Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 16:31:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fx8_29526/04_2023/8fx8_29526_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fx8_29526/04_2023/8fx8_29526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fx8_29526/04_2023/8fx8_29526.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fx8_29526/04_2023/8fx8_29526.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fx8_29526/04_2023/8fx8_29526_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fx8_29526/04_2023/8fx8_29526_neut_updated.pdb" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 84 5.16 5 Na 1 4.78 5 C 11956 2.51 5 N 3028 2.21 5 O 3008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 18077 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4495 Classifications: {'peptide': 597} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 18, 'TRANS': 578} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 394 Unresolved non-hydrogen angles: 492 Unresolved non-hydrogen dihedrals: 327 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 13, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 19, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 262 Chain: "B" Number of atoms: 4495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4495 Classifications: {'peptide': 597} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 18, 'TRANS': 578} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 394 Unresolved non-hydrogen angles: 492 Unresolved non-hydrogen dihedrals: 327 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 13, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 19, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 262 Chain: "C" Number of atoms: 4495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4495 Classifications: {'peptide': 597} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 18, 'TRANS': 578} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 394 Unresolved non-hydrogen angles: 492 Unresolved non-hydrogen dihedrals: 327 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 13, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 19, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 262 Chain: "D" Number of atoms: 4495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4495 Classifications: {'peptide': 597} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 18, 'TRANS': 578} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 394 Unresolved non-hydrogen angles: 492 Unresolved non-hydrogen dihedrals: 327 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 13, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 19, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 262 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' NA': 1, 'P0T': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'P0T': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'P0T': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'P0T': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 9.36, per 1000 atoms: 0.52 Number of scatterers: 18077 At special positions: 0 Unit cell: (159.1, 159.1, 115.24, 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) S 84 16.00 Na 1 11.00 O 3008 8.00 N 3028 7.00 C 11956 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.58 Conformation dependent library (CDL) restraints added in 3.0 seconds 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4520 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 112 helices and 4 sheets defined 58.3% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 95 through 102 Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 136 through 145 Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 167 through 173 Processing helix chain 'A' and resid 177 through 185 Processing helix chain 'A' and resid 197 through 199 No H-bonds generated for 'chain 'A' and resid 197 through 199' Processing helix chain 'A' and resid 213 through 219 Processing helix chain 'A' and resid 223 through 230 Processing helix chain 'A' and resid 249 through 255 Processing helix chain 'A' and resid 261 through 281 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 298 through 305 Processing helix chain 'A' and resid 308 through 315 Processing helix chain 'A' and resid 324 through 326 No H-bonds generated for 'chain 'A' and resid 324 through 326' Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 367 through 373 removed outlier: 4.653A pdb=" N HIS A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG A 371 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 373 " --> pdb=" O HIS A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 412 removed outlier: 3.900A pdb=" N LYS A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 458 removed outlier: 3.609A pdb=" N LEU A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 465 Processing helix chain 'A' and resid 473 through 491 removed outlier: 3.540A pdb=" N PHE A 491 " --> pdb=" O GLN A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 518 removed outlier: 3.884A pdb=" N LEU A 505 " --> pdb=" O LEU A 501 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL A 506 " --> pdb=" O VAL A 502 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLY A 508 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU A 513 " --> pdb=" O TRP A 509 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR A 514 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N TYR A 515 " --> pdb=" O ASN A 511 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N THR A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ARG A 517 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N GLY A 518 " --> pdb=" O TYR A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 536 removed outlier: 3.793A pdb=" N ILE A 524 " --> pdb=" O GLN A 520 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 534 " --> pdb=" O GLN A 530 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG A 535 " --> pdb=" O LYS A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 559 removed outlier: 3.996A pdb=" N LEU A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A 543 " --> pdb=" O ARG A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 605 removed outlier: 3.668A pdb=" N LEU A 598 " --> pdb=" O LEU A 594 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR A 604 " --> pdb=" O LEU A 600 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE A 605 " --> pdb=" O PHE A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 650 removed outlier: 3.605A pdb=" N TYR A 634 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN A 650 " --> pdb=" O SER A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 673 removed outlier: 4.018A pdb=" N ASN A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 86 Processing helix chain 'B' and resid 95 through 102 Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 136 through 145 Processing helix chain 'B' and resid 152 through 154 No H-bonds generated for 'chain 'B' and resid 152 through 154' Processing helix chain 'B' and resid 167 through 173 Processing helix chain 'B' and resid 177 through 185 Processing helix chain 'B' and resid 197 through 199 No H-bonds generated for 'chain 'B' and resid 197 through 199' Processing helix chain 'B' and resid 213 through 219 Processing helix chain 'B' and resid 223 through 230 Processing helix chain 'B' and resid 249 through 255 Processing helix chain 'B' and resid 261 through 281 Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 298 through 305 Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 324 through 326 No H-bonds generated for 'chain 'B' and resid 324 through 326' Processing helix chain 'B' and resid 356 through 362 Processing helix chain 'B' and resid 367 through 373 removed outlier: 4.653A pdb=" N HIS B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG B 371 " --> pdb=" O ASN B 368 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 373 " --> pdb=" O HIS B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 412 removed outlier: 3.899A pdb=" N LYS B 380 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 458 removed outlier: 3.609A pdb=" N LEU B 443 " --> pdb=" O ILE B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 465 Processing helix chain 'B' and resid 473 through 491 removed outlier: 3.540A pdb=" N PHE B 491 " --> pdb=" O GLN B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 518 removed outlier: 3.884A pdb=" N LEU B 505 " --> pdb=" O LEU B 501 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL B 506 " --> pdb=" O VAL B 502 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU B 507 " --> pdb=" O LEU B 503 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLY B 508 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU B 513 " --> pdb=" O TRP B 509 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR B 514 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N TYR B 515 " --> pdb=" O ASN B 511 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N THR B 516 " --> pdb=" O LEU B 512 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ARG B 517 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N GLY B 518 " --> pdb=" O TYR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 536 removed outlier: 3.793A pdb=" N ILE B 524 " --> pdb=" O GLN B 520 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU B 534 " --> pdb=" O GLN B 530 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG B 535 " --> pdb=" O LYS B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 559 removed outlier: 3.997A pdb=" N LEU B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B 543 " --> pdb=" O ARG B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 605 removed outlier: 3.668A pdb=" N LEU B 598 " --> pdb=" O LEU B 594 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR B 604 " --> pdb=" O LEU B 600 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE B 605 " --> pdb=" O PHE B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 650 removed outlier: 3.606A pdb=" N TYR B 634 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN B 650 " --> pdb=" O SER B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 673 removed outlier: 4.018A pdb=" N ASN B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 86 Processing helix chain 'C' and resid 95 through 102 Processing helix chain 'C' and resid 120 through 126 Processing helix chain 'C' and resid 136 through 145 Processing helix chain 'C' and resid 152 through 154 No H-bonds generated for 'chain 'C' and resid 152 through 154' Processing helix chain 'C' and resid 167 through 173 Processing helix chain 'C' and resid 177 through 185 Processing helix chain 'C' and resid 197 through 199 No H-bonds generated for 'chain 'C' and resid 197 through 199' Processing helix chain 'C' and resid 213 through 219 Processing helix chain 'C' and resid 223 through 230 Processing helix chain 'C' and resid 249 through 255 Processing helix chain 'C' and resid 261 through 281 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 298 through 305 Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 324 through 326 No H-bonds generated for 'chain 'C' and resid 324 through 326' Processing helix chain 'C' and resid 356 through 362 Processing helix chain 'C' and resid 367 through 373 removed outlier: 4.653A pdb=" N HIS C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG C 371 " --> pdb=" O ASN C 368 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL C 373 " --> pdb=" O HIS C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 412 removed outlier: 3.900A pdb=" N LYS C 380 " --> pdb=" O GLU C 376 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 458 removed outlier: 3.609A pdb=" N LEU C 443 " --> pdb=" O ILE C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 465 Processing helix chain 'C' and resid 473 through 491 removed outlier: 3.540A pdb=" N PHE C 491 " --> pdb=" O GLN C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 518 removed outlier: 3.884A pdb=" N LEU C 505 " --> pdb=" O LEU C 501 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL C 506 " --> pdb=" O VAL C 502 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU C 507 " --> pdb=" O LEU C 503 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLY C 508 " --> pdb=" O SER C 504 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU C 513 " --> pdb=" O TRP C 509 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR C 514 " --> pdb=" O LEU C 510 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N TYR C 515 " --> pdb=" O ASN C 511 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N THR C 516 " --> pdb=" O LEU C 512 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ARG C 517 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N GLY C 518 " --> pdb=" O TYR C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 536 removed outlier: 3.793A pdb=" N ILE C 524 " --> pdb=" O GLN C 520 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU C 534 " --> pdb=" O GLN C 530 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG C 535 " --> pdb=" O LYS C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 559 removed outlier: 3.996A pdb=" N LEU C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL C 543 " --> pdb=" O ARG C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 605 removed outlier: 3.669A pdb=" N LEU C 598 " --> pdb=" O LEU C 594 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE C 603 " --> pdb=" O GLU C 599 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR C 604 " --> pdb=" O LEU C 600 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE C 605 " --> pdb=" O PHE C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 650 removed outlier: 3.605A pdb=" N TYR C 634 " --> pdb=" O VAL C 630 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN C 650 " --> pdb=" O SER C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 673 removed outlier: 4.018A pdb=" N ASN C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 86 Processing helix chain 'D' and resid 95 through 102 Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'D' and resid 136 through 145 Processing helix chain 'D' and resid 152 through 154 No H-bonds generated for 'chain 'D' and resid 152 through 154' Processing helix chain 'D' and resid 167 through 173 Processing helix chain 'D' and resid 177 through 185 Processing helix chain 'D' and resid 197 through 199 No H-bonds generated for 'chain 'D' and resid 197 through 199' Processing helix chain 'D' and resid 213 through 219 Processing helix chain 'D' and resid 223 through 230 Processing helix chain 'D' and resid 249 through 255 Processing helix chain 'D' and resid 261 through 281 Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 298 through 305 Processing helix chain 'D' and resid 308 through 315 Processing helix chain 'D' and resid 324 through 326 No H-bonds generated for 'chain 'D' and resid 324 through 326' Processing helix chain 'D' and resid 356 through 362 Processing helix chain 'D' and resid 367 through 373 removed outlier: 4.654A pdb=" N HIS D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG D 371 " --> pdb=" O ASN D 368 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL D 373 " --> pdb=" O HIS D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 412 removed outlier: 3.900A pdb=" N LYS D 380 " --> pdb=" O GLU D 376 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 458 removed outlier: 3.609A pdb=" N LEU D 443 " --> pdb=" O ILE D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 465 Processing helix chain 'D' and resid 473 through 491 removed outlier: 3.540A pdb=" N PHE D 491 " --> pdb=" O GLN D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 518 removed outlier: 3.884A pdb=" N LEU D 505 " --> pdb=" O LEU D 501 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL D 506 " --> pdb=" O VAL D 502 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU D 507 " --> pdb=" O LEU D 503 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLY D 508 " --> pdb=" O SER D 504 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU D 513 " --> pdb=" O TRP D 509 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TYR D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N TYR D 515 " --> pdb=" O ASN D 511 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N THR D 516 " --> pdb=" O LEU D 512 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARG D 517 " --> pdb=" O LEU D 513 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N GLY D 518 " --> pdb=" O TYR D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 536 removed outlier: 3.793A pdb=" N ILE D 524 " --> pdb=" O GLN D 520 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU D 534 " --> pdb=" O GLN D 530 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 559 removed outlier: 3.996A pdb=" N LEU D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL D 543 " --> pdb=" O ARG D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 605 removed outlier: 3.669A pdb=" N LEU D 598 " --> pdb=" O LEU D 594 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE D 603 " --> pdb=" O GLU D 599 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR D 604 " --> pdb=" O LEU D 600 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE D 605 " --> pdb=" O PHE D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 650 removed outlier: 3.606A pdb=" N TYR D 634 " --> pdb=" O VAL D 630 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN D 650 " --> pdb=" O SER D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 673 removed outlier: 4.018A pdb=" N ASN D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 687 through 690 removed outlier: 4.100A pdb=" N TRP A 333 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU A 342 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N THR A 331 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ASP A 344 " --> pdb=" O LYS A 329 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LYS A 329 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 687 through 690 removed outlier: 4.100A pdb=" N TRP B 333 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU B 342 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N THR B 331 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ASP B 344 " --> pdb=" O LYS B 329 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LYS B 329 " --> pdb=" O ASP B 344 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 687 through 690 removed outlier: 4.099A pdb=" N TRP C 333 " --> pdb=" O VAL C 340 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU C 342 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N THR C 331 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ASP C 344 " --> pdb=" O LYS C 329 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LYS C 329 " --> pdb=" O ASP C 344 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 687 through 690 removed outlier: 4.100A pdb=" N TRP D 333 " --> pdb=" O VAL D 340 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU D 342 " --> pdb=" O THR D 331 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N THR D 331 " --> pdb=" O LEU D 342 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ASP D 344 " --> pdb=" O LYS D 329 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LYS D 329 " --> pdb=" O ASP D 344 " (cutoff:3.500A) 896 hydrogen bonds defined for protein. 2652 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: 5.14 Time building geometry restraints manager: 8.10 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: 5608 1.34 - 1.46: 4533 1.46 - 1.58: 8239 1.58 - 1.69: 12 1.69 - 1.81: 120 Bond restraints: 18512 Sorted by residual: bond pdb=" C05 P0T C 801 " pdb=" C06 P0T C 801 " ideal model delta sigma weight residual 1.521 1.659 -0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" C05 P0T A 801 " pdb=" C06 P0T A 801 " ideal model delta sigma weight residual 1.521 1.659 -0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" C05 P0T D 801 " pdb=" C06 P0T D 801 " ideal model delta sigma weight residual 1.521 1.659 -0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" C05 P0T B 801 " pdb=" C06 P0T B 801 " ideal model delta sigma weight residual 1.521 1.659 -0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" C03 P0T D 801 " pdb=" C04 P0T D 801 " ideal model delta sigma weight residual 1.548 1.684 -0.136 2.00e-02 2.50e+03 4.60e+01 ... (remaining 18507 not shown) Histogram of bond angle deviations from ideal: 100.56 - 107.26: 528 107.26 - 113.97: 10615 113.97 - 120.67: 7948 120.67 - 127.37: 5933 127.37 - 134.07: 240 Bond angle restraints: 25264 Sorted by residual: angle pdb=" C04 P0T D 801 " pdb=" C07 P0T D 801 " pdb=" C09 P0T D 801 " ideal model delta sigma weight residual 125.00 117.98 7.02 3.00e+00 1.11e-01 5.48e+00 angle pdb=" C04 P0T B 801 " pdb=" C07 P0T B 801 " pdb=" C09 P0T B 801 " ideal model delta sigma weight residual 125.00 117.98 7.02 3.00e+00 1.11e-01 5.48e+00 angle pdb=" C04 P0T A 801 " pdb=" C07 P0T A 801 " pdb=" C09 P0T A 801 " ideal model delta sigma weight residual 125.00 117.98 7.02 3.00e+00 1.11e-01 5.48e+00 angle pdb=" C04 P0T C 801 " pdb=" C07 P0T C 801 " pdb=" C09 P0T C 801 " ideal model delta sigma weight residual 125.00 117.99 7.01 3.00e+00 1.11e-01 5.45e+00 angle pdb=" C GLY B 204 " pdb=" N THR B 205 " pdb=" CA THR B 205 " ideal model delta sigma weight residual 122.82 125.37 -2.55 1.42e+00 4.96e-01 3.22e+00 ... (remaining 25259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.93: 10400 29.93 - 59.86: 240 59.86 - 89.79: 24 89.79 - 119.71: 0 119.71 - 149.64: 4 Dihedral angle restraints: 10668 sinusoidal: 3688 harmonic: 6980 Sorted by residual: dihedral pdb=" C18 P0T D 801 " pdb=" C20 P0T D 801 " pdb=" C21 P0T D 801 " pdb=" C22 P0T D 801 " ideal model delta sinusoidal sigma weight residual 179.29 29.65 149.64 1 3.00e+01 1.11e-03 1.99e+01 dihedral pdb=" C18 P0T C 801 " pdb=" C20 P0T C 801 " pdb=" C21 P0T C 801 " pdb=" C22 P0T C 801 " ideal model delta sinusoidal sigma weight residual 179.29 29.68 149.61 1 3.00e+01 1.11e-03 1.99e+01 dihedral pdb=" C18 P0T B 801 " pdb=" C20 P0T B 801 " pdb=" C21 P0T B 801 " pdb=" C22 P0T B 801 " ideal model delta sinusoidal sigma weight residual 179.29 29.70 149.59 1 3.00e+01 1.11e-03 1.99e+01 ... (remaining 10665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 2944 0.100 - 0.200: 40 0.200 - 0.300: 0 0.300 - 0.400: 0 0.400 - 0.500: 4 Chirality restraints: 2988 Sorted by residual: chirality pdb=" C03 P0T B 801 " pdb=" C04 P0T B 801 " pdb=" C05 P0T B 801 " pdb=" C10 P0T B 801 " both_signs ideal model delta sigma weight residual False -2.55 -3.05 0.50 2.00e-01 2.50e+01 6.24e+00 chirality pdb=" C03 P0T D 801 " pdb=" C04 P0T D 801 " pdb=" C05 P0T D 801 " pdb=" C10 P0T D 801 " both_signs ideal model delta sigma weight residual False -2.55 -3.05 0.50 2.00e-01 2.50e+01 6.24e+00 chirality pdb=" C03 P0T A 801 " pdb=" C04 P0T A 801 " pdb=" C05 P0T A 801 " pdb=" C10 P0T A 801 " both_signs ideal model delta sigma weight residual False -2.55 -3.05 0.50 2.00e-01 2.50e+01 6.23e+00 ... (remaining 2985 not shown) Planarity restraints: 3096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 297 " -0.026 5.00e-02 4.00e+02 3.87e-02 2.39e+00 pdb=" N PRO B 298 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 298 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 298 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 297 " 0.026 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO D 298 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO D 298 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 298 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 297 " 0.026 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO A 298 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 298 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 298 " 0.022 5.00e-02 4.00e+02 ... (remaining 3093 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 4037 2.78 - 3.31: 17087 3.31 - 3.84: 28136 3.84 - 4.37: 30193 4.37 - 4.90: 54540 Nonbonded interactions: 133993 Sorted by model distance: nonbonded pdb=" OH TYR C 271 " pdb=" OE2 GLU C 288 " model vdw 2.256 2.440 nonbonded pdb=" OH TYR D 271 " pdb=" OE2 GLU D 288 " model vdw 2.256 2.440 nonbonded pdb=" OH TYR A 271 " pdb=" OE2 GLU A 288 " model vdw 2.256 2.440 nonbonded pdb=" OH TYR B 271 " pdb=" OE2 GLU B 288 " model vdw 2.257 2.440 nonbonded pdb=" O ARG D 197 " pdb=" NE2 GLN D 203 " model vdw 2.311 2.520 ... (remaining 133988 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 75 through 728 or resid 801)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.430 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 46.030 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.138 18512 Z= 0.317 Angle : 0.562 7.024 25264 Z= 0.285 Chirality : 0.041 0.500 2988 Planarity : 0.003 0.039 3096 Dihedral : 13.468 149.643 6148 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.18), residues: 2348 helix: 2.09 (0.14), residues: 1424 sheet: 1.41 (0.50), residues: 84 loop : -0.72 (0.21), residues: 840 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 2.353 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.2131 time to fit residues: 75.2031 Evaluate side-chains 166 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 2.228 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 3.9990 chunk 178 optimal weight: 30.0000 chunk 99 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 184 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 112 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 chunk 214 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 18512 Z= 0.352 Angle : 0.577 7.355 25264 Z= 0.296 Chirality : 0.039 0.132 2988 Planarity : 0.003 0.037 3096 Dihedral : 6.174 88.270 2572 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 2.53 % 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: 1.77 (0.18), residues: 2348 helix: 2.24 (0.14), residues: 1396 sheet: 1.62 (0.56), residues: 84 loop : -0.67 (0.21), residues: 868 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 169 time to evaluate : 2.415 Fit side-chains outliers start: 43 outliers final: 31 residues processed: 191 average time/residue: 0.2132 time to fit residues: 71.9885 Evaluate side-chains 181 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 150 time to evaluate : 2.312 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1639 time to fit residues: 12.6079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 178 optimal weight: 0.0980 chunk 145 optimal weight: 9.9990 chunk 59 optimal weight: 20.0000 chunk 214 optimal weight: 20.0000 chunk 231 optimal weight: 0.7980 chunk 191 optimal weight: 1.9990 chunk 212 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 18512 Z= 0.152 Angle : 0.455 7.274 25264 Z= 0.234 Chirality : 0.035 0.134 2988 Planarity : 0.003 0.034 3096 Dihedral : 4.871 54.080 2572 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 1.18 % 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: 2.15 (0.18), residues: 2348 helix: 2.59 (0.14), residues: 1392 sheet: 1.76 (0.56), residues: 84 loop : -0.59 (0.22), residues: 872 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 181 time to evaluate : 2.159 Fit side-chains outliers start: 20 outliers final: 7 residues processed: 194 average time/residue: 0.2050 time to fit residues: 70.8296 Evaluate side-chains 172 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 165 time to evaluate : 2.080 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1498 time to fit residues: 4.9410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 0.5980 chunk 161 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 228 optimal weight: 7.9990 chunk 112 optimal weight: 7.9990 chunk 204 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 18512 Z= 0.217 Angle : 0.491 7.268 25264 Z= 0.246 Chirality : 0.036 0.131 2988 Planarity : 0.003 0.033 3096 Dihedral : 4.266 43.167 2572 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 2.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.18), residues: 2348 helix: 2.65 (0.14), residues: 1396 sheet: 1.65 (0.56), residues: 84 loop : -0.57 (0.22), residues: 868 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 173 time to evaluate : 2.371 Fit side-chains outliers start: 39 outliers final: 27 residues processed: 194 average time/residue: 0.2215 time to fit residues: 75.2521 Evaluate side-chains 187 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 160 time to evaluate : 2.240 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1648 time to fit residues: 11.7027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 0.4980 chunk 129 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 194 optimal weight: 0.7980 chunk 157 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 116 optimal weight: 7.9990 chunk 204 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 18512 Z= 0.221 Angle : 0.491 7.204 25264 Z= 0.246 Chirality : 0.036 0.130 2988 Planarity : 0.003 0.032 3096 Dihedral : 4.264 43.307 2572 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 0.82 % 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: 2.25 (0.18), residues: 2348 helix: 2.66 (0.14), residues: 1396 sheet: 1.62 (0.56), residues: 84 loop : -0.53 (0.22), residues: 868 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 179 time to evaluate : 2.221 Fit side-chains outliers start: 14 outliers final: 0 residues processed: 188 average time/residue: 0.2158 time to fit residues: 71.2714 Evaluate side-chains 163 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 2.156 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 7.9990 chunk 205 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 228 optimal weight: 2.9990 chunk 189 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 119 optimal weight: 20.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 18512 Z= 0.179 Angle : 0.473 8.011 25264 Z= 0.235 Chirality : 0.036 0.129 2988 Planarity : 0.003 0.032 3096 Dihedral : 4.192 45.813 2572 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer Outliers : 1.71 % 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: 2.26 (0.18), residues: 2348 helix: 2.71 (0.14), residues: 1400 sheet: 1.64 (0.55), residues: 84 loop : -0.63 (0.22), residues: 864 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 179 time to evaluate : 2.187 Fit side-chains outliers start: 29 outliers final: 13 residues processed: 192 average time/residue: 0.2162 time to fit residues: 73.1010 Evaluate side-chains 181 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 168 time to evaluate : 2.288 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1626 time to fit residues: 6.8758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 166 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 192 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 227 optimal weight: 4.9990 chunk 142 optimal weight: 7.9990 chunk 138 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 18512 Z= 0.231 Angle : 0.496 7.784 25264 Z= 0.248 Chirality : 0.036 0.139 2988 Planarity : 0.003 0.032 3096 Dihedral : 4.281 46.022 2572 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer Outliers : 1.47 % 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: 2.21 (0.18), residues: 2348 helix: 2.67 (0.14), residues: 1400 sheet: 1.57 (0.54), residues: 84 loop : -0.65 (0.22), residues: 864 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 183 time to evaluate : 2.374 Fit side-chains outliers start: 25 outliers final: 9 residues processed: 197 average time/residue: 0.2151 time to fit residues: 74.9447 Evaluate side-chains 169 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 160 time to evaluate : 2.360 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1631 time to fit residues: 5.7674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 144 optimal weight: 6.9990 chunk 154 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 178 optimal weight: 8.9990 chunk 206 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 18512 Z= 0.189 Angle : 0.486 9.640 25264 Z= 0.240 Chirality : 0.036 0.137 2988 Planarity : 0.003 0.032 3096 Dihedral : 4.246 48.604 2572 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 0.76 % 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: 2.20 (0.18), residues: 2348 helix: 2.69 (0.14), residues: 1396 sheet: 1.58 (0.55), residues: 84 loop : -0.68 (0.22), residues: 868 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 174 time to evaluate : 2.285 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 187 average time/residue: 0.2202 time to fit residues: 73.2435 Evaluate side-chains 164 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 159 time to evaluate : 2.108 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1558 time to fit residues: 4.2694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 6.9990 chunk 198 optimal weight: 5.9990 chunk 211 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 166 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 191 optimal weight: 0.9990 chunk 200 optimal weight: 6.9990 chunk 139 optimal weight: 9.9990 chunk 224 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 18512 Z= 0.192 Angle : 0.491 8.901 25264 Z= 0.242 Chirality : 0.036 0.142 2988 Planarity : 0.003 0.032 3096 Dihedral : 4.217 48.341 2572 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 0.41 % 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: 2.20 (0.18), residues: 2348 helix: 2.69 (0.14), residues: 1396 sheet: 1.60 (0.55), residues: 84 loop : -0.69 (0.22), residues: 868 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 177 time to evaluate : 2.265 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 184 average time/residue: 0.2155 time to fit residues: 70.2017 Evaluate side-chains 167 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 163 time to evaluate : 2.229 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1603 time to fit residues: 3.9885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 235 optimal weight: 3.9990 chunk 216 optimal weight: 1.9990 chunk 187 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 114 optimal weight: 0.4980 chunk 148 optimal weight: 0.6980 chunk 199 optimal weight: 5.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 18512 Z= 0.170 Angle : 0.482 8.914 25264 Z= 0.238 Chirality : 0.036 0.160 2988 Planarity : 0.003 0.032 3096 Dihedral : 4.177 49.408 2572 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 0.59 % 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: 2.27 (0.18), residues: 2348 helix: 2.72 (0.14), residues: 1396 sheet: 1.62 (0.55), residues: 84 loop : -0.61 (0.22), residues: 868 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 177 time to evaluate : 2.135 Fit side-chains outliers start: 10 outliers final: 1 residues processed: 183 average time/residue: 0.2185 time to fit residues: 70.2274 Evaluate side-chains 172 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 2.203 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1644 time to fit residues: 3.2613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 9.9990 chunk 172 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 187 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 192 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 164 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.092002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.077439 restraints weight = 57881.114| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 3.44 r_work: 0.3292 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 18512 Z= 0.157 Angle : 0.480 8.897 25264 Z= 0.234 Chirality : 0.036 0.148 2988 Planarity : 0.003 0.032 3096 Dihedral : 4.110 50.287 2572 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.18), residues: 2348 helix: 2.76 (0.14), residues: 1392 sheet: 1.65 (0.54), residues: 84 loop : -0.62 (0.22), residues: 872 =============================================================================== Job complete usr+sys time: 3049.10 seconds wall clock time: 56 minutes 33.38 seconds (3393.38 seconds total)