Starting phenix.real_space_refine (version: dev) on Thu Feb 23 20:35:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cud_7620/02_2023/6cud_7620_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cud_7620/02_2023/6cud_7620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cud_7620/02_2023/6cud_7620.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cud_7620/02_2023/6cud_7620.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cud_7620/02_2023/6cud_7620_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cud_7620/02_2023/6cud_7620_neut_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.004 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 Process input model Symmetric amino acids flipped Residue "A ARG 89": "NH1" <-> "NH2" Residue "A TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 248": "NH1" <-> "NH2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "A ARG 395": "NH1" <-> "NH2" Residue "A ARG 475": "NH1" <-> "NH2" Residue "A ARG 514": "NH1" <-> "NH2" Residue "A ARG 540": "NH1" <-> "NH2" Residue "A ARG 560": "NH1" <-> "NH2" Residue "A ARG 769": "NH1" <-> "NH2" Residue "B ARG 89": "NH1" <-> "NH2" Residue "B TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 248": "NH1" <-> "NH2" Residue "B ARG 266": "NH1" <-> "NH2" Residue "B ARG 395": "NH1" <-> "NH2" Residue "B ARG 475": "NH1" <-> "NH2" Residue "B ARG 514": "NH1" <-> "NH2" Residue "B ARG 540": "NH1" <-> "NH2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B ARG 769": "NH1" <-> "NH2" Residue "C ARG 89": "NH1" <-> "NH2" Residue "C TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 248": "NH1" <-> "NH2" Residue "C ARG 266": "NH1" <-> "NH2" Residue "C ARG 395": "NH1" <-> "NH2" Residue "C ARG 475": "NH1" <-> "NH2" Residue "C ARG 514": "NH1" <-> "NH2" Residue "C ARG 540": "NH1" <-> "NH2" Residue "C ARG 560": "NH1" <-> "NH2" Residue "C ARG 769": "NH1" <-> "NH2" Residue "D ARG 89": "NH1" <-> "NH2" Residue "D TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 248": "NH1" <-> "NH2" Residue "D ARG 266": "NH1" <-> "NH2" Residue "D ARG 395": "NH1" <-> "NH2" Residue "D ARG 475": "NH1" <-> "NH2" Residue "D ARG 514": "NH1" <-> "NH2" Residue "D ARG 540": "NH1" <-> "NH2" Residue "D ARG 560": "NH1" <-> "NH2" Residue "D ARG 769": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 21028 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5196 Classifications: {'peptide': 704} Incomplete info: {'truncation_to_alanine': 148} Link IDs: {'PTRANS': 22, 'TRANS': 681} Chain breaks: 2 Unresolved non-hydrogen bonds: 493 Unresolved non-hydrogen angles: 615 Unresolved non-hydrogen dihedrals: 380 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 3, 'ASN:plan1': 9, 'ASP:plan': 25, 'GLU:plan': 38, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 333 Chain: "B" Number of atoms: 5196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5196 Classifications: {'peptide': 704} Incomplete info: {'truncation_to_alanine': 148} Link IDs: {'PTRANS': 22, 'TRANS': 681} Chain breaks: 2 Unresolved non-hydrogen bonds: 493 Unresolved non-hydrogen angles: 615 Unresolved non-hydrogen dihedrals: 380 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 3, 'ASN:plan1': 9, 'ASP:plan': 25, 'GLU:plan': 38, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 333 Chain: "C" Number of atoms: 5196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5196 Classifications: {'peptide': 704} Incomplete info: {'truncation_to_alanine': 148} Link IDs: {'PTRANS': 22, 'TRANS': 681} Chain breaks: 2 Unresolved non-hydrogen bonds: 493 Unresolved non-hydrogen angles: 615 Unresolved non-hydrogen dihedrals: 380 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 3, 'ASN:plan1': 9, 'ASP:plan': 25, 'GLU:plan': 38, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 333 Chain: "D" Number of atoms: 5196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5196 Classifications: {'peptide': 704} Incomplete info: {'truncation_to_alanine': 148} Link IDs: {'PTRANS': 22, 'TRANS': 681} Chain breaks: 2 Unresolved non-hydrogen bonds: 493 Unresolved non-hydrogen angles: 615 Unresolved non-hydrogen dihedrals: 380 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 3, 'ASN:plan1': 9, 'ASP:plan': 25, 'GLU:plan': 38, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 333 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {'6OE': 1, 'FGJ': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {'6OE': 1, 'FGJ': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {'6OE': 1, 'FGJ': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {'6OE': 1, 'FGJ': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 12.22, per 1000 atoms: 0.58 Number of scatterers: 21028 At special positions: 0 Unit cell: (123.51, 123.51, 148.212, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 104 16.00 P 4 15.00 O 3592 8.00 N 3484 7.00 C 13844 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 182 " - pdb=" SG CYS A 184 " distance=2.05 Simple disulfide: pdb=" SG CYS B 182 " - pdb=" SG CYS B 184 " distance=2.05 Simple disulfide: pdb=" SG CYS C 182 " - pdb=" SG CYS C 184 " distance=2.05 Simple disulfide: pdb=" SG CYS D 182 " - pdb=" SG CYS D 184 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 903 " - " ASN A 404 " " NAG B 903 " - " ASN B 404 " " NAG C 903 " - " ASN C 404 " " NAG D 903 " - " ASN D 404 " Time building additional restraints: 8.27 Conformation dependent library (CDL) restraints added in 3.6 seconds 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5392 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 144 helices and 0 sheets defined 68.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.77 Creating SS restraints... Processing helix chain 'A' and resid 26 through 37 removed outlier: 3.953A pdb=" N ALA A 34 " --> pdb=" O ARG A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 49 removed outlier: 3.718A pdb=" N MET A 46 " --> pdb=" O VAL A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 75 through 81 removed outlier: 3.633A pdb=" N LEU A 80 " --> pdb=" O GLU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 99 Processing helix chain 'A' and resid 104 through 110 Processing helix chain 'A' and resid 113 through 116 No H-bonds generated for 'chain 'A' and resid 113 through 116' Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 161 through 170 removed outlier: 3.632A pdb=" N HIS A 165 " --> pdb=" O TYR A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 192 Processing helix chain 'A' and resid 195 through 209 removed outlier: 3.723A pdb=" N ILE A 203 " --> pdb=" O SER A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 218 Processing helix chain 'A' and resid 222 through 240 removed outlier: 3.965A pdb=" N ASN A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 239 " --> pdb=" O LYS A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 264 removed outlier: 3.642A pdb=" N MET A 252 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL A 258 " --> pdb=" O CYS A 254 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 274 Processing helix chain 'A' and resid 295 through 302 removed outlier: 3.956A pdb=" N LYS A 302 " --> pdb=" O LYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 312 through 322 removed outlier: 4.185A pdb=" N GLN A 317 " --> pdb=" O ASN A 313 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A 321 " --> pdb=" O GLN A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 334 through 356 Proline residue: A 349 - end of helix removed outlier: 4.609A pdb=" N ALA A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ILE A 353 " --> pdb=" O PRO A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'A' and resid 415 through 420 removed outlier: 3.923A pdb=" N THR A 419 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 415 through 420' Processing helix chain 'A' and resid 424 through 447 removed outlier: 3.536A pdb=" N LEU A 428 " --> pdb=" O TRP A 424 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 434 " --> pdb=" O MET A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 454 Processing helix chain 'A' and resid 456 through 492 removed outlier: 3.923A pdb=" N GLN A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA A 482 " --> pdb=" O ALA A 478 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A 491 " --> pdb=" O GLN A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 511 removed outlier: 3.577A pdb=" N TYR A 509 " --> pdb=" O PRO A 505 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N PHE A 510 " --> pdb=" O GLU A 506 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR A 511 " --> pdb=" O ILE A 507 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 505 through 511' Processing helix chain 'A' and resid 522 through 543 removed outlier: 3.523A pdb=" N VAL A 534 " --> pdb=" O TYR A 530 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL A 535 " --> pdb=" O ALA A 531 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE A 538 " --> pdb=" O VAL A 534 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER A 539 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ARG A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ILE A 541 " --> pdb=" O SER A 537 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ALA A 542 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N TYR A 543 " --> pdb=" O SER A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 589 removed outlier: 3.666A pdb=" N ILE A 556 " --> pdb=" O GLY A 552 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER A 557 " --> pdb=" O PRO A 553 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N PHE A 566 " --> pdb=" O VAL A 562 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LYS A 567 " --> pdb=" O LYS A 563 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE A 568 " --> pdb=" O ASP A 564 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 571 " --> pdb=" O LYS A 567 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N TYR A 589 " --> pdb=" O ILE A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 614 removed outlier: 4.284A pdb=" N ILE A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE A 614 " --> pdb=" O PHE A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 621 No H-bonds generated for 'chain 'A' and resid 619 through 621' Processing helix chain 'A' and resid 629 through 664 removed outlier: 3.867A pdb=" N VAL A 647 " --> pdb=" O ASN A 643 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER A 661 " --> pdb=" O MET A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 684 removed outlier: 3.904A pdb=" N LYS A 679 " --> pdb=" O PHE A 675 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 785 Processing helix chain 'A' and resid 788 through 805 Processing helix chain 'B' and resid 26 through 37 removed outlier: 3.953A pdb=" N ALA B 34 " --> pdb=" O ARG B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 49 removed outlier: 3.717A pdb=" N MET B 46 " --> pdb=" O VAL B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 71 Processing helix chain 'B' and resid 75 through 81 removed outlier: 3.634A pdb=" N LEU B 80 " --> pdb=" O GLU B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 99 Processing helix chain 'B' and resid 104 through 110 Processing helix chain 'B' and resid 113 through 116 No H-bonds generated for 'chain 'B' and resid 113 through 116' Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 161 through 170 removed outlier: 3.632A pdb=" N HIS B 165 " --> pdb=" O TYR B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 195 through 209 removed outlier: 3.724A pdb=" N ILE B 203 " --> pdb=" O SER B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 218 Processing helix chain 'B' and resid 222 through 240 removed outlier: 3.965A pdb=" N ASN B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN B 238 " --> pdb=" O ALA B 234 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE B 239 " --> pdb=" O LYS B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 264 removed outlier: 3.641A pdb=" N MET B 252 " --> pdb=" O ARG B 248 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN B 253 " --> pdb=" O LYS B 249 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL B 258 " --> pdb=" O CYS B 254 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 274 Processing helix chain 'B' and resid 295 through 302 removed outlier: 3.957A pdb=" N LYS B 302 " --> pdb=" O LYS B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 312 through 322 removed outlier: 4.185A pdb=" N GLN B 317 " --> pdb=" O ASN B 313 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE B 321 " --> pdb=" O GLN B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 331 No H-bonds generated for 'chain 'B' and resid 329 through 331' Processing helix chain 'B' and resid 334 through 356 Proline residue: B 349 - end of helix removed outlier: 4.608A pdb=" N ALA B 352 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ILE B 353 " --> pdb=" O PRO B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 360 No H-bonds generated for 'chain 'B' and resid 358 through 360' Processing helix chain 'B' and resid 362 through 367 Processing helix chain 'B' and resid 370 through 391 Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.924A pdb=" N THR B 419 " --> pdb=" O PHE B 415 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR B 420 " --> pdb=" O ARG B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 415 through 420' Processing helix chain 'B' and resid 424 through 447 removed outlier: 3.535A pdb=" N LEU B 428 " --> pdb=" O TRP B 424 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 434 " --> pdb=" O MET B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 454 Processing helix chain 'B' and resid 456 through 492 removed outlier: 3.923A pdb=" N GLN B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA B 482 " --> pdb=" O ALA B 478 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER B 491 " --> pdb=" O GLN B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 511 removed outlier: 3.577A pdb=" N TYR B 509 " --> pdb=" O PRO B 505 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N PHE B 510 " --> pdb=" O GLU B 506 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR B 511 " --> pdb=" O ILE B 507 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 505 through 511' Processing helix chain 'B' and resid 522 through 543 removed outlier: 3.523A pdb=" N VAL B 534 " --> pdb=" O TYR B 530 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 535 " --> pdb=" O ALA B 531 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE B 538 " --> pdb=" O VAL B 534 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER B 539 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ARG B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ILE B 541 " --> pdb=" O SER B 537 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ALA B 542 " --> pdb=" O PHE B 538 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N TYR B 543 " --> pdb=" O SER B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 589 removed outlier: 3.666A pdb=" N ILE B 556 " --> pdb=" O GLY B 552 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 557 " --> pdb=" O PRO B 553 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N PHE B 566 " --> pdb=" O VAL B 562 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LYS B 567 " --> pdb=" O LYS B 563 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE B 568 " --> pdb=" O ASP B 564 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B 571 " --> pdb=" O LYS B 567 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N TYR B 589 " --> pdb=" O ILE B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 614 removed outlier: 4.285A pdb=" N ILE B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE B 614 " --> pdb=" O PHE B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 621 No H-bonds generated for 'chain 'B' and resid 619 through 621' Processing helix chain 'B' and resid 629 through 664 removed outlier: 3.867A pdb=" N VAL B 647 " --> pdb=" O ASN B 643 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER B 660 " --> pdb=" O ALA B 656 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER B 661 " --> pdb=" O MET B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 684 removed outlier: 3.904A pdb=" N LYS B 679 " --> pdb=" O PHE B 675 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR B 684 " --> pdb=" O LEU B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 785 Processing helix chain 'B' and resid 788 through 805 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.954A pdb=" N ALA C 34 " --> pdb=" O ARG C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 49 removed outlier: 3.718A pdb=" N MET C 46 " --> pdb=" O VAL C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 71 Processing helix chain 'C' and resid 75 through 81 removed outlier: 3.634A pdb=" N LEU C 80 " --> pdb=" O GLU C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 99 Processing helix chain 'C' and resid 104 through 110 Processing helix chain 'C' and resid 113 through 116 No H-bonds generated for 'chain 'C' and resid 113 through 116' Processing helix chain 'C' and resid 151 through 158 Processing helix chain 'C' and resid 161 through 170 removed outlier: 3.632A pdb=" N HIS C 165 " --> pdb=" O TYR C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 192 Processing helix chain 'C' and resid 195 through 209 removed outlier: 3.724A pdb=" N ILE C 203 " --> pdb=" O SER C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 218 Processing helix chain 'C' and resid 222 through 240 removed outlier: 3.965A pdb=" N ASN C 231 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN C 238 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE C 239 " --> pdb=" O LYS C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 264 removed outlier: 3.642A pdb=" N MET C 252 " --> pdb=" O ARG C 248 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN C 253 " --> pdb=" O LYS C 249 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL C 258 " --> pdb=" O CYS C 254 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU C 264 " --> pdb=" O GLY C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 274 Processing helix chain 'C' and resid 295 through 302 removed outlier: 3.956A pdb=" N LYS C 302 " --> pdb=" O LYS C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 309 No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 312 through 322 removed outlier: 4.185A pdb=" N GLN C 317 " --> pdb=" O ASN C 313 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE C 321 " --> pdb=" O GLN C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 334 through 356 Proline residue: C 349 - end of helix removed outlier: 4.609A pdb=" N ALA C 352 " --> pdb=" O LEU C 348 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ILE C 353 " --> pdb=" O PRO C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 360 No H-bonds generated for 'chain 'C' and resid 358 through 360' Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 370 through 391 Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.923A pdb=" N THR C 419 " --> pdb=" O PHE C 415 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR C 420 " --> pdb=" O ARG C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 415 through 420' Processing helix chain 'C' and resid 424 through 447 removed outlier: 3.536A pdb=" N LEU C 428 " --> pdb=" O TRP C 424 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 434 " --> pdb=" O MET C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 454 Processing helix chain 'C' and resid 456 through 492 removed outlier: 3.924A pdb=" N GLN C 481 " --> pdb=" O LEU C 477 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA C 482 " --> pdb=" O ALA C 478 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER C 491 " --> pdb=" O GLN C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 511 removed outlier: 3.578A pdb=" N TYR C 509 " --> pdb=" O PRO C 505 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N PHE C 510 " --> pdb=" O GLU C 506 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR C 511 " --> pdb=" O ILE C 507 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 505 through 511' Processing helix chain 'C' and resid 522 through 543 removed outlier: 3.524A pdb=" N VAL C 534 " --> pdb=" O TYR C 530 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL C 535 " --> pdb=" O ALA C 531 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE C 538 " --> pdb=" O VAL C 534 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER C 539 " --> pdb=" O VAL C 535 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ARG C 540 " --> pdb=" O LEU C 536 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ILE C 541 " --> pdb=" O SER C 537 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ALA C 542 " --> pdb=" O PHE C 538 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N TYR C 543 " --> pdb=" O SER C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 589 removed outlier: 3.666A pdb=" N ILE C 556 " --> pdb=" O GLY C 552 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER C 557 " --> pdb=" O PRO C 553 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N PHE C 566 " --> pdb=" O VAL C 562 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LYS C 567 " --> pdb=" O LYS C 563 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE C 568 " --> pdb=" O ASP C 564 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU C 571 " --> pdb=" O LYS C 567 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET C 574 " --> pdb=" O VAL C 570 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N TYR C 589 " --> pdb=" O ILE C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 614 removed outlier: 4.284A pdb=" N ILE C 613 " --> pdb=" O LEU C 609 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE C 614 " --> pdb=" O PHE C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 621 No H-bonds generated for 'chain 'C' and resid 619 through 621' Processing helix chain 'C' and resid 629 through 664 removed outlier: 3.868A pdb=" N VAL C 647 " --> pdb=" O ASN C 643 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER C 660 " --> pdb=" O ALA C 656 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER C 661 " --> pdb=" O MET C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 684 removed outlier: 3.904A pdb=" N LYS C 679 " --> pdb=" O PHE C 675 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR C 684 " --> pdb=" O LEU C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 785 Processing helix chain 'C' and resid 788 through 805 Processing helix chain 'D' and resid 26 through 37 removed outlier: 3.953A pdb=" N ALA D 34 " --> pdb=" O ARG D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 49 removed outlier: 3.718A pdb=" N MET D 46 " --> pdb=" O VAL D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 71 Processing helix chain 'D' and resid 75 through 81 removed outlier: 3.634A pdb=" N LEU D 80 " --> pdb=" O GLU D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 99 Processing helix chain 'D' and resid 104 through 110 Processing helix chain 'D' and resid 113 through 116 No H-bonds generated for 'chain 'D' and resid 113 through 116' Processing helix chain 'D' and resid 151 through 158 Processing helix chain 'D' and resid 161 through 170 removed outlier: 3.632A pdb=" N HIS D 165 " --> pdb=" O TYR D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 192 Processing helix chain 'D' and resid 195 through 209 removed outlier: 3.724A pdb=" N ILE D 203 " --> pdb=" O SER D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 218 Processing helix chain 'D' and resid 222 through 240 removed outlier: 3.965A pdb=" N ASN D 231 " --> pdb=" O LEU D 227 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN D 238 " --> pdb=" O ALA D 234 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE D 239 " --> pdb=" O LYS D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 264 removed outlier: 3.641A pdb=" N MET D 252 " --> pdb=" O ARG D 248 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN D 253 " --> pdb=" O LYS D 249 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL D 258 " --> pdb=" O CYS D 254 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU D 264 " --> pdb=" O GLY D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 274 Processing helix chain 'D' and resid 295 through 302 removed outlier: 3.956A pdb=" N LYS D 302 " --> pdb=" O LYS D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 312 through 322 removed outlier: 4.185A pdb=" N GLN D 317 " --> pdb=" O ASN D 313 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE D 321 " --> pdb=" O GLN D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 331 No H-bonds generated for 'chain 'D' and resid 329 through 331' Processing helix chain 'D' and resid 334 through 356 Proline residue: D 349 - end of helix removed outlier: 4.609A pdb=" N ALA D 352 " --> pdb=" O LEU D 348 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ILE D 353 " --> pdb=" O PRO D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 360 No H-bonds generated for 'chain 'D' and resid 358 through 360' Processing helix chain 'D' and resid 362 through 367 Processing helix chain 'D' and resid 370 through 391 Processing helix chain 'D' and resid 415 through 420 removed outlier: 3.924A pdb=" N THR D 419 " --> pdb=" O PHE D 415 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR D 420 " --> pdb=" O ARG D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 415 through 420' Processing helix chain 'D' and resid 424 through 447 removed outlier: 3.536A pdb=" N LEU D 428 " --> pdb=" O TRP D 424 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU D 434 " --> pdb=" O MET D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 454 Processing helix chain 'D' and resid 456 through 492 removed outlier: 3.923A pdb=" N GLN D 481 " --> pdb=" O LEU D 477 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA D 482 " --> pdb=" O ALA D 478 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER D 491 " --> pdb=" O GLN D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 511 removed outlier: 3.578A pdb=" N TYR D 509 " --> pdb=" O PRO D 505 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N PHE D 510 " --> pdb=" O GLU D 506 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR D 511 " --> pdb=" O ILE D 507 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 505 through 511' Processing helix chain 'D' and resid 522 through 543 removed outlier: 3.523A pdb=" N VAL D 534 " --> pdb=" O TYR D 530 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL D 535 " --> pdb=" O ALA D 531 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE D 538 " --> pdb=" O VAL D 534 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER D 539 " --> pdb=" O VAL D 535 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ARG D 540 " --> pdb=" O LEU D 536 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ILE D 541 " --> pdb=" O SER D 537 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ALA D 542 " --> pdb=" O PHE D 538 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N TYR D 543 " --> pdb=" O SER D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 589 removed outlier: 3.666A pdb=" N ILE D 556 " --> pdb=" O GLY D 552 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER D 557 " --> pdb=" O PRO D 553 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N PHE D 566 " --> pdb=" O VAL D 562 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LYS D 567 " --> pdb=" O LYS D 563 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE D 568 " --> pdb=" O ASP D 564 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU D 571 " --> pdb=" O LYS D 567 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N TYR D 589 " --> pdb=" O ILE D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 614 removed outlier: 4.283A pdb=" N ILE D 613 " --> pdb=" O LEU D 609 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE D 614 " --> pdb=" O PHE D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 621 No H-bonds generated for 'chain 'D' and resid 619 through 621' Processing helix chain 'D' and resid 629 through 664 removed outlier: 3.867A pdb=" N VAL D 647 " --> pdb=" O ASN D 643 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER D 660 " --> pdb=" O ALA D 656 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER D 661 " --> pdb=" O MET D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 684 removed outlier: 3.904A pdb=" N LYS D 679 " --> pdb=" O PHE D 675 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR D 684 " --> pdb=" O LEU D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 762 through 785 Processing helix chain 'D' and resid 788 through 805 1136 hydrogen bonds defined for protein. 3408 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.83 Time building geometry restraints manager: 8.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3334 1.32 - 1.45: 5818 1.45 - 1.57: 12168 1.57 - 1.69: 8 1.69 - 1.81: 176 Bond restraints: 21504 Sorted by residual: bond pdb=" C ILE C 40 " pdb=" N PRO C 41 " ideal model delta sigma weight residual 1.336 1.386 -0.050 1.20e-02 6.94e+03 1.73e+01 bond pdb=" C ILE D 40 " pdb=" N PRO D 41 " ideal model delta sigma weight residual 1.336 1.385 -0.049 1.20e-02 6.94e+03 1.68e+01 bond pdb=" C ILE A 40 " pdb=" N PRO A 41 " ideal model delta sigma weight residual 1.336 1.385 -0.049 1.20e-02 6.94e+03 1.68e+01 bond pdb=" C ILE B 40 " pdb=" N PRO B 41 " ideal model delta sigma weight residual 1.336 1.385 -0.049 1.20e-02 6.94e+03 1.67e+01 bond pdb=" N TYR C 410 " pdb=" CA TYR C 410 " ideal model delta sigma weight residual 1.453 1.489 -0.035 9.20e-03 1.18e+04 1.48e+01 ... (remaining 21499 not shown) Histogram of bond angle deviations from ideal: 98.42 - 105.59: 422 105.59 - 112.76: 11357 112.76 - 119.93: 7444 119.93 - 127.09: 9826 127.09 - 134.26: 239 Bond angle restraints: 29288 Sorted by residual: angle pdb=" N LEU D 217 " pdb=" CA LEU D 217 " pdb=" C LEU D 217 " ideal model delta sigma weight residual 113.17 121.07 -7.90 1.26e+00 6.30e-01 3.93e+01 angle pdb=" N LEU B 217 " pdb=" CA LEU B 217 " pdb=" C LEU B 217 " ideal model delta sigma weight residual 113.17 121.07 -7.90 1.26e+00 6.30e-01 3.93e+01 angle pdb=" N LEU A 217 " pdb=" CA LEU A 217 " pdb=" C LEU A 217 " ideal model delta sigma weight residual 113.17 121.05 -7.88 1.26e+00 6.30e-01 3.91e+01 angle pdb=" N LEU C 217 " pdb=" CA LEU C 217 " pdb=" C LEU C 217 " ideal model delta sigma weight residual 113.17 121.01 -7.84 1.26e+00 6.30e-01 3.87e+01 angle pdb=" N SER D 216 " pdb=" CA SER D 216 " pdb=" C SER D 216 " ideal model delta sigma weight residual 111.36 117.42 -6.06 1.09e+00 8.42e-01 3.09e+01 ... (remaining 29283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.02: 12312 30.02 - 60.05: 252 60.05 - 90.07: 24 90.07 - 120.10: 0 120.10 - 150.12: 8 Dihedral angle restraints: 12596 sinusoidal: 4280 harmonic: 8316 Sorted by residual: dihedral pdb=" CD ARG A 540 " pdb=" NE ARG A 540 " pdb=" CZ ARG A 540 " pdb=" NH1 ARG A 540 " ideal model delta sinusoidal sigma weight residual 0.00 -67.50 67.50 1 1.00e+01 1.00e-02 5.93e+01 dihedral pdb=" CD ARG B 540 " pdb=" NE ARG B 540 " pdb=" CZ ARG B 540 " pdb=" NH1 ARG B 540 " ideal model delta sinusoidal sigma weight residual 0.00 -67.49 67.49 1 1.00e+01 1.00e-02 5.92e+01 dihedral pdb=" CD ARG D 540 " pdb=" NE ARG D 540 " pdb=" CZ ARG D 540 " pdb=" NH1 ARG D 540 " ideal model delta sinusoidal sigma weight residual 0.00 -67.45 67.45 1 1.00e+01 1.00e-02 5.92e+01 ... (remaining 12593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2640 0.060 - 0.121: 664 0.121 - 0.181: 133 0.181 - 0.241: 23 0.241 - 0.302: 16 Chirality restraints: 3476 Sorted by residual: chirality pdb=" CA SER B 218 " pdb=" N SER B 218 " pdb=" C SER B 218 " pdb=" CB SER B 218 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CA SER A 218 " pdb=" N SER A 218 " pdb=" C SER A 218 " pdb=" CB SER A 218 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA SER C 218 " pdb=" N SER C 218 " pdb=" C SER C 218 " pdb=" CB SER C 218 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 3473 not shown) Planarity restraints: 3620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 540 " -1.013 9.50e-02 1.11e+02 4.54e-01 1.25e+02 pdb=" NE ARG B 540 " 0.061 2.00e-02 2.50e+03 pdb=" CZ ARG B 540 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 540 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 540 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 540 " -1.013 9.50e-02 1.11e+02 4.54e-01 1.24e+02 pdb=" NE ARG C 540 " 0.060 2.00e-02 2.50e+03 pdb=" CZ ARG C 540 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG C 540 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 540 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 540 " -1.013 9.50e-02 1.11e+02 4.54e-01 1.24e+02 pdb=" NE ARG A 540 " 0.061 2.00e-02 2.50e+03 pdb=" CZ ARG A 540 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 540 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 540 " -0.023 2.00e-02 2.50e+03 ... (remaining 3617 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 976 2.72 - 3.26: 20820 3.26 - 3.81: 31349 3.81 - 4.35: 37494 4.35 - 4.90: 64589 Nonbonded interactions: 155228 Sorted by model distance: nonbonded pdb=" OD1 ASP B 92 " pdb=" NH2 ARG B 144 " model vdw 2.171 2.520 nonbonded pdb=" OD1 ASP A 92 " pdb=" NH2 ARG A 144 " model vdw 2.172 2.520 nonbonded pdb=" OD1 ASP C 92 " pdb=" NH2 ARG C 144 " model vdw 2.172 2.520 nonbonded pdb=" OD1 ASP D 92 " pdb=" NH2 ARG D 144 " model vdw 2.172 2.520 nonbonded pdb=" OE1 GLU B 440 " pdb=" OH TYR B 452 " model vdw 2.279 2.440 ... (remaining 155223 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 104 5.16 5 C 13844 2.51 5 N 3484 2.21 5 O 3592 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 13.480 Check model and map are aligned: 0.290 Process input model: 52.680 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.190 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 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 : 0.007 0.059 21504 Z= 0.438 Angle : 1.133 11.573 29288 Z= 0.705 Chirality : 0.059 0.302 3476 Planarity : 0.017 0.454 3616 Dihedral : 12.629 150.120 7192 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.37 % Favored : 95.49 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.13), residues: 2792 helix: -1.63 (0.10), residues: 1948 sheet: None (None), residues: 0 loop : -2.59 (0.17), residues: 844 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 209 time to evaluate : 2.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 12 residues processed: 233 average time/residue: 0.3207 time to fit residues: 117.7766 Evaluate side-chains 163 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 151 time to evaluate : 2.593 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2489 time to fit residues: 8.6772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 236 optimal weight: 0.9990 chunk 212 optimal weight: 0.0770 chunk 117 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 chunk 219 optimal weight: 0.0170 chunk 84 optimal weight: 0.8980 chunk 133 optimal weight: 8.9990 chunk 163 optimal weight: 0.5980 chunk 254 optimal weight: 0.8980 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 112 HIS A 198 HIS ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 HIS B 198 HIS ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 HIS C 198 HIS C 508 GLN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 HIS D 198 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 21504 Z= 0.162 Angle : 0.565 9.856 29288 Z= 0.290 Chirality : 0.039 0.123 3476 Planarity : 0.005 0.063 3616 Dihedral : 9.772 111.409 3132 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.87 % Favored : 95.99 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.15), residues: 2792 helix: 0.27 (0.12), residues: 1948 sheet: None (None), residues: 0 loop : -2.16 (0.18), residues: 844 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 182 time to evaluate : 2.442 Fit side-chains outliers start: 17 outliers final: 10 residues processed: 189 average time/residue: 0.2869 time to fit residues: 89.6163 Evaluate side-chains 164 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 154 time to evaluate : 2.397 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1776 time to fit residues: 6.6933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 141 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 211 optimal weight: 10.0000 chunk 173 optimal weight: 2.9990 chunk 70 optimal weight: 20.0000 chunk 254 optimal weight: 0.9980 chunk 275 optimal weight: 3.9990 chunk 226 optimal weight: 0.6980 chunk 252 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 204 optimal weight: 0.5980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 21504 Z= 0.305 Angle : 0.576 11.257 29288 Z= 0.296 Chirality : 0.040 0.126 3476 Planarity : 0.004 0.034 3616 Dihedral : 9.131 112.236 3132 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.05 % Favored : 95.81 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.16), residues: 2792 helix: 1.04 (0.12), residues: 1968 sheet: None (None), residues: 0 loop : -2.05 (0.19), residues: 824 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 157 time to evaluate : 2.620 Fit side-chains outliers start: 25 outliers final: 12 residues processed: 180 average time/residue: 0.2566 time to fit residues: 81.1573 Evaluate side-chains 161 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 149 time to evaluate : 2.463 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2020 time to fit residues: 8.1462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 251 optimal weight: 0.8980 chunk 191 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 255 optimal weight: 1.9990 chunk 270 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 242 optimal weight: 0.0370 chunk 72 optimal weight: 0.0570 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS C 193 HIS D 193 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 21504 Z= 0.167 Angle : 0.505 12.397 29288 Z= 0.251 Chirality : 0.038 0.119 3476 Planarity : 0.003 0.034 3616 Dihedral : 8.582 102.255 3132 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.33 % Favored : 96.53 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.16), residues: 2792 helix: 1.61 (0.12), residues: 1964 sheet: None (None), residues: 0 loop : -1.83 (0.20), residues: 828 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 155 time to evaluate : 2.669 Fit side-chains outliers start: 26 outliers final: 12 residues processed: 173 average time/residue: 0.2622 time to fit residues: 79.0025 Evaluate side-chains 164 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 152 time to evaluate : 2.470 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1887 time to fit residues: 7.8521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 225 optimal weight: 4.9990 chunk 153 optimal weight: 0.7980 chunk 3 optimal weight: 0.0980 chunk 201 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 230 optimal weight: 0.0070 chunk 187 optimal weight: 0.0370 chunk 0 optimal weight: 30.0000 chunk 138 optimal weight: 40.0000 chunk 242 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 GLN B 193 HIS B 508 GLN C 193 HIS D 508 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 21504 Z= 0.119 Angle : 0.487 11.554 29288 Z= 0.237 Chirality : 0.037 0.115 3476 Planarity : 0.003 0.033 3616 Dihedral : 7.948 93.317 3132 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.04 % Favored : 96.81 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.16), residues: 2792 helix: 1.99 (0.12), residues: 1984 sheet: None (None), residues: 0 loop : -1.83 (0.20), residues: 808 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 167 time to evaluate : 2.526 Fit side-chains outliers start: 25 outliers final: 10 residues processed: 189 average time/residue: 0.2641 time to fit residues: 86.7421 Evaluate side-chains 159 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 149 time to evaluate : 2.471 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2056 time to fit residues: 6.9682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 91 optimal weight: 1.9990 chunk 243 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 158 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 270 optimal weight: 0.7980 chunk 224 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 142 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS B 193 HIS D 193 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 21504 Z= 0.176 Angle : 0.492 10.133 29288 Z= 0.241 Chirality : 0.038 0.117 3476 Planarity : 0.003 0.032 3616 Dihedral : 7.591 91.602 3132 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.15 % Favored : 96.70 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.16), residues: 2792 helix: 2.17 (0.12), residues: 1984 sheet: None (None), residues: 0 loop : -1.74 (0.20), residues: 808 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 153 time to evaluate : 2.380 Fit side-chains outliers start: 20 outliers final: 13 residues processed: 167 average time/residue: 0.2566 time to fit residues: 74.3686 Evaluate side-chains 158 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 145 time to evaluate : 2.348 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2520 time to fit residues: 8.8748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 261 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 154 optimal weight: 0.4980 chunk 197 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 228 optimal weight: 0.9980 chunk 151 optimal weight: 0.7980 chunk 269 optimal weight: 0.7980 chunk 168 optimal weight: 0.6980 chunk 164 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS B 193 HIS C 193 HIS D 193 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 21504 Z= 0.150 Angle : 0.480 13.065 29288 Z= 0.235 Chirality : 0.037 0.115 3476 Planarity : 0.003 0.033 3616 Dihedral : 7.318 90.930 3132 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.40 % Favored : 96.45 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.16), residues: 2792 helix: 2.31 (0.12), residues: 1984 sheet: None (None), residues: 0 loop : -1.66 (0.20), residues: 808 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 150 time to evaluate : 2.333 Fit side-chains outliers start: 16 outliers final: 7 residues processed: 158 average time/residue: 0.2762 time to fit residues: 73.8335 Evaluate side-chains 147 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 140 time to evaluate : 2.548 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1820 time to fit residues: 5.7912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 166 optimal weight: 0.7980 chunk 107 optimal weight: 6.9990 chunk 161 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 171 optimal weight: 6.9990 chunk 183 optimal weight: 0.9980 chunk 133 optimal weight: 0.8980 chunk 25 optimal weight: 0.0570 chunk 212 optimal weight: 0.2980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS B 193 HIS C 193 HIS D 193 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 21504 Z= 0.134 Angle : 0.464 12.186 29288 Z= 0.228 Chirality : 0.037 0.116 3476 Planarity : 0.003 0.033 3616 Dihedral : 6.963 88.864 3132 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.15 % Favored : 96.70 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.17), residues: 2792 helix: 2.53 (0.12), residues: 1984 sheet: None (None), residues: 0 loop : -1.65 (0.20), residues: 808 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 146 time to evaluate : 2.685 Fit side-chains outliers start: 12 outliers final: 0 residues processed: 154 average time/residue: 0.2675 time to fit residues: 72.0982 Evaluate side-chains 140 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 2.638 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 245 optimal weight: 0.5980 chunk 258 optimal weight: 1.9990 chunk 235 optimal weight: 0.6980 chunk 251 optimal weight: 10.0000 chunk 151 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 197 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 227 optimal weight: 0.9980 chunk 237 optimal weight: 8.9990 chunk 250 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS B 193 HIS C 193 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 21504 Z= 0.152 Angle : 0.488 14.394 29288 Z= 0.235 Chirality : 0.037 0.116 3476 Planarity : 0.003 0.033 3616 Dihedral : 6.809 87.873 3132 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.55 % Favored : 96.31 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.17), residues: 2792 helix: 2.56 (0.12), residues: 1988 sheet: None (None), residues: 0 loop : -1.59 (0.20), residues: 804 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 141 time to evaluate : 2.713 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 145 average time/residue: 0.2668 time to fit residues: 67.5237 Evaluate side-chains 141 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 2.434 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1812 time to fit residues: 3.6425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 165 optimal weight: 0.7980 chunk 265 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 126 optimal weight: 0.0570 chunk 184 optimal weight: 2.9990 chunk 278 optimal weight: 20.0000 chunk 256 optimal weight: 20.0000 chunk 222 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 171 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS B 193 HIS C 193 HIS D 193 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 21504 Z= 0.139 Angle : 0.473 13.959 29288 Z= 0.230 Chirality : 0.037 0.122 3476 Planarity : 0.003 0.033 3616 Dihedral : 6.619 86.790 3132 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.33 % Favored : 96.53 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.17), residues: 2792 helix: 2.64 (0.12), residues: 1988 sheet: None (None), residues: 0 loop : -1.59 (0.20), residues: 804 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 138 time to evaluate : 2.558 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 138 average time/residue: 0.2708 time to fit residues: 65.2050 Evaluate side-chains 136 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 2.330 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 176 optimal weight: 0.9980 chunk 236 optimal weight: 0.2980 chunk 68 optimal weight: 9.9990 chunk 204 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 61 optimal weight: 0.6980 chunk 222 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 228 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS B 193 HIS C 193 HIS D 193 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.098490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.072953 restraints weight = 46346.149| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.92 r_work: 0.2924 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 21504 Z= 0.153 Angle : 0.487 13.825 29288 Z= 0.235 Chirality : 0.037 0.125 3476 Planarity : 0.003 0.032 3616 Dihedral : 6.426 85.606 3132 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.72 % Favored : 96.13 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.17), residues: 2792 helix: 2.69 (0.12), residues: 1984 sheet: None (None), residues: 0 loop : -1.60 (0.20), residues: 808 =============================================================================== Job complete usr+sys time: 3343.66 seconds wall clock time: 61 minutes 53.33 seconds (3713.33 seconds total)