Starting phenix.real_space_refine on Sun Jun 22 18:03:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dre_27676/06_2025/8dre_27676.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dre_27676/06_2025/8dre_27676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dre_27676/06_2025/8dre_27676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dre_27676/06_2025/8dre_27676.map" model { file = "/net/cci-nas-00/data/ceres_data/8dre_27676/06_2025/8dre_27676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dre_27676/06_2025/8dre_27676.cif" } resolution = 3.18 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= 0.019 sd= 0.067 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 9 5.49 5 S 138 5.16 5 C 17031 2.51 5 N 4192 2.21 5 O 4570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25940 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5915 Classifications: {'peptide': 717} Link IDs: {'PTRANS': 27, 'TRANS': 689} Chain breaks: 2 Chain: "B" Number of atoms: 5911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 5911 Classifications: {'peptide': 716} Link IDs: {'PTRANS': 27, 'TRANS': 688} Chain breaks: 2 Chain: "C" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2519 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 9, 'TRANS': 290} Chain breaks: 2 Chain: "D" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2653 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "E" Number of atoms: 2651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2651 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "F" Number of atoms: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5751 Classifications: {'peptide': 704} Link IDs: {'PTRANS': 24, 'TRANS': 679} Chain breaks: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 116 Unusual residues: {'PEE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 115 Unusual residues: {'PEE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {'PEE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 15.35, per 1000 atoms: 0.59 Number of scatterers: 25940 At special positions: 0 Unit cell: (119.472, 124.712, 195.976, 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 138 16.00 P 9 15.00 O 4570 8.00 N 4192 7.00 C 17031 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.04 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 308 " distance=2.03 Simple disulfide: pdb=" SG CYS F 115 " - pdb=" SG CYS F 293 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.17 Conformation dependent library (CDL) restraints added in 3.4 seconds 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5966 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 17 sheets defined 59.2% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.83 Creating SS restraints... Processing helix chain 'A' and resid 15 through 21 removed outlier: 4.202A pdb=" N ARG A 18 " --> pdb=" O PRO A 15 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE A 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 50 removed outlier: 3.937A pdb=" N ASP A 50 " --> pdb=" O GLN A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 117 Processing helix chain 'A' and resid 119 through 141 Proline residue: A 126 - end of helix Processing helix chain 'A' and resid 141 through 146 removed outlier: 3.569A pdb=" N LYS A 145 " --> pdb=" O ASN A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 165 removed outlier: 4.203A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 175 removed outlier: 4.191A pdb=" N THR A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 Processing helix chain 'A' and resid 258 through 286 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 315 through 346 removed outlier: 4.141A pdb=" N ARG A 346 " --> pdb=" O TRP A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 360 Processing helix chain 'A' and resid 369 through 383 Processing helix chain 'A' and resid 383 through 392 removed outlier: 4.100A pdb=" N SER A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 411 Processing helix chain 'A' and resid 412 through 420 Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.637A pdb=" N PHE A 443 " --> pdb=" O PRO A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 467 removed outlier: 3.527A pdb=" N ILE A 465 " --> pdb=" O PRO A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 495 Processing helix chain 'A' and resid 536 through 542 removed outlier: 3.889A pdb=" N GLY A 539 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 541 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 566 removed outlier: 3.694A pdb=" N THR A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 590 removed outlier: 3.911A pdb=" N LYS A 588 " --> pdb=" O ASN A 585 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS A 589 " --> pdb=" O SER A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 613 Processing helix chain 'A' and resid 629 through 638 removed outlier: 3.954A pdb=" N ILE A 633 " --> pdb=" O GLU A 630 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN A 636 " --> pdb=" O ILE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 661 Processing helix chain 'A' and resid 680 through 684 removed outlier: 3.606A pdb=" N CYS A 684 " --> pdb=" O LEU A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 706 Processing helix chain 'A' and resid 724 through 730 removed outlier: 3.644A pdb=" N CYS A 730 " --> pdb=" O LEU A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 753 removed outlier: 3.549A pdb=" N VAL A 750 " --> pdb=" O PRO A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 776 removed outlier: 3.655A pdb=" N CYS A 776 " --> pdb=" O LEU A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 793 Processing helix chain 'A' and resid 795 through 808 Processing helix chain 'B' and resid 16 through 21 removed outlier: 4.053A pdb=" N ILE B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 49 Processing helix chain 'B' and resid 102 through 117 Processing helix chain 'B' and resid 119 through 146 Proline residue: B 126 - end of helix removed outlier: 4.559A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 165 removed outlier: 3.917A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 175 removed outlier: 4.226A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 Processing helix chain 'B' and resid 259 through 286 Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 314 through 343 removed outlier: 4.095A pdb=" N PHE B 324 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR B 325 " --> pdb=" O LEU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 360 Processing helix chain 'B' and resid 369 through 383 Processing helix chain 'B' and resid 383 through 391 removed outlier: 4.127A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 395 through 411 Processing helix chain 'B' and resid 412 through 419 Processing helix chain 'B' and resid 440 through 445 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 484 through 495 removed outlier: 3.647A pdb=" N GLU B 493 " --> pdb=" O ALA B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 508 removed outlier: 3.878A pdb=" N GLU B 507 " --> pdb=" O ASP B 504 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 508 " --> pdb=" O ILE B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 566 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 586 through 590 removed outlier: 4.011A pdb=" N LYS B 589 " --> pdb=" O SER B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 removed outlier: 3.512A pdb=" N LEU B 613 " --> pdb=" O ILE B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 638 removed outlier: 3.756A pdb=" N HIS B 637 " --> pdb=" O SER B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 661 removed outlier: 3.718A pdb=" N ILE B 658 " --> pdb=" O PRO B 655 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 661 " --> pdb=" O ILE B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 684 removed outlier: 3.866A pdb=" N CYS B 684 " --> pdb=" O LEU B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 705 removed outlier: 3.619A pdb=" N ILE B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 729 Processing helix chain 'B' and resid 747 through 752 removed outlier: 3.638A pdb=" N VAL B 750 " --> pdb=" O PRO B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 776 removed outlier: 3.510A pdb=" N CYS B 776 " --> pdb=" O LEU B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 792 Processing helix chain 'B' and resid 795 through 808 Processing helix chain 'C' and resid 22 through 49 removed outlier: 3.577A pdb=" N GLN C 49 " --> pdb=" O LEU C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 117 Processing helix chain 'C' and resid 119 through 146 Proline residue: C 126 - end of helix removed outlier: 4.420A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 165 Processing helix chain 'C' and resid 167 through 175 removed outlier: 3.767A pdb=" N ARG C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 255 Processing helix chain 'C' and resid 258 through 286 removed outlier: 3.577A pdb=" N PHE C 275 " --> pdb=" O LYS C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 314 through 343 removed outlier: 3.500A pdb=" N ALA C 322 " --> pdb=" O PHE C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 360 Processing helix chain 'C' and resid 370 through 383 Processing helix chain 'C' and resid 383 through 392 removed outlier: 4.284A pdb=" N SER C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 401 Processing helix chain 'D' and resid 15 through 21 removed outlier: 3.959A pdb=" N ILE D 19 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 49 Processing helix chain 'D' and resid 102 through 117 Processing helix chain 'D' and resid 119 through 146 Proline residue: D 126 - end of helix removed outlier: 4.706A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 166 Processing helix chain 'D' and resid 166 through 175 removed outlier: 4.019A pdb=" N THR D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU D 175 " --> pdb=" O ARG D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 removed outlier: 3.644A pdb=" N GLU D 255 " --> pdb=" O ARG D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 286 Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 314 through 346 removed outlier: 4.171A pdb=" N ARG D 346 " --> pdb=" O TRP D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 360 Processing helix chain 'D' and resid 369 through 383 Processing helix chain 'D' and resid 383 through 391 removed outlier: 4.217A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 394 No H-bonds generated for 'chain 'D' and resid 392 through 394' Processing helix chain 'D' and resid 395 through 410 Processing helix chain 'E' and resid 15 through 19 removed outlier: 3.686A pdb=" N ARG E 18 " --> pdb=" O PRO E 15 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE E 19 " --> pdb=" O ALA E 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 15 through 19' Processing helix chain 'E' and resid 22 through 50 removed outlier: 3.632A pdb=" N ASP E 50 " --> pdb=" O GLN E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 117 Processing helix chain 'E' and resid 119 through 146 Proline residue: E 126 - end of helix removed outlier: 4.499A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 165 Processing helix chain 'E' and resid 166 through 175 removed outlier: 4.226A pdb=" N THR E 170 " --> pdb=" O SER E 166 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG E 171 " --> pdb=" O PRO E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 Processing helix chain 'E' and resid 259 through 286 Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 314 through 345 removed outlier: 3.542A pdb=" N ALA E 322 " --> pdb=" O PHE E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 358 removed outlier: 3.596A pdb=" N GLU E 358 " --> pdb=" O GLU E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 383 Processing helix chain 'E' and resid 383 through 391 removed outlier: 4.198A pdb=" N SER E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 394 No H-bonds generated for 'chain 'E' and resid 392 through 394' Processing helix chain 'E' and resid 395 through 409 removed outlier: 3.524A pdb=" N GLU E 399 " --> pdb=" O SER E 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 47 Processing helix chain 'F' and resid 104 through 119 Processing helix chain 'F' and resid 121 through 143 Proline residue: F 128 - end of helix removed outlier: 4.236A pdb=" N ASN F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 167 Processing helix chain 'F' and resid 168 through 179 removed outlier: 3.949A pdb=" N THR F 172 " --> pdb=" O SER F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 253 Processing helix chain 'F' and resid 256 through 284 removed outlier: 3.593A pdb=" N ALA F 260 " --> pdb=" O ASP F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 287 No H-bonds generated for 'chain 'F' and resid 285 through 287' Processing helix chain 'F' and resid 297 through 302 Processing helix chain 'F' and resid 312 through 344 removed outlier: 4.001A pdb=" N ARG F 344 " --> pdb=" O TRP F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 358 removed outlier: 4.191A pdb=" N GLU F 357 " --> pdb=" O TYR F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 381 removed outlier: 3.608A pdb=" N ALA F 371 " --> pdb=" O LYS F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 389 removed outlier: 4.010A pdb=" N SER F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 392 No H-bonds generated for 'chain 'F' and resid 390 through 392' Processing helix chain 'F' and resid 394 through 409 Processing helix chain 'F' and resid 410 through 418 Processing helix chain 'F' and resid 460 through 466 removed outlier: 3.649A pdb=" N ILE F 463 " --> pdb=" O PRO F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 493 Processing helix chain 'F' and resid 502 through 506 Processing helix chain 'F' and resid 508 through 513 removed outlier: 3.710A pdb=" N TYR F 511 " --> pdb=" O PRO F 508 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU F 513 " --> pdb=" O MET F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 540 removed outlier: 4.042A pdb=" N ARG F 539 " --> pdb=" O GLU F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 563 removed outlier: 3.573A pdb=" N VAL F 561 " --> pdb=" O PRO F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 582 through 587 Processing helix chain 'F' and resid 605 through 610 Processing helix chain 'F' and resid 629 through 636 removed outlier: 4.564A pdb=" N GLN F 634 " --> pdb=" O VAL F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 653 through 659 removed outlier: 3.797A pdb=" N ILE F 656 " --> pdb=" O PRO F 653 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU F 659 " --> pdb=" O ILE F 656 " (cutoff:3.500A) Processing helix chain 'F' and resid 676 through 682 removed outlier: 3.938A pdb=" N PHE F 680 " --> pdb=" O PRO F 676 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N CYS F 682 " --> pdb=" O HIS F 678 " (cutoff:3.500A) Processing helix chain 'F' and resid 699 through 705 removed outlier: 3.537A pdb=" N ILE F 702 " --> pdb=" O PRO F 699 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY F 703 " --> pdb=" O PRO F 700 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 728 Processing helix chain 'F' and resid 768 through 774 removed outlier: 3.696A pdb=" N CYS F 774 " --> pdb=" O LEU F 771 " (cutoff:3.500A) Processing helix chain 'F' and resid 785 through 791 Processing helix chain 'F' and resid 793 through 802 removed outlier: 3.839A pdb=" N MET F 800 " --> pdb=" O VAL F 796 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 3.683A pdb=" N VAL A 60 " --> pdb=" O VAL F 94 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL F 94 " --> pdb=" O VAL A 60 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 421 through 422 removed outlier: 6.379A pdb=" N LEU A 428 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LYS A 452 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU A 430 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLU A 454 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU A 432 " --> pdb=" O GLU A 454 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU A 451 " --> pdb=" O TRP A 475 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N TYR A 477 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU A 453 " --> pdb=" O TYR A 477 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU A 572 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE A 599 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ILE A 574 " --> pdb=" O ILE A 599 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU A 596 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE A 619 " --> pdb=" O LYS A 645 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 459 through 461 removed outlier: 6.351A pdb=" N VAL A 459 " --> pdb=" O LYS A 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 666 through 668 removed outlier: 3.660A pdb=" N ASP A 691 " --> pdb=" O LEU A 667 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 759 through 760 removed outlier: 6.341A pdb=" N ILE A 759 " --> pdb=" O VAL A 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA8, first strand: chain 'B' and resid 420 through 422 removed outlier: 6.518A pdb=" N LEU B 428 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LYS B 452 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU B 430 " --> pdb=" O LYS B 452 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLU B 454 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU B 432 " --> pdb=" O GLU B 454 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEU B 451 " --> pdb=" O TRP B 475 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N TYR B 477 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU B 453 " --> pdb=" O TYR B 477 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU B 474 " --> pdb=" O HIS B 499 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LYS B 501 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LEU B 476 " --> pdb=" O LYS B 501 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU B 498 " --> pdb=" O HIS B 522 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N THR B 524 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE B 500 " --> pdb=" O THR B 524 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER B 573 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU B 644 " --> pdb=" O TYR B 668 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU B 667 " --> pdb=" O ASP B 691 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 459 through 461 Processing sheet with id=AB1, first strand: chain 'B' and resid 712 through 714 removed outlier: 7.029A pdb=" N LEU B 713 " --> pdb=" O HIS B 737 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AB3, first strand: chain 'C' and resid 350 through 351 Processing sheet with id=AB4, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AB5, first strand: chain 'E' and resid 53 through 56 Processing sheet with id=AB6, first strand: chain 'F' and resid 52 through 56 Processing sheet with id=AB7, first strand: chain 'F' and resid 419 through 420 removed outlier: 6.080A pdb=" N LEU F 426 " --> pdb=" O SER F 448 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LYS F 450 " --> pdb=" O LEU F 426 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LEU F 428 " --> pdb=" O LYS F 450 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLU F 452 " --> pdb=" O LEU F 428 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU F 430 " --> pdb=" O GLU F 452 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU F 449 " --> pdb=" O CYS F 473 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N HIS F 475 " --> pdb=" O LEU F 449 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU F 451 " --> pdb=" O HIS F 475 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU F 472 " --> pdb=" O SER F 497 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N LYS F 499 " --> pdb=" O LEU F 472 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU F 474 " --> pdb=" O LYS F 499 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N MET F 570 " --> pdb=" O GLU F 595 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL F 597 " --> pdb=" O MET F 570 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N VAL F 572 " --> pdb=" O VAL F 597 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU F 617 " --> pdb=" O LYS F 643 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS F 735 " --> pdb=" O PHE F 711 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP F 758 " --> pdb=" O LEU F 734 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU F 757 " --> pdb=" O VAL F 783 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 457 through 459 removed outlier: 5.735A pdb=" N VAL F 457 " --> pdb=" O LYS F 480 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 1303 hydrogen bonds defined for protein. 3657 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: 12.09 Time building geometry restraints manager: 7.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4501 1.33 - 1.45: 6761 1.45 - 1.57: 15055 1.57 - 1.70: 10 1.70 - 1.82: 204 Bond restraints: 26531 Sorted by residual: bond pdb=" C LYS F 399 " pdb=" N LEU F 400 " ideal model delta sigma weight residual 1.335 1.445 -0.110 1.31e-02 5.83e+03 7.02e+01 bond pdb=" C10 PEE F 902 " pdb=" O4 PEE F 902 " ideal model delta sigma weight residual 1.206 1.358 -0.152 2.00e-02 2.50e+03 5.79e+01 bond pdb=" C10 PEE E 902 " pdb=" O4 PEE E 902 " ideal model delta sigma weight residual 1.206 1.358 -0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" C10 PEE F 903 " pdb=" O4 PEE F 903 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" C10 PEE C 902 " pdb=" O4 PEE C 902 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 26526 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 35316 2.78 - 5.57: 360 5.57 - 8.35: 84 8.35 - 11.13: 15 11.13 - 13.91: 15 Bond angle restraints: 35790 Sorted by residual: angle pdb=" C LYS F 399 " pdb=" N LEU F 400 " pdb=" CA LEU F 400 " ideal model delta sigma weight residual 120.28 110.14 10.14 1.34e+00 5.57e-01 5.73e+01 angle pdb=" CA LYS F 399 " pdb=" C LYS F 399 " pdb=" N LEU F 400 " ideal model delta sigma weight residual 117.17 109.59 7.58 1.18e+00 7.18e-01 4.12e+01 angle pdb=" O LYS F 399 " pdb=" C LYS F 399 " pdb=" N LEU F 400 " ideal model delta sigma weight residual 122.09 128.79 -6.70 1.08e+00 8.57e-01 3.85e+01 angle pdb=" C ASN F 368 " pdb=" CA ASN F 368 " pdb=" CB ASN F 368 " ideal model delta sigma weight residual 116.63 109.95 6.68 1.16e+00 7.43e-01 3.32e+01 angle pdb=" C ASN E 370 " pdb=" CA ASN E 370 " pdb=" CB ASN E 370 " ideal model delta sigma weight residual 116.63 110.17 6.46 1.16e+00 7.43e-01 3.10e+01 ... (remaining 35785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 15461 35.76 - 71.51: 556 71.51 - 107.27: 35 107.27 - 143.02: 19 143.02 - 178.78: 16 Dihedral angle restraints: 16087 sinusoidal: 6916 harmonic: 9171 Sorted by residual: dihedral pdb=" CB CYS C 57 " pdb=" SG CYS C 57 " pdb=" SG CYS C 65 " pdb=" CB CYS C 65 " ideal model delta sinusoidal sigma weight residual -86.00 -6.58 -79.42 1 1.00e+01 1.00e-02 7.84e+01 dihedral pdb=" CB CYS E 113 " pdb=" SG CYS E 113 " pdb=" SG CYS E 295 " pdb=" CB CYS E 295 " ideal model delta sinusoidal sigma weight residual 93.00 48.87 44.13 1 1.00e+01 1.00e-02 2.71e+01 dihedral pdb=" CB CYS D 113 " pdb=" SG CYS D 113 " pdb=" SG CYS D 295 " pdb=" CB CYS D 295 " ideal model delta sinusoidal sigma weight residual 93.00 51.95 41.05 1 1.00e+01 1.00e-02 2.36e+01 ... (remaining 16084 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 3762 0.084 - 0.168: 227 0.168 - 0.252: 9 0.252 - 0.336: 2 0.336 - 0.420: 7 Chirality restraints: 4007 Sorted by residual: chirality pdb=" C2 PEE D 901 " pdb=" C1 PEE D 901 " pdb=" C3 PEE D 901 " pdb=" O2 PEE D 901 " both_signs ideal model delta sigma weight residual False -2.33 -2.75 0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" C2 PEE D 904 " pdb=" C1 PEE D 904 " pdb=" C3 PEE D 904 " pdb=" O2 PEE D 904 " both_signs ideal model delta sigma weight residual False -2.33 -2.74 0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" C2 PEE C 901 " pdb=" C1 PEE C 901 " pdb=" C3 PEE C 901 " pdb=" O2 PEE C 901 " both_signs ideal model delta sigma weight residual False -2.33 -2.74 0.41 2.00e-01 2.50e+01 4.18e+00 ... (remaining 4004 not shown) Planarity restraints: 4356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 23 " -0.023 2.00e-02 2.50e+03 2.21e-02 1.23e+01 pdb=" CG TRP C 23 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP C 23 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP C 23 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 23 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 23 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 23 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 23 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 23 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 23 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 399 " 0.016 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C LYS F 399 " -0.059 2.00e-02 2.50e+03 pdb=" O LYS F 399 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU F 400 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 795 " 0.047 5.00e-02 4.00e+02 7.16e-02 8.20e+00 pdb=" N PRO A 796 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 796 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 796 " 0.039 5.00e-02 4.00e+02 ... (remaining 4353 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2990 2.75 - 3.29: 25337 3.29 - 3.83: 45169 3.83 - 4.36: 53575 4.36 - 4.90: 90688 Nonbonded interactions: 217759 Sorted by model distance: nonbonded pdb=" O SER F 168 " pdb=" OG1 THR F 171 " model vdw 2.216 3.040 nonbonded pdb=" O ILE B 356 " pdb=" OG SER B 360 " model vdw 2.240 3.040 nonbonded pdb=" O ILE F 556 " pdb=" ND2 ASN F 584 " model vdw 2.257 3.120 nonbonded pdb=" O THR A 44 " pdb=" OG1 THR A 48 " model vdw 2.260 3.040 nonbonded pdb=" O TRP A 411 " pdb=" OG1 THR A 441 " model vdw 2.272 3.040 ... (remaining 217754 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 175 or resid 231 through 808 or resid 901 or (r \ esid 902 and (name C10 or name C11 or name C12 or name C13 or name C14 or name C \ 15 or name C16 or name C17 or name C18 or name O2 or name O4 )) or (resid 903 an \ d (name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name \ C16 or name C17 or name O2 or name O4 )))) selection = (chain 'B' and (resid 15 through 808 or resid 901 through 903)) } ncs_group { reference = (chain 'C' and (resid 15 through 402 or (resid 901 through 902 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 \ or name O2 or name O4 )))) selection = (chain 'D' and (resid 15 through 175 or resid 240 through 402 or (resid 903 thro \ ugh 904 and (name C10 or name C11 or name C12 or name C13 or name C14 or name C1 \ 5 or name C16 or name C17 or name O2 or name O4 )))) selection = (chain 'E' and (resid 15 through 175 or resid 240 through 402 or resid 902 throu \ gh 903)) } 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: 6.790 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: 0.030 Extract box with map and model: 1.010 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 59.950 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 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 : 0.006 0.152 26548 Z= 0.283 Angle : 0.803 13.914 35824 Z= 0.404 Chirality : 0.047 0.420 4007 Planarity : 0.005 0.072 4356 Dihedral : 19.104 178.780 10070 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.25 % Allowed : 21.36 % Favored : 78.40 % 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: -0.71 (0.15), residues: 3033 helix: 0.17 (0.12), residues: 1638 sheet: -1.32 (0.32), residues: 286 loop : -1.05 (0.18), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP C 23 HIS 0.020 0.001 HIS A 253 PHE 0.043 0.002 PHE E 390 TYR 0.036 0.001 TYR C 284 ARG 0.013 0.001 ARG F 118 Details of bonding type rmsd hydrogen bonds : bond 0.14210 ( 1303) hydrogen bonds : angle 6.27686 ( 3657) SS BOND : bond 0.00356 ( 17) SS BOND : angle 1.32058 ( 34) covalent geometry : bond 0.00563 (26531) covalent geometry : angle 0.80282 (35790) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 256 time to evaluate : 2.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8583 (mt-10) REVERT: A 689 TYR cc_start: 0.7514 (t80) cc_final: 0.7220 (m-80) REVERT: B 171 ARG cc_start: 0.8204 (mmm160) cc_final: 0.7683 (ttm-80) REVERT: B 234 LYS cc_start: 0.8852 (tptp) cc_final: 0.8149 (tptp) REVERT: B 238 GLU cc_start: 0.8395 (tt0) cc_final: 0.7781 (pt0) REVERT: B 239 GLN cc_start: 0.8212 (pp30) cc_final: 0.7969 (pp30) REVERT: B 429 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8199 (mm-30) REVERT: B 545 ARG cc_start: 0.8742 (mtm180) cc_final: 0.8510 (mtp85) REVERT: C 47 VAL cc_start: 0.8585 (t) cc_final: 0.8384 (p) REVERT: C 168 TRP cc_start: 0.5497 (t60) cc_final: 0.4886 (t-100) REVERT: D 30 TYR cc_start: 0.7979 (m-80) cc_final: 0.7728 (m-80) REVERT: D 375 MET cc_start: 0.8189 (mtm) cc_final: 0.7770 (mtm) REVERT: E 24 TRP cc_start: 0.7009 (p90) cc_final: 0.6618 (p90) REVERT: E 33 ILE cc_start: 0.8759 (mm) cc_final: 0.8452 (mt) REVERT: E 341 TRP cc_start: 0.7645 (t60) cc_final: 0.7351 (t60) REVERT: F 96 MET cc_start: 0.7967 (mtm) cc_final: 0.7691 (mtm) REVERT: F 144 PHE cc_start: 0.7811 (t80) cc_final: 0.7537 (t80) REVERT: F 300 MET cc_start: 0.7803 (mmm) cc_final: 0.7316 (mmm) outliers start: 7 outliers final: 3 residues processed: 259 average time/residue: 0.3842 time to fit residues: 159.8381 Evaluate side-chains 218 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 215 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain E residue 52 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 0.7980 chunk 230 optimal weight: 1.9990 chunk 127 optimal weight: 0.0870 chunk 78 optimal weight: 0.6980 chunk 155 optimal weight: 8.9990 chunk 123 optimal weight: 20.0000 chunk 238 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 chunk 276 optimal weight: 0.8980 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 ASN A 467 GLN B 499 HIS ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN F 402 GLN ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 GLN F 635 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.130842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.096864 restraints weight = 62399.769| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 3.48 r_work: 0.3415 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26548 Z= 0.131 Angle : 0.519 8.223 35824 Z= 0.275 Chirality : 0.040 0.167 4007 Planarity : 0.004 0.053 4356 Dihedral : 15.480 171.554 3802 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.93 % Allowed : 20.38 % Favored : 77.70 % 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: -0.16 (0.15), residues: 3033 helix: 0.76 (0.13), residues: 1667 sheet: -1.37 (0.32), residues: 279 loop : -1.00 (0.18), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 23 HIS 0.009 0.001 HIS C 253 PHE 0.021 0.001 PHE F 609 TYR 0.016 0.001 TYR F 756 ARG 0.017 0.001 ARG C 103 Details of bonding type rmsd hydrogen bonds : bond 0.04140 ( 1303) hydrogen bonds : angle 4.80115 ( 3657) SS BOND : bond 0.00304 ( 17) SS BOND : angle 0.86534 ( 34) covalent geometry : bond 0.00285 (26531) covalent geometry : angle 0.51827 (35790) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 229 time to evaluate : 3.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.9115 (tp) cc_final: 0.8837 (tt) REVERT: A 451 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8084 (pt) REVERT: A 452 LYS cc_start: 0.7628 (mtpp) cc_final: 0.7426 (mtpp) REVERT: A 467 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8168 (mp10) REVERT: A 475 TRP cc_start: 0.8402 (m-10) cc_final: 0.8048 (m-10) REVERT: A 645 LYS cc_start: 0.7932 (mttt) cc_final: 0.7311 (mtmm) REVERT: B 37 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8386 (ttp) REVERT: B 171 ARG cc_start: 0.8434 (mmm160) cc_final: 0.7871 (ttm-80) REVERT: B 234 LYS cc_start: 0.8884 (tptp) cc_final: 0.8203 (tptp) REVERT: B 238 GLU cc_start: 0.8455 (tt0) cc_final: 0.8034 (pt0) REVERT: B 239 GLN cc_start: 0.7974 (pp30) cc_final: 0.7733 (pp30) REVERT: B 337 MET cc_start: 0.8134 (mtp) cc_final: 0.7863 (mtp) REVERT: B 521 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7344 (tt) REVERT: B 590 MET cc_start: 0.6692 (mmm) cc_final: 0.6001 (tpt) REVERT: C 47 VAL cc_start: 0.8832 (t) cc_final: 0.8591 (p) REVERT: C 168 TRP cc_start: 0.5063 (t60) cc_final: 0.4565 (t-100) REVERT: C 286 VAL cc_start: 0.8179 (OUTLIER) cc_final: 0.7772 (p) REVERT: D 375 MET cc_start: 0.8207 (mtm) cc_final: 0.7996 (mtm) REVERT: E 24 TRP cc_start: 0.7147 (p90) cc_final: 0.6450 (p90) REVERT: E 33 ILE cc_start: 0.8473 (mm) cc_final: 0.8163 (mt) REVERT: E 341 TRP cc_start: 0.7946 (t60) cc_final: 0.7628 (t60) REVERT: F 38 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7218 (tt) REVERT: F 144 PHE cc_start: 0.7946 (t80) cc_final: 0.7698 (t80) REVERT: F 261 MET cc_start: 0.6696 (ttm) cc_final: 0.6482 (ttm) outliers start: 55 outliers final: 25 residues processed: 274 average time/residue: 0.3706 time to fit residues: 165.5447 Evaluate side-chains 241 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 210 time to evaluate : 2.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 467 GLN Chi-restraints excluded: chain A residue 568 HIS Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 250 PHE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 312 MET Chi-restraints excluded: chain F residue 694 ASP Chi-restraints excluded: chain F residue 753 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 282 optimal weight: 8.9990 chunk 202 optimal weight: 0.8980 chunk 108 optimal weight: 6.9990 chunk 239 optimal weight: 3.9990 chunk 118 optimal weight: 30.0000 chunk 162 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 270 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 242 optimal weight: 0.9990 chunk 234 optimal weight: 0.0050 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN A 711 GLN ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN F 112 ASN ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.130061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.093925 restraints weight = 61606.461| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 3.05 r_work: 0.3400 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26548 Z= 0.128 Angle : 0.501 8.174 35824 Z= 0.263 Chirality : 0.040 0.166 4007 Planarity : 0.004 0.050 4356 Dihedral : 13.816 174.681 3795 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.03 % Allowed : 20.45 % Favored : 77.52 % 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: -0.03 (0.15), residues: 3033 helix: 0.90 (0.13), residues: 1673 sheet: -1.31 (0.32), residues: 279 loop : -1.02 (0.19), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 23 HIS 0.010 0.001 HIS C 253 PHE 0.016 0.001 PHE F 609 TYR 0.012 0.001 TYR D 281 ARG 0.012 0.000 ARG A 533 Details of bonding type rmsd hydrogen bonds : bond 0.03788 ( 1303) hydrogen bonds : angle 4.58049 ( 3657) SS BOND : bond 0.00292 ( 17) SS BOND : angle 0.98254 ( 34) covalent geometry : bond 0.00284 (26531) covalent geometry : angle 0.50050 (35790) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 221 time to evaluate : 2.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.9075 (tp) cc_final: 0.8869 (tt) REVERT: A 275 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8267 (t80) REVERT: A 451 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7962 (pt) REVERT: A 467 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8032 (mp10) REVERT: A 475 TRP cc_start: 0.8391 (m-10) cc_final: 0.8132 (m-10) REVERT: A 581 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8051 (mm) REVERT: A 645 LYS cc_start: 0.7838 (mttt) cc_final: 0.7196 (mtmm) REVERT: A 689 TYR cc_start: 0.7510 (t80) cc_final: 0.7233 (m-80) REVERT: B 37 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8425 (ttp) REVERT: B 171 ARG cc_start: 0.8475 (mmm160) cc_final: 0.7914 (ttm-80) REVERT: B 234 LYS cc_start: 0.8898 (tptp) cc_final: 0.8669 (tptp) REVERT: B 239 GLN cc_start: 0.8010 (pp30) cc_final: 0.7711 (pp30) REVERT: B 337 MET cc_start: 0.8138 (mtp) cc_final: 0.7836 (mtp) REVERT: B 521 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.7081 (tt) REVERT: B 590 MET cc_start: 0.6598 (mmm) cc_final: 0.5973 (tpt) REVERT: B 644 LEU cc_start: 0.8553 (pt) cc_final: 0.8144 (tp) REVERT: B 700 LEU cc_start: 0.6391 (OUTLIER) cc_final: 0.6129 (tt) REVERT: C 47 VAL cc_start: 0.8825 (t) cc_final: 0.8587 (p) REVERT: C 168 TRP cc_start: 0.5146 (t60) cc_final: 0.4634 (t-100) REVERT: C 375 MET cc_start: 0.6046 (mtm) cc_final: 0.5696 (mtm) REVERT: D 134 LEU cc_start: 0.8403 (mm) cc_final: 0.8101 (mp) REVERT: D 375 MET cc_start: 0.8139 (mtm) cc_final: 0.7887 (mtm) REVERT: E 24 TRP cc_start: 0.7111 (p90) cc_final: 0.6602 (p90) REVERT: E 33 ILE cc_start: 0.8413 (mm) cc_final: 0.8118 (mt) REVERT: E 37 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8152 (ttp) REVERT: E 341 TRP cc_start: 0.7888 (t60) cc_final: 0.7608 (t60) REVERT: F 38 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.7129 (tt) REVERT: F 144 PHE cc_start: 0.7881 (t80) cc_final: 0.7636 (t80) REVERT: F 386 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7832 (pttp) REVERT: F 509 TRP cc_start: 0.7947 (p-90) cc_final: 0.7746 (p-90) outliers start: 58 outliers final: 29 residues processed: 268 average time/residue: 0.3653 time to fit residues: 158.3465 Evaluate side-chains 248 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 209 time to evaluate : 2.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 467 GLN Chi-restraints excluded: chain A residue 568 HIS Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 250 PHE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 312 MET Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 386 LYS Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain F residue 694 ASP Chi-restraints excluded: chain F residue 753 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 170 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 275 optimal weight: 6.9990 chunk 284 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 200 optimal weight: 0.9980 chunk 287 optimal weight: 7.9990 chunk 260 optimal weight: 2.9990 chunk 117 optimal weight: 20.0000 chunk 255 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 GLN B 409 ASN ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN E 312 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.127078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.087999 restraints weight = 61853.092| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.59 r_work: 0.3351 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 26548 Z= 0.318 Angle : 0.631 13.983 35824 Z= 0.327 Chirality : 0.045 0.183 4007 Planarity : 0.004 0.038 4356 Dihedral : 13.349 169.982 3795 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.33 % Allowed : 19.96 % Favored : 76.72 % 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: -0.29 (0.15), residues: 3033 helix: 0.65 (0.13), residues: 1667 sheet: -1.10 (0.33), residues: 265 loop : -1.17 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 143 HIS 0.017 0.002 HIS D 253 PHE 0.036 0.002 PHE B 393 TYR 0.021 0.002 TYR F 279 ARG 0.006 0.001 ARG D 346 Details of bonding type rmsd hydrogen bonds : bond 0.04401 ( 1303) hydrogen bonds : angle 4.78964 ( 3657) SS BOND : bond 0.00739 ( 17) SS BOND : angle 1.25669 ( 34) covalent geometry : bond 0.00752 (26531) covalent geometry : angle 0.63012 (35790) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 228 time to evaluate : 2.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.8998 (tp) cc_final: 0.8773 (tt) REVERT: A 275 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.8338 (t80) REVERT: A 430 LEU cc_start: 0.9181 (tp) cc_final: 0.8779 (mt) REVERT: A 451 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7865 (pt) REVERT: A 452 LYS cc_start: 0.7789 (mtpp) cc_final: 0.7347 (mtpp) REVERT: A 581 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7969 (mm) REVERT: B 171 ARG cc_start: 0.8430 (mmm160) cc_final: 0.7848 (ttm-80) REVERT: B 244 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.8192 (t80) REVERT: B 337 MET cc_start: 0.8194 (mtp) cc_final: 0.7983 (mtp) REVERT: B 438 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.7987 (mp) REVERT: B 644 LEU cc_start: 0.8392 (pt) cc_final: 0.7990 (tp) REVERT: B 700 LEU cc_start: 0.6502 (OUTLIER) cc_final: 0.6284 (tt) REVERT: C 17 TYR cc_start: 0.7670 (OUTLIER) cc_final: 0.7183 (m-80) REVERT: C 47 VAL cc_start: 0.8943 (t) cc_final: 0.8678 (p) REVERT: C 49 GLN cc_start: 0.8040 (pm20) cc_final: 0.7830 (pm20) REVERT: C 168 TRP cc_start: 0.5138 (t60) cc_final: 0.4549 (t-100) REVERT: C 372 PHE cc_start: 0.5055 (OUTLIER) cc_final: 0.4727 (t80) REVERT: D 134 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8250 (mt) REVERT: D 372 PHE cc_start: 0.7313 (OUTLIER) cc_final: 0.6395 (t80) REVERT: D 375 MET cc_start: 0.8207 (mtm) cc_final: 0.7893 (mtm) REVERT: E 24 TRP cc_start: 0.7344 (p90) cc_final: 0.6422 (p90) REVERT: E 33 ILE cc_start: 0.8404 (mm) cc_final: 0.8094 (mt) REVERT: E 341 TRP cc_start: 0.7734 (t60) cc_final: 0.7354 (t60) REVERT: F 144 PHE cc_start: 0.7984 (t80) cc_final: 0.7669 (t80) REVERT: F 517 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7945 (mm-30) REVERT: F 520 TYR cc_start: 0.7328 (m-80) cc_final: 0.7094 (m-80) REVERT: F 581 MET cc_start: 0.6945 (tpt) cc_final: 0.6581 (tpt) REVERT: F 645 TRP cc_start: 0.6637 (OUTLIER) cc_final: 0.6238 (p90) REVERT: F 756 TYR cc_start: 0.5668 (t80) cc_final: 0.5465 (t80) outliers start: 95 outliers final: 55 residues processed: 305 average time/residue: 0.3767 time to fit residues: 188.9872 Evaluate side-chains 271 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 204 time to evaluate : 3.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 568 HIS Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 749 ARG Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 372 PHE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 372 PHE Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 312 MET Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 517 GLU Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain F residue 645 TRP Chi-restraints excluded: chain F residue 694 ASP Chi-restraints excluded: chain F residue 753 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 50 optimal weight: 5.9990 chunk 248 optimal weight: 0.6980 chunk 264 optimal weight: 10.0000 chunk 300 optimal weight: 9.9990 chunk 295 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 280 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 266 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 HIS E 155 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 670 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.126963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.088775 restraints weight = 61669.783| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.95 r_work: 0.3325 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 26548 Z= 0.307 Angle : 0.606 11.386 35824 Z= 0.316 Chirality : 0.044 0.177 4007 Planarity : 0.004 0.038 4356 Dihedral : 12.981 168.827 3795 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.47 % Allowed : 21.01 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.15), residues: 3033 helix: 0.58 (0.12), residues: 1667 sheet: -1.20 (0.33), residues: 272 loop : -1.20 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP F 509 HIS 0.010 0.001 HIS C 253 PHE 0.030 0.002 PHE D 244 TYR 0.016 0.002 TYR C 281 ARG 0.005 0.000 ARG B 749 Details of bonding type rmsd hydrogen bonds : bond 0.04314 ( 1303) hydrogen bonds : angle 4.77263 ( 3657) SS BOND : bond 0.00706 ( 17) SS BOND : angle 1.04224 ( 34) covalent geometry : bond 0.00722 (26531) covalent geometry : angle 0.60504 (35790) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 219 time to evaluate : 3.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.9012 (tp) cc_final: 0.8791 (tt) REVERT: A 235 LYS cc_start: 0.8861 (mmtt) cc_final: 0.8615 (mmmt) REVERT: A 275 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.8349 (t80) REVERT: A 407 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8171 (mp) REVERT: A 419 ARG cc_start: 0.8637 (tpt90) cc_final: 0.8166 (tpt90) REVERT: A 430 LEU cc_start: 0.9172 (tp) cc_final: 0.8668 (mt) REVERT: A 451 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7985 (pt) REVERT: A 452 LYS cc_start: 0.7822 (mtpp) cc_final: 0.7325 (mtpp) REVERT: A 475 TRP cc_start: 0.8538 (m-10) cc_final: 0.8004 (m-10) REVERT: B 168 TRP cc_start: 0.8704 (OUTLIER) cc_final: 0.7849 (t-100) REVERT: B 171 ARG cc_start: 0.8327 (mmm160) cc_final: 0.7858 (ttm-80) REVERT: B 244 PHE cc_start: 0.8610 (OUTLIER) cc_final: 0.8329 (t80) REVERT: B 510 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8802 (mm) REVERT: B 644 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8162 (tp) REVERT: C 17 TYR cc_start: 0.7748 (OUTLIER) cc_final: 0.7161 (m-80) REVERT: C 33 ILE cc_start: 0.8167 (mm) cc_final: 0.7869 (mm) REVERT: C 168 TRP cc_start: 0.4970 (t60) cc_final: 0.4388 (t-100) REVERT: D 134 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8251 (mt) REVERT: D 343 MET cc_start: 0.7552 (mmm) cc_final: 0.7091 (mmm) REVERT: D 372 PHE cc_start: 0.7321 (OUTLIER) cc_final: 0.6439 (t80) REVERT: D 375 MET cc_start: 0.8224 (mtm) cc_final: 0.7902 (mtm) REVERT: E 24 TRP cc_start: 0.7475 (p90) cc_final: 0.6581 (p90) REVERT: E 263 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7417 (mp) REVERT: F 357 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7946 (pm20) REVERT: F 520 TYR cc_start: 0.7329 (m-80) cc_final: 0.7048 (m-80) REVERT: F 581 MET cc_start: 0.6981 (tpt) cc_final: 0.6620 (tpt) REVERT: F 645 TRP cc_start: 0.6778 (OUTLIER) cc_final: 0.6277 (p90) REVERT: F 756 TYR cc_start: 0.5869 (t80) cc_final: 0.5571 (t80) outliers start: 99 outliers final: 61 residues processed: 301 average time/residue: 0.4577 time to fit residues: 225.6456 Evaluate side-chains 285 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 211 time to evaluate : 3.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 568 HIS Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 168 TRP Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 749 ARG Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 372 PHE Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 250 PHE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 232 LYS Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain F residue 645 TRP Chi-restraints excluded: chain F residue 694 ASP Chi-restraints excluded: chain F residue 753 PHE Chi-restraints excluded: chain F residue 783 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 252 optimal weight: 0.7980 chunk 111 optimal weight: 7.9990 chunk 296 optimal weight: 6.9990 chunk 176 optimal weight: 0.3980 chunk 165 optimal weight: 0.9980 chunk 116 optimal weight: 20.0000 chunk 270 optimal weight: 9.9990 chunk 215 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 169 optimal weight: 0.9980 chunk 196 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.129016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.091154 restraints weight = 61043.336| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.91 r_work: 0.3376 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26548 Z= 0.134 Angle : 0.526 10.434 35824 Z= 0.271 Chirality : 0.040 0.163 4007 Planarity : 0.003 0.043 4356 Dihedral : 12.122 165.083 3795 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.14 % Allowed : 22.41 % Favored : 75.46 % 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: -0.04 (0.16), residues: 3033 helix: 0.89 (0.13), residues: 1648 sheet: -1.40 (0.32), residues: 301 loop : -0.93 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 509 HIS 0.013 0.001 HIS C 253 PHE 0.021 0.001 PHE E 390 TYR 0.019 0.001 TYR D 281 ARG 0.006 0.000 ARG F 504 Details of bonding type rmsd hydrogen bonds : bond 0.03716 ( 1303) hydrogen bonds : angle 4.50991 ( 3657) SS BOND : bond 0.00274 ( 17) SS BOND : angle 1.10774 ( 34) covalent geometry : bond 0.00302 (26531) covalent geometry : angle 0.52537 (35790) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 229 time to evaluate : 2.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.8974 (tp) cc_final: 0.8755 (tt) REVERT: A 235 LYS cc_start: 0.8773 (mmtt) cc_final: 0.8554 (mmmt) REVERT: A 275 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.8292 (t80) REVERT: A 419 ARG cc_start: 0.8657 (tpt90) cc_final: 0.8236 (tpt90) REVERT: A 430 LEU cc_start: 0.9178 (tp) cc_final: 0.8699 (mt) REVERT: A 452 LYS cc_start: 0.7926 (mtpp) cc_final: 0.7381 (mtpp) REVERT: A 475 TRP cc_start: 0.8444 (m-10) cc_final: 0.7938 (m-10) REVERT: B 171 ARG cc_start: 0.8239 (mmm160) cc_final: 0.7777 (ttm-80) REVERT: B 510 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8804 (mm) REVERT: B 644 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7986 (tp) REVERT: C 33 ILE cc_start: 0.8137 (mm) cc_final: 0.7807 (mm) REVERT: C 47 VAL cc_start: 0.8842 (p) cc_final: 0.8565 (p) REVERT: C 168 TRP cc_start: 0.5077 (t60) cc_final: 0.4493 (t-100) REVERT: D 134 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8031 (mp) REVERT: D 254 VAL cc_start: 0.7076 (OUTLIER) cc_final: 0.6767 (m) REVERT: D 343 MET cc_start: 0.7330 (mmm) cc_final: 0.6864 (mmm) REVERT: D 372 PHE cc_start: 0.7158 (OUTLIER) cc_final: 0.6333 (t80) REVERT: D 375 MET cc_start: 0.8187 (mtm) cc_final: 0.7846 (mtm) REVERT: E 24 TRP cc_start: 0.7385 (p90) cc_final: 0.6375 (p90) REVERT: E 33 ILE cc_start: 0.8493 (mm) cc_final: 0.8155 (mt) REVERT: E 263 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7391 (mp) REVERT: F 357 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7752 (pm20) REVERT: F 377 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7702 (mm) REVERT: F 504 ARG cc_start: 0.7959 (tpt90) cc_final: 0.7695 (tpt90) REVERT: F 509 TRP cc_start: 0.8002 (p-90) cc_final: 0.7503 (p-90) REVERT: F 520 TYR cc_start: 0.7231 (m-80) cc_final: 0.6981 (m-80) REVERT: F 581 MET cc_start: 0.6769 (tpt) cc_final: 0.6533 (tpt) REVERT: F 679 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6548 (mt) REVERT: F 756 TYR cc_start: 0.5986 (t80) cc_final: 0.5749 (t80) outliers start: 61 outliers final: 38 residues processed: 278 average time/residue: 0.3626 time to fit residues: 162.5716 Evaluate side-chains 267 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 219 time to evaluate : 2.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 568 HIS Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 372 PHE Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 250 PHE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 232 LYS Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain F residue 679 LEU Chi-restraints excluded: chain F residue 694 ASP Chi-restraints excluded: chain F residue 783 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 245 optimal weight: 0.5980 chunk 157 optimal weight: 7.9990 chunk 221 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 206 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 27 optimal weight: 0.2980 chunk 51 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 281 optimal weight: 10.0000 chunk 177 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 ASN ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.129035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.092475 restraints weight = 61030.181| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.79 r_work: 0.3371 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26548 Z= 0.132 Angle : 0.519 12.027 35824 Z= 0.266 Chirality : 0.040 0.160 4007 Planarity : 0.003 0.040 4356 Dihedral : 11.588 163.034 3795 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.31 % Allowed : 22.76 % Favored : 74.93 % 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: 0.09 (0.16), residues: 3033 helix: 1.01 (0.13), residues: 1638 sheet: -1.39 (0.32), residues: 308 loop : -0.86 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 509 HIS 0.013 0.001 HIS C 253 PHE 0.023 0.001 PHE E 390 TYR 0.017 0.001 TYR D 281 ARG 0.005 0.000 ARG B 749 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 1303) hydrogen bonds : angle 4.43976 ( 3657) SS BOND : bond 0.00333 ( 17) SS BOND : angle 0.91273 ( 34) covalent geometry : bond 0.00300 (26531) covalent geometry : angle 0.51830 (35790) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 214 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.8980 (tp) cc_final: 0.8765 (tt) REVERT: A 275 PHE cc_start: 0.8792 (OUTLIER) cc_final: 0.8287 (t80) REVERT: A 430 LEU cc_start: 0.9174 (tp) cc_final: 0.8803 (mt) REVERT: A 452 LYS cc_start: 0.7848 (mtpp) cc_final: 0.7377 (mtpp) REVERT: A 475 TRP cc_start: 0.8447 (m-10) cc_final: 0.7980 (m-10) REVERT: B 171 ARG cc_start: 0.8204 (mmm160) cc_final: 0.7756 (ttm-80) REVERT: B 510 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8803 (mm) REVERT: B 644 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8051 (tp) REVERT: C 33 ILE cc_start: 0.8186 (mm) cc_final: 0.7837 (mm) REVERT: C 168 TRP cc_start: 0.4984 (t60) cc_final: 0.4474 (t-100) REVERT: D 134 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8201 (mt) REVERT: D 372 PHE cc_start: 0.7227 (OUTLIER) cc_final: 0.6326 (t80) REVERT: D 375 MET cc_start: 0.8209 (mtm) cc_final: 0.8002 (mtm) REVERT: E 24 TRP cc_start: 0.7384 (p90) cc_final: 0.6367 (p90) REVERT: E 33 ILE cc_start: 0.8506 (mm) cc_final: 0.8175 (mt) REVERT: E 263 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7422 (mp) REVERT: F 232 LYS cc_start: 0.7002 (OUTLIER) cc_final: 0.6017 (ptpp) REVERT: F 357 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8036 (pm20) REVERT: F 377 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7698 (mm) REVERT: F 504 ARG cc_start: 0.7982 (tpt90) cc_final: 0.7741 (tpt90) REVERT: F 509 TRP cc_start: 0.8001 (p-90) cc_final: 0.7597 (p-90) REVERT: F 520 TYR cc_start: 0.7215 (m-80) cc_final: 0.6947 (m-80) REVERT: F 581 MET cc_start: 0.6706 (tpt) cc_final: 0.6498 (tpp) REVERT: F 679 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6559 (mt) REVERT: F 756 TYR cc_start: 0.5868 (t80) cc_final: 0.5635 (t80) outliers start: 66 outliers final: 47 residues processed: 268 average time/residue: 0.3568 time to fit residues: 156.7947 Evaluate side-chains 267 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 210 time to evaluate : 3.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 568 HIS Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 372 PHE Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 250 PHE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 232 LYS Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain F residue 679 LEU Chi-restraints excluded: chain F residue 694 ASP Chi-restraints excluded: chain F residue 783 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 211 optimal weight: 0.6980 chunk 145 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 266 optimal weight: 7.9990 chunk 73 optimal weight: 0.7980 chunk 247 optimal weight: 3.9990 chunk 181 optimal weight: 0.5980 chunk 265 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 270 optimal weight: 10.0000 chunk 188 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 ASN ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 423 HIS ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.129203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.092142 restraints weight = 61651.605| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.79 r_work: 0.3386 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26548 Z= 0.131 Angle : 0.516 11.033 35824 Z= 0.264 Chirality : 0.040 0.185 4007 Planarity : 0.003 0.038 4356 Dihedral : 10.957 160.125 3795 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.38 % Allowed : 22.79 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.16), residues: 3033 helix: 1.07 (0.13), residues: 1639 sheet: -1.43 (0.31), residues: 313 loop : -0.78 (0.19), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 143 HIS 0.014 0.001 HIS C 253 PHE 0.026 0.001 PHE E 390 TYR 0.022 0.001 TYR A 653 ARG 0.004 0.000 ARG D 346 Details of bonding type rmsd hydrogen bonds : bond 0.03519 ( 1303) hydrogen bonds : angle 4.37246 ( 3657) SS BOND : bond 0.00320 ( 17) SS BOND : angle 0.82536 ( 34) covalent geometry : bond 0.00301 (26531) covalent geometry : angle 0.51556 (35790) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 216 time to evaluate : 2.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.8928 (tp) cc_final: 0.8688 (tt) REVERT: A 275 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8224 (t80) REVERT: A 430 LEU cc_start: 0.9144 (tp) cc_final: 0.8771 (mt) REVERT: A 452 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7518 (mtpp) REVERT: A 465 ILE cc_start: 0.9121 (tt) cc_final: 0.8880 (tp) REVERT: A 568 HIS cc_start: 0.8131 (OUTLIER) cc_final: 0.7739 (p-80) REVERT: B 171 ARG cc_start: 0.8282 (mmm160) cc_final: 0.7769 (ttm-80) REVERT: B 434 MET cc_start: 0.8300 (mtt) cc_final: 0.8008 (mtt) REVERT: B 644 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8082 (tp) REVERT: C 33 ILE cc_start: 0.8195 (mm) cc_final: 0.7849 (mm) REVERT: C 47 VAL cc_start: 0.8940 (t) cc_final: 0.8708 (p) REVERT: C 168 TRP cc_start: 0.5057 (t60) cc_final: 0.4544 (t-100) REVERT: D 134 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8120 (mt) REVERT: D 372 PHE cc_start: 0.7112 (OUTLIER) cc_final: 0.6248 (t80) REVERT: D 375 MET cc_start: 0.8090 (mtm) cc_final: 0.7870 (mtp) REVERT: E 24 TRP cc_start: 0.7283 (p90) cc_final: 0.6324 (p90) REVERT: E 33 ILE cc_start: 0.8403 (mm) cc_final: 0.8076 (mt) REVERT: F 232 LYS cc_start: 0.6900 (OUTLIER) cc_final: 0.5904 (ptpp) REVERT: F 357 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8023 (pm20) REVERT: F 377 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7659 (mm) REVERT: F 504 ARG cc_start: 0.8031 (tpt90) cc_final: 0.7727 (tpt170) REVERT: F 509 TRP cc_start: 0.7957 (p-90) cc_final: 0.7596 (p-90) REVERT: F 520 TYR cc_start: 0.7255 (m-80) cc_final: 0.6986 (m-80) REVERT: F 581 MET cc_start: 0.6815 (tpt) cc_final: 0.6569 (tpp) REVERT: F 598 HIS cc_start: 0.8477 (t70) cc_final: 0.8212 (t70) REVERT: F 679 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.6567 (mt) REVERT: F 756 TYR cc_start: 0.5836 (t80) cc_final: 0.5542 (t80) outliers start: 68 outliers final: 49 residues processed: 272 average time/residue: 0.3555 time to fit residues: 157.7700 Evaluate side-chains 266 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 207 time to evaluate : 2.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 452 LYS Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 568 HIS Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 372 PHE Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 250 PHE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 232 LYS Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain F residue 679 LEU Chi-restraints excluded: chain F residue 694 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 225 optimal weight: 0.9990 chunk 43 optimal weight: 0.0010 chunk 243 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 chunk 232 optimal weight: 0.9980 chunk 274 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 199 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 ASN B 585 ASN ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.129279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.092107 restraints weight = 61453.404| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.95 r_work: 0.3390 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26548 Z= 0.125 Angle : 0.511 10.990 35824 Z= 0.261 Chirality : 0.040 0.219 4007 Planarity : 0.003 0.040 4356 Dihedral : 10.443 157.686 3795 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.42 % Allowed : 22.83 % Favored : 74.75 % 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: 0.20 (0.16), residues: 3033 helix: 1.09 (0.13), residues: 1647 sheet: -1.44 (0.31), residues: 313 loop : -0.75 (0.19), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 143 HIS 0.013 0.001 HIS B 522 PHE 0.027 0.001 PHE E 390 TYR 0.017 0.001 TYR D 281 ARG 0.005 0.000 ARG B 600 Details of bonding type rmsd hydrogen bonds : bond 0.03455 ( 1303) hydrogen bonds : angle 4.34579 ( 3657) SS BOND : bond 0.00308 ( 17) SS BOND : angle 0.78249 ( 34) covalent geometry : bond 0.00286 (26531) covalent geometry : angle 0.51021 (35790) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 209 time to evaluate : 3.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.8938 (tp) cc_final: 0.8690 (tt) REVERT: A 275 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.8287 (t80) REVERT: A 430 LEU cc_start: 0.9120 (tp) cc_final: 0.8775 (mt) REVERT: A 452 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7506 (mtpp) REVERT: A 568 HIS cc_start: 0.8135 (OUTLIER) cc_final: 0.7745 (p-80) REVERT: B 171 ARG cc_start: 0.8290 (mmm160) cc_final: 0.7761 (ttm-80) REVERT: B 434 MET cc_start: 0.8241 (mtt) cc_final: 0.7938 (mtt) REVERT: B 644 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8052 (tp) REVERT: C 33 ILE cc_start: 0.8144 (mm) cc_final: 0.7788 (mm) REVERT: C 168 TRP cc_start: 0.5068 (t60) cc_final: 0.4594 (t-100) REVERT: D 134 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8115 (mt) REVERT: D 372 PHE cc_start: 0.7064 (OUTLIER) cc_final: 0.6183 (t80) REVERT: E 24 TRP cc_start: 0.7276 (p90) cc_final: 0.6315 (p90) REVERT: E 33 ILE cc_start: 0.8397 (mm) cc_final: 0.8067 (mt) REVERT: F 232 LYS cc_start: 0.6871 (OUTLIER) cc_final: 0.5895 (ptpp) REVERT: F 357 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8101 (pm20) REVERT: F 377 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7687 (mm) REVERT: F 504 ARG cc_start: 0.8112 (tpt90) cc_final: 0.7785 (tpt170) REVERT: F 509 TRP cc_start: 0.7977 (p-90) cc_final: 0.7686 (p-90) REVERT: F 520 TYR cc_start: 0.7284 (m-80) cc_final: 0.7010 (m-80) REVERT: F 581 MET cc_start: 0.6987 (tpt) cc_final: 0.6720 (tpp) REVERT: F 598 HIS cc_start: 0.8520 (t70) cc_final: 0.8255 (t70) REVERT: F 679 LEU cc_start: 0.6898 (OUTLIER) cc_final: 0.6550 (mt) REVERT: F 756 TYR cc_start: 0.5820 (t80) cc_final: 0.5560 (t80) outliers start: 69 outliers final: 50 residues processed: 267 average time/residue: 0.3600 time to fit residues: 157.0103 Evaluate side-chains 268 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 208 time to evaluate : 2.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 452 LYS Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 568 HIS Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 372 PHE Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 250 PHE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 232 LYS Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain F residue 679 LEU Chi-restraints excluded: chain F residue 694 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 91 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 271 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 ASN B 585 ASN C 155 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.128315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.090448 restraints weight = 61227.035| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.92 r_work: 0.3359 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26548 Z= 0.186 Angle : 0.548 14.382 35824 Z= 0.281 Chirality : 0.041 0.300 4007 Planarity : 0.003 0.038 4356 Dihedral : 10.290 158.137 3795 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.31 % Allowed : 22.79 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.16), residues: 3033 helix: 0.98 (0.13), residues: 1652 sheet: -1.49 (0.32), residues: 314 loop : -0.78 (0.20), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 143 HIS 0.015 0.001 HIS C 253 PHE 0.028 0.002 PHE E 390 TYR 0.019 0.001 TYR A 332 ARG 0.004 0.000 ARG B 600 Details of bonding type rmsd hydrogen bonds : bond 0.03674 ( 1303) hydrogen bonds : angle 4.42610 ( 3657) SS BOND : bond 0.00444 ( 17) SS BOND : angle 0.86342 ( 34) covalent geometry : bond 0.00433 (26531) covalent geometry : angle 0.54791 (35790) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 211 time to evaluate : 4.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.8966 (tp) cc_final: 0.8725 (tt) REVERT: A 275 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.8362 (t80) REVERT: A 419 ARG cc_start: 0.8624 (tpt90) cc_final: 0.8108 (tpt90) REVERT: A 430 LEU cc_start: 0.9162 (tp) cc_final: 0.8620 (mt) REVERT: A 452 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7532 (mtpp) REVERT: A 645 LYS cc_start: 0.8103 (mttt) cc_final: 0.7365 (mtmm) REVERT: B 171 ARG cc_start: 0.8233 (mmm160) cc_final: 0.7739 (ttm-80) REVERT: B 434 MET cc_start: 0.8205 (mtt) cc_final: 0.7935 (mtt) REVERT: B 510 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8784 (mm) REVERT: B 644 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8045 (tp) REVERT: C 33 ILE cc_start: 0.8177 (mm) cc_final: 0.7824 (mm) REVERT: C 168 TRP cc_start: 0.5111 (t60) cc_final: 0.4626 (t-100) REVERT: D 134 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8210 (mt) REVERT: D 372 PHE cc_start: 0.7229 (OUTLIER) cc_final: 0.6375 (t80) REVERT: E 24 TRP cc_start: 0.7369 (p90) cc_final: 0.6401 (p90) REVERT: E 33 ILE cc_start: 0.8481 (mm) cc_final: 0.8156 (mt) REVERT: F 232 LYS cc_start: 0.6982 (OUTLIER) cc_final: 0.6019 (ptpp) REVERT: F 357 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8034 (pm20) REVERT: F 377 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7890 (mm) REVERT: F 504 ARG cc_start: 0.8164 (tpt90) cc_final: 0.7830 (tpt170) REVERT: F 509 TRP cc_start: 0.8030 (p-90) cc_final: 0.7675 (p-90) REVERT: F 520 TYR cc_start: 0.7371 (m-80) cc_final: 0.7140 (m-80) REVERT: F 581 MET cc_start: 0.7054 (tpt) cc_final: 0.6767 (tpp) REVERT: F 598 HIS cc_start: 0.8533 (t70) cc_final: 0.8205 (t70) REVERT: F 756 TYR cc_start: 0.5939 (t80) cc_final: 0.5688 (t80) outliers start: 66 outliers final: 51 residues processed: 264 average time/residue: 0.5079 time to fit residues: 223.3425 Evaluate side-chains 270 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 210 time to evaluate : 4.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 452 LYS Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 568 HIS Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 372 PHE Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 250 PHE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 232 LYS Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain F residue 694 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 74 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 61 optimal weight: 0.0170 chunk 29 optimal weight: 0.9980 chunk 285 optimal weight: 7.9990 chunk 49 optimal weight: 0.0370 chunk 273 optimal weight: 9.9990 chunk 144 optimal weight: 3.9990 chunk 289 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 overall best weight: 0.6096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 554 ASN B 239 GLN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 ASN C 155 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.129181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.092680 restraints weight = 61256.577| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.76 r_work: 0.3395 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26548 Z= 0.120 Angle : 0.517 12.302 35824 Z= 0.263 Chirality : 0.040 0.312 4007 Planarity : 0.003 0.040 4356 Dihedral : 9.821 157.057 3795 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.10 % Allowed : 23.11 % Favored : 74.79 % 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: 0.23 (0.16), residues: 3033 helix: 1.11 (0.13), residues: 1647 sheet: -1.42 (0.32), residues: 308 loop : -0.74 (0.20), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 143 HIS 0.014 0.001 HIS C 253 PHE 0.027 0.001 PHE E 390 TYR 0.016 0.001 TYR D 281 ARG 0.003 0.000 ARG F 603 Details of bonding type rmsd hydrogen bonds : bond 0.03432 ( 1303) hydrogen bonds : angle 4.32297 ( 3657) SS BOND : bond 0.00241 ( 17) SS BOND : angle 0.74971 ( 34) covalent geometry : bond 0.00272 (26531) covalent geometry : angle 0.51681 (35790) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16276.16 seconds wall clock time: 285 minutes 38.67 seconds (17138.67 seconds total)