Starting phenix.real_space_refine on Mon Mar 18 13:23:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cud_7620/03_2024/6cud_7620_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cud_7620/03_2024/6cud_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_7620/03_2024/6cud_7620.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cud_7620/03_2024/6cud_7620.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cud_7620/03_2024/6cud_7620_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cud_7620/03_2024/6cud_7620_neut_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 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 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. 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.12, per 1000 atoms: 0.53 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: 7.79 Conformation dependent library (CDL) restraints added in 4.0 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: 4.18 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: 6.17 Time building geometry restraints manager: 8.48 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 - 31.33: 12432 31.33 - 62.67: 232 62.67 - 94.00: 40 94.00 - 125.34: 0 125.34 - 156.67: 24 Dihedral angle restraints: 12728 sinusoidal: 4412 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 12725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2636 0.060 - 0.121: 668 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 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: 6.010 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: 13.750 Check model and map are aligned: 0.290 Set scattering table: 0.200 Process input model: 53.750 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 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= 0.441 Angle : 1.135 11.573 29288 Z= 0.705 Chirality : 0.059 0.302 3476 Planarity : 0.017 0.454 3616 Dihedral : 14.710 156.670 7324 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 % Allowed : 5.53 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 611 HIS 0.006 0.002 HIS C 377 PHE 0.031 0.002 PHE D 538 TYR 0.035 0.002 TYR B 636 ARG 0.007 0.001 ARG B 677 *********************** 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 : 2.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 ASP cc_start: 0.7747 (m-30) cc_final: 0.7520 (m-30) REVERT: A 351 LEU cc_start: 0.7410 (mt) cc_final: 0.7055 (mt) REVERT: A 410 TYR cc_start: 0.5312 (OUTLIER) cc_final: 0.4272 (p90) REVERT: A 430 MET cc_start: 0.8349 (mmm) cc_final: 0.8100 (tpp) REVERT: A 521 ASP cc_start: 0.7881 (t0) cc_final: 0.7573 (t0) REVERT: B 246 ASP cc_start: 0.7717 (m-30) cc_final: 0.7506 (m-30) REVERT: B 351 LEU cc_start: 0.7448 (mt) cc_final: 0.7090 (mt) REVERT: B 410 TYR cc_start: 0.5533 (OUTLIER) cc_final: 0.4312 (p90) REVERT: B 430 MET cc_start: 0.8350 (mmm) cc_final: 0.8066 (tpp) REVERT: B 521 ASP cc_start: 0.8044 (t0) cc_final: 0.7662 (t0) REVERT: C 246 ASP cc_start: 0.7762 (m-30) cc_final: 0.7550 (m-30) REVERT: C 351 LEU cc_start: 0.7416 (mt) cc_final: 0.7051 (mt) REVERT: C 410 TYR cc_start: 0.5315 (OUTLIER) cc_final: 0.4327 (p90) REVERT: C 430 MET cc_start: 0.8352 (mmm) cc_final: 0.8093 (tpp) REVERT: C 521 ASP cc_start: 0.7909 (t0) cc_final: 0.7620 (t0) REVERT: D 351 LEU cc_start: 0.7426 (mt) cc_final: 0.7069 (mt) REVERT: D 410 TYR cc_start: 0.5433 (OUTLIER) cc_final: 0.4347 (p90) REVERT: D 430 MET cc_start: 0.8367 (mmm) cc_final: 0.8094 (tpp) REVERT: D 521 ASP cc_start: 0.7882 (t0) cc_final: 0.7569 (t0) outliers start: 28 outliers final: 12 residues processed: 233 average time/residue: 0.2883 time to fit residues: 106.2681 Evaluate side-chains 171 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 155 time to evaluate : 2.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 445 TRP Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 410 TYR Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 445 TRP Chi-restraints excluded: chain C residue 181 PHE Chi-restraints excluded: chain C residue 410 TYR Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 445 TRP Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain D residue 410 TYR Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 445 TRP 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: 0.6980 overall best weight: 0.4576 ------------------------------------------------------------------------------- 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 A 508 GLN ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 HIS B 198 HIS B 508 GLN ** 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 D 508 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21504 Z= 0.167 Angle : 0.574 8.817 29288 Z= 0.296 Chirality : 0.039 0.117 3476 Planarity : 0.004 0.047 3616 Dihedral : 15.000 154.687 3296 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.87 % Favored : 95.99 % Rotamer: Outliers : 1.42 % Allowed : 8.89 % Favored : 89.68 % 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: -0.88 (0.15), residues: 2792 helix: 0.14 (0.11), residues: 1948 sheet: None (None), residues: 0 loop : -2.21 (0.18), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 673 HIS 0.003 0.001 HIS C 628 PHE 0.018 0.001 PHE C 181 TYR 0.016 0.002 TYR B 488 ARG 0.007 0.001 ARG D 330 *********************** 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 206 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 179 time to evaluate : 2.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 LEU cc_start: 0.7373 (mt) cc_final: 0.7046 (mt) REVERT: A 445 TRP cc_start: 0.6527 (OUTLIER) cc_final: 0.5939 (t-100) REVERT: A 521 ASP cc_start: 0.7943 (t0) cc_final: 0.7644 (t0) REVERT: B 351 LEU cc_start: 0.7416 (mt) cc_final: 0.7084 (mt) REVERT: B 445 TRP cc_start: 0.6501 (OUTLIER) cc_final: 0.5867 (t-100) REVERT: C 351 LEU cc_start: 0.7332 (mt) cc_final: 0.7001 (mt) REVERT: C 445 TRP cc_start: 0.6424 (OUTLIER) cc_final: 0.5829 (t-100) REVERT: C 521 ASP cc_start: 0.7951 (t0) cc_final: 0.7670 (t0) REVERT: C 583 MET cc_start: 0.8937 (mmm) cc_final: 0.8717 (mmt) REVERT: D 351 LEU cc_start: 0.7357 (mt) cc_final: 0.7028 (mt) REVERT: D 445 TRP cc_start: 0.6444 (OUTLIER) cc_final: 0.5805 (t-100) REVERT: D 521 ASP cc_start: 0.7923 (t0) cc_final: 0.7617 (t0) outliers start: 27 outliers final: 15 residues processed: 199 average time/residue: 0.2918 time to fit residues: 95.1146 Evaluate side-chains 179 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 160 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 445 TRP Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 445 TRP Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain C residue 181 PHE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 445 TRP Chi-restraints excluded: chain C residue 550 SER Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 445 TRP Chi-restraints excluded: chain D residue 550 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 141 optimal weight: 10.0000 chunk 78 optimal weight: 0.4980 chunk 211 optimal weight: 9.9990 chunk 173 optimal weight: 0.8980 chunk 70 optimal weight: 20.0000 chunk 254 optimal weight: 0.6980 chunk 275 optimal weight: 0.7980 chunk 226 optimal weight: 0.9980 chunk 252 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 204 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 508 GLN B 508 GLN C 508 GLN D 508 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21504 Z= 0.175 Angle : 0.517 10.556 29288 Z= 0.262 Chirality : 0.038 0.118 3476 Planarity : 0.003 0.039 3616 Dihedral : 14.018 155.733 3288 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.40 % Favored : 96.45 % Rotamer: Outliers : 2.26 % Allowed : 10.53 % Favored : 87.21 % 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: 0.33 (0.16), residues: 2792 helix: 1.12 (0.12), residues: 1960 sheet: None (None), residues: 0 loop : -1.99 (0.19), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 356 HIS 0.003 0.001 HIS A 198 PHE 0.013 0.001 PHE C 181 TYR 0.016 0.001 TYR B 636 ARG 0.007 0.000 ARG C 330 *********************** 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 205 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 162 time to evaluate : 2.355 Fit side-chains REVERT: A 351 LEU cc_start: 0.7342 (mt) cc_final: 0.7009 (mt) REVERT: A 572 PHE cc_start: 0.8334 (t80) cc_final: 0.8046 (t80) REVERT: A 680 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9111 (tp) REVERT: B 351 LEU cc_start: 0.7377 (mt) cc_final: 0.7042 (mt) REVERT: B 452 TYR cc_start: 0.4501 (OUTLIER) cc_final: 0.4239 (m-80) REVERT: B 680 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9118 (tp) REVERT: C 351 LEU cc_start: 0.7396 (mt) cc_final: 0.7063 (mt) REVERT: C 572 PHE cc_start: 0.8319 (t80) cc_final: 0.8052 (t80) REVERT: C 680 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9126 (tp) REVERT: D 351 LEU cc_start: 0.7364 (mt) cc_final: 0.7032 (mt) REVERT: D 572 PHE cc_start: 0.8266 (t80) cc_final: 0.7996 (t80) REVERT: D 680 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9125 (tp) outliers start: 43 outliers final: 28 residues processed: 200 average time/residue: 0.2635 time to fit residues: 89.8345 Evaluate side-chains 185 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 152 time to evaluate : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 452 TYR Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain C residue 181 PHE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 550 SER Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 550 SER Chi-restraints excluded: chain D residue 680 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 251 optimal weight: 1.9990 chunk 191 optimal weight: 0.0070 chunk 132 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 255 optimal weight: 0.9990 chunk 270 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 242 optimal weight: 3.9990 chunk 72 optimal weight: 0.4980 overall best weight: 0.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 GLN B 508 GLN C 508 GLN D 193 HIS D 508 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 21504 Z= 0.183 Angle : 0.488 9.667 29288 Z= 0.247 Chirality : 0.038 0.121 3476 Planarity : 0.003 0.044 3616 Dihedral : 13.274 157.167 3280 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.55 % Favored : 96.31 % Rotamer: Outliers : 1.68 % Allowed : 11.47 % Favored : 86.84 % 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: 1.00 (0.16), residues: 2792 helix: 1.63 (0.12), residues: 1992 sheet: None (None), residues: 0 loop : -1.90 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 356 HIS 0.006 0.001 HIS D 193 PHE 0.018 0.001 PHE C 350 TYR 0.013 0.001 TYR B 488 ARG 0.011 0.001 ARG C 248 *********************** 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 193 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 161 time to evaluate : 2.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 LEU cc_start: 0.7322 (mt) cc_final: 0.7067 (mt) REVERT: A 464 MET cc_start: 0.7990 (ttp) cc_final: 0.7729 (ttp) REVERT: B 351 LEU cc_start: 0.7344 (mt) cc_final: 0.7083 (mt) REVERT: B 464 MET cc_start: 0.7973 (ttp) cc_final: 0.7722 (ttp) REVERT: B 569 MET cc_start: 0.6849 (tpt) cc_final: 0.6614 (tpt) REVERT: B 572 PHE cc_start: 0.8128 (t80) cc_final: 0.7912 (t80) REVERT: C 351 LEU cc_start: 0.7524 (mt) cc_final: 0.7247 (mt) REVERT: C 464 MET cc_start: 0.7961 (ttp) cc_final: 0.7710 (ttp) REVERT: C 572 PHE cc_start: 0.8129 (t80) cc_final: 0.7893 (t80) REVERT: C 583 MET cc_start: 0.9000 (mmm) cc_final: 0.8775 (mmt) REVERT: D 194 ASP cc_start: 0.8217 (t0) cc_final: 0.7955 (t0) REVERT: D 351 LEU cc_start: 0.7337 (mt) cc_final: 0.7075 (mt) REVERT: D 464 MET cc_start: 0.7971 (ttp) cc_final: 0.7724 (ttp) REVERT: D 569 MET cc_start: 0.6868 (tpt) cc_final: 0.6618 (tpt) REVERT: D 572 PHE cc_start: 0.8092 (t80) cc_final: 0.7845 (t80) outliers start: 32 outliers final: 28 residues processed: 190 average time/residue: 0.2611 time to fit residues: 83.0996 Evaluate side-chains 179 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 151 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain C residue 181 PHE Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 550 SER Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain D residue 184 CYS Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 550 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 225 optimal weight: 0.7980 chunk 153 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 201 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 230 optimal weight: 0.0970 chunk 187 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 138 optimal weight: 40.0000 chunk 242 optimal weight: 1.9990 chunk 68 optimal weight: 0.0030 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 HIS C 193 HIS D 193 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 21504 Z= 0.131 Angle : 0.465 9.361 29288 Z= 0.231 Chirality : 0.037 0.117 3476 Planarity : 0.003 0.032 3616 Dihedral : 12.836 156.280 3280 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.01 % Favored : 96.85 % Rotamer: Outliers : 3.05 % Allowed : 10.63 % Favored : 86.32 % 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: 1.48 (0.16), residues: 2792 helix: 2.04 (0.12), residues: 1984 sheet: None (None), residues: 0 loop : -1.85 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 356 HIS 0.008 0.001 HIS A 193 PHE 0.012 0.001 PHE C 350 TYR 0.011 0.001 TYR B 488 ARG 0.004 0.000 ARG C 248 *********************** 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 212 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 154 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 MET cc_start: 0.7939 (ttp) cc_final: 0.7708 (ttp) REVERT: A 564 ASP cc_start: 0.8228 (t0) cc_final: 0.7997 (t0) REVERT: A 680 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9085 (tp) REVERT: B 464 MET cc_start: 0.7962 (ttp) cc_final: 0.7751 (ttp) REVERT: B 572 PHE cc_start: 0.8069 (t80) cc_final: 0.7847 (t80) REVERT: B 680 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9085 (tp) REVERT: C 464 MET cc_start: 0.7954 (ttp) cc_final: 0.7740 (ttp) REVERT: C 583 MET cc_start: 0.9001 (mmm) cc_final: 0.8780 (mmt) REVERT: C 680 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9093 (tp) REVERT: D 194 ASP cc_start: 0.8096 (t0) cc_final: 0.7794 (t0) REVERT: D 464 MET cc_start: 0.7946 (ttp) cc_final: 0.7730 (ttp) REVERT: D 569 MET cc_start: 0.6915 (tpt) cc_final: 0.6697 (tpt) REVERT: D 572 PHE cc_start: 0.8031 (t80) cc_final: 0.7800 (t80) REVERT: D 680 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9093 (tp) outliers start: 58 outliers final: 37 residues processed: 203 average time/residue: 0.2637 time to fit residues: 89.9463 Evaluate side-chains 189 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 148 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain C residue 181 PHE Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain D residue 184 CYS Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 680 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 91 optimal weight: 0.8980 chunk 243 optimal weight: 0.0270 chunk 53 optimal weight: 4.9990 chunk 158 optimal weight: 0.6980 chunk 66 optimal weight: 0.0170 chunk 270 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- 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: 0.8015 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 21504 Z= 0.131 Angle : 0.461 8.138 29288 Z= 0.228 Chirality : 0.037 0.118 3476 Planarity : 0.003 0.031 3616 Dihedral : 12.585 155.819 3280 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.08 % Favored : 96.78 % Rotamer: Outliers : 2.68 % Allowed : 11.11 % Favored : 86.21 % 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: 1.75 (0.16), residues: 2792 helix: 2.28 (0.12), residues: 1964 sheet: None (None), residues: 0 loop : -1.73 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 356 HIS 0.007 0.001 HIS A 193 PHE 0.012 0.001 PHE C 350 TYR 0.010 0.001 TYR B 488 ARG 0.005 0.000 ARG C 248 *********************** 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 207 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 156 time to evaluate : 2.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 680 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9108 (tp) REVERT: B 572 PHE cc_start: 0.8046 (t80) cc_final: 0.7824 (t80) REVERT: B 680 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9113 (tp) REVERT: C 569 MET cc_start: 0.6942 (tpt) cc_final: 0.6741 (tpt) REVERT: C 680 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9123 (tp) REVERT: D 194 ASP cc_start: 0.8076 (t0) cc_final: 0.7771 (t0) REVERT: D 572 PHE cc_start: 0.7999 (t80) cc_final: 0.7759 (t80) REVERT: D 680 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9119 (tp) outliers start: 51 outliers final: 36 residues processed: 197 average time/residue: 0.2719 time to fit residues: 89.4930 Evaluate side-chains 180 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 140 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain C residue 181 PHE Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 550 SER Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 680 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 261 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 197 optimal weight: 0.6980 chunk 153 optimal weight: 0.9980 chunk 228 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 269 optimal weight: 0.0980 chunk 168 optimal weight: 0.8980 chunk 164 optimal weight: 0.2980 chunk 124 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.8012 moved from start: 0.2780 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= 0.128 Angle : 0.456 8.288 29288 Z= 0.226 Chirality : 0.037 0.122 3476 Planarity : 0.003 0.031 3616 Dihedral : 12.365 154.838 3280 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.47 % Favored : 96.38 % Rotamer: Outliers : 2.42 % Allowed : 12.16 % Favored : 85.42 % 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: 1.96 (0.17), residues: 2792 helix: 2.46 (0.12), residues: 1960 sheet: None (None), residues: 0 loop : -1.70 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 356 HIS 0.006 0.001 HIS B 193 PHE 0.011 0.001 PHE B 350 TYR 0.010 0.001 TYR B 488 ARG 0.004 0.000 ARG C 248 *********************** 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 192 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 146 time to evaluate : 2.198 Fit side-chains REVERT: A 680 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9104 (tp) REVERT: B 572 PHE cc_start: 0.8007 (t80) cc_final: 0.7791 (t80) REVERT: B 680 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9106 (tp) REVERT: C 680 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9117 (tp) REVERT: D 194 ASP cc_start: 0.8076 (t0) cc_final: 0.7781 (t0) REVERT: D 572 PHE cc_start: 0.7979 (t80) cc_final: 0.7741 (t80) REVERT: D 680 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9118 (tp) outliers start: 46 outliers final: 37 residues processed: 179 average time/residue: 0.2799 time to fit residues: 84.4904 Evaluate side-chains 176 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 135 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain D residue 184 CYS Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 550 SER Chi-restraints excluded: chain D residue 680 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 166 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 161 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 171 optimal weight: 0.1980 chunk 183 optimal weight: 0.9980 chunk 133 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 212 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.8032 moved from start: 0.2830 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= 0.157 Angle : 0.460 9.097 29288 Z= 0.229 Chirality : 0.037 0.125 3476 Planarity : 0.003 0.030 3616 Dihedral : 12.221 154.462 3276 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.30 % Favored : 96.56 % Rotamer: Outliers : 3.00 % Allowed : 12.32 % Favored : 84.68 % 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: 2.10 (0.17), residues: 2792 helix: 2.52 (0.12), residues: 1980 sheet: None (None), residues: 0 loop : -1.63 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 356 HIS 0.006 0.001 HIS A 193 PHE 0.011 0.001 PHE B 350 TYR 0.009 0.001 TYR B 488 ARG 0.002 0.000 ARG D 330 *********************** 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 199 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 142 time to evaluate : 2.460 Fit side-chains REVERT: A 680 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9102 (tp) REVERT: B 572 PHE cc_start: 0.7994 (t80) cc_final: 0.7766 (t80) REVERT: B 680 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9104 (tp) REVERT: C 583 MET cc_start: 0.8925 (mmm) cc_final: 0.8720 (mmt) REVERT: C 680 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9115 (tp) REVERT: D 194 ASP cc_start: 0.8094 (t0) cc_final: 0.7810 (t0) REVERT: D 680 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9113 (tp) outliers start: 57 outliers final: 41 residues processed: 186 average time/residue: 0.2424 time to fit residues: 78.3129 Evaluate side-chains 183 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 138 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 550 SER Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 184 CYS Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 550 SER Chi-restraints excluded: chain D residue 680 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 245 optimal weight: 0.7980 chunk 258 optimal weight: 0.0030 chunk 235 optimal weight: 2.9990 chunk 251 optimal weight: 3.9990 chunk 151 optimal weight: 0.0980 chunk 109 optimal weight: 0.6980 chunk 197 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 227 optimal weight: 4.9990 chunk 237 optimal weight: 0.4980 chunk 250 optimal weight: 0.7980 overall best weight: 0.4190 ------------------------------------------------------------------------------- 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: 0.8003 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21504 Z= 0.116 Angle : 0.450 9.236 29288 Z= 0.221 Chirality : 0.037 0.129 3476 Planarity : 0.003 0.030 3616 Dihedral : 12.011 152.520 3272 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.12 % Favored : 96.74 % Rotamer: Outliers : 2.68 % Allowed : 12.58 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.17), residues: 2792 helix: 2.64 (0.12), residues: 1960 sheet: None (None), residues: 0 loop : -1.57 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP B 356 HIS 0.006 0.001 HIS A 193 PHE 0.009 0.001 PHE C 350 TYR 0.010 0.001 TYR B 488 ARG 0.003 0.000 ARG D 330 *********************** 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 196 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 145 time to evaluate : 2.502 Fit side-chains REVERT: A 680 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9096 (tp) REVERT: B 572 PHE cc_start: 0.7927 (t80) cc_final: 0.7713 (t80) REVERT: B 680 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9095 (tp) REVERT: C 680 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9109 (tp) REVERT: D 194 ASP cc_start: 0.8012 (t0) cc_final: 0.7732 (t0) REVERT: D 572 PHE cc_start: 0.7790 (t80) cc_final: 0.7583 (t80) REVERT: D 680 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9101 (tp) outliers start: 51 outliers final: 43 residues processed: 184 average time/residue: 0.2447 time to fit residues: 77.8035 Evaluate side-chains 183 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 136 time to evaluate : 2.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 550 SER Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 184 CYS Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 550 SER Chi-restraints excluded: chain D residue 680 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 165 optimal weight: 0.9990 chunk 265 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 126 optimal weight: 0.0980 chunk 184 optimal weight: 3.9990 chunk 278 optimal weight: 30.0000 chunk 256 optimal weight: 6.9990 chunk 222 optimal weight: 0.0270 chunk 23 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 overall best weight: 0.5842 ------------------------------------------------------------------------------- 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: 0.8015 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 21504 Z= 0.134 Angle : 0.453 9.750 29288 Z= 0.223 Chirality : 0.037 0.132 3476 Planarity : 0.003 0.030 3616 Dihedral : 11.939 152.209 3272 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.40 % Favored : 96.45 % Rotamer: Outliers : 2.74 % Allowed : 12.89 % Favored : 84.37 % 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: 2.29 (0.17), residues: 2792 helix: 2.71 (0.12), residues: 1956 sheet: None (None), residues: 0 loop : -1.56 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 356 HIS 0.006 0.001 HIS A 193 PHE 0.010 0.001 PHE C 350 TYR 0.008 0.001 TYR B 488 ARG 0.003 0.000 ARG C 248 ********************** 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 191 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 139 time to evaluate : 2.526 Fit side-chains REVERT: A 680 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9089 (tp) REVERT: B 572 PHE cc_start: 0.7931 (t80) cc_final: 0.7691 (t80) REVERT: B 680 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9091 (tp) REVERT: C 680 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9102 (tp) REVERT: D 194 ASP cc_start: 0.8024 (t0) cc_final: 0.7746 (t0) REVERT: D 572 PHE cc_start: 0.7786 (t80) cc_final: 0.7581 (t80) REVERT: D 680 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9100 (tp) outliers start: 52 outliers final: 38 residues processed: 179 average time/residue: 0.2431 time to fit residues: 75.5484 Evaluate side-chains 178 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 136 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 550 SER Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 184 CYS Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 550 SER Chi-restraints excluded: chain D residue 680 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 176 optimal weight: 4.9990 chunk 236 optimal weight: 0.0470 chunk 68 optimal weight: 3.9990 chunk 204 optimal weight: 0.7980 chunk 32 optimal weight: 0.0870 chunk 61 optimal weight: 0.5980 chunk 222 optimal weight: 0.0010 chunk 93 optimal weight: 0.9990 chunk 228 optimal weight: 0.9990 chunk 28 optimal weight: 0.0980 chunk 40 optimal weight: 3.9990 overall best weight: 0.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN A 193 HIS C 191 GLN C 193 HIS D 191 GLN D 193 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.101500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.076551 restraints weight = 46163.123| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.89 r_work: 0.2992 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21504 Z= 0.101 Angle : 0.444 9.320 29288 Z= 0.219 Chirality : 0.036 0.137 3476 Planarity : 0.003 0.030 3616 Dihedral : 11.752 150.170 3272 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.01 % Favored : 96.85 % Rotamer: Outliers : 2.47 % Allowed : 12.95 % Favored : 84.58 % 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: 2.46 (0.17), residues: 2792 helix: 2.83 (0.12), residues: 1960 sheet: None (None), residues: 0 loop : -1.49 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP C 356 HIS 0.007 0.001 HIS A 193 PHE 0.009 0.001 PHE B 350 TYR 0.011 0.001 TYR B 488 ARG 0.003 0.000 ARG C 248 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3487.36 seconds wall clock time: 63 minutes 47.67 seconds (3827.67 seconds total)