Starting phenix.real_space_refine on Sun May 25 01:58:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dre_27676/05_2025/8dre_27676.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dre_27676/05_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_27676/05_2025/8dre_27676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dre_27676/05_2025/8dre_27676.map" model { file = "/net/cci-nas-00/data/ceres_data/8dre_27676/05_2025/8dre_27676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dre_27676/05_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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 16.38, per 1000 atoms: 0.63 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: 6.90 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: 2.84 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: 9.73 Time building geometry restraints manager: 8.01 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: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.900 Check model and map are aligned: 0.170 Set scattering table: 0.250 Process input model: 59.250 Find NCS groups from input model: 1.090 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.600 ------------------------------------------------------------------------------- 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 : 3.004 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: 0.3637 time to fit residues: 150.0336 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 : 3.013 ------------------------------------------------------------------------------- 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 = 0.4301 r_free = 0.4301 target = 0.130759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.095192 restraints weight = 62298.318| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.90 r_work: 0.3431 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 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 4.80116 ( 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 : 3.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.9122 (tp) cc_final: 0.8844 (tt) REVERT: A 451 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8062 (pt) REVERT: A 467 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8160 (mp10) REVERT: A 475 TRP cc_start: 0.8410 (m-10) cc_final: 0.8048 (m-10) REVERT: A 645 LYS cc_start: 0.7909 (mttt) cc_final: 0.7283 (mtmm) REVERT: B 37 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8371 (ttp) REVERT: B 171 ARG cc_start: 0.8452 (mmm160) cc_final: 0.7894 (ttm-80) REVERT: B 234 LYS cc_start: 0.8890 (tptp) cc_final: 0.8213 (tptp) REVERT: B 238 GLU cc_start: 0.8467 (tt0) cc_final: 0.8046 (pt0) REVERT: B 239 GLN cc_start: 0.7949 (pp30) cc_final: 0.7714 (pp30) REVERT: B 337 MET cc_start: 0.8102 (mtp) cc_final: 0.7832 (mtp) REVERT: B 521 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7303 (tt) REVERT: B 590 MET cc_start: 0.6652 (mmm) cc_final: 0.5953 (tpt) REVERT: C 47 VAL cc_start: 0.8848 (t) cc_final: 0.8609 (p) REVERT: C 168 TRP cc_start: 0.5027 (t60) cc_final: 0.4549 (t-100) REVERT: C 286 VAL cc_start: 0.8191 (OUTLIER) cc_final: 0.7784 (p) REVERT: D 375 MET cc_start: 0.8193 (mtm) cc_final: 0.7979 (mtm) REVERT: E 24 TRP cc_start: 0.7142 (p90) cc_final: 0.6446 (p90) REVERT: E 33 ILE cc_start: 0.8472 (mm) cc_final: 0.8163 (mt) REVERT: E 341 TRP cc_start: 0.7937 (t60) cc_final: 0.7618 (t60) REVERT: F 38 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7266 (tt) REVERT: F 144 PHE cc_start: 0.7963 (t80) cc_final: 0.7707 (t80) REVERT: F 261 MET cc_start: 0.6685 (ttm) cc_final: 0.6474 (ttm) outliers start: 55 outliers final: 25 residues processed: 274 average time/residue: 0.3529 time to fit residues: 156.8903 Evaluate side-chains 240 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 209 time to evaluate : 2.760 ------------------------------------------------------------------------------- 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: 3.9990 chunk 202 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 239 optimal weight: 3.9990 chunk 118 optimal weight: 20.0000 chunk 162 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 270 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 242 optimal weight: 0.8980 chunk 234 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.4290 r_free = 0.4290 target = 0.129622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.092514 restraints weight = 61321.087| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.70 r_work: 0.3404 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 26548 Z= 0.158 Angle : 0.514 8.076 35824 Z= 0.271 Chirality : 0.040 0.170 4007 Planarity : 0.004 0.046 4356 Dihedral : 13.794 177.913 3795 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.17 % Allowed : 20.48 % Favored : 77.35 % 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: -0.07 (0.15), residues: 3033 helix: 0.86 (0.13), residues: 1673 sheet: -1.36 (0.32), residues: 285 loop : -1.01 (0.19), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 23 HIS 0.009 0.001 HIS C 253 PHE 0.016 0.001 PHE F 609 TYR 0.013 0.001 TYR F 279 ARG 0.006 0.000 ARG D 346 Details of bonding type rmsd hydrogen bonds : bond 0.03882 ( 1303) hydrogen bonds : angle 4.61013 ( 3657) SS BOND : bond 0.00569 ( 17) SS BOND : angle 1.12955 ( 34) covalent geometry : bond 0.00362 (26531) covalent geometry : angle 0.51341 (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 284 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 222 time to evaluate : 3.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.9083 (tp) cc_final: 0.8874 (tt) REVERT: A 275 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.8294 (t80) REVERT: A 375 MET cc_start: 0.7411 (ptp) cc_final: 0.7179 (mtp) REVERT: A 451 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7988 (pt) REVERT: A 467 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8131 (mp10) REVERT: A 475 TRP cc_start: 0.8423 (m-10) cc_final: 0.8210 (m-10) REVERT: A 581 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8030 (mm) REVERT: A 645 LYS cc_start: 0.7942 (mttt) cc_final: 0.7313 (mtmm) REVERT: A 689 TYR cc_start: 0.7495 (t80) cc_final: 0.7214 (m-80) REVERT: B 171 ARG cc_start: 0.8350 (mmm160) cc_final: 0.7831 (ttm-80) REVERT: B 234 LYS cc_start: 0.8845 (tptp) cc_final: 0.8634 (tptp) REVERT: B 239 GLN cc_start: 0.7945 (pp30) cc_final: 0.7668 (pp30) REVERT: B 521 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7241 (tt) REVERT: B 590 MET cc_start: 0.6675 (mmm) cc_final: 0.6055 (tpt) REVERT: B 644 LEU cc_start: 0.8512 (pt) cc_final: 0.8113 (tp) REVERT: B 700 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.6314 (tt) REVERT: C 47 VAL cc_start: 0.8829 (t) cc_final: 0.8585 (p) REVERT: C 168 TRP cc_start: 0.5220 (t60) cc_final: 0.4640 (t-100) REVERT: C 375 MET cc_start: 0.6113 (mtm) cc_final: 0.5733 (mtm) REVERT: D 134 LEU cc_start: 0.8477 (mm) cc_final: 0.8178 (mp) REVERT: E 24 TRP cc_start: 0.7190 (p90) cc_final: 0.6411 (p90) REVERT: E 33 ILE cc_start: 0.8385 (mm) cc_final: 0.8101 (mt) REVERT: E 341 TRP cc_start: 0.7969 (t60) cc_final: 0.7641 (t60) REVERT: F 144 PHE cc_start: 0.7870 (t80) cc_final: 0.7598 (t80) REVERT: F 386 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7817 (pttp) REVERT: F 509 TRP cc_start: 0.7995 (p-90) cc_final: 0.7787 (p-90) outliers start: 62 outliers final: 32 residues processed: 274 average time/residue: 0.3490 time to fit residues: 154.9865 Evaluate side-chains 253 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 214 time to evaluate : 2.718 ------------------------------------------------------------------------------- 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 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 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 37 MET 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 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 135 THR Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 312 MET 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: 3.9990 chunk 36 optimal weight: 0.0070 chunk 275 optimal weight: 6.9990 chunk 284 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 287 optimal weight: 0.0040 chunk 260 optimal weight: 0.4980 chunk 117 optimal weight: 20.0000 chunk 255 optimal weight: 0.5980 chunk 52 optimal weight: 6.9990 overall best weight: 0.6212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 155 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 312 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.130016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.093671 restraints weight = 61976.270| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 3.02 r_work: 0.3394 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 26548 Z= 0.118 Angle : 0.499 11.739 35824 Z= 0.257 Chirality : 0.039 0.160 4007 Planarity : 0.003 0.042 4356 Dihedral : 12.915 176.937 3795 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.96 % Allowed : 20.83 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.15), residues: 3033 helix: 1.00 (0.13), residues: 1665 sheet: -1.34 (0.32), residues: 273 loop : -1.00 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 143 HIS 0.010 0.001 HIS C 253 PHE 0.025 0.001 PHE B 393 TYR 0.019 0.001 TYR D 382 ARG 0.004 0.000 ARG D 346 Details of bonding type rmsd hydrogen bonds : bond 0.03605 ( 1303) hydrogen bonds : angle 4.45828 ( 3657) SS BOND : bond 0.00449 ( 17) SS BOND : angle 0.91334 ( 34) covalent geometry : bond 0.00262 (26531) covalent geometry : angle 0.49822 (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 275 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 219 time to evaluate : 2.855 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: 0.9003 (tp) cc_final: 0.8792 (tt) REVERT: A 275 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.8232 (t80) REVERT: A 430 LEU cc_start: 0.9162 (tp) cc_final: 0.8695 (mt) REVERT: A 451 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7947 (pt) REVERT: A 475 TRP cc_start: 0.8469 (m-10) cc_final: 0.8199 (m-10) REVERT: A 581 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8083 (mm) REVERT: A 645 LYS cc_start: 0.7861 (mttt) cc_final: 0.7223 (mtmm) REVERT: A 689 TYR cc_start: 0.7478 (t80) cc_final: 0.7183 (m-80) REVERT: B 171 ARG cc_start: 0.8461 (mmm160) cc_final: 0.7902 (ttm-80) REVERT: B 234 LYS cc_start: 0.8861 (tptp) cc_final: 0.8630 (tptp) REVERT: B 337 MET cc_start: 0.8305 (mtp) cc_final: 0.8007 (mtp) REVERT: B 590 MET cc_start: 0.6562 (mmm) cc_final: 0.5930 (tpt) REVERT: B 644 LEU cc_start: 0.8336 (pt) cc_final: 0.7958 (tp) REVERT: C 18 ARG cc_start: 0.7395 (ptp-170) cc_final: 0.7183 (ptp90) REVERT: C 33 ILE cc_start: 0.8117 (mm) cc_final: 0.7816 (mm) REVERT: C 47 VAL cc_start: 0.8828 (t) cc_final: 0.8575 (p) REVERT: C 168 TRP cc_start: 0.5142 (t60) cc_final: 0.4638 (t-100) REVERT: D 134 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8079 (mp) REVERT: D 372 PHE cc_start: 0.7193 (OUTLIER) cc_final: 0.6281 (t80) REVERT: E 24 TRP cc_start: 0.7130 (p90) cc_final: 0.6567 (p90) REVERT: E 33 ILE cc_start: 0.8452 (mm) cc_final: 0.8139 (mt) REVERT: E 341 TRP cc_start: 0.7913 (t60) cc_final: 0.7629 (t60) REVERT: F 144 PHE cc_start: 0.7837 (t80) cc_final: 0.7611 (t80) REVERT: F 386 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7877 (pttp) REVERT: F 504 ARG cc_start: 0.7953 (tpt90) cc_final: 0.7481 (tpt90) REVERT: F 509 TRP cc_start: 0.7969 (p-90) cc_final: 0.7732 (p-90) REVERT: F 517 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.8006 (mm-30) REVERT: F 756 TYR cc_start: 0.5453 (t80) cc_final: 0.5173 (t80) outliers start: 56 outliers final: 32 residues processed: 263 average time/residue: 0.3615 time to fit residues: 153.8370 Evaluate side-chains 252 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 213 time to evaluate : 2.831 ------------------------------------------------------------------------------- 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 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 674 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 749 ARG 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 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 134 LEU Chi-restraints excluded: chain D residue 143 TRP 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 250 PHE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 386 LYS 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 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: 6.9990 chunk 248 optimal weight: 2.9990 chunk 264 optimal weight: 6.9990 chunk 300 optimal weight: 0.0170 chunk 295 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 280 optimal weight: 0.0570 chunk 42 optimal weight: 8.9990 chunk 266 optimal weight: 10.0000 overall best weight: 1.0140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN B 381 GLN ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** E 288 ASN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN F 423 HIS ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 670 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.128986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.092108 restraints weight = 61340.824| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.73 r_work: 0.3399 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26548 Z= 0.150 Angle : 0.501 8.658 35824 Z= 0.260 Chirality : 0.040 0.156 4007 Planarity : 0.003 0.036 4356 Dihedral : 12.253 177.789 3795 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.66 % Allowed : 20.87 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.16), residues: 3033 helix: 1.09 (0.13), residues: 1649 sheet: -1.21 (0.33), residues: 274 loop : -0.94 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 143 HIS 0.011 0.001 HIS C 253 PHE 0.030 0.001 PHE D 244 TYR 0.013 0.001 TYR F 279 ARG 0.004 0.000 ARG D 346 Details of bonding type rmsd hydrogen bonds : bond 0.03635 ( 1303) hydrogen bonds : angle 4.41552 ( 3657) SS BOND : bond 0.00495 ( 17) SS BOND : angle 0.87759 ( 34) covalent geometry : bond 0.00345 (26531) covalent geometry : angle 0.50093 (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 298 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 222 time to evaluate : 2.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.8942 (tp) cc_final: 0.8734 (tt) REVERT: A 275 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.8208 (t80) REVERT: A 430 LEU cc_start: 0.9151 (tp) cc_final: 0.8690 (mt) REVERT: A 451 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7855 (pt) REVERT: A 581 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8112 (mm) REVERT: B 171 ARG cc_start: 0.8422 (mmm160) cc_final: 0.7830 (ttm-80) REVERT: B 337 MET cc_start: 0.8275 (mtp) cc_final: 0.7962 (mtp) REVERT: B 590 MET cc_start: 0.6357 (mmm) cc_final: 0.5708 (tpt) REVERT: B 644 LEU cc_start: 0.8323 (pt) cc_final: 0.7965 (tp) REVERT: C 18 ARG cc_start: 0.7464 (ptp-170) cc_final: 0.7241 (mtm180) REVERT: C 33 ILE cc_start: 0.8174 (mm) cc_final: 0.7848 (mm) REVERT: C 47 VAL cc_start: 0.8872 (t) cc_final: 0.8610 (p) REVERT: C 168 TRP cc_start: 0.5195 (t60) cc_final: 0.4652 (t-100) REVERT: D 337 MET cc_start: 0.8268 (mmm) cc_final: 0.8056 (mmm) REVERT: D 372 PHE cc_start: 0.7146 (OUTLIER) cc_final: 0.6252 (t80) REVERT: E 24 TRP cc_start: 0.7164 (p90) cc_final: 0.6313 (p90) REVERT: E 33 ILE cc_start: 0.8349 (mm) cc_final: 0.8077 (mt) REVERT: E 37 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.8062 (ttp) REVERT: E 263 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.7150 (mp) REVERT: E 341 TRP cc_start: 0.7811 (t60) cc_final: 0.7457 (t60) REVERT: F 144 PHE cc_start: 0.7778 (t80) cc_final: 0.7553 (t80) REVERT: F 232 LYS cc_start: 0.6801 (OUTLIER) cc_final: 0.5821 (ptpp) REVERT: F 357 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7695 (pm20) REVERT: F 377 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7724 (mm) REVERT: F 386 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7931 (pttt) REVERT: F 504 ARG cc_start: 0.7973 (tpt90) cc_final: 0.7578 (tpt90) REVERT: F 509 TRP cc_start: 0.8043 (p-90) cc_final: 0.7831 (p-90) REVERT: F 517 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7995 (mm-30) REVERT: F 521 LEU cc_start: 0.7812 (tp) cc_final: 0.7566 (tt) REVERT: F 756 TYR cc_start: 0.5851 (t80) cc_final: 0.5492 (t80) outliers start: 76 outliers final: 46 residues processed: 284 average time/residue: 0.3487 time to fit residues: 160.1961 Evaluate side-chains 268 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 211 time to evaluate : 3.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET 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 440 ASP 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 274 LYS 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 396 GLU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C residue 104 HIS 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 44 THR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 143 TRP 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 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 263 LEU 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 159 ILE Chi-restraints excluded: chain F residue 232 LYS Chi-restraints excluded: chain F residue 312 MET 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 386 LYS 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 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: 2.9990 chunk 111 optimal weight: 20.0000 chunk 296 optimal weight: 0.8980 chunk 176 optimal weight: 0.9990 chunk 165 optimal weight: 0.9980 chunk 116 optimal weight: 20.0000 chunk 270 optimal weight: 4.9990 chunk 215 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN ** 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 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 = 0.4268 r_free = 0.4268 target = 0.128056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.091104 restraints weight = 61465.362| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.86 r_work: 0.3355 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 26548 Z= 0.227 Angle : 0.556 9.683 35824 Z= 0.289 Chirality : 0.042 0.161 4007 Planarity : 0.004 0.037 4356 Dihedral : 11.973 166.305 3795 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.26 % Allowed : 20.73 % Favored : 76.02 % 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: 0.05 (0.16), residues: 3033 helix: 0.96 (0.13), residues: 1644 sheet: -1.35 (0.33), residues: 290 loop : -0.90 (0.19), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 475 HIS 0.011 0.001 HIS C 253 PHE 0.038 0.002 PHE D 390 TYR 0.021 0.002 TYR B 386 ARG 0.006 0.000 ARG B 749 Details of bonding type rmsd hydrogen bonds : bond 0.03980 ( 1303) hydrogen bonds : angle 4.52810 ( 3657) SS BOND : bond 0.00595 ( 17) SS BOND : angle 0.97674 ( 34) covalent geometry : bond 0.00532 (26531) covalent geometry : angle 0.55572 (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 315 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 222 time to evaluate : 3.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.8984 (tp) cc_final: 0.8767 (tt) REVERT: A 275 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8315 (t80) REVERT: A 430 LEU cc_start: 0.9175 (tp) cc_final: 0.8753 (mt) REVERT: A 451 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7870 (pt) REVERT: A 467 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8244 (mp10) REVERT: B 171 ARG cc_start: 0.8217 (mmm160) cc_final: 0.7720 (ttm-80) REVERT: B 590 MET cc_start: 0.6376 (mmm) cc_final: 0.5733 (tpt) REVERT: B 644 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8118 (tp) REVERT: C 33 ILE cc_start: 0.8130 (mm) cc_final: 0.7816 (mm) REVERT: C 168 TRP cc_start: 0.5140 (t60) cc_final: 0.4577 (t-100) REVERT: C 372 PHE cc_start: 0.5165 (OUTLIER) cc_final: 0.4947 (t80) REVERT: D 343 MET cc_start: 0.7397 (mmm) cc_final: 0.6868 (mmt) REVERT: D 372 PHE cc_start: 0.7279 (OUTLIER) cc_final: 0.6398 (t80) REVERT: E 24 TRP cc_start: 0.7364 (p90) cc_final: 0.6361 (p90) REVERT: E 263 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7292 (mp) REVERT: E 341 TRP cc_start: 0.7784 (t60) cc_final: 0.7370 (t60) REVERT: F 144 PHE cc_start: 0.7923 (t80) cc_final: 0.7636 (t80) REVERT: F 357 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7679 (pm20) REVERT: F 504 ARG cc_start: 0.8090 (tpt90) cc_final: 0.7653 (tpt90) REVERT: F 509 TRP cc_start: 0.8101 (p-90) cc_final: 0.7883 (p-90) REVERT: F 517 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7959 (mm-30) REVERT: F 520 TYR cc_start: 0.7141 (m-80) cc_final: 0.6870 (m-80) REVERT: F 521 LEU cc_start: 0.8031 (tp) cc_final: 0.7814 (tp) REVERT: F 645 TRP cc_start: 0.6732 (OUTLIER) cc_final: 0.6466 (p90) REVERT: F 679 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.6563 (mt) REVERT: F 756 TYR cc_start: 0.5989 (t80) cc_final: 0.5699 (t80) outliers start: 93 outliers final: 59 residues processed: 298 average time/residue: 0.3654 time to fit residues: 176.6559 Evaluate side-chains 278 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 208 time to evaluate : 3.005 ------------------------------------------------------------------------------- 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 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 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 158 SER Chi-restraints excluded: chain B residue 274 LYS 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 396 GLU Chi-restraints excluded: chain B residue 521 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 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 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 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 140 SER 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 280 CYS 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 141 CYS Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 252 VAL 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 517 GLU Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain F residue 645 TRP Chi-restraints excluded: chain F residue 679 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 245 optimal weight: 0.9980 chunk 157 optimal weight: 7.9990 chunk 221 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 206 optimal weight: 0.7980 chunk 34 optimal weight: 0.0070 chunk 27 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 18 optimal weight: 0.5980 chunk 281 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.129104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.092478 restraints weight = 61357.068| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.93 r_work: 0.3375 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2174 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= 0.140 Angle : 0.513 9.900 35824 Z= 0.266 Chirality : 0.040 0.151 4007 Planarity : 0.003 0.036 4356 Dihedral : 11.453 163.549 3795 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.28 % Allowed : 22.02 % Favored : 75.70 % 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 (0.16), residues: 3033 helix: 1.07 (0.13), residues: 1640 sheet: -1.47 (0.32), residues: 305 loop : -0.80 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 475 HIS 0.011 0.001 HIS C 253 PHE 0.030 0.001 PHE D 390 TYR 0.021 0.001 TYR A 653 ARG 0.006 0.000 ARG B 749 Details of bonding type rmsd hydrogen bonds : bond 0.03632 ( 1303) hydrogen bonds : angle 4.39986 ( 3657) SS BOND : bond 0.00316 ( 17) SS BOND : angle 0.83086 ( 34) covalent geometry : bond 0.00321 (26531) covalent geometry : angle 0.51235 (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 279 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 214 time to evaluate : 3.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.8977 (tp) cc_final: 0.8762 (tt) REVERT: A 235 LYS cc_start: 0.8870 (mmtt) cc_final: 0.8633 (mmmt) REVERT: A 275 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.8283 (t80) REVERT: A 430 LEU cc_start: 0.9045 (tp) cc_final: 0.8712 (mt) REVERT: A 467 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8343 (mp10) REVERT: B 171 ARG cc_start: 0.8240 (mmm160) cc_final: 0.7780 (ttm-80) REVERT: B 510 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8744 (mm) REVERT: B 590 MET cc_start: 0.6234 (mmm) cc_final: 0.5682 (tpt) REVERT: B 644 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7928 (tp) REVERT: C 33 ILE cc_start: 0.8143 (mm) cc_final: 0.7792 (mm) REVERT: C 47 VAL cc_start: 0.8838 (p) cc_final: 0.8372 (p) REVERT: C 168 TRP cc_start: 0.5121 (t60) cc_final: 0.4489 (t-100) REVERT: D 343 MET cc_start: 0.7272 (mmm) cc_final: 0.6731 (mmt) REVERT: D 372 PHE cc_start: 0.7239 (OUTLIER) cc_final: 0.6345 (t80) REVERT: D 375 MET cc_start: 0.8240 (mtm) cc_final: 0.7973 (mtm) REVERT: E 24 TRP cc_start: 0.7320 (p90) cc_final: 0.6327 (p90) REVERT: E 341 TRP cc_start: 0.7789 (t60) cc_final: 0.7366 (t60) REVERT: F 144 PHE cc_start: 0.7876 (t80) cc_final: 0.7626 (t80) REVERT: F 357 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7666 (pm20) REVERT: F 377 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7746 (mm) REVERT: F 504 ARG cc_start: 0.8171 (tpt90) cc_final: 0.7653 (tpt90) REVERT: F 509 TRP cc_start: 0.8108 (p-90) cc_final: 0.7846 (p-90) REVERT: F 517 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7935 (mm-30) REVERT: F 521 LEU cc_start: 0.8160 (tp) cc_final: 0.7938 (tp) REVERT: F 679 LEU cc_start: 0.6846 (OUTLIER) cc_final: 0.6574 (mt) REVERT: F 756 TYR cc_start: 0.6002 (t80) cc_final: 0.5715 (t80) outliers start: 65 outliers final: 44 residues processed: 268 average time/residue: 0.3535 time to fit residues: 153.7321 Evaluate side-chains 262 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 209 time to evaluate : 3.153 ------------------------------------------------------------------------------- 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 459 VAL Chi-restraints excluded: chain A residue 467 GLN 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 95 THR Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 280 CYS 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 275 PHE Chi-restraints excluded: chain C residue 292 ASP 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 37 MET 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 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 275 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 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 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 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: 0.0970 chunk 145 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 266 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 247 optimal weight: 10.0000 chunk 181 optimal weight: 0.7980 chunk 265 optimal weight: 6.9990 chunk 153 optimal weight: 3.9990 chunk 270 optimal weight: 10.0000 chunk 188 optimal weight: 2.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN ** 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 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 = 0.4293 r_free = 0.4293 target = 0.129605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.092914 restraints weight = 61406.857| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.88 r_work: 0.3390 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26548 Z= 0.126 Angle : 0.509 12.223 35824 Z= 0.262 Chirality : 0.040 0.210 4007 Planarity : 0.003 0.036 4356 Dihedral : 10.911 160.275 3795 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.21 % Allowed : 22.37 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.16), residues: 3033 helix: 1.14 (0.13), residues: 1642 sheet: -1.56 (0.31), residues: 309 loop : -0.73 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 475 HIS 0.012 0.001 HIS C 253 PHE 0.028 0.001 PHE D 390 TYR 0.014 0.001 TYR D 281 ARG 0.006 0.000 ARG B 749 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 1303) hydrogen bonds : angle 4.34005 ( 3657) SS BOND : bond 0.00330 ( 17) SS BOND : angle 0.86704 ( 34) covalent geometry : bond 0.00286 (26531) covalent geometry : angle 0.50831 (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 271 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 208 time to evaluate : 2.734 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: 0.8946 (tp) cc_final: 0.8713 (tt) REVERT: A 235 LYS cc_start: 0.8831 (mmtt) cc_final: 0.8605 (mmmt) REVERT: A 275 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.8285 (t80) REVERT: A 467 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8133 (mp10) REVERT: A 568 HIS cc_start: 0.8161 (OUTLIER) cc_final: 0.7778 (p-80) REVERT: B 171 ARG cc_start: 0.8223 (mmm160) cc_final: 0.7769 (ttm-80) REVERT: B 434 MET cc_start: 0.8370 (mtt) cc_final: 0.7890 (mtt) REVERT: B 644 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8059 (tp) REVERT: C 33 ILE cc_start: 0.8161 (mm) cc_final: 0.7802 (mm) REVERT: C 47 VAL cc_start: 0.8798 (p) cc_final: 0.8521 (p) REVERT: C 168 TRP cc_start: 0.5042 (t60) cc_final: 0.4555 (t-100) REVERT: D 343 MET cc_start: 0.7212 (mmm) cc_final: 0.6834 (mmt) REVERT: D 372 PHE cc_start: 0.7245 (OUTLIER) cc_final: 0.6361 (t80) REVERT: D 375 MET cc_start: 0.8199 (mtm) cc_final: 0.7936 (mtm) REVERT: E 24 TRP cc_start: 0.7256 (p90) cc_final: 0.6378 (p90) REVERT: E 341 TRP cc_start: 0.7761 (t60) cc_final: 0.7332 (t60) REVERT: F 144 PHE cc_start: 0.7860 (t80) cc_final: 0.7577 (t80) REVERT: F 232 LYS cc_start: 0.6928 (OUTLIER) cc_final: 0.5891 (ptpp) REVERT: F 357 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7637 (pm20) REVERT: F 377 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7778 (mm) REVERT: F 504 ARG cc_start: 0.8281 (tpt90) cc_final: 0.7802 (tpt90) REVERT: F 509 TRP cc_start: 0.8045 (p-90) cc_final: 0.7821 (p-90) REVERT: F 517 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7093 (mp0) REVERT: F 598 HIS cc_start: 0.8492 (t70) cc_final: 0.8222 (t70) REVERT: F 679 LEU cc_start: 0.6854 (OUTLIER) cc_final: 0.6567 (mt) REVERT: F 756 TYR cc_start: 0.5864 (t80) cc_final: 0.5525 (t80) outliers start: 63 outliers final: 43 residues processed: 258 average time/residue: 0.3497 time to fit residues: 146.4503 Evaluate side-chains 252 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 199 time to evaluate : 2.840 ------------------------------------------------------------------------------- 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 467 GLN 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 95 THR Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 274 LYS 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 396 GLU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 644 LEU 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 330 ILE Chi-restraints excluded: chain D residue 37 MET 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 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 40 VAL 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 383 LEU Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 462 THR Chi-restraints excluded: chain F residue 517 GLU 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: 1.9990 chunk 43 optimal weight: 0.9990 chunk 243 optimal weight: 0.9990 chunk 6 optimal weight: 0.2980 chunk 192 optimal weight: 1.9990 chunk 232 optimal weight: 7.9990 chunk 274 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 199 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- 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 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 ASN B 650 HIS ** 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 112 ASN ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 532 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.129472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.092275 restraints weight = 61230.602| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.65 r_work: 0.3412 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26548 Z= 0.137 Angle : 0.523 14.755 35824 Z= 0.267 Chirality : 0.040 0.281 4007 Planarity : 0.003 0.035 4356 Dihedral : 10.576 157.998 3795 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.24 % Allowed : 22.48 % Favored : 75.28 % 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: 0.21 (0.16), residues: 3033 helix: 1.08 (0.13), residues: 1658 sheet: -1.64 (0.31), residues: 314 loop : -0.68 (0.20), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 475 HIS 0.014 0.001 HIS B 522 PHE 0.027 0.001 PHE E 390 TYR 0.016 0.001 TYR A 332 ARG 0.006 0.000 ARG B 749 Details of bonding type rmsd hydrogen bonds : bond 0.03501 ( 1303) hydrogen bonds : angle 4.33754 ( 3657) SS BOND : bond 0.00355 ( 17) SS BOND : angle 1.25922 ( 34) covalent geometry : bond 0.00315 (26531) covalent geometry : angle 0.52137 (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 270 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 206 time to evaluate : 3.241 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: 0.8953 (tp) cc_final: 0.8705 (tt) REVERT: A 235 LYS cc_start: 0.8766 (mmtt) cc_final: 0.8532 (mmmt) REVERT: A 275 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.8260 (t80) REVERT: A 419 ARG cc_start: 0.8524 (tpt90) cc_final: 0.8061 (tpt90) REVERT: A 568 HIS cc_start: 0.8193 (OUTLIER) cc_final: 0.7807 (p-80) REVERT: B 171 ARG cc_start: 0.8167 (mmm160) cc_final: 0.7706 (ttm-80) REVERT: B 510 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8740 (mm) REVERT: B 644 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8032 (tp) REVERT: C 33 ILE cc_start: 0.8183 (mm) cc_final: 0.7804 (mm) REVERT: C 46 GLN cc_start: 0.7966 (tm-30) cc_final: 0.7619 (tm-30) REVERT: C 47 VAL cc_start: 0.8842 (p) cc_final: 0.8548 (p) REVERT: C 168 TRP cc_start: 0.5146 (t60) cc_final: 0.4629 (t-100) REVERT: D 244 PHE cc_start: 0.5914 (m-80) cc_final: 0.5699 (m-10) REVERT: D 343 MET cc_start: 0.7221 (mmm) cc_final: 0.6844 (mmt) REVERT: D 372 PHE cc_start: 0.7222 (OUTLIER) cc_final: 0.6321 (t80) REVERT: D 375 MET cc_start: 0.8192 (mtm) cc_final: 0.7908 (mtm) REVERT: E 24 TRP cc_start: 0.7257 (p90) cc_final: 0.6336 (p90) REVERT: F 144 PHE cc_start: 0.7833 (t80) cc_final: 0.7537 (t80) REVERT: F 232 LYS cc_start: 0.6905 (OUTLIER) cc_final: 0.5866 (ptpp) REVERT: F 357 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7676 (pm20) REVERT: F 377 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7732 (mm) REVERT: F 504 ARG cc_start: 0.8351 (tpt90) cc_final: 0.7845 (tpt90) REVERT: F 509 TRP cc_start: 0.8092 (p-90) cc_final: 0.7800 (p-90) REVERT: F 598 HIS cc_start: 0.8562 (t70) cc_final: 0.8256 (t70) REVERT: F 679 LEU cc_start: 0.6844 (OUTLIER) cc_final: 0.6559 (mt) REVERT: F 756 TYR cc_start: 0.5920 (t80) cc_final: 0.5629 (t80) outliers start: 64 outliers final: 50 residues processed: 258 average time/residue: 0.3838 time to fit residues: 160.0881 Evaluate side-chains 263 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 204 time to evaluate : 3.280 ------------------------------------------------------------------------------- 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 459 VAL 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 95 THR Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 274 LYS 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 396 GLU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 521 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 330 ILE Chi-restraints excluded: chain D residue 37 MET 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 275 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 277 ILE 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 462 THR 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: 0.6980 chunk 167 optimal weight: 6.9990 chunk 166 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 271 optimal weight: 5.9990 chunk 135 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 128 optimal weight: 8.9990 chunk 132 optimal weight: 0.8980 chunk 146 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 HIS A 467 GLN ** B 288 ASN ** 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 112 ASN ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 532 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.128949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.092372 restraints weight = 61141.311| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.83 r_work: 0.3374 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26548 Z= 0.159 Angle : 0.528 11.256 35824 Z= 0.271 Chirality : 0.040 0.234 4007 Planarity : 0.003 0.036 4356 Dihedral : 10.135 155.467 3795 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.14 % Allowed : 22.48 % Favored : 75.39 % 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 (0.16), residues: 3033 helix: 1.04 (0.13), residues: 1658 sheet: -1.56 (0.32), residues: 298 loop : -0.76 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 143 HIS 0.015 0.001 HIS C 253 PHE 0.029 0.001 PHE E 390 TYR 0.015 0.001 TYR A 332 ARG 0.007 0.000 ARG B 749 Details of bonding type rmsd hydrogen bonds : bond 0.03583 ( 1303) hydrogen bonds : angle 4.36561 ( 3657) SS BOND : bond 0.00402 ( 17) SS BOND : angle 1.02440 ( 34) covalent geometry : bond 0.00369 (26531) covalent geometry : angle 0.52696 (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 267 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 206 time to evaluate : 2.906 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: 0.8954 (tp) cc_final: 0.8717 (tt) REVERT: A 275 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.8295 (t80) REVERT: A 419 ARG cc_start: 0.8560 (tpt90) cc_final: 0.8151 (tpt90) REVERT: A 467 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8390 (mp10) REVERT: A 568 HIS cc_start: 0.8195 (OUTLIER) cc_final: 0.7806 (p-80) REVERT: B 171 ARG cc_start: 0.8246 (mmm160) cc_final: 0.7740 (ttm-80) REVERT: B 434 MET cc_start: 0.8133 (mtt) cc_final: 0.7869 (mtt) REVERT: B 510 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8692 (mm) REVERT: B 590 MET cc_start: 0.6312 (mmm) cc_final: 0.5672 (tpt) REVERT: B 644 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8003 (tp) REVERT: C 33 ILE cc_start: 0.8210 (mm) cc_final: 0.7831 (mm) REVERT: C 46 GLN cc_start: 0.8002 (tm-30) cc_final: 0.7665 (tm-30) REVERT: C 47 VAL cc_start: 0.8855 (p) cc_final: 0.8553 (p) REVERT: C 168 TRP cc_start: 0.5181 (t60) cc_final: 0.4649 (t-100) REVERT: D 343 MET cc_start: 0.7253 (mmm) cc_final: 0.6942 (mmt) REVERT: D 372 PHE cc_start: 0.7271 (OUTLIER) cc_final: 0.6334 (t80) REVERT: D 375 MET cc_start: 0.8230 (mtm) cc_final: 0.7957 (mtm) REVERT: E 24 TRP cc_start: 0.7325 (p90) cc_final: 0.6382 (p90) REVERT: F 232 LYS cc_start: 0.6962 (OUTLIER) cc_final: 0.5959 (ptpp) REVERT: F 357 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7994 (pm20) REVERT: F 377 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7857 (mm) REVERT: F 504 ARG cc_start: 0.8371 (tpt90) cc_final: 0.8075 (tpt170) REVERT: F 509 TRP cc_start: 0.8099 (p-90) cc_final: 0.7847 (p-90) REVERT: F 598 HIS cc_start: 0.8603 (t70) cc_final: 0.8270 (t70) REVERT: F 679 LEU cc_start: 0.6845 (OUTLIER) cc_final: 0.6527 (mt) REVERT: F 756 TYR cc_start: 0.6058 (t80) cc_final: 0.5831 (t80) outliers start: 61 outliers final: 49 residues processed: 255 average time/residue: 0.3559 time to fit residues: 146.8604 Evaluate side-chains 262 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 203 time to evaluate : 3.015 ------------------------------------------------------------------------------- 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 459 VAL Chi-restraints excluded: chain A residue 467 GLN 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 95 THR Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 274 LYS 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 396 GLU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 521 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 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 275 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 383 LEU Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 462 THR 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 74 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 285 optimal weight: 4.9990 chunk 49 optimal weight: 0.0770 chunk 273 optimal weight: 7.9990 chunk 144 optimal weight: 0.9980 chunk 289 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN ** B 288 ASN ** 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 112 ASN ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 532 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.128954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.091821 restraints weight = 61115.704| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.56 r_work: 0.3404 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.165 26548 Z= 0.180 Angle : 0.677 59.200 35824 Z= 0.380 Chirality : 0.041 0.606 4007 Planarity : 0.003 0.035 4356 Dihedral : 10.135 155.454 3795 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.10 % Allowed : 22.69 % Favored : 75.21 % Cbeta Deviations : 0.03 % 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: 0.17 (0.16), residues: 3033 helix: 1.05 (0.13), residues: 1658 sheet: -1.56 (0.32), residues: 298 loop : -0.76 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 143 HIS 0.013 0.001 HIS C 253 PHE 0.036 0.001 PHE A 156 TYR 0.014 0.001 TYR A 332 ARG 0.005 0.000 ARG B 749 Details of bonding type rmsd hydrogen bonds : bond 0.03623 ( 1303) hydrogen bonds : angle 4.36687 ( 3657) SS BOND : bond 0.00342 ( 17) SS BOND : angle 0.98899 ( 34) covalent geometry : bond 0.00396 (26531) covalent geometry : angle 0.67619 (35790) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16122.75 seconds wall clock time: 279 minutes 12.26 seconds (16752.26 seconds total)