Starting phenix.real_space_refine on Mon Aug 25 07:35:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dre_27676/08_2025/8dre_27676.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dre_27676/08_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_27676/08_2025/8dre_27676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dre_27676/08_2025/8dre_27676.map" model { file = "/net/cci-nas-00/data/ceres_data/8dre_27676/08_2025/8dre_27676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dre_27676/08_2025/8dre_27676.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.019 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 5.69, per 1000 atoms: 0.22 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: 2.34 Conformation dependent library (CDL) restraints added in 982.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.78 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: 4.61 Time building geometry restraints manager: 2.97 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 901 or (resid 902 and \ (name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C1 \ 6 or name C17 or name C18 or name O2 or name O4 )) or (resid 903 and (name C10 o \ r name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C \ 17 or name O2 or name O4 )))) selection = (chain 'B' and resid 15 through 903) } ncs_group { reference = (chain 'C' and (resid 15 through 402 or (resid 901 through 902 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 \ or name O2 or name O4 )))) selection = (chain 'D' and (resid 15 through 175 or resid 240 through 402 or (resid 903 thro \ ugh 904 and (name C10 or name C11 or name C12 or name C13 or name C14 or name C1 \ 5 or name C16 or name C17 or name O2 or name O4 )))) selection = (chain 'E' and (resid 15 through 175 or resid 240 through 402 or resid 902 throu \ gh 903)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.140 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: 0.040 Extract box with map and model: 0.440 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 22.100 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.430 ------------------------------------------------------------------------------- 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 : 8.34 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (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 ARG 0.013 0.001 ARG F 118 TYR 0.036 0.001 TYR C 284 PHE 0.043 0.002 PHE E 390 TRP 0.060 0.002 TRP C 23 HIS 0.020 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00563 (26531) covalent geometry : angle 0.80282 (35790) SS BOND : bond 0.00356 ( 17) SS BOND : angle 1.32058 ( 34) hydrogen bonds : bond 0.14210 ( 1303) hydrogen bonds : angle 6.27686 ( 3657) *********************** 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 : 0.970 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: A 738 LEU cc_start: 0.8117 (mm) cc_final: 0.7895 (mp) REVERT: B 171 ARG cc_start: 0.8204 (mmm160) cc_final: 0.7682 (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: 0.7352 (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: 0.1677 time to fit residues: 68.7970 Evaluate side-chains 219 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 216 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.0980 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 ASN A 409 ASN ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 GLN B 499 HIS ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN F 402 GLN ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 GLN F 635 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.130902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.096734 restraints weight = 62606.258| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 3.34 r_work: 0.3424 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 26548 Z= 0.128 Angle : 0.518 8.368 35824 Z= 0.274 Chirality : 0.040 0.170 4007 Planarity : 0.004 0.052 4356 Dihedral : 15.229 170.987 3802 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.93 % Allowed : 20.52 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.15), residues: 3033 helix: 0.77 (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 ARG 0.008 0.000 ARG F 539 TYR 0.016 0.001 TYR F 756 PHE 0.023 0.001 PHE F 609 TRP 0.027 0.001 TRP C 23 HIS 0.009 0.001 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00271 (26531) covalent geometry : angle 0.51728 (35790) SS BOND : bond 0.00294 ( 17) SS BOND : angle 0.83422 ( 34) hydrogen bonds : bond 0.04052 ( 1303) hydrogen bonds : angle 4.76386 ( 3657) *********************** 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 286 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 231 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.9116 (tp) cc_final: 0.8841 (tt) REVERT: A 467 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8144 (mp10) REVERT: A 475 TRP cc_start: 0.8416 (m-10) cc_final: 0.7999 (m-10) REVERT: A 477 TYR cc_start: 0.8754 (m-80) cc_final: 0.8549 (m-80) REVERT: A 645 LYS cc_start: 0.7945 (mttt) cc_final: 0.7328 (mtmm) REVERT: A 738 LEU cc_start: 0.8773 (mm) cc_final: 0.8539 (mp) REVERT: B 37 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8398 (ttp) REVERT: B 171 ARG cc_start: 0.8433 (mmm160) cc_final: 0.7883 (ttm-80) REVERT: B 234 LYS cc_start: 0.8841 (tptp) cc_final: 0.8144 (tptp) REVERT: B 238 GLU cc_start: 0.8401 (tt0) cc_final: 0.7981 (pt0) REVERT: B 239 GLN cc_start: 0.7995 (pp30) cc_final: 0.7758 (pp30) REVERT: B 337 MET cc_start: 0.8128 (mtp) cc_final: 0.7863 (mtp) REVERT: B 521 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7365 (tt) REVERT: B 590 MET cc_start: 0.6702 (mmm) cc_final: 0.6145 (tpt) REVERT: B 598 LEU cc_start: 0.6882 (mt) cc_final: 0.6557 (mp) REVERT: C 47 VAL cc_start: 0.8832 (t) cc_final: 0.8600 (p) REVERT: C 168 TRP cc_start: 0.5150 (t60) cc_final: 0.4591 (t-100) REVERT: C 286 VAL cc_start: 0.8103 (OUTLIER) cc_final: 0.7731 (p) REVERT: D 375 MET cc_start: 0.8195 (mtm) cc_final: 0.7992 (mtm) REVERT: E 24 TRP cc_start: 0.7133 (p90) cc_final: 0.6433 (p90) REVERT: E 33 ILE cc_start: 0.8428 (mm) cc_final: 0.8120 (mt) REVERT: E 341 TRP cc_start: 0.7975 (t60) cc_final: 0.7694 (t60) REVERT: F 38 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7202 (tt) REVERT: F 144 PHE cc_start: 0.7900 (t80) cc_final: 0.7679 (t80) REVERT: F 236 GLU cc_start: 0.8552 (pt0) cc_final: 0.8154 (tm-30) REVERT: F 261 MET cc_start: 0.6557 (ttm) cc_final: 0.6351 (ttm) REVERT: F 521 LEU cc_start: 0.8237 (tp) cc_final: 0.7883 (tt) outliers start: 55 outliers final: 22 residues processed: 278 average time/residue: 0.1581 time to fit residues: 71.6157 Evaluate side-chains 242 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 215 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 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 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 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 159 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 283 optimal weight: 2.9990 chunk 236 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 241 optimal weight: 0.8980 chunk 213 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 226 optimal weight: 1.9990 chunk 224 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 ASN A 711 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 E 312 HIS ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.129245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.092497 restraints weight = 61945.399| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.91 r_work: 0.3380 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 26548 Z= 0.179 Angle : 0.529 12.060 35824 Z= 0.276 Chirality : 0.041 0.174 4007 Planarity : 0.004 0.045 4356 Dihedral : 13.575 179.424 3795 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.35 % Allowed : 20.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.15), residues: 3033 helix: 0.85 (0.13), residues: 1670 sheet: -1.16 (0.32), residues: 281 loop : -1.07 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 533 TYR 0.015 0.001 TYR F 279 PHE 0.018 0.002 PHE E 390 TRP 0.019 0.001 TRP C 23 HIS 0.009 0.001 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00415 (26531) covalent geometry : angle 0.52788 (35790) SS BOND : bond 0.00426 ( 17) SS BOND : angle 1.06797 ( 34) hydrogen bonds : bond 0.03927 ( 1303) hydrogen bonds : angle 4.62189 ( 3657) *********************** 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 299 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 232 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.9088 (tp) cc_final: 0.8878 (tt) REVERT: A 275 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8305 (t80) REVERT: A 375 MET cc_start: 0.7557 (ptp) cc_final: 0.7353 (mtp) REVERT: A 451 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7965 (pt) REVERT: A 475 TRP cc_start: 0.8443 (m-10) cc_final: 0.8241 (m-10) REVERT: A 581 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8114 (mm) REVERT: A 645 LYS cc_start: 0.7951 (mttt) cc_final: 0.7322 (mtmm) REVERT: A 689 TYR cc_start: 0.7538 (t80) cc_final: 0.7251 (m-80) REVERT: B 171 ARG cc_start: 0.8404 (mmm160) cc_final: 0.7876 (ttm-80) REVERT: B 234 LYS cc_start: 0.8800 (tptp) cc_final: 0.8584 (tptp) REVERT: B 239 GLN cc_start: 0.7963 (pp30) cc_final: 0.7701 (pp30) REVERT: B 521 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.7151 (tt) REVERT: B 590 MET cc_start: 0.6541 (mmm) cc_final: 0.5937 (tpt) REVERT: B 644 LEU cc_start: 0.8508 (pt) cc_final: 0.8111 (tp) REVERT: B 700 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.6192 (tt) REVERT: C 17 TYR cc_start: 0.7444 (OUTLIER) cc_final: 0.7087 (m-80) REVERT: C 47 VAL cc_start: 0.8851 (t) cc_final: 0.8606 (p) REVERT: C 168 TRP cc_start: 0.5176 (t60) cc_final: 0.4616 (t-100) REVERT: C 375 MET cc_start: 0.6189 (mtm) cc_final: 0.5825 (mtm) REVERT: D 134 LEU cc_start: 0.8470 (mm) cc_final: 0.8262 (mt) REVERT: E 24 TRP cc_start: 0.7223 (p90) cc_final: 0.6438 (p90) REVERT: E 33 ILE cc_start: 0.8381 (mm) cc_final: 0.8079 (mt) REVERT: E 341 TRP cc_start: 0.7937 (t60) cc_final: 0.7613 (t60) REVERT: F 144 PHE cc_start: 0.7891 (t80) cc_final: 0.7621 (t80) REVERT: F 236 GLU cc_start: 0.8572 (pt0) cc_final: 0.8061 (tm-30) REVERT: F 521 LEU cc_start: 0.8031 (tp) cc_final: 0.7690 (tt) REVERT: F 581 MET cc_start: 0.7030 (tpt) cc_final: 0.6712 (tpt) outliers start: 67 outliers final: 35 residues processed: 284 average time/residue: 0.1592 time to fit residues: 74.0436 Evaluate side-chains 262 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 221 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 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 158 SER 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 521 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 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 143 TRP 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 19 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 377 ILE Chi-restraints excluded: chain F residue 449 LEU 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 11 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 302 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 59 optimal weight: 0.4980 chunk 114 optimal weight: 9.9990 chunk 176 optimal weight: 0.3980 chunk 287 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN B 409 ASN ** B 499 HIS ** 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 ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.129795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.093105 restraints weight = 61251.818| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.95 r_work: 0.3396 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 26548 Z= 0.117 Angle : 0.497 10.669 35824 Z= 0.257 Chirality : 0.039 0.162 4007 Planarity : 0.003 0.040 4356 Dihedral : 12.654 174.460 3795 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.16), residues: 3033 helix: 1.04 (0.13), residues: 1653 sheet: -1.26 (0.32), residues: 273 loop : -0.97 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 346 TYR 0.020 0.001 TYR D 382 PHE 0.020 0.001 PHE B 393 TRP 0.028 0.001 TRP F 509 HIS 0.011 0.001 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00262 (26531) covalent geometry : angle 0.49664 (35790) SS BOND : bond 0.00286 ( 17) SS BOND : angle 0.85382 ( 34) hydrogen bonds : bond 0.03577 ( 1303) hydrogen bonds : angle 4.44292 ( 3657) *********************** 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 284 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 228 time to evaluate : 1.043 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: 0.8993 (tp) cc_final: 0.8780 (tt) REVERT: A 275 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.8213 (t80) REVERT: A 430 LEU cc_start: 0.9157 (tp) cc_final: 0.8695 (mt) REVERT: A 451 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7872 (pt) REVERT: A 581 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8087 (mm) REVERT: A 689 TYR cc_start: 0.7404 (t80) cc_final: 0.7129 (m-80) REVERT: B 171 ARG cc_start: 0.8399 (mmm160) cc_final: 0.7878 (ttm-80) REVERT: B 337 MET cc_start: 0.8290 (mtp) cc_final: 0.7970 (mtp) REVERT: B 590 MET cc_start: 0.6527 (mmm) cc_final: 0.5863 (tpt) REVERT: B 644 LEU cc_start: 0.8267 (pt) cc_final: 0.7920 (tp) REVERT: C 18 ARG cc_start: 0.7461 (ptp-170) cc_final: 0.7121 (mtm180) REVERT: C 33 ILE cc_start: 0.8179 (mm) cc_final: 0.7875 (mm) REVERT: C 47 VAL cc_start: 0.8855 (t) cc_final: 0.8604 (p) REVERT: C 168 TRP cc_start: 0.5172 (t60) cc_final: 0.4627 (t-100) REVERT: D 134 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8033 (mp) REVERT: D 372 PHE cc_start: 0.7157 (OUTLIER) cc_final: 0.6233 (t80) REVERT: E 24 TRP cc_start: 0.7138 (p90) cc_final: 0.6561 (p90) REVERT: E 33 ILE cc_start: 0.8447 (mm) cc_final: 0.8138 (mt) REVERT: E 341 TRP cc_start: 0.7838 (t60) cc_final: 0.7544 (t60) REVERT: F 144 PHE cc_start: 0.7806 (t80) cc_final: 0.7595 (t80) REVERT: F 386 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7818 (pttp) REVERT: F 504 ARG cc_start: 0.7981 (tpt90) cc_final: 0.7494 (tpt90) REVERT: F 517 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8024 (mm-30) REVERT: F 521 LEU cc_start: 0.7842 (tp) cc_final: 0.7539 (tt) REVERT: F 581 MET cc_start: 0.6802 (tpt) cc_final: 0.6486 (tpt) REVERT: F 756 TYR cc_start: 0.5334 (t80) cc_final: 0.5011 (t80) outliers start: 56 outliers final: 28 residues processed: 271 average time/residue: 0.1606 time to fit residues: 70.9907 Evaluate side-chains 250 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 215 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 440 ASP 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 674 ILE Chi-restraints excluded: chain B residue 95 THR 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 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 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 250 PHE Chi-restraints excluded: chain E residue 275 PHE 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 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 0 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 123 optimal weight: 20.0000 chunk 283 optimal weight: 6.9990 chunk 191 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 129 optimal weight: 9.9990 chunk 213 optimal weight: 2.9990 chunk 214 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 670 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.128798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.090777 restraints weight = 61528.094| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.96 r_work: 0.3365 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 26548 Z= 0.191 Angle : 0.526 9.271 35824 Z= 0.272 Chirality : 0.041 0.158 4007 Planarity : 0.003 0.040 4356 Dihedral : 12.299 169.045 3795 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.84 % Allowed : 20.87 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.16), residues: 3033 helix: 1.01 (0.13), residues: 1658 sheet: -1.15 (0.33), residues: 274 loop : -1.01 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 749 TYR 0.015 0.001 TYR F 279 PHE 0.029 0.002 PHE D 244 TRP 0.025 0.002 TRP F 509 HIS 0.011 0.001 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00446 (26531) covalent geometry : angle 0.52509 (35790) SS BOND : bond 0.00484 ( 17) SS BOND : angle 0.90144 ( 34) hydrogen bonds : bond 0.03786 ( 1303) hydrogen bonds : angle 4.48255 ( 3657) *********************** 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 302 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 221 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.8995 (tp) cc_final: 0.8769 (tt) REVERT: A 275 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8296 (t80) REVERT: A 430 LEU cc_start: 0.9184 (tp) cc_final: 0.8738 (mt) REVERT: A 451 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7887 (pt) REVERT: A 452 LYS cc_start: 0.7224 (mtpp) cc_final: 0.6726 (ttmt) REVERT: A 581 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8033 (mm) REVERT: B 171 ARG cc_start: 0.8391 (mmm160) cc_final: 0.7835 (ttm-80) REVERT: B 337 MET cc_start: 0.8267 (mtp) cc_final: 0.7987 (mtp) REVERT: B 438 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8084 (mp) REVERT: B 443 PHE cc_start: 0.8784 (m-10) cc_final: 0.8566 (m-10) REVERT: B 590 MET cc_start: 0.6381 (mmm) cc_final: 0.5750 (tpt) REVERT: B 644 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7942 (tp) REVERT: C 18 ARG cc_start: 0.7568 (ptp-170) cc_final: 0.7229 (mtm180) REVERT: C 33 ILE cc_start: 0.8218 (mm) cc_final: 0.7882 (mm) REVERT: C 47 VAL cc_start: 0.8906 (t) cc_final: 0.8642 (p) REVERT: C 168 TRP cc_start: 0.5134 (t60) cc_final: 0.4583 (t-100) REVERT: C 372 PHE cc_start: 0.4714 (OUTLIER) cc_final: 0.4358 (t80) REVERT: D 134 LEU cc_start: 0.8404 (mm) cc_final: 0.8204 (mt) REVERT: D 343 MET cc_start: 0.7287 (mmm) cc_final: 0.6716 (mmt) REVERT: D 372 PHE cc_start: 0.7288 (OUTLIER) cc_final: 0.6399 (t80) REVERT: E 24 TRP cc_start: 0.7254 (p90) cc_final: 0.6400 (p90) REVERT: E 263 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7308 (mp) REVERT: E 341 TRP cc_start: 0.7845 (t60) cc_final: 0.7485 (t60) REVERT: F 144 PHE cc_start: 0.7809 (t80) cc_final: 0.7559 (t80) REVERT: F 357 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7715 (pm20) REVERT: F 386 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7830 (pttp) REVERT: F 504 ARG cc_start: 0.8044 (tpt90) cc_final: 0.7540 (tpt90) REVERT: F 517 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7924 (mm-30) REVERT: F 521 LEU cc_start: 0.8142 (tp) cc_final: 0.7764 (tt) REVERT: F 581 MET cc_start: 0.7179 (tpt) cc_final: 0.6748 (tpp) REVERT: F 679 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6638 (mp) REVERT: F 756 TYR cc_start: 0.5870 (t80) cc_final: 0.5592 (t80) outliers start: 81 outliers final: 49 residues processed: 287 average time/residue: 0.1564 time to fit residues: 72.2292 Evaluate side-chains 275 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 214 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 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 438 ILE Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 749 ARG Chi-restraints excluded: chain C residue 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 330 ILE Chi-restraints excluded: chain C residue 372 PHE Chi-restraints excluded: chain D residue 37 MET 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 143 TRP Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 372 PHE Chi-restraints excluded: chain E residue 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 232 LYS Chi-restraints excluded: chain F residue 252 VAL 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 174 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 231 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 229 optimal weight: 0.0020 chunk 160 optimal weight: 0.0770 chunk 136 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 247 optimal weight: 0.6980 overall best weight: 0.4546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.130202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.093700 restraints weight = 61703.500| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.93 r_work: 0.3405 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 26548 Z= 0.104 Angle : 0.489 9.374 35824 Z= 0.252 Chirality : 0.039 0.152 4007 Planarity : 0.003 0.037 4356 Dihedral : 11.538 165.264 3795 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.89 % Allowed : 22.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.16), residues: 3033 helix: 1.20 (0.13), residues: 1643 sheet: -1.30 (0.33), residues: 287 loop : -0.81 (0.19), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 749 TYR 0.017 0.001 TYR A 653 PHE 0.022 0.001 PHE E 390 TRP 0.032 0.002 TRP A 475 HIS 0.011 0.001 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00226 (26531) covalent geometry : angle 0.48891 (35790) SS BOND : bond 0.00282 ( 17) SS BOND : angle 0.78856 ( 34) hydrogen bonds : bond 0.03427 ( 1303) hydrogen bonds : angle 4.31777 ( 3657) *********************** 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 279 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 225 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.8939 (tp) cc_final: 0.8717 (tt) REVERT: A 275 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.8190 (t80) REVERT: A 430 LEU cc_start: 0.9179 (tp) cc_final: 0.8777 (mt) REVERT: A 581 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8136 (mm) REVERT: B 171 ARG cc_start: 0.8240 (mmm160) cc_final: 0.7741 (ttm-80) REVERT: B 337 MET cc_start: 0.8285 (mtp) cc_final: 0.8014 (mtp) REVERT: B 590 MET cc_start: 0.6411 (mmm) cc_final: 0.5737 (tpt) REVERT: B 644 LEU cc_start: 0.8287 (pt) cc_final: 0.7943 (tp) REVERT: C 33 ILE cc_start: 0.8165 (mm) cc_final: 0.7840 (mm) REVERT: C 47 VAL cc_start: 0.8871 (t) cc_final: 0.8655 (p) REVERT: C 168 TRP cc_start: 0.5170 (t60) cc_final: 0.4647 (t-100) REVERT: D 134 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8068 (mp) REVERT: D 343 MET cc_start: 0.7122 (mmm) cc_final: 0.6655 (mmt) REVERT: D 372 PHE cc_start: 0.7094 (OUTLIER) cc_final: 0.6190 (t80) REVERT: D 375 MET cc_start: 0.8104 (mtm) cc_final: 0.7856 (mtm) REVERT: E 24 TRP cc_start: 0.7182 (p90) cc_final: 0.6615 (p90) REVERT: E 341 TRP cc_start: 0.7833 (t60) cc_final: 0.7439 (t60) REVERT: F 144 PHE cc_start: 0.7773 (t80) cc_final: 0.7545 (t80) REVERT: F 357 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7660 (pm20) REVERT: F 377 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7645 (mm) REVERT: F 386 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7879 (pttt) REVERT: F 504 ARG cc_start: 0.8030 (tpt90) cc_final: 0.7681 (tpt90) REVERT: F 517 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8007 (mm-30) REVERT: F 520 TYR cc_start: 0.7012 (m-80) cc_final: 0.6741 (m-80) REVERT: F 521 LEU cc_start: 0.7853 (tp) cc_final: 0.7519 (tt) REVERT: F 581 MET cc_start: 0.7112 (tpt) cc_final: 0.6772 (tpp) REVERT: F 598 HIS cc_start: 0.8490 (t70) cc_final: 0.8127 (t-170) REVERT: F 679 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6578 (mp) REVERT: F 756 TYR cc_start: 0.5735 (t80) cc_final: 0.5441 (t80) outliers start: 54 outliers final: 31 residues processed: 272 average time/residue: 0.1563 time to fit residues: 69.0736 Evaluate side-chains 252 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 212 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 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 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 307 THR Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 641 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 60 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 372 PHE Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 250 PHE Chi-restraints excluded: chain F residue 59 VAL 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 386 LYS Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 517 GLU Chi-restraints excluded: chain F residue 679 LEU Chi-restraints excluded: chain F residue 694 ASP Chi-restraints excluded: chain F residue 783 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 127 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 130 optimal weight: 0.4980 chunk 50 optimal weight: 5.9990 chunk 239 optimal weight: 1.9990 chunk 83 optimal weight: 0.0870 chunk 32 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 291 optimal weight: 3.9990 chunk 294 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.9164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 ASN ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.128117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.090621 restraints weight = 61386.321| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.57 r_work: 0.3376 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 26548 Z= 0.241 Angle : 0.564 10.115 35824 Z= 0.292 Chirality : 0.042 0.156 4007 Planarity : 0.004 0.037 4356 Dihedral : 11.548 163.842 3795 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.56 % Allowed : 21.50 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.16), residues: 3033 helix: 1.00 (0.13), residues: 1645 sheet: -1.47 (0.31), residues: 317 loop : -0.77 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG B 749 TYR 0.020 0.002 TYR A 653 PHE 0.040 0.002 PHE D 390 TRP 0.041 0.002 TRP A 475 HIS 0.011 0.001 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00568 (26531) covalent geometry : angle 0.56352 (35790) SS BOND : bond 0.00562 ( 17) SS BOND : angle 0.96176 ( 34) hydrogen bonds : bond 0.03957 ( 1303) hydrogen bonds : angle 4.49756 ( 3657) *********************** 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 294 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 221 time to evaluate : 0.858 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: 0.8964 (tp) cc_final: 0.8752 (tt) REVERT: A 275 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.8292 (t80) REVERT: A 430 LEU cc_start: 0.9195 (tp) cc_final: 0.8799 (mt) REVERT: A 645 LYS cc_start: 0.7950 (mttt) cc_final: 0.7254 (mtmm) REVERT: B 171 ARG cc_start: 0.8204 (mmm160) cc_final: 0.7674 (ttm-80) REVERT: B 510 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8797 (mm) REVERT: B 590 MET cc_start: 0.6454 (mmm) cc_final: 0.5745 (tpt) REVERT: B 644 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8057 (tp) REVERT: C 33 ILE cc_start: 0.8224 (mm) cc_final: 0.7896 (mm) REVERT: C 168 TRP cc_start: 0.5175 (t60) cc_final: 0.4584 (t-100) REVERT: D 134 LEU cc_start: 0.8416 (mm) cc_final: 0.8206 (mt) REVERT: D 343 MET cc_start: 0.7347 (mmm) cc_final: 0.7010 (mmt) REVERT: D 372 PHE cc_start: 0.7291 (OUTLIER) cc_final: 0.6432 (t80) REVERT: E 24 TRP cc_start: 0.7344 (p90) cc_final: 0.6327 (p90) REVERT: E 341 TRP cc_start: 0.7789 (t60) cc_final: 0.7372 (t60) REVERT: F 144 PHE cc_start: 0.7956 (t80) cc_final: 0.7674 (t80) REVERT: F 357 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7694 (pm20) REVERT: F 386 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7914 (pttt) REVERT: F 504 ARG cc_start: 0.8117 (tpt90) cc_final: 0.7746 (tpt90) REVERT: F 509 TRP cc_start: 0.8016 (p-90) cc_final: 0.7445 (p-90) REVERT: F 520 TYR cc_start: 0.7178 (m-80) cc_final: 0.6890 (m-80) REVERT: F 521 LEU cc_start: 0.7944 (tp) cc_final: 0.7578 (tt) REVERT: F 581 MET cc_start: 0.7259 (tpt) cc_final: 0.6878 (tpp) REVERT: F 679 LEU cc_start: 0.6970 (OUTLIER) cc_final: 0.6659 (mp) REVERT: F 756 TYR cc_start: 0.5821 (t80) cc_final: 0.5595 (t80) outliers start: 73 outliers final: 49 residues processed: 282 average time/residue: 0.1425 time to fit residues: 65.6797 Evaluate side-chains 273 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 217 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 459 VAL 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 A residue 738 LEU 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 307 THR Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 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 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 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 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 141 CYS 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 363 ILE Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 386 LYS Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 604 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 128 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 218 optimal weight: 0.8980 chunk 125 optimal weight: 10.0000 chunk 29 optimal weight: 0.5980 chunk 199 optimal weight: 0.6980 chunk 226 optimal weight: 0.9980 chunk 274 optimal weight: 10.0000 chunk 159 optimal weight: 0.6980 chunk 241 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 ASN B 650 HIS B 764 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.129466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.092299 restraints weight = 61231.742| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.69 r_work: 0.3397 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26548 Z= 0.130 Angle : 0.509 12.531 35824 Z= 0.262 Chirality : 0.040 0.178 4007 Planarity : 0.003 0.036 4356 Dihedral : 10.967 160.350 3795 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.00 % Allowed : 22.41 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.16), residues: 3033 helix: 1.13 (0.13), residues: 1641 sheet: -1.55 (0.31), residues: 319 loop : -0.69 (0.19), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 346 TYR 0.015 0.001 TYR D 281 PHE 0.030 0.001 PHE D 390 TRP 0.043 0.002 TRP A 475 HIS 0.011 0.001 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00298 (26531) covalent geometry : angle 0.50842 (35790) SS BOND : bond 0.00429 ( 17) SS BOND : angle 0.93784 ( 34) hydrogen bonds : bond 0.03544 ( 1303) hydrogen bonds : angle 4.35776 ( 3657) *********************** 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 272 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 215 time to evaluate : 0.731 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: 0.8950 (tp) cc_final: 0.8711 (tt) REVERT: A 275 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.8285 (t80) REVERT: A 430 LEU cc_start: 0.9159 (tp) cc_final: 0.8660 (mt) REVERT: A 447 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8134 (pm20) REVERT: A 452 LYS cc_start: 0.7196 (mtpp) cc_final: 0.6915 (ttmt) REVERT: B 171 ARG cc_start: 0.8175 (mmm160) cc_final: 0.7733 (ttm-80) REVERT: B 510 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8727 (mm) REVERT: B 590 MET cc_start: 0.6384 (mmm) cc_final: 0.5714 (tpt) REVERT: B 644 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8014 (tp) REVERT: C 33 ILE cc_start: 0.8146 (mm) cc_final: 0.7799 (mm) REVERT: C 46 GLN cc_start: 0.8113 (tm-30) cc_final: 0.7744 (tm-30) REVERT: C 47 VAL cc_start: 0.8762 (p) cc_final: 0.8483 (p) REVERT: C 168 TRP cc_start: 0.5117 (t60) cc_final: 0.4571 (t-100) REVERT: D 134 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8091 (mp) REVERT: D 372 PHE cc_start: 0.7223 (OUTLIER) cc_final: 0.6309 (t80) REVERT: D 375 MET cc_start: 0.8199 (mtm) cc_final: 0.7914 (mtm) REVERT: E 24 TRP cc_start: 0.7305 (p90) cc_final: 0.6368 (p90) REVERT: F 144 PHE cc_start: 0.7841 (t80) cc_final: 0.7559 (t80) REVERT: F 357 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7675 (pm20) REVERT: F 377 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7680 (mm) REVERT: F 386 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7827 (pttt) REVERT: F 504 ARG cc_start: 0.8246 (tpt90) cc_final: 0.7879 (tpt90) REVERT: F 509 TRP cc_start: 0.8027 (p-90) cc_final: 0.7449 (p-90) REVERT: F 517 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.6912 (mp0) REVERT: F 520 TYR cc_start: 0.7227 (m-80) cc_final: 0.6922 (m-80) REVERT: F 521 LEU cc_start: 0.8070 (tp) cc_final: 0.7661 (tt) REVERT: F 581 MET cc_start: 0.7297 (tpt) cc_final: 0.6913 (tpp) REVERT: F 598 HIS cc_start: 0.8578 (t70) cc_final: 0.8267 (t70) REVERT: F 679 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6567 (mp) REVERT: F 756 TYR cc_start: 0.5987 (t80) cc_final: 0.5695 (t80) outliers start: 57 outliers final: 33 residues processed: 261 average time/residue: 0.1403 time to fit residues: 59.4507 Evaluate side-chains 253 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 209 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 447 GLU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 546 LEU 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 307 THR 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 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 134 LEU Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 372 PHE Chi-restraints excluded: chain E residue 250 PHE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 159 ILE 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 386 LYS Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 517 GLU 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 245 optimal weight: 0.5980 chunk 277 optimal weight: 6.9990 chunk 204 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 241 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 188 optimal weight: 0.5980 chunk 195 optimal weight: 0.7980 chunk 167 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.128583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.091360 restraints weight = 61355.493| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.58 r_work: 0.3395 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26548 Z= 0.190 Angle : 0.542 11.970 35824 Z= 0.279 Chirality : 0.041 0.151 4007 Planarity : 0.003 0.044 4356 Dihedral : 10.750 158.968 3795 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.03 % Allowed : 22.44 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.16), residues: 3033 helix: 1.04 (0.13), residues: 1646 sheet: -1.62 (0.31), residues: 325 loop : -0.70 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 346 TYR 0.015 0.001 TYR F 279 PHE 0.030 0.002 PHE D 390 TRP 0.051 0.002 TRP A 475 HIS 0.014 0.001 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00445 (26531) covalent geometry : angle 0.54056 (35790) SS BOND : bond 0.00402 ( 17) SS BOND : angle 1.29025 ( 34) hydrogen bonds : bond 0.03725 ( 1303) hydrogen bonds : angle 4.41721 ( 3657) *********************** 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 271 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 213 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.8946 (tp) cc_final: 0.8718 (tt) REVERT: A 275 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8280 (t80) REVERT: A 430 LEU cc_start: 0.9138 (tp) cc_final: 0.8671 (mt) REVERT: A 447 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8146 (pm20) REVERT: A 452 LYS cc_start: 0.7188 (mtpp) cc_final: 0.6778 (ttmt) REVERT: A 568 HIS cc_start: 0.8114 (OUTLIER) cc_final: 0.7741 (p-80) REVERT: B 171 ARG cc_start: 0.8161 (mmm160) cc_final: 0.7706 (ttm-80) REVERT: B 434 MET cc_start: 0.8282 (mtt) cc_final: 0.8031 (mtt) REVERT: B 510 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8772 (mm) REVERT: B 590 MET cc_start: 0.6380 (mmm) cc_final: 0.5642 (tpt) REVERT: B 644 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8048 (tp) REVERT: C 33 ILE cc_start: 0.8219 (mm) cc_final: 0.7869 (mm) REVERT: C 46 GLN cc_start: 0.8172 (tm-30) cc_final: 0.7791 (tm-30) REVERT: C 47 VAL cc_start: 0.8794 (p) cc_final: 0.8486 (p) REVERT: C 168 TRP cc_start: 0.5126 (t60) cc_final: 0.4564 (t-100) REVERT: D 134 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8222 (mt) REVERT: D 372 PHE cc_start: 0.7278 (OUTLIER) cc_final: 0.6411 (t80) REVERT: E 24 TRP cc_start: 0.7343 (p90) cc_final: 0.6333 (p90) REVERT: E 33 ILE cc_start: 0.8505 (mm) cc_final: 0.8173 (mt) REVERT: F 144 PHE cc_start: 0.7872 (t80) cc_final: 0.7565 (t80) REVERT: F 357 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7966 (pm20) REVERT: F 377 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7875 (mm) REVERT: F 386 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7832 (pttt) REVERT: F 504 ARG cc_start: 0.8275 (tpt90) cc_final: 0.7898 (tpt90) REVERT: F 509 TRP cc_start: 0.8077 (p-90) cc_final: 0.7579 (p-90) REVERT: F 517 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: F 520 TYR cc_start: 0.7242 (m-80) cc_final: 0.6896 (m-80) REVERT: F 521 LEU cc_start: 0.7995 (tp) cc_final: 0.7754 (tp) REVERT: F 581 MET cc_start: 0.7311 (tpt) cc_final: 0.6945 (tpp) REVERT: F 598 HIS cc_start: 0.8548 (t70) cc_final: 0.8235 (t70) REVERT: F 679 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6586 (mp) REVERT: F 756 TYR cc_start: 0.5976 (t80) cc_final: 0.5697 (t80) outliers start: 58 outliers final: 42 residues processed: 264 average time/residue: 0.1654 time to fit residues: 71.4468 Evaluate side-chains 264 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 210 time to evaluate : 1.084 ------------------------------------------------------------------------------- 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 447 GLU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 546 LEU 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 307 THR Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 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 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 134 LEU Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 372 PHE Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 59 VAL 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 386 LYS Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 517 GLU 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 128 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 178 optimal weight: 0.7980 chunk 117 optimal weight: 20.0000 chunk 281 optimal weight: 0.5980 chunk 261 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 177 optimal weight: 0.0040 chunk 113 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 532 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.129390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.092396 restraints weight = 61509.137| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.96 r_work: 0.3389 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2463 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= 0.130 Angle : 0.518 13.431 35824 Z= 0.265 Chirality : 0.040 0.147 4007 Planarity : 0.003 0.043 4356 Dihedral : 10.134 155.864 3795 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.00 % Allowed : 22.48 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.16), residues: 3033 helix: 1.15 (0.13), residues: 1642 sheet: -1.57 (0.31), residues: 324 loop : -0.64 (0.20), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 18 TYR 0.014 0.001 TYR D 281 PHE 0.028 0.001 PHE D 390 TRP 0.044 0.002 TRP A 475 HIS 0.015 0.001 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00298 (26531) covalent geometry : angle 0.51702 (35790) SS BOND : bond 0.00313 ( 17) SS BOND : angle 1.00960 ( 34) hydrogen bonds : bond 0.03468 ( 1303) hydrogen bonds : angle 4.31807 ( 3657) ********************** 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 273 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 216 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.8908 (tp) cc_final: 0.8669 (tt) REVERT: A 275 PHE cc_start: 0.8724 (OUTLIER) cc_final: 0.8268 (t80) REVERT: A 430 LEU cc_start: 0.9098 (tp) cc_final: 0.8608 (mt) REVERT: A 447 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8084 (pm20) REVERT: A 568 HIS cc_start: 0.8149 (OUTLIER) cc_final: 0.7750 (p-80) REVERT: B 171 ARG cc_start: 0.8316 (mmm160) cc_final: 0.7769 (ttm-80) REVERT: B 434 MET cc_start: 0.8252 (mtt) cc_final: 0.7974 (mtt) REVERT: B 510 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8777 (mm) REVERT: B 590 MET cc_start: 0.6193 (mmm) cc_final: 0.5456 (tpt) REVERT: B 644 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8046 (tp) REVERT: C 33 ILE cc_start: 0.8122 (mm) cc_final: 0.7783 (mm) REVERT: C 46 GLN cc_start: 0.8212 (tm-30) cc_final: 0.7805 (tm-30) REVERT: C 47 VAL cc_start: 0.8779 (p) cc_final: 0.8505 (p) REVERT: C 168 TRP cc_start: 0.5025 (t60) cc_final: 0.4554 (t-100) REVERT: D 134 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7947 (mp) REVERT: D 372 PHE cc_start: 0.7028 (OUTLIER) cc_final: 0.6208 (t80) REVERT: D 375 MET cc_start: 0.8093 (mtm) cc_final: 0.7831 (mtm) REVERT: E 24 TRP cc_start: 0.7220 (p90) cc_final: 0.6287 (p90) REVERT: F 357 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8003 (pm20) REVERT: F 377 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7668 (mm) REVERT: F 386 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7823 (pttt) REVERT: F 500 PHE cc_start: 0.6967 (p90) cc_final: 0.6763 (p90) REVERT: F 504 ARG cc_start: 0.8282 (tpt90) cc_final: 0.7877 (tpt90) REVERT: F 509 TRP cc_start: 0.8010 (p-90) cc_final: 0.7535 (p-90) REVERT: F 520 TYR cc_start: 0.7107 (m-80) cc_final: 0.6828 (m-80) REVERT: F 581 MET cc_start: 0.7243 (tpt) cc_final: 0.6893 (tpp) REVERT: F 598 HIS cc_start: 0.8464 (t70) cc_final: 0.8193 (t70) REVERT: F 679 LEU cc_start: 0.6860 (OUTLIER) cc_final: 0.6572 (mp) REVERT: F 756 TYR cc_start: 0.5932 (t80) cc_final: 0.5724 (t80) REVERT: F 800 MET cc_start: 0.8079 (mmt) cc_final: 0.7877 (mmt) outliers start: 57 outliers final: 43 residues processed: 259 average time/residue: 0.1721 time to fit residues: 72.8961 Evaluate side-chains 262 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 208 time to evaluate : 1.096 ------------------------------------------------------------------------------- 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 447 GLU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 546 LEU 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 307 THR Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 521 LEU 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 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 D residue 379 ILE Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 250 PHE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 159 ILE 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 386 LYS Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 604 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 90 optimal weight: 0.6980 chunk 243 optimal weight: 0.0270 chunk 239 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 257 optimal weight: 1.9990 chunk 110 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 221 optimal weight: 0.6980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 585 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 532 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.129633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.093358 restraints weight = 60543.463| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.93 r_work: 0.3405 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 26548 Z= 0.111 Angle : 0.523 18.949 35824 Z= 0.263 Chirality : 0.039 0.151 4007 Planarity : 0.003 0.042 4356 Dihedral : 9.738 153.816 3795 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.86 % Allowed : 22.79 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.16), residues: 3033 helix: 1.21 (0.13), residues: 1642 sheet: -1.55 (0.30), residues: 330 loop : -0.64 (0.20), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.015 0.001 TYR D 281 PHE 0.028 0.001 PHE D 390 TRP 0.048 0.002 TRP A 475 HIS 0.014 0.001 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00249 (26531) covalent geometry : angle 0.52264 (35790) SS BOND : bond 0.00260 ( 17) SS BOND : angle 0.86394 ( 34) hydrogen bonds : bond 0.03366 ( 1303) hydrogen bonds : angle 4.27894 ( 3657) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7182.04 seconds wall clock time: 123 minutes 39.25 seconds (7419.25 seconds total)