Starting phenix.real_space_refine on Thu Sep 18 09:51:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5vca_8659/09_2025/5vca_8659.cif Found real_map, /net/cci-nas-00/data/ceres_data/5vca_8659/09_2025/5vca_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/cci-nas-00/data/ceres_data/5vca_8659/09_2025/5vca_8659.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5vca_8659/09_2025/5vca_8659.map" model { file = "/net/cci-nas-00/data/ceres_data/5vca_8659/09_2025/5vca_8659.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5vca_8659/09_2025/5vca_8659.cif" } resolution = 4.8 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 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 55, 'ARG:plan': 37, 'TYR:plan': 12, 'ASP:plan': 33, 'GLN:plan1': 9, 'HIS:plan': 5, 'PHE:plan': 16, 'ASN:plan1': 21, 'TRP:plan': 2} 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: {'GLU:plan': 55, 'ARG:plan': 37, 'TYR:plan': 12, 'ASP:plan': 33, 'GLN:plan1': 9, 'HIS:plan': 5, 'PHE:plan': 16, 'ASN:plan1': 21, 'TRP:plan': 2} 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: {'GLU:plan': 55, 'ARG:plan': 37, 'TYR:plan': 12, 'ASP:plan': 33, 'GLN:plan1': 9, 'HIS:plan': 5, 'PHE:plan': 16, 'ASN:plan1': 21, 'TRP:plan': 2} 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: {'GLU:plan': 55, 'ARG:plan': 37, 'TYR:plan': 12, 'ASP:plan': 33, 'GLN:plan1': 9, 'HIS:plan': 5, 'PHE:plan': 16, 'ASN:plan1': 21, 'TRP:plan': 2} 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: {'GLU:plan': 55, 'ARG:plan': 37, 'TYR:plan': 12, 'ASP:plan': 33, 'GLN:plan1': 9, 'HIS:plan': 5, 'PHE:plan': 16, 'ASN:plan1': 21, 'TRP:plan': 2} 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: {'GLU:plan': 55, 'ARG:plan': 37, 'TYR:plan': 12, 'ASP:plan': 33, 'GLN:plan1': 9, 'HIS:plan': 5, 'PHE:plan': 16, 'ASN:plan1': 21, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 826 Time building chain proxies: 5.15, per 1000 atoms: 0.32 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: 1.91 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 1.2 microseconds 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: 0.76 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: 3.18 Time building geometry restraints manager: 2.36 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: 0.02 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: 1.310 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.900 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.280 ------------------------------------------------------------------------------- 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= 1.645 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 TYR 0.000 0.000 TYR P 189 PHE 0.000 0.000 PHE P 216 TRP 0.000 0.000 TRP P 466 Details of bonding type rmsd covalent geometry : bond 0.02149 (16074) covalent geometry : angle 2.64310 (22356) hydrogen bonds : bond 0.24055 ( 1162) hydrogen bonds : angle 9.48245 ( 3318) *********************** 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 to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.094 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0143 time to fit residues: 0.5144 Evaluate side-chains 15 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 0.2980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 40.0000 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 3.9990 overall best weight: 6.0588 ------------------------------------------------------------------------------- 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 = 0.3064 r_free = 0.3064 target = 0.064480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.051542 restraints weight = 17179.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.052490 restraints weight = 13994.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.053221 restraints weight = 11785.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.053930 restraints weight = 10225.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.054480 restraints weight = 9021.492| |-----------------------------------------------------------------------------| r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 moved from start: 1.8406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 16074 Z= 0.292 Angle : 0.814 8.566 22356 Z= 0.533 Chirality : 0.045 0.133 3030 Planarity : 0.005 0.034 3258 Dihedral : 8.552 51.417 3258 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 2.03 % Allowed : 6.64 % Favored : 91.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (0.13), residues: 3252 helix: -0.26 (0.12), residues: 1650 sheet: -0.25 (0.27), residues: 258 loop : -2.63 (0.15), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR P 189 PHE 0.000 0.000 PHE P 216 TRP 0.000 0.000 TRP P 466 Details of bonding type rmsd covalent geometry : bond 0.00385 (16074) covalent geometry : angle 0.81357 (22356) hydrogen bonds : bond 0.06903 ( 1162) hydrogen bonds : angle 6.51752 ( 3318) *********************** 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 to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.098 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0132 time to fit residues: 0.4994 Evaluate side-chains 15 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 157 optimal weight: 0.0970 chunk 165 optimal weight: 20.0000 chunk 17 optimal weight: 8.9990 chunk 43 optimal weight: 20.0000 chunk 313 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 chunk 58 optimal weight: 20.0000 chunk 85 optimal weight: 9.9990 chunk 140 optimal weight: 30.0000 chunk 103 optimal weight: 10.0000 overall best weight: 6.4186 ------------------------------------------------------------------------------- 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 = 0.3153 r_free = 0.3153 target = 0.070338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.056530 restraints weight = 16553.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.057486 restraints weight = 13883.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.058262 restraints weight = 11931.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.058929 restraints weight = 10477.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.059470 restraints weight = 9356.205| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 1.8289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 16074 Z= 0.256 Angle : 0.650 7.905 22356 Z= 0.436 Chirality : 0.043 0.135 3030 Planarity : 0.004 0.022 3258 Dihedral : 6.842 44.876 3258 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.41 % Favored : 90.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.14), residues: 3252 helix: 0.32 (0.12), residues: 1692 sheet: -1.20 (0.26), residues: 372 loop : -2.76 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR P 189 PHE 0.000 0.000 PHE P 216 TRP 0.000 0.000 TRP P 466 Details of bonding type rmsd covalent geometry : bond 0.00340 (16074) covalent geometry : angle 0.64965 (22356) hydrogen bonds : bond 0.05850 ( 1162) hydrogen bonds : angle 6.44254 ( 3318) *********************** 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 to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.097 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0132 time to fit residues: 0.5002 Evaluate side-chains 15 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 237 optimal weight: 7.9990 chunk 303 optimal weight: 9.9990 chunk 90 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 chunk 201 optimal weight: 7.9990 chunk 118 optimal weight: 20.0000 chunk 149 optimal weight: 20.0000 chunk 320 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 chunk 217 optimal weight: 9.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- 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 = 0.3232 r_free = 0.3232 target = 0.078200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.061376 restraints weight = 15262.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.061913 restraints weight = 13308.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.062634 restraints weight = 12172.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.063319 restraints weight = 10936.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.063811 restraints weight = 10056.810| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 1.8430 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= 0.311 Angle : 0.673 9.295 22356 Z= 0.456 Chirality : 0.043 0.117 3030 Planarity : 0.004 0.021 3258 Dihedral : 6.963 33.320 3258 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.14), residues: 3252 helix: -0.07 (0.12), residues: 1656 sheet: -1.78 (0.26), residues: 348 loop : -2.63 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR P 189 PHE 0.000 0.000 PHE P 216 TRP 0.000 0.000 TRP P 466 Details of bonding type rmsd covalent geometry : bond 0.00414 (16074) covalent geometry : angle 0.67284 (22356) hydrogen bonds : bond 0.06233 ( 1162) hydrogen bonds : angle 6.84330 ( 3318) *********************** REFINEMENT MACRO_CYCLE 4 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 to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.101 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0136 time to fit residues: 0.5188 Evaluate side-chains 15 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 227 optimal weight: 8.9990 chunk 175 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 111 optimal weight: 20.0000 chunk 314 optimal weight: 5.9990 chunk 244 optimal weight: 30.0000 chunk 158 optimal weight: 10.0000 chunk 300 optimal weight: 6.9990 chunk 53 optimal weight: 30.0000 chunk 11 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 overall best weight: 8.3992 ------------------------------------------------------------------------------- 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 = 0.3188 r_free = 0.3188 target = 0.073101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.058608 restraints weight = 17142.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.059531 restraints weight = 14583.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.060076 restraints weight = 12714.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.060810 restraints weight = 11499.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.061397 restraints weight = 10361.325| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 1.8649 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 : 0.636 8.152 22356 Z= 0.433 Chirality : 0.042 0.115 3030 Planarity : 0.003 0.017 3258 Dihedral : 6.288 32.008 3258 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.44 % 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 : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.15), residues: 3252 helix: 0.19 (0.12), residues: 1626 sheet: -2.00 (0.26), residues: 348 loop : -2.58 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR P 189 PHE 0.000 0.000 PHE P 216 TRP 0.000 0.000 TRP P 466 Details of bonding type rmsd covalent geometry : bond 0.00388 (16074) covalent geometry : angle 0.63575 (22356) hydrogen bonds : bond 0.05595 ( 1162) hydrogen bonds : angle 6.70781 ( 3318) *********************** REFINEMENT MACRO_CYCLE 5 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 to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.136 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0137 time to fit residues: 0.5110 Evaluate side-chains 15 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 8 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 282 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 123 optimal weight: 20.0000 chunk 249 optimal weight: 4.9990 chunk 283 optimal weight: 20.0000 chunk 256 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 112 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.3220 r_free = 0.3220 target = 0.074882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.060109 restraints weight = 17014.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.061052 restraints weight = 14379.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.061908 restraints weight = 12473.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.062612 restraints weight = 11026.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.063150 restraints weight = 9887.051| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 1.8715 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= 0.224 Angle : 0.574 6.432 22356 Z= 0.389 Chirality : 0.042 0.117 3030 Planarity : 0.003 0.016 3258 Dihedral : 5.706 30.066 3258 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.15), residues: 3252 helix: 0.81 (0.13), residues: 1656 sheet: -2.03 (0.27), residues: 318 loop : -2.57 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR P 189 PHE 0.000 0.000 PHE P 216 TRP 0.000 0.000 TRP P 466 Details of bonding type rmsd covalent geometry : bond 0.00299 (16074) covalent geometry : angle 0.57418 (22356) hydrogen bonds : bond 0.04807 ( 1162) hydrogen bonds : angle 6.17354 ( 3318) *********************** REFINEMENT MACRO_CYCLE 6 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 to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.095 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0125 time to fit residues: 0.4531 Evaluate side-chains 15 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 246 optimal weight: 10.0000 chunk 280 optimal weight: 20.0000 chunk 230 optimal weight: 10.0000 chunk 154 optimal weight: 20.0000 chunk 287 optimal weight: 4.9990 chunk 181 optimal weight: 30.0000 chunk 278 optimal weight: 0.9990 chunk 89 optimal weight: 0.3980 chunk 18 optimal weight: 0.0040 chunk 118 optimal weight: 7.9990 chunk 146 optimal weight: 20.0000 overall best weight: 2.8798 ------------------------------------------------------------------------------- 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 = 0.3260 r_free = 0.3260 target = 0.077441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.061859 restraints weight = 16355.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.062853 restraints weight = 13980.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.063614 restraints weight = 12214.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.064408 restraints weight = 10879.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.064989 restraints weight = 9796.293| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 1.8783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 16074 Z= 0.144 Angle : 0.509 6.123 22356 Z= 0.342 Chirality : 0.042 0.118 3030 Planarity : 0.002 0.014 3258 Dihedral : 4.793 26.339 3258 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.16), residues: 3252 helix: 1.64 (0.13), residues: 1692 sheet: -1.94 (0.26), residues: 330 loop : -2.57 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR P 189 PHE 0.000 0.000 PHE P 216 TRP 0.000 0.000 TRP P 466 Details of bonding type rmsd covalent geometry : bond 0.00191 (16074) covalent geometry : angle 0.50895 (22356) hydrogen bonds : bond 0.03793 ( 1162) hydrogen bonds : angle 5.39982 ( 3318) *********************** REFINEMENT MACRO_CYCLE 7 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 to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.112 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0132 time to fit residues: 0.5001 Evaluate side-chains 15 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 321 optimal weight: 20.0000 chunk 45 optimal weight: 30.0000 chunk 113 optimal weight: 10.0000 chunk 254 optimal weight: 30.0000 chunk 3 optimal weight: 10.0000 chunk 214 optimal weight: 20.0000 chunk 310 optimal weight: 10.0000 chunk 105 optimal weight: 30.0000 chunk 117 optimal weight: 10.0000 chunk 323 optimal weight: 40.0000 chunk 141 optimal weight: 3.9990 overall best weight: 8.7998 ------------------------------------------------------------------------------- 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 = 0.3197 r_free = 0.3197 target = 0.073803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.059365 restraints weight = 17716.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.060255 restraints weight = 15165.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.061047 restraints weight = 13270.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.061705 restraints weight = 11781.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.062231 restraints weight = 10592.948| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 1.8885 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= 0.307 Angle : 0.638 8.755 22356 Z= 0.434 Chirality : 0.042 0.118 3030 Planarity : 0.003 0.016 3258 Dihedral : 6.101 32.548 3258 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.73 % Favored : 87.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.15), residues: 3252 helix: 0.77 (0.13), residues: 1626 sheet: -2.30 (0.27), residues: 324 loop : -2.35 (0.18), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR P 189 PHE 0.000 0.000 PHE P 216 TRP 0.000 0.000 TRP P 466 Details of bonding type rmsd covalent geometry : bond 0.00408 (16074) covalent geometry : angle 0.63843 (22356) hydrogen bonds : bond 0.05726 ( 1162) hydrogen bonds : angle 6.62542 ( 3318) *********************** REFINEMENT MACRO_CYCLE 8 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 to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.096 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0132 time to fit residues: 0.4864 Evaluate side-chains 15 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 283 optimal weight: 20.0000 chunk 163 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 239 optimal weight: 9.9990 chunk 31 optimal weight: 0.0980 chunk 177 optimal weight: 9.9990 chunk 189 optimal weight: 20.0000 chunk 27 optimal weight: 30.0000 chunk 128 optimal weight: 20.0000 chunk 67 optimal weight: 20.0000 chunk 132 optimal weight: 30.0000 overall best weight: 8.0190 ------------------------------------------------------------------------------- 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 = 0.3213 r_free = 0.3213 target = 0.074845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.060138 restraints weight = 17869.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.061099 restraints weight = 15207.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.061869 restraints weight = 13241.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.062568 restraints weight = 11762.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.063124 restraints weight = 10595.949| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 1.9045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 16074 Z= 0.277 Angle : 0.614 7.944 22356 Z= 0.417 Chirality : 0.042 0.116 3030 Planarity : 0.003 0.016 3258 Dihedral : 5.854 32.283 3258 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.28 % Favored : 86.72 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.15), residues: 3252 helix: 0.68 (0.13), residues: 1668 sheet: -2.43 (0.30), residues: 234 loop : -2.66 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR P 189 PHE 0.000 0.000 PHE P 216 TRP 0.000 0.000 TRP P 466 Details of bonding type rmsd covalent geometry : bond 0.00369 (16074) covalent geometry : angle 0.61400 (22356) hydrogen bonds : bond 0.05235 ( 1162) hydrogen bonds : angle 6.47474 ( 3318) *********************** REFINEMENT MACRO_CYCLE 9 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 to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.103 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0146 time to fit residues: 0.5563 Evaluate side-chains 15 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 210 optimal weight: 20.0000 chunk 255 optimal weight: 10.0000 chunk 81 optimal weight: 30.0000 chunk 237 optimal weight: 20.0000 chunk 164 optimal weight: 20.0000 chunk 105 optimal weight: 20.0000 chunk 290 optimal weight: 20.0000 chunk 80 optimal weight: 9.9990 chunk 36 optimal weight: 0.0070 chunk 323 optimal weight: 0.2980 chunk 42 optimal weight: 0.0040 overall best weight: 4.0616 ------------------------------------------------------------------------------- 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 = 0.3245 r_free = 0.3245 target = 0.076863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.060990 restraints weight = 16211.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.062036 restraints weight = 13755.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.062921 restraints weight = 11949.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.063678 restraints weight = 10579.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.064255 restraints weight = 9516.309| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 1.9082 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= 0.170 Angle : 0.526 6.000 22356 Z= 0.354 Chirality : 0.042 0.118 3030 Planarity : 0.002 0.014 3258 Dihedral : 5.053 27.641 3258 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.89 % Favored : 89.11 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.16), residues: 3252 helix: 1.53 (0.13), residues: 1680 sheet: -2.36 (0.26), residues: 324 loop : -2.53 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR P 189 PHE 0.000 0.000 PHE P 216 TRP 0.000 0.000 TRP P 466 Details of bonding type rmsd covalent geometry : bond 0.00227 (16074) covalent geometry : angle 0.52611 (22356) hydrogen bonds : bond 0.04074 ( 1162) hydrogen bonds : angle 5.73677 ( 3318) ********************** REFINEMENT MACRO_CYCLE 10 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 to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.094 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0130 time to fit residues: 0.4906 Evaluate side-chains 15 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 209 optimal weight: 30.0000 chunk 297 optimal weight: 20.0000 chunk 258 optimal weight: 30.0000 chunk 273 optimal weight: 30.0000 chunk 17 optimal weight: 30.0000 chunk 44 optimal weight: 10.0000 chunk 171 optimal weight: 9.9990 chunk 223 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 150 optimal weight: 0.4980 chunk 172 optimal weight: 2.9990 overall best weight: 6.6988 ------------------------------------------------------------------------------- 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 = 0.3224 r_free = 0.3224 target = 0.075470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.060524 restraints weight = 17127.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.061495 restraints weight = 14637.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.062291 restraints weight = 12783.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 15)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.062851 restraints weight = 11397.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.063487 restraints weight = 10376.009| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 1.9171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 16074 Z= 0.244 Angle : 0.580 7.362 22356 Z= 0.393 Chirality : 0.042 0.116 3030 Planarity : 0.003 0.016 3258 Dihedral : 5.555 30.793 3258 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.73 % Favored : 87.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.15), residues: 3252 helix: 1.13 (0.13), residues: 1674 sheet: -2.53 (0.30), residues: 234 loop : -2.50 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR P 189 PHE 0.000 0.000 PHE P 216 TRP 0.000 0.000 TRP P 466 Details of bonding type rmsd covalent geometry : bond 0.00324 (16074) covalent geometry : angle 0.57980 (22356) hydrogen bonds : bond 0.04879 ( 1162) hydrogen bonds : angle 6.24084 ( 3318) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1090.79 seconds wall clock time: 19 minutes 32.87 seconds (1172.87 seconds total)