Starting phenix.real_space_refine on Fri Sep 27 11:37:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vca_8659/09_2024/5vca_8659.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vca_8659/09_2024/5vca_8659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vca_8659/09_2024/5vca_8659.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vca_8659/09_2024/5vca_8659.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vca_8659/09_2024/5vca_8659.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vca_8659/09_2024/5vca_8659.cif" } resolution = 4.8 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= -0.000 sd= 0.027 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: 3 Type Number sf(0) Gaussians C 9558 2.51 5 N 3264 2.21 5 O 3258 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-5461/modules/chem_data/mon_lib" Total number of atoms: 16080 Number of models: 1 Model: "" Number of chains: 6 Chain: "P" Number of atoms: 2680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 2680 Classifications: {'peptide': 544} Incomplete info: {'truncation_to_alanine': 466} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 508} Unresolved chain link angles: 35 Unresolved non-hydrogen bonds: 1645 Unresolved non-hydrogen angles: 2084 Unresolved non-hydrogen dihedrals: 1332 Unresolved non-hydrogen chiralities: 161 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 33, 'TYR:plan': 12, 'ASN:plan1': 21, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 16, 'GLU:plan': 55, 'ARG:plan': 37} Unresolved non-hydrogen planarities: 826 Chain: "M" Number of atoms: 2680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 2680 Classifications: {'peptide': 544} Incomplete info: {'truncation_to_alanine': 466} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 508} Unresolved chain link angles: 35 Unresolved non-hydrogen bonds: 1645 Unresolved non-hydrogen angles: 2084 Unresolved non-hydrogen dihedrals: 1332 Unresolved non-hydrogen chiralities: 161 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 33, 'TYR:plan': 12, 'ASN:plan1': 21, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 16, 'GLU:plan': 55, 'ARG:plan': 37} Unresolved non-hydrogen planarities: 826 Chain: "N" Number of atoms: 2680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 2680 Classifications: {'peptide': 544} Incomplete info: {'truncation_to_alanine': 466} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 508} Unresolved chain link angles: 35 Unresolved non-hydrogen bonds: 1645 Unresolved non-hydrogen angles: 2084 Unresolved non-hydrogen dihedrals: 1332 Unresolved non-hydrogen chiralities: 161 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 33, 'TYR:plan': 12, 'ASN:plan1': 21, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 16, 'GLU:plan': 55, 'ARG:plan': 37} Unresolved non-hydrogen planarities: 826 Chain: "O" Number of atoms: 2680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 2680 Classifications: {'peptide': 544} Incomplete info: {'truncation_to_alanine': 466} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 508} Unresolved chain link angles: 35 Unresolved non-hydrogen bonds: 1645 Unresolved non-hydrogen angles: 2084 Unresolved non-hydrogen dihedrals: 1332 Unresolved non-hydrogen chiralities: 161 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 33, 'TYR:plan': 12, 'ASN:plan1': 21, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 16, 'GLU:plan': 55, 'ARG:plan': 37} Unresolved non-hydrogen planarities: 826 Chain: "Q" Number of atoms: 2680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 2680 Classifications: {'peptide': 544} Incomplete info: {'truncation_to_alanine': 466} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 508} Unresolved chain link angles: 35 Unresolved non-hydrogen bonds: 1645 Unresolved non-hydrogen angles: 2084 Unresolved non-hydrogen dihedrals: 1332 Unresolved non-hydrogen chiralities: 161 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 33, 'TYR:plan': 12, 'ASN:plan1': 21, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 16, 'GLU:plan': 55, 'ARG:plan': 37} Unresolved non-hydrogen planarities: 826 Chain: "R" Number of atoms: 2680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 2680 Classifications: {'peptide': 544} Incomplete info: {'truncation_to_alanine': 466} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 508} Unresolved chain link angles: 35 Unresolved non-hydrogen bonds: 1645 Unresolved non-hydrogen angles: 2084 Unresolved non-hydrogen dihedrals: 1332 Unresolved non-hydrogen chiralities: 161 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 33, 'TYR:plan': 12, 'ASN:plan1': 21, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 16, 'GLU:plan': 55, 'ARG:plan': 37} Unresolved non-hydrogen planarities: 826 Time building chain proxies: 10.83, per 1000 atoms: 0.67 Number of scatterers: 16080 At special positions: 0 Unit cell: (140.65, 139.2, 105.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 3258 8.00 N 3264 7.00 C 9558 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: 5.11 Conformation dependent library (CDL) restraints added in 3.3 seconds 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6060 Finding SS restraints... Secondary structure from input PDB file: 175 helices and 13 sheets defined 58.2% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.37 Creating SS restraints... Processing helix chain 'P' and resid 188 through 193 removed outlier: 4.340A pdb=" N ILE P 192 " --> pdb=" O SER P 188 " (cutoff:3.500A) Processing helix chain 'P' and resid 195 through 206 removed outlier: 3.664A pdb=" N LYS P 201 " --> pdb=" O GLU P 197 " (cutoff:3.500A) Processing helix chain 'P' and resid 206 through 212 Processing helix chain 'P' and resid 213 through 219 Processing helix chain 'P' and resid 236 through 249 removed outlier: 3.544A pdb=" N ALA P 241 " --> pdb=" O LYS P 237 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN P 246 " --> pdb=" O ARG P 242 " (cutoff:3.500A) Processing helix chain 'P' and resid 256 through 261 Processing helix chain 'P' and resid 266 through 283 removed outlier: 3.799A pdb=" N GLN P 270 " --> pdb=" O GLY P 266 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS P 271 " --> pdb=" O GLN P 267 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU P 272 " --> pdb=" O SER P 268 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG P 273 " --> pdb=" O GLU P 269 " (cutoff:3.500A) Processing helix chain 'P' and resid 291 through 296 Processing helix chain 'P' and resid 304 through 320 Processing helix chain 'P' and resid 340 through 345 removed outlier: 3.620A pdb=" N ARG P 344 " --> pdb=" O ASP P 340 " (cutoff:3.500A) Processing helix chain 'P' and resid 359 through 372 removed outlier: 3.628A pdb=" N LYS P 364 " --> pdb=" O ARG P 360 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU P 365 " --> pdb=" O ASN P 361 " (cutoff:3.500A) Processing helix chain 'P' and resid 380 through 393 Processing helix chain 'P' and resid 398 through 417 Processing helix chain 'P' and resid 417 through 422 Processing helix chain 'P' and resid 438 through 447 removed outlier: 3.813A pdb=" N PHE P 442 " --> pdb=" O THR P 438 " (cutoff:3.500A) Processing helix chain 'P' and resid 465 through 469 Processing helix chain 'P' and resid 472 through 489 removed outlier: 3.508A pdb=" N LEU P 485 " --> pdb=" O GLU P 481 " (cutoff:3.500A) Proline residue: P 486 - end of helix Processing helix chain 'P' and resid 490 through 497 Processing helix chain 'P' and resid 513 through 525 Processing helix chain 'P' and resid 533 through 540 Processing helix chain 'P' and resid 546 through 560 Processing helix chain 'P' and resid 568 through 573 Processing helix chain 'P' and resid 583 through 598 removed outlier: 4.032A pdb=" N ASN P 590 " --> pdb=" O GLU P 586 " (cutoff:3.500A) Processing helix chain 'P' and resid 613 through 617 Processing helix chain 'P' and resid 618 through 623 Processing helix chain 'P' and resid 637 through 649 removed outlier: 3.600A pdb=" N LEU P 642 " --> pdb=" O LYS P 638 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER P 643 " --> pdb=" O GLU P 639 " (cutoff:3.500A) Processing helix chain 'P' and resid 659 through 667 removed outlier: 3.649A pdb=" N ILE P 663 " --> pdb=" O ASP P 659 " (cutoff:3.500A) Processing helix chain 'P' and resid 671 through 690 removed outlier: 3.674A pdb=" N LEU P 675 " --> pdb=" O VAL P 671 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG P 688 " --> pdb=" O MET P 684 " (cutoff:3.500A) Processing helix chain 'P' and resid 697 through 706 removed outlier: 3.671A pdb=" N ALA P 704 " --> pdb=" O ASN P 700 " (cutoff:3.500A) Processing helix chain 'P' and resid 713 through 724 removed outlier: 3.574A pdb=" N LYS P 718 " --> pdb=" O GLU P 714 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 206 Processing helix chain 'M' and resid 206 through 212 removed outlier: 3.595A pdb=" N LEU M 210 " --> pdb=" O ILE M 206 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HIS M 212 " --> pdb=" O LEU M 208 " (cutoff:3.500A) Processing helix chain 'M' and resid 213 through 219 Processing helix chain 'M' and resid 236 through 243 Processing helix chain 'M' and resid 256 through 261 removed outlier: 3.664A pdb=" N MET M 261 " --> pdb=" O GLY M 257 " (cutoff:3.500A) Processing helix chain 'M' and resid 267 through 283 removed outlier: 3.576A pdb=" N LEU M 272 " --> pdb=" O SER M 268 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR M 282 " --> pdb=" O LYS M 278 " (cutoff:3.500A) Processing helix chain 'M' and resid 304 through 320 Processing helix chain 'M' and resid 340 through 345 Processing helix chain 'M' and resid 359 through 371 removed outlier: 3.685A pdb=" N LYS M 364 " --> pdb=" O ARG M 360 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU M 365 " --> pdb=" O ASN M 361 " (cutoff:3.500A) Processing helix chain 'M' and resid 380 through 394 Processing helix chain 'M' and resid 398 through 417 Processing helix chain 'M' and resid 417 through 422 removed outlier: 4.411A pdb=" N ASP M 422 " --> pdb=" O LEU M 418 " (cutoff:3.500A) Processing helix chain 'M' and resid 438 through 446 removed outlier: 3.915A pdb=" N PHE M 442 " --> pdb=" O THR M 438 " (cutoff:3.500A) Processing helix chain 'M' and resid 465 through 469 Processing helix chain 'M' and resid 472 through 489 Proline residue: M 486 - end of helix Processing helix chain 'M' and resid 489 through 497 removed outlier: 4.274A pdb=" N PHE M 493 " --> pdb=" O LYS M 489 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU M 496 " --> pdb=" O VAL M 492 " (cutoff:3.500A) Processing helix chain 'M' and resid 513 through 525 Processing helix chain 'M' and resid 533 through 540 Processing helix chain 'M' and resid 546 through 560 removed outlier: 3.613A pdb=" N PHE M 553 " --> pdb=" O ILE M 549 " (cutoff:3.500A) Processing helix chain 'M' and resid 568 through 573 removed outlier: 3.619A pdb=" N ILE M 572 " --> pdb=" O GLU M 568 " (cutoff:3.500A) Processing helix chain 'M' and resid 583 through 598 removed outlier: 3.815A pdb=" N ASN M 590 " --> pdb=" O GLU M 586 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN M 591 " --> pdb=" O ARG M 587 " (cutoff:3.500A) Processing helix chain 'M' and resid 613 through 617 Processing helix chain 'M' and resid 618 through 623 Processing helix chain 'M' and resid 637 through 650 removed outlier: 3.731A pdb=" N SER M 643 " --> pdb=" O GLU M 639 " (cutoff:3.500A) Processing helix chain 'M' and resid 659 through 665 removed outlier: 3.640A pdb=" N ILE M 663 " --> pdb=" O ASP M 659 " (cutoff:3.500A) Processing helix chain 'M' and resid 671 through 690 Processing helix chain 'M' and resid 697 through 706 removed outlier: 3.872A pdb=" N ALA M 704 " --> pdb=" O ASN M 700 " (cutoff:3.500A) Processing helix chain 'M' and resid 713 through 724 Processing helix chain 'N' and resid 195 through 206 removed outlier: 3.606A pdb=" N LYS N 201 " --> pdb=" O GLU N 197 " (cutoff:3.500A) Processing helix chain 'N' and resid 206 through 212 removed outlier: 3.544A pdb=" N LEU N 210 " --> pdb=" O ILE N 206 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS N 212 " --> pdb=" O LEU N 208 " (cutoff:3.500A) Processing helix chain 'N' and resid 213 through 219 Processing helix chain 'N' and resid 236 through 246 removed outlier: 3.558A pdb=" N VAL N 244 " --> pdb=" O ILE N 240 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASN N 246 " --> pdb=" O ARG N 242 " (cutoff:3.500A) Processing helix chain 'N' and resid 256 through 261 removed outlier: 3.519A pdb=" N ILE N 260 " --> pdb=" O ASN N 256 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET N 261 " --> pdb=" O GLY N 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 256 through 261' Processing helix chain 'N' and resid 267 through 283 removed outlier: 3.745A pdb=" N LEU N 272 " --> pdb=" O SER N 268 " (cutoff:3.500A) Processing helix chain 'N' and resid 304 through 320 Processing helix chain 'N' and resid 340 through 345 removed outlier: 3.814A pdb=" N ARG N 344 " --> pdb=" O ASP N 340 " (cutoff:3.500A) Processing helix chain 'N' and resid 359 through 372 removed outlier: 4.014A pdb=" N LYS N 364 " --> pdb=" O ARG N 360 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU N 365 " --> pdb=" O ASN N 361 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG N 372 " --> pdb=" O MET N 368 " (cutoff:3.500A) Processing helix chain 'N' and resid 380 through 393 Processing helix chain 'N' and resid 398 through 417 Processing helix chain 'N' and resid 417 through 422 Processing helix chain 'N' and resid 438 through 447 removed outlier: 3.550A pdb=" N LYS N 447 " --> pdb=" O LYS N 443 " (cutoff:3.500A) Processing helix chain 'N' and resid 465 through 469 Processing helix chain 'N' and resid 472 through 489 Proline residue: N 486 - end of helix Processing helix chain 'N' and resid 489 through 497 Processing helix chain 'N' and resid 513 through 525 removed outlier: 3.574A pdb=" N LEU N 517 " --> pdb=" O GLY N 513 " (cutoff:3.500A) Processing helix chain 'N' and resid 534 through 540 Processing helix chain 'N' and resid 546 through 560 Processing helix chain 'N' and resid 568 through 573 Processing helix chain 'N' and resid 583 through 597 removed outlier: 3.515A pdb=" N ASN N 590 " --> pdb=" O GLU N 586 " (cutoff:3.500A) Processing helix chain 'N' and resid 613 through 617 removed outlier: 3.692A pdb=" N ILE N 616 " --> pdb=" O ARG N 613 " (cutoff:3.500A) Processing helix chain 'N' and resid 618 through 623 Processing helix chain 'N' and resid 637 through 650 removed outlier: 3.701A pdb=" N SER N 643 " --> pdb=" O GLU N 639 " (cutoff:3.500A) Processing helix chain 'N' and resid 659 through 667 removed outlier: 3.644A pdb=" N ILE N 663 " --> pdb=" O ASP N 659 " (cutoff:3.500A) Processing helix chain 'N' and resid 671 through 690 Processing helix chain 'N' and resid 697 through 706 removed outlier: 3.831A pdb=" N ALA N 704 " --> pdb=" O ASN N 700 " (cutoff:3.500A) Processing helix chain 'N' and resid 713 through 724 Processing helix chain 'O' and resid 195 through 206 Processing helix chain 'O' and resid 206 through 212 removed outlier: 3.658A pdb=" N LEU O 210 " --> pdb=" O ILE O 206 " (cutoff:3.500A) Processing helix chain 'O' and resid 213 through 219 Processing helix chain 'O' and resid 236 through 243 removed outlier: 3.617A pdb=" N ALA O 241 " --> pdb=" O LYS O 237 " (cutoff:3.500A) Processing helix chain 'O' and resid 256 through 261 removed outlier: 3.808A pdb=" N ILE O 260 " --> pdb=" O ASN O 256 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET O 261 " --> pdb=" O GLY O 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 256 through 261' Processing helix chain 'O' and resid 266 through 283 removed outlier: 4.166A pdb=" N GLN O 270 " --> pdb=" O GLY O 266 " (cutoff:3.500A) Processing helix chain 'O' and resid 304 through 320 Processing helix chain 'O' and resid 340 through 345 Processing helix chain 'O' and resid 359 through 372 removed outlier: 4.069A pdb=" N LYS O 364 " --> pdb=" O ARG O 360 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLU O 365 " --> pdb=" O ASN O 361 " (cutoff:3.500A) Processing helix chain 'O' and resid 380 through 393 Processing helix chain 'O' and resid 398 through 417 Processing helix chain 'O' and resid 417 through 422 Processing helix chain 'O' and resid 438 through 447 removed outlier: 3.794A pdb=" N PHE O 442 " --> pdb=" O THR O 438 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS O 447 " --> pdb=" O LYS O 443 " (cutoff:3.500A) Processing helix chain 'O' and resid 465 through 469 Processing helix chain 'O' and resid 472 through 489 Proline residue: O 486 - end of helix Processing helix chain 'O' and resid 489 through 497 removed outlier: 3.843A pdb=" N PHE O 493 " --> pdb=" O LYS O 489 " (cutoff:3.500A) Processing helix chain 'O' and resid 513 through 525 removed outlier: 3.719A pdb=" N LEU O 517 " --> pdb=" O GLY O 513 " (cutoff:3.500A) Processing helix chain 'O' and resid 533 through 539 Processing helix chain 'O' and resid 546 through 560 Processing helix chain 'O' and resid 568 through 573 Processing helix chain 'O' and resid 582 through 598 removed outlier: 3.862A pdb=" N ASN O 590 " --> pdb=" O GLU O 586 " (cutoff:3.500A) Processing helix chain 'O' and resid 613 through 617 Processing helix chain 'O' and resid 618 through 623 Processing helix chain 'O' and resid 637 through 650 removed outlier: 3.506A pdb=" N SER O 643 " --> pdb=" O GLU O 639 " (cutoff:3.500A) Processing helix chain 'O' and resid 659 through 667 removed outlier: 3.894A pdb=" N ILE O 663 " --> pdb=" O ASP O 659 " (cutoff:3.500A) Processing helix chain 'O' and resid 671 through 690 removed outlier: 3.502A pdb=" N GLY O 683 " --> pdb=" O CYS O 679 " (cutoff:3.500A) Processing helix chain 'O' and resid 697 through 706 removed outlier: 3.771A pdb=" N ALA O 704 " --> pdb=" O ASN O 700 " (cutoff:3.500A) Processing helix chain 'O' and resid 713 through 724 Processing helix chain 'Q' and resid 188 through 192 Processing helix chain 'Q' and resid 195 through 206 Processing helix chain 'Q' and resid 206 through 212 removed outlier: 3.592A pdb=" N LEU Q 210 " --> pdb=" O ILE Q 206 " (cutoff:3.500A) Processing helix chain 'Q' and resid 213 through 219 Processing helix chain 'Q' and resid 236 through 243 Processing helix chain 'Q' and resid 243 through 249 Processing helix chain 'Q' and resid 256 through 261 removed outlier: 3.724A pdb=" N ILE Q 260 " --> pdb=" O ASN Q 256 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N MET Q 261 " --> pdb=" O GLY Q 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 256 through 261' Processing helix chain 'Q' and resid 267 through 282 removed outlier: 3.689A pdb=" N LYS Q 271 " --> pdb=" O GLN Q 267 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU Q 272 " --> pdb=" O SER Q 268 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG Q 273 " --> pdb=" O GLU Q 269 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS Q 278 " --> pdb=" O GLU Q 274 " (cutoff:3.500A) Processing helix chain 'Q' and resid 291 through 296 removed outlier: 3.861A pdb=" N ILE Q 295 " --> pdb=" O GLU Q 291 " (cutoff:3.500A) Processing helix chain 'Q' and resid 304 through 321 removed outlier: 3.934A pdb=" N MET Q 321 " --> pdb=" O LEU Q 317 " (cutoff:3.500A) Processing helix chain 'Q' and resid 335 through 339 removed outlier: 3.555A pdb=" N ILE Q 339 " --> pdb=" O ILE Q 336 " (cutoff:3.500A) Processing helix chain 'Q' and resid 340 through 345 Processing helix chain 'Q' and resid 359 through 374 removed outlier: 4.145A pdb=" N LYS Q 364 " --> pdb=" O ARG Q 360 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLU Q 365 " --> pdb=" O ASN Q 361 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASN Q 373 " --> pdb=" O ILE Q 369 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET Q 374 " --> pdb=" O HIS Q 370 " (cutoff:3.500A) Processing helix chain 'Q' and resid 380 through 393 Processing helix chain 'Q' and resid 398 through 417 removed outlier: 3.605A pdb=" N ARG Q 416 " --> pdb=" O ASN Q 412 " (cutoff:3.500A) Processing helix chain 'Q' and resid 417 through 422 Processing helix chain 'Q' and resid 438 through 447 removed outlier: 3.514A pdb=" N PHE Q 442 " --> pdb=" O THR Q 438 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS Q 447 " --> pdb=" O LYS Q 443 " (cutoff:3.500A) Processing helix chain 'Q' and resid 465 through 469 Processing helix chain 'Q' and resid 472 through 489 Proline residue: Q 486 - end of helix Processing helix chain 'Q' and resid 489 through 497 removed outlier: 3.779A pdb=" N PHE Q 493 " --> pdb=" O LYS Q 489 " (cutoff:3.500A) Processing helix chain 'Q' and resid 513 through 525 removed outlier: 4.156A pdb=" N LEU Q 517 " --> pdb=" O GLY Q 513 " (cutoff:3.500A) Processing helix chain 'Q' and resid 533 through 539 Processing helix chain 'Q' and resid 546 through 560 removed outlier: 3.771A pdb=" N PHE Q 553 " --> pdb=" O ILE Q 549 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS Q 554 " --> pdb=" O ARG Q 550 " (cutoff:3.500A) Processing helix chain 'Q' and resid 568 through 573 Processing helix chain 'Q' and resid 583 through 598 removed outlier: 4.052A pdb=" N ASN Q 590 " --> pdb=" O GLU Q 586 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN Q 591 " --> pdb=" O ARG Q 587 " (cutoff:3.500A) Processing helix chain 'Q' and resid 613 through 617 Processing helix chain 'Q' and resid 618 through 623 Processing helix chain 'Q' and resid 637 through 650 removed outlier: 3.715A pdb=" N SER Q 643 " --> pdb=" O GLU Q 639 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS Q 646 " --> pdb=" O LEU Q 642 " (cutoff:3.500A) Processing helix chain 'Q' and resid 659 through 667 removed outlier: 3.623A pdb=" N ILE Q 663 " --> pdb=" O ASP Q 659 " (cutoff:3.500A) Processing helix chain 'Q' and resid 671 through 690 Processing helix chain 'Q' and resid 697 through 706 removed outlier: 3.821A pdb=" N ALA Q 704 " --> pdb=" O ASN Q 700 " (cutoff:3.500A) Processing helix chain 'Q' and resid 713 through 724 Processing helix chain 'R' and resid 195 through 206 Processing helix chain 'R' and resid 206 through 212 removed outlier: 3.587A pdb=" N LEU R 210 " --> pdb=" O ILE R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 219 Processing helix chain 'R' and resid 236 through 243 removed outlier: 3.569A pdb=" N ALA R 241 " --> pdb=" O LYS R 237 " (cutoff:3.500A) Processing helix chain 'R' and resid 244 through 248 Processing helix chain 'R' and resid 256 through 261 removed outlier: 3.605A pdb=" N MET R 261 " --> pdb=" O GLY R 257 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 282 removed outlier: 3.784A pdb=" N LYS R 271 " --> pdb=" O GLN R 267 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU R 272 " --> pdb=" O SER R 268 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR R 282 " --> pdb=" O LYS R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 320 Processing helix chain 'R' and resid 340 through 345 Processing helix chain 'R' and resid 359 through 372 removed outlier: 3.682A pdb=" N LYS R 364 " --> pdb=" O ARG R 360 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU R 365 " --> pdb=" O ASN R 361 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG R 372 " --> pdb=" O MET R 368 " (cutoff:3.500A) Processing helix chain 'R' and resid 380 through 393 removed outlier: 3.961A pdb=" N TYR R 393 " --> pdb=" O GLU R 389 " (cutoff:3.500A) Processing helix chain 'R' and resid 398 through 417 Processing helix chain 'R' and resid 417 through 422 Processing helix chain 'R' and resid 438 through 447 removed outlier: 3.607A pdb=" N PHE R 442 " --> pdb=" O THR R 438 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS R 447 " --> pdb=" O LYS R 443 " (cutoff:3.500A) Processing helix chain 'R' and resid 465 through 469 Processing helix chain 'R' and resid 472 through 489 Proline residue: R 486 - end of helix Processing helix chain 'R' and resid 489 through 497 removed outlier: 3.793A pdb=" N PHE R 493 " --> pdb=" O LYS R 489 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU R 496 " --> pdb=" O VAL R 492 " (cutoff:3.500A) Processing helix chain 'R' and resid 513 through 525 Processing helix chain 'R' and resid 534 through 539 removed outlier: 3.518A pdb=" N SER R 539 " --> pdb=" O PRO R 535 " (cutoff:3.500A) Processing helix chain 'R' and resid 546 through 560 removed outlier: 3.573A pdb=" N ARG R 550 " --> pdb=" O GLU R 546 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE R 553 " --> pdb=" O ILE R 549 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS R 554 " --> pdb=" O ARG R 550 " (cutoff:3.500A) Processing helix chain 'R' and resid 568 through 573 Processing helix chain 'R' and resid 583 through 598 removed outlier: 3.608A pdb=" N ASN R 590 " --> pdb=" O GLU R 586 " (cutoff:3.500A) Processing helix chain 'R' and resid 613 through 617 Processing helix chain 'R' and resid 618 through 623 Processing helix chain 'R' and resid 637 through 649 Processing helix chain 'R' and resid 660 through 667 Processing helix chain 'R' and resid 671 through 690 Processing helix chain 'R' and resid 697 through 706 removed outlier: 4.347A pdb=" N ALA R 704 " --> pdb=" O ASN R 700 " (cutoff:3.500A) Processing helix chain 'R' and resid 713 through 724 removed outlier: 3.542A pdb=" N ILE R 717 " --> pdb=" O ASP R 713 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'P' and resid 251 through 254 removed outlier: 5.723A pdb=" N ASN P 251 " --> pdb=" O ILE P 286 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N PHE P 288 " --> pdb=" O ASN P 251 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU P 253 " --> pdb=" O PHE P 288 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N SER P 285 " --> pdb=" O ILE P 328 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ILE P 330 " --> pdb=" O SER P 285 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE P 287 " --> pdb=" O ILE P 330 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N ALA P 332 " --> pdb=" O ILE P 287 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR P 333 " --> pdb=" O LEU P 229 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG P 351 " --> pdb=" O GLY P 226 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE P 228 " --> pdb=" O ARG P 351 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE P 353 " --> pdb=" O ILE P 228 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 504 through 507 Processing sheet with id=AA3, first strand: chain 'P' and resid 528 through 531 removed outlier: 6.461A pdb=" N ASN P 528 " --> pdb=" O ILE P 563 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N PHE P 565 " --> pdb=" O ASN P 528 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ILE P 530 " --> pdb=" O PHE P 565 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ASP P 567 " --> pdb=" O ILE P 530 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA P 562 " --> pdb=" O VAL P 606 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ILE P 608 " --> pdb=" O ALA P 562 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL P 564 " --> pdb=" O ILE P 608 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ALA P 610 " --> pdb=" O VAL P 564 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU P 566 " --> pdb=" O ALA P 610 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'M' and resid 251 through 254 removed outlier: 5.665A pdb=" N ASN M 251 " --> pdb=" O ILE M 286 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE M 288 " --> pdb=" O ASN M 251 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU M 253 " --> pdb=" O PHE M 288 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ILE M 228 " --> pdb=" O ILE M 353 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 528 through 531 removed outlier: 6.285A pdb=" N PHE M 504 " --> pdb=" O GLY M 609 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS M 629 " --> pdb=" O GLY M 503 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 253 through 254 removed outlier: 5.362A pdb=" N LEU N 253 " --> pdb=" O PHE N 288 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE N 330 " --> pdb=" O ILE N 287 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ILE N 228 " --> pdb=" O ILE N 353 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 528 through 533 removed outlier: 6.238A pdb=" N ASN N 528 " --> pdb=" O ILE N 563 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N PHE N 565 " --> pdb=" O ASN N 528 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ILE N 530 " --> pdb=" O PHE N 565 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ASP N 567 " --> pdb=" O ILE N 530 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE N 532 " --> pdb=" O ASP N 567 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 251 through 254 removed outlier: 6.563A pdb=" N ASN O 251 " --> pdb=" O ILE O 286 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N PHE O 288 " --> pdb=" O ASN O 251 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU O 253 " --> pdb=" O PHE O 288 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N SER O 285 " --> pdb=" O ILE O 328 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ILE O 330 " --> pdb=" O SER O 285 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE O 287 " --> pdb=" O ILE O 330 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N ALA O 332 " --> pdb=" O ILE O 287 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'O' and resid 529 through 531 removed outlier: 6.257A pdb=" N PHE O 504 " --> pdb=" O GLY O 609 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N THR O 611 " --> pdb=" O PHE O 504 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LEU O 506 " --> pdb=" O THR O 611 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Q' and resid 251 through 254 removed outlier: 5.649A pdb=" N ASN Q 251 " --> pdb=" O ILE Q 286 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N PHE Q 288 " --> pdb=" O ASN Q 251 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LEU Q 253 " --> pdb=" O PHE Q 288 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ILE Q 228 " --> pdb=" O ILE Q 353 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Q' and resid 528 through 531 removed outlier: 7.881A pdb=" N ILE Q 608 " --> pdb=" O ALA Q 562 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL Q 564 " --> pdb=" O ILE Q 608 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ALA Q 610 " --> pdb=" O VAL Q 564 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU Q 566 " --> pdb=" O ALA Q 610 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE Q 504 " --> pdb=" O GLY Q 609 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N THR Q 611 " --> pdb=" O PHE Q 504 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LEU Q 506 " --> pdb=" O THR Q 611 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS Q 629 " --> pdb=" O GLY Q 503 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 251 through 254 removed outlier: 5.752A pdb=" N SER R 285 " --> pdb=" O ILE R 328 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ILE R 330 " --> pdb=" O SER R 285 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ILE R 287 " --> pdb=" O ILE R 330 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ALA R 332 " --> pdb=" O ILE R 287 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLY R 226 " --> pdb=" O ARG R 351 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ILE R 353 " --> pdb=" O GLY R 226 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ILE R 228 " --> pdb=" O ILE R 353 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 528 through 533 removed outlier: 3.971A pdb=" N ASP R 567 " --> pdb=" O ILE R 532 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE R 504 " --> pdb=" O GLY R 609 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N THR R 611 " --> pdb=" O PHE R 504 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU R 506 " --> pdb=" O THR R 611 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU R 505 " --> pdb=" O ILE R 631 " (cutoff:3.500A) 1162 hydrogen bonds defined for protein. 3318 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: 5.36 Time building geometry restraints manager: 5.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.28: 3258 1.28 - 1.35: 2580 1.35 - 1.43: 1235 1.43 - 1.50: 5383 1.50 - 1.58: 3618 Bond restraints: 16074 Sorted by residual: bond pdb=" CA SER Q 531 " pdb=" C SER Q 531 " ideal model delta sigma weight residual 1.520 1.451 0.069 1.17e-02 7.31e+03 3.48e+01 bond pdb=" CA GLY P 331 " pdb=" C GLY P 331 " ideal model delta sigma weight residual 1.511 1.448 0.063 1.10e-02 8.26e+03 3.29e+01 bond pdb=" CA ASN O 612 " pdb=" C ASN O 612 " ideal model delta sigma weight residual 1.525 1.468 0.057 1.02e-02 9.61e+03 3.16e+01 bond pdb=" CA ILE P 289 " pdb=" C ILE P 289 " ideal model delta sigma weight residual 1.522 1.451 0.071 1.26e-02 6.30e+03 3.15e+01 bond pdb=" CA ASN N 256 " pdb=" C ASN N 256 " ideal model delta sigma weight residual 1.521 1.454 0.067 1.20e-02 6.94e+03 3.09e+01 ... (remaining 16069 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.39: 18644 3.39 - 6.78: 3156 6.78 - 10.17: 478 10.17 - 13.57: 65 13.57 - 16.96: 13 Bond angle restraints: 22356 Sorted by residual: angle pdb=" N ASP O 319 " pdb=" CA ASP O 319 " pdb=" C ASP O 319 " ideal model delta sigma weight residual 111.28 124.28 -13.00 1.09e+00 8.42e-01 1.42e+02 angle pdb=" N ASP R 319 " pdb=" CA ASP R 319 " pdb=" C ASP R 319 " ideal model delta sigma weight residual 111.28 122.23 -10.95 1.09e+00 8.42e-01 1.01e+02 angle pdb=" N LEU P 376 " pdb=" CA LEU P 376 " pdb=" C LEU P 376 " ideal model delta sigma weight residual 114.75 102.71 12.04 1.26e+00 6.30e-01 9.14e+01 angle pdb=" N ILE R 633 " pdb=" CA ILE R 633 " pdb=" C ILE R 633 " ideal model delta sigma weight residual 108.15 98.92 9.23 9.90e-01 1.02e+00 8.69e+01 angle pdb=" N GLY P 513 " pdb=" CA GLY P 513 " pdb=" C GLY P 513 " ideal model delta sigma weight residual 115.08 99.96 15.12 1.64e+00 3.72e-01 8.50e+01 ... (remaining 22351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 4.66: 7151 4.66 - 9.33: 1750 9.33 - 13.99: 326 13.99 - 18.65: 75 18.65 - 23.31: 16 Dihedral angle restraints: 9318 sinusoidal: 0 harmonic: 9318 Sorted by residual: dihedral pdb=" N ASP R 674 " pdb=" C ASP R 674 " pdb=" CA ASP R 674 " pdb=" CB ASP R 674 " ideal model delta harmonic sigma weight residual 122.80 138.27 -15.47 0 2.50e+00 1.60e-01 3.83e+01 dihedral pdb=" C ASP R 674 " pdb=" N ASP R 674 " pdb=" CA ASP R 674 " pdb=" CB ASP R 674 " ideal model delta harmonic sigma weight residual -122.60 -137.67 15.07 0 2.50e+00 1.60e-01 3.63e+01 dihedral pdb=" N ASP N 674 " pdb=" C ASP N 674 " pdb=" CA ASP N 674 " pdb=" CB ASP N 674 " ideal model delta harmonic sigma weight residual 122.80 137.26 -14.46 0 2.50e+00 1.60e-01 3.35e+01 ... (remaining 9315 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 1927 0.127 - 0.254: 848 0.254 - 0.381: 200 0.381 - 0.508: 49 0.508 - 0.635: 6 Chirality restraints: 3030 Sorted by residual: chirality pdb=" CA ASP R 674 " pdb=" N ASP R 674 " pdb=" C ASP R 674 " pdb=" CB ASP R 674 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" CA ASP N 674 " pdb=" N ASP N 674 " pdb=" C ASP N 674 " pdb=" CB ASP N 674 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.52e+00 chirality pdb=" CA ARG M 455 " pdb=" N ARG M 455 " pdb=" C ARG M 455 " pdb=" CB ARG M 455 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.33e+00 ... (remaining 3027 not shown) Planarity restraints: 3258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG P 666 " 0.027 2.00e-02 2.50e+03 5.30e-02 2.81e+01 pdb=" C ARG P 666 " -0.092 2.00e-02 2.50e+03 pdb=" O ARG P 666 " 0.034 2.00e-02 2.50e+03 pdb=" N THR P 667 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 542 " 0.025 2.00e-02 2.50e+03 5.07e-02 2.57e+01 pdb=" C VAL R 542 " -0.088 2.00e-02 2.50e+03 pdb=" O VAL R 542 " 0.034 2.00e-02 2.50e+03 pdb=" N GLY R 543 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR M 394 " 0.024 2.00e-02 2.50e+03 4.93e-02 2.43e+01 pdb=" C THR M 394 " -0.085 2.00e-02 2.50e+03 pdb=" O THR M 394 " 0.033 2.00e-02 2.50e+03 pdb=" N TYR M 395 " 0.027 2.00e-02 2.50e+03 ... (remaining 3255 not shown) Histogram of nonbonded interaction distances: 1.10 - 1.86: 4 1.86 - 2.62: 605 2.62 - 3.38: 24135 3.38 - 4.14: 31149 4.14 - 4.90: 51354 Nonbonded interactions: 107247 Sorted by model distance: nonbonded pdb=" CB SER M 580 " pdb=" CB SER N 582 " model vdw 1.097 3.840 nonbonded pdb=" CB SER M 580 " pdb=" CA SER N 582 " model vdw 1.230 3.870 nonbonded pdb=" CB SER O 262 " pdb=" O GLY Q 266 " model vdw 1.450 3.440 nonbonded pdb=" CB SER N 262 " pdb=" O GLY O 266 " model vdw 1.661 3.440 nonbonded pdb=" CA SER M 580 " pdb=" CB SER N 582 " model vdw 1.924 3.870 ... (remaining 107242 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 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set refine NCS operators NCS operators will be refined. 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 group one per residue 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 42.090 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 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 : 0.021 0.071 16074 Z= 1.594 Angle : 2.643 16.958 22356 Z= 1.830 Chirality : 0.147 0.635 3030 Planarity : 0.012 0.053 3258 Dihedral : 5.911 23.313 3258 Min Nonbonded Distance : 1.097 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 3.08 % Allowed : 6.92 % Favored : 90.01 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 1.65 % Peptide Plane: Cis-proline : 5.71 % 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: -4.41 (0.12), residues: 3252 helix: -3.41 (0.08), residues: 1539 sheet: -1.38 (0.24), residues: 304 loop : -2.54 (0.15), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP P 466 PHE 0.000 0.000 PHE P 216 TYR 0.000 0.000 TYR P 189 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.318 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0334 time to fit residues: 1.2962 Evaluate side-chains 15 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 8.9990 chunk 245 optimal weight: 9.9990 chunk 136 optimal weight: 30.0000 chunk 83 optimal weight: 8.9990 chunk 165 optimal weight: 5.9990 chunk 131 optimal weight: 20.0000 chunk 253 optimal weight: 10.0000 chunk 98 optimal weight: 30.0000 chunk 154 optimal weight: 20.0000 chunk 189 optimal weight: 20.0000 chunk 294 optimal weight: 30.0000 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5943 moved from start: 1.8307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 16074 Z= 0.353 Angle : 0.871 9.343 22356 Z= 0.574 Chirality : 0.046 0.147 3030 Planarity : 0.006 0.034 3258 Dihedral : 9.035 58.066 3258 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 2.40 % Allowed : 7.01 % Favored : 90.59 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.18 % 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: -2.12 (0.13), residues: 3252 helix: -0.58 (0.11), residues: 1662 sheet: -0.52 (0.28), residues: 258 loop : -2.66 (0.15), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP P 466 PHE 0.000 0.000 PHE P 216 TYR 0.000 0.000 TYR P 189 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.301 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0280 time to fit residues: 1.2038 Evaluate side-chains 15 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 8.9990 chunk 91 optimal weight: 20.0000 chunk 244 optimal weight: 20.0000 chunk 200 optimal weight: 20.0000 chunk 81 optimal weight: 30.0000 chunk 294 optimal weight: 20.0000 chunk 318 optimal weight: 30.0000 chunk 262 optimal weight: 9.9990 chunk 292 optimal weight: 8.9990 chunk 100 optimal weight: 30.0000 chunk 236 optimal weight: 20.0000 overall best weight: 13.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6164 moved from start: 1.8426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.026 16074 Z= 0.458 Angle : 0.869 13.726 22356 Z= 0.582 Chirality : 0.044 0.124 3030 Planarity : 0.005 0.026 3258 Dihedral : 8.993 44.102 3258 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.55 % Allowed : 10.89 % Favored : 88.56 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.57 % 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: -2.89 (0.13), residues: 3252 helix: -1.20 (0.11), residues: 1674 sheet: -1.43 (0.32), residues: 222 loop : -2.90 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP P 466 PHE 0.000 0.000 PHE P 216 TYR 0.000 0.000 TYR P 189 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.283 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0284 time to fit residues: 1.2134 Evaluate side-chains 15 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 20.0000 chunk 221 optimal weight: 9.9990 chunk 152 optimal weight: 20.0000 chunk 32 optimal weight: 0.0370 chunk 140 optimal weight: 20.0000 chunk 197 optimal weight: 0.8980 chunk 295 optimal weight: 30.0000 chunk 313 optimal weight: 3.9990 chunk 154 optimal weight: 20.0000 chunk 280 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 overall best weight: 4.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6016 moved from start: 1.8401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 16074 Z= 0.183 Angle : 0.575 6.036 22356 Z= 0.386 Chirality : 0.042 0.118 3030 Planarity : 0.003 0.021 3258 Dihedral : 6.340 33.429 3258 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.23 % Favored : 90.59 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.59 % 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: -1.70 (0.14), residues: 3252 helix: 0.41 (0.12), residues: 1662 sheet: -2.43 (0.23), residues: 384 loop : -2.89 (0.16), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP P 466 PHE 0.000 0.000 PHE P 216 TYR 0.000 0.000 TYR P 189 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.313 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0288 time to fit residues: 1.2132 Evaluate side-chains 15 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 20.0000 chunk 177 optimal weight: 4.9990 chunk 4 optimal weight: 0.0870 chunk 233 optimal weight: 6.9990 chunk 129 optimal weight: 20.0000 chunk 267 optimal weight: 30.0000 chunk 216 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 159 optimal weight: 30.0000 chunk 281 optimal weight: 9.9990 chunk 79 optimal weight: 20.0000 overall best weight: 6.4168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6078 moved from start: 1.8532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 16074 Z= 0.242 Angle : 0.591 7.331 22356 Z= 0.401 Chirality : 0.042 0.122 3030 Planarity : 0.003 0.016 3258 Dihedral : 6.123 30.580 3258 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.36 % Favored : 87.45 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.72 (0.15), residues: 3252 helix: 0.31 (0.13), residues: 1650 sheet: -2.56 (0.25), residues: 348 loop : -2.71 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP P 466 PHE 0.000 0.000 PHE P 216 TYR 0.000 0.000 TYR P 189 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.315 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0286 time to fit residues: 1.2205 Evaluate side-chains 15 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 30.0000 chunk 282 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 313 optimal weight: 30.0000 chunk 260 optimal weight: 9.9990 chunk 145 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 164 optimal weight: 8.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6047 moved from start: 1.8681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 16074 Z= 0.207 Angle : 0.558 5.943 22356 Z= 0.378 Chirality : 0.042 0.118 3030 Planarity : 0.002 0.014 3258 Dihedral : 5.322 28.869 3258 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.07 % Favored : 88.75 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.27 (0.15), residues: 3252 helix: 0.91 (0.13), residues: 1692 sheet: -3.00 (0.22), residues: 390 loop : -2.74 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP P 466 PHE 0.000 0.000 PHE P 216 TYR 0.000 0.000 TYR P 189 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.319 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0295 time to fit residues: 1.2214 Evaluate side-chains 15 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 30.0000 chunk 35 optimal weight: 0.0370 chunk 178 optimal weight: 9.9990 chunk 228 optimal weight: 0.0970 chunk 177 optimal weight: 0.0050 chunk 263 optimal weight: 0.0010 chunk 175 optimal weight: 10.0000 chunk 312 optimal weight: 30.0000 chunk 195 optimal weight: 2.9990 chunk 190 optimal weight: 20.0000 chunk 144 optimal weight: 8.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5889 moved from start: 1.8784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.015 16074 Z= 0.108 Angle : 0.488 6.056 22356 Z= 0.323 Chirality : 0.042 0.120 3030 Planarity : 0.002 0.013 3258 Dihedral : 4.319 24.996 3258 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 0.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.09 (0.16), residues: 3252 helix: 1.91 (0.13), residues: 1692 sheet: -2.30 (0.24), residues: 366 loop : -2.32 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP P 466 PHE 0.000 0.000 PHE P 216 TYR 0.000 0.000 TYR P 189 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.290 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0285 time to fit residues: 1.2309 Evaluate side-chains 15 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 10.0000 chunk 124 optimal weight: 30.0000 chunk 186 optimal weight: 20.0000 chunk 94 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 198 optimal weight: 4.9990 chunk 212 optimal weight: 10.0000 chunk 154 optimal weight: 30.0000 chunk 29 optimal weight: 30.0000 chunk 245 optimal weight: 10.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6087 moved from start: 1.8778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 16074 Z= 0.254 Angle : 0.585 7.319 22356 Z= 0.397 Chirality : 0.042 0.125 3030 Planarity : 0.003 0.015 3258 Dihedral : 5.430 29.426 3258 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.81 % Favored : 88.19 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.88 (0.15), residues: 3252 helix: 1.04 (0.13), residues: 1686 sheet: -2.44 (0.25), residues: 324 loop : -2.39 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP P 466 PHE 0.000 0.000 PHE P 216 TYR 0.000 0.000 TYR P 189 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.335 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0300 time to fit residues: 1.2929 Evaluate side-chains 15 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 20.0000 chunk 299 optimal weight: 30.0000 chunk 272 optimal weight: 20.0000 chunk 291 optimal weight: 20.0000 chunk 175 optimal weight: 10.0000 chunk 126 optimal weight: 0.9980 chunk 228 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 262 optimal weight: 20.0000 chunk 275 optimal weight: 8.9990 chunk 289 optimal weight: 0.0470 overall best weight: 4.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6042 moved from start: 1.8847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 16074 Z= 0.179 Angle : 0.527 5.974 22356 Z= 0.356 Chirality : 0.042 0.117 3030 Planarity : 0.002 0.013 3258 Dihedral : 4.934 28.447 3258 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.25 % Favored : 88.75 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.16), residues: 3252 helix: 1.39 (0.13), residues: 1692 sheet: -2.44 (0.26), residues: 318 loop : -2.35 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP P 466 PHE 0.000 0.000 PHE P 216 TYR 0.000 0.000 TYR P 189 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.316 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0291 time to fit residues: 1.2507 Evaluate side-chains 15 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 9.9990 chunk 307 optimal weight: 20.0000 chunk 187 optimal weight: 30.0000 chunk 145 optimal weight: 20.0000 chunk 213 optimal weight: 20.0000 chunk 322 optimal weight: 9.9990 chunk 297 optimal weight: 20.0000 chunk 257 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 198 optimal weight: 9.9990 chunk 157 optimal weight: 1.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6140 moved from start: 1.8959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 16074 Z= 0.291 Angle : 0.619 7.936 22356 Z= 0.422 Chirality : 0.042 0.120 3030 Planarity : 0.003 0.015 3258 Dihedral : 5.791 32.001 3258 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.21 % Favored : 85.79 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -1.44 (0.15), residues: 3252 helix: 0.43 (0.13), residues: 1662 sheet: -2.76 (0.29), residues: 234 loop : -2.41 (0.18), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP P 466 PHE 0.000 0.000 PHE P 216 TYR 0.000 0.000 TYR P 189 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.328 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0299 time to fit residues: 1.2900 Evaluate side-chains 15 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 0.0040 chunk 273 optimal weight: 20.0000 chunk 78 optimal weight: 50.0000 chunk 237 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 71 optimal weight: 9.9990 chunk 257 optimal weight: 1.9990 chunk 107 optimal weight: 30.0000 chunk 264 optimal weight: 30.0000 chunk 32 optimal weight: 9.9990 chunk 47 optimal weight: 0.0050 overall best weight: 4.4012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.079422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.063371 restraints weight = 14790.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.064333 restraints weight = 12712.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.065151 restraints weight = 11167.935| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 1.9005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 16074 Z= 0.176 Angle : 0.532 5.999 22356 Z= 0.359 Chirality : 0.042 0.121 3030 Planarity : 0.002 0.013 3258 Dihedral : 5.065 28.842 3258 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.36 % Favored : 87.64 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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 (0.16), residues: 3252 helix: 1.15 (0.13), residues: 1674 sheet: -2.60 (0.29), residues: 234 loop : -2.35 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP P 466 PHE 0.000 0.000 PHE P 216 TYR 0.000 0.000 TYR P 189 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1770.62 seconds wall clock time: 31 minutes 57.93 seconds (1917.93 seconds total)