 average time/residue: 0.2301 time to fit residues: 37.9073 Evaluate side-chains 110 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 443 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 1 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 89 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 26 optimal weight: 0.0370 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 ASN B 265 ASN ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 ASN C 265 ASN ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9201 Z= 0.151 Angle : 0.548 12.058 12600 Z= 0.264 Chirality : 0.040 0.146 1425 Planarity : 0.005 0.059 1518 Dihedral : 8.749 59.980 1398 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.86 % Allowed : 13.48 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.26), residues: 1098 helix: 1.24 (0.21), residues: 666 sheet: None (None), residues: 0 loop : -0.59 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 229 HIS 0.002 0.000 HIS A 364 PHE 0.028 0.001 PHE A 362 TYR 0.011 0.001 TYR C 312 ARG 0.003 0.000 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 1.156 Fit side-chains REVERT: A 405 ASN cc_start: 0.8098 (t0) cc_final: 0.7816 (t0) REVERT: A 441 PHE cc_start: 0.7122 (t80) cc_final: 0.6549 (t80) REVERT: A 485 MET cc_start: 0.7431 (mmm) cc_final: 0.7224 (tpt) REVERT: B 306 PHE cc_start: 0.6807 (t80) cc_final: 0.6574 (t80) REVERT: B 441 PHE cc_start: 0.6701 (t80) cc_final: 0.6368 (t80) REVERT: C 407 ILE cc_start: 0.7559 (OUTLIER) cc_final: 0.7139 (mp) REVERT: C 441 PHE cc_start: 0.6562 (t80) cc_final: 0.6297 (t80) outliers start: 8 outliers final: 5 residues processed: 111 average time/residue: 0.1785 time to fit residues: 29.6705 Evaluate side-chains 114 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 443 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 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 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 ASN ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 9201 Z= 0.236 Angle : 0.606 11.962 12600 Z= 0.292 Chirality : 0.042 0.167 1425 Planarity : 0.005 0.059 1518 Dihedral : 8.973 58.225 1398 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.08 % Allowed : 14.35 % Favored : 84.57 % 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: 0.53 (0.26), residues: 1098 helix: 1.05 (0.21), residues: 666 sheet: None (None), residues: 0 loop : -0.68 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 229 HIS 0.002 0.001 HIS A 260 PHE 0.013 0.001 PHE A 450 TYR 0.011 0.001 TYR C 365 ARG 0.004 0.000 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.948 Fit side-chains REVERT: A 375 ARG cc_start: 0.6917 (ttp-170) cc_final: 0.6454 (ptt90) REVERT: A 405 ASN cc_start: 0.8372 (t0) cc_final: 0.8013 (t0) REVERT: A 441 PHE cc_start: 0.6904 (t80) cc_final: 0.6463 (t80) REVERT: B 155 ARG cc_start: 0.7543 (mmm160) cc_final: 0.7342 (tpt90) REVERT: B 306 PHE cc_start: 0.6943 (t80) cc_final: 0.6687 (t80) REVERT: B 375 ARG cc_start: 0.7040 (ttm170) cc_final: 0.6767 (ttp-110) REVERT: B 441 PHE cc_start: 0.6726 (t80) cc_final: 0.6422 (t80) REVERT: C 375 ARG cc_start: 0.7021 (ttm170) cc_final: 0.6720 (ttp-170) REVERT: C 407 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7290 (mp) REVERT: C 441 PHE cc_start: 0.6677 (t80) cc_final: 0.6418 (t80) outliers start: 10 outliers final: 6 residues processed: 118 average time/residue: 0.2324 time to fit residues: 37.7257 Evaluate side-chains 119 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 443 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 0.0050 chunk 76 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 9201 Z= 0.160 Angle : 0.553 12.324 12600 Z= 0.265 Chirality : 0.040 0.149 1425 Planarity : 0.005 0.058 1518 Dihedral : 8.876 59.539 1398 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.19 % Allowed : 14.89 % Favored : 83.93 % 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: 0.80 (0.26), residues: 1098 helix: 1.29 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -0.59 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 229 HIS 0.002 0.001 HIS A 364 PHE 0.026 0.001 PHE C 362 TYR 0.009 0.001 TYR C 312 ARG 0.002 0.000 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 1.006 Fit side-chains REVERT: A 405 ASN cc_start: 0.8276 (t0) cc_final: 0.7960 (t0) REVERT: B 306 PHE cc_start: 0.6822 (t80) cc_final: 0.6555 (t80) REVERT: B 441 PHE cc_start: 0.6713 (t80) cc_final: 0.6432 (t80) REVERT: C 407 ILE cc_start: 0.7634 (OUTLIER) cc_final: 0.7229 (mp) REVERT: C 441 PHE cc_start: 0.6673 (t80) cc_final: 0.6364 (t80) outliers start: 11 outliers final: 6 residues processed: 115 average time/residue: 0.1753 time to fit residues: 30.0730 Evaluate side-chains 114 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 443 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.7980 chunk 62 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 9201 Z= 0.156 Angle : 0.551 12.355 12600 Z= 0.262 Chirality : 0.040 0.136 1425 Planarity : 0.005 0.058 1518 Dihedral : 8.938 59.472 1398 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.97 % Allowed : 15.21 % Favored : 83.82 % 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: 0.87 (0.26), residues: 1098 helix: 1.37 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -0.60 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 229 HIS 0.002 0.001 HIS A 364 PHE 0.012 0.001 PHE C 362 TYR 0.009 0.001 TYR C 312 ARG 0.002 0.000 ARG C 375 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.946 Fit side-chains REVERT: A 405 ASN cc_start: 0.8278 (t0) cc_final: 0.7950 (t0) REVERT: B 306 PHE cc_start: 0.6838 (t80) cc_final: 0.6545 (t80) REVERT: C 407 ILE cc_start: 0.7459 (OUTLIER) cc_final: 0.7060 (mp) REVERT: C 441 PHE cc_start: 0.6636 (t80) cc_final: 0.6347 (t80) outliers start: 9 outliers final: 6 residues processed: 114 average time/residue: 0.1821 time to fit residues: 30.8716 Evaluate side-chains 114 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 443 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9201 Z= 0.192 Angle : 0.571 12.368 12600 Z= 0.274 Chirality : 0.041 0.169 1425 Planarity : 0.005 0.060 1518 Dihedral : 8.858 59.672 1398 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.76 % Allowed : 15.64 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.26), residues: 1098 helix: 1.26 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -0.63 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 445 HIS 0.002 0.001 HIS A 364 PHE 0.025 0.001 PHE A 362 TYR 0.010 0.001 TYR C 312 ARG 0.003 0.000 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 1.044 Fit side-chains REVERT: A 405 ASN cc_start: 0.8327 (t0) cc_final: 0.7988 (t0) REVERT: B 306 PHE cc_start: 0.6807 (t80) cc_final: 0.6512 (t80) REVERT: C 407 ILE cc_start: 0.7675 (OUTLIER) cc_final: 0.7294 (mp) REVERT: C 441 PHE cc_start: 0.6648 (t80) cc_final: 0.6345 (t80) outliers start: 7 outliers final: 5 residues processed: 110 average time/residue: 0.1842 time to fit residues: 30.2861 Evaluate side-chains 113 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 430 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.8980 chunk 62 optimal weight: 0.0020 chunk 48 optimal weight: 0.7980 chunk 71 optimal weight: 0.0070 chunk 107 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 85 optimal weight: 0.3980 chunk 8 optimal weight: 0.5980 chunk 66 optimal weight: 0.0670 chunk 52 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 overall best weight: 0.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN C 265 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 9201 Z= 0.123 Angle : 0.524 12.371 12600 Z= 0.249 Chirality : 0.039 0.110 1425 Planarity : 0.005 0.059 1518 Dihedral : 8.804 59.100 1398 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.54 % Allowed : 15.75 % Favored : 83.71 % 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: 1.10 (0.26), residues: 1098 helix: 1.58 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -0.56 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 229 HIS 0.004 0.001 HIS A 364 PHE 0.026 0.001 PHE A 362 TYR 0.008 0.001 TYR C 312 ARG 0.002 0.000 ARG C 375 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 0.876 Fit side-chains REVERT: A 405 ASN cc_start: 0.8126 (t0) cc_final: 0.7799 (t0) REVERT: B 306 PHE cc_start: 0.6724 (t80) cc_final: 0.6419 (t80) REVERT: B 485 MET cc_start: 0.7530 (mmm) cc_final: 0.7271 (tpt) REVERT: C 215 THR cc_start: 0.8074 (m) cc_final: 0.7805 (p) REVERT: C 407 ILE cc_start: 0.7531 (OUTLIER) cc_final: 0.7081 (mp) REVERT: C 441 PHE cc_start: 0.6505 (t80) cc_final: 0.6174 (t80) outliers start: 5 outliers final: 4 residues processed: 112 average time/residue: 0.1795 time to fit residues: 29.6472 Evaluate side-chains 110 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 430 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 0.0870 chunk 85 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 75 optimal weight: 0.0470 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 ASN ** 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 = 0.3912 r_free = 0.3912 target = 0.173656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.137672 restraints weight = 26333.254| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 3.35 r_work: 0.3351 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3337 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3337 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 9201 Z= 0.145 Angle : 0.531 12.431 12600 Z= 0.252 Chirality : 0.039 0.148 1425 Planarity : 0.005 0.059 1518 Dihedral : 8.763 59.362 1398 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.65 % Allowed : 16.07 % Favored : 83.28 % 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: 1.04 (0.26), residues: 1098 helix: 1.47 (0.21), residues: 681 sheet: None (None), residues: 0 loop : -0.56 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 229 HIS 0.002 0.000 HIS A 364 PHE 0.025 0.001 PHE A 362 TYR 0.008 0.001 TYR C 312 ARG 0.002 0.000 ARG B 375 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1818.03 seconds wall clock time: 34 minutes 1.22 seconds (2041.22 seconds total)