Starting phenix.real_space_refine on Mon Jul 6 04:00:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8f79_28898/07_2026/8f79_28898.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f79_28898/07_2026/8f79_28898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8f79_28898/07_2026/8f79_28898.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8f79_28898/07_2026/8f79_28898.cif" model { file = "/net/cci-nas-00/data/ceres_data/8f79_28898/07_2026/8f79_28898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f79_28898/07_2026/8f79_28898.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8f79_28898/07_2026/8f79_28898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f79_28898/07_2026/8f79_28898.map" } resolution = 3.15 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= 0.003 sd= 0.060 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 6 5.49 5 S 154 5.16 5 C 21092 2.51 5 N 5349 2.21 5 O 5732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 139 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32333 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5916 Classifications: {'peptide': 717} Link IDs: {'PTRANS': 27, 'TRANS': 689} Chain breaks: 2 Chain: "B" Number of atoms: 5912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 5912 Classifications: {'peptide': 716} Link IDs: {'PTRANS': 27, 'TRANS': 688} Chain breaks: 2 Chain: "C" Number of atoms: 5898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 714, 5898 Classifications: {'peptide': 714} Link IDs: {'PTRANS': 27, 'TRANS': 686} Chain breaks: 2 Chain: "D" Number of atoms: 2648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2648 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "E" Number of atoms: 5905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 715, 5905 Classifications: {'peptide': 715} Link IDs: {'PTRANS': 27, 'TRANS': 687} 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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 49 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 47 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 73 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: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 47 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 72 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: 5.94, per 1000 atoms: 0.18 Number of scatterers: 32333 At special positions: 0 Unit cell: (145.672, 139.384, 192.832, 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 154 16.00 P 6 15.00 O 5732 8.00 N 5349 7.00 C 21092 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=2.04 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=2.03 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=2.02 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: 1.86 Conformation dependent library (CDL) restraints added in 1.3 seconds 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7536 Finding SS restraints... Secondary structure from input PDB file: 170 helices and 24 sheets defined 53.2% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 15 through 21 removed outlier: 4.188A pdb=" N ILE A 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 21 " --> pdb=" O ARG A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 49 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 146 through 165 removed outlier: 3.966A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N CYS A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 175 removed outlier: 3.944A pdb=" N THR A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 removed outlier: 3.581A pdb=" N THR A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 286 removed outlier: 3.920A pdb=" N VAL A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) 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: 3.887A 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 370 through 383 Processing helix chain 'A' and resid 383 through 391 removed outlier: 4.141A pdb=" N SER A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' 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 445 removed outlier: 3.724A pdb=" N LEU A 445 " --> pdb=" O THR A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 484 through 495 Processing helix chain 'A' and resid 509 through 515 removed outlier: 3.635A pdb=" N ILE A 512 " --> pdb=" O PRO A 509 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR A 513 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A 515 " --> pdb=" O ILE A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 542 removed outlier: 4.238A pdb=" N GLY A 539 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG A 541 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 566 Processing helix chain 'A' and resid 585 through 589 removed outlier: 3.912A pdb=" N LYS A 588 " --> pdb=" O ASN A 585 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS A 589 " --> pdb=" O SER A 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 585 through 589' Processing helix chain 'A' and resid 633 through 638 removed outlier: 3.508A pdb=" N GLN A 636 " --> pdb=" O ILE A 633 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HIS A 637 " --> pdb=" O SER A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 661 removed outlier: 3.628A pdb=" N ILE A 658 " --> pdb=" O PRO A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 684 removed outlier: 3.568A pdb=" N CYS A 684 " --> pdb=" O LEU A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 707 removed outlier: 3.771A pdb=" N ILE A 704 " --> pdb=" O PRO A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 730 removed outlier: 3.936A pdb=" N PHE A 728 " --> pdb=" O PRO A 724 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS A 730 " --> pdb=" O GLU A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 753 Processing helix chain 'A' and resid 770 through 776 Processing helix chain 'A' and resid 787 through 793 Processing helix chain 'A' and resid 795 through 808 Processing helix chain 'B' and resid 17 through 21 Processing helix chain 'B' and resid 22 through 50 removed outlier: 3.983A pdb=" N ASP B 50 " --> pdb=" O GLN B 46 " (cutoff:3.500A) 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: 4.569A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 165 Processing helix chain 'B' and resid 167 through 175 Processing helix chain 'B' and resid 233 through 255 Processing helix chain 'B' and resid 258 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 345 removed outlier: 3.544A pdb=" N CYS B 336 " --> pdb=" O TYR B 332 " (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: 4.251A 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 removed outlier: 3.529A pdb=" N GLU B 399 " --> pdb=" O SER B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 419 Processing helix chain 'B' and resid 439 through 445 removed outlier: 3.843A pdb=" N PHE B 443 " --> pdb=" O PRO B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 467 Processing helix chain 'B' and resid 484 through 495 removed outlier: 3.740A pdb=" N GLU B 493 " --> pdb=" O ALA B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 508 removed outlier: 3.854A pdb=" N GLU B 507 " --> pdb=" O ASP B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 515 removed outlier: 4.279A pdb=" N SER B 514 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 515 " --> pdb=" O TRP B 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 510 through 515' Processing helix chain 'B' and resid 535 through 543 removed outlier: 3.532A pdb=" N ASP B 538 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY B 539 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG B 541 " --> pdb=" O ASP B 538 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLU B 542 " --> pdb=" O GLY B 539 " (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 634 through 638 Processing helix chain 'B' and resid 655 through 661 removed outlier: 3.684A pdb=" N ILE B 658 " --> pdb=" O PRO B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 684 removed outlier: 3.508A pdb=" N TYR B 683 " --> pdb=" O GLN B 680 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N CYS B 684 " --> pdb=" O LEU B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 707 Processing helix chain 'B' and resid 724 through 730 removed outlier: 3.638A pdb=" N CYS B 730 " --> pdb=" O GLU B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 752 removed outlier: 3.508A pdb=" N GLY B 751 " --> pdb=" O PRO B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 774 removed outlier: 3.776A pdb=" N LEU B 773 " --> pdb=" O PRO B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 792 removed outlier: 3.557A pdb=" N SER B 792 " --> pdb=" O GLU B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 808 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 22 through 50 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: 4.619A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 5.061A 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: 3.870A pdb=" N ARG C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 Processing helix chain 'C' and resid 258 through 286 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 315 through 345 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 391 removed outlier: 4.117A pdb=" N SER C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 394 No H-bonds generated for 'chain 'C' and resid 392 through 394' Processing helix chain 'C' and resid 395 through 411 Processing helix chain 'C' and resid 412 through 419 removed outlier: 4.003A pdb=" N GLN C 418 " --> pdb=" O ASP C 414 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG C 419 " --> pdb=" O LYS C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 444 removed outlier: 3.635A pdb=" N PHE C 443 " --> pdb=" O PRO C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 484 through 494 Processing helix chain 'C' and resid 535 through 541 removed outlier: 3.755A pdb=" N ASP C 538 " --> pdb=" O ILE C 535 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY C 539 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG C 541 " --> pdb=" O ASP C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 566 Processing helix chain 'C' and resid 607 through 612 removed outlier: 4.247A pdb=" N PHE C 611 " --> pdb=" O PRO C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 638 removed outlier: 3.525A pdb=" N ILE C 632 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE C 633 " --> pdb=" O GLU C 630 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN C 636 " --> pdb=" O ILE C 633 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N HIS C 637 " --> pdb=" O SER C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 661 removed outlier: 3.823A pdb=" N LEU C 661 " --> pdb=" O ILE C 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 678 through 684 removed outlier: 3.750A pdb=" N CYS C 684 " --> pdb=" O LEU C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 707 removed outlier: 3.662A pdb=" N ILE C 704 " --> pdb=" O PRO C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 730 removed outlier: 3.762A pdb=" N CYS C 730 " --> pdb=" O LEU C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 753 Processing helix chain 'C' and resid 770 through 775 Processing helix chain 'C' and resid 787 through 792 Processing helix chain 'C' and resid 795 through 807 Processing helix chain 'D' and resid 22 through 50 removed outlier: 3.639A pdb=" N ASP D 50 " --> pdb=" O GLN D 46 " (cutoff:3.500A) 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: 4.602A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.021A 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: 3.896A pdb=" N THR D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 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 315 through 346 removed outlier: 4.261A 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 removed outlier: 3.617A pdb=" N ALA D 373 " --> pdb=" O LYS D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 395 removed outlier: 4.262A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL D 392 " --> pdb=" O LYS D 388 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N PHE D 393 " --> pdb=" O ARG D 389 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU D 394 " --> pdb=" O PHE D 390 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER D 395 " --> pdb=" O ALA D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 408 removed outlier: 3.542A pdb=" N GLU D 399 " --> pdb=" O SER D 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 50 removed outlier: 3.831A 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: 4.498A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 4.965A 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: 3.545A pdb=" N THR E 170 " --> pdb=" O SER E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 Processing helix chain 'E' and resid 258 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 317 through 345 removed outlier: 3.577A pdb=" N SER E 327 " --> pdb=" O SER E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 360 removed outlier: 3.566A pdb=" N GLU E 359 " --> pdb=" O SER E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 383 Processing helix chain 'E' and resid 383 through 392 removed outlier: 4.263A pdb=" N SER E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 411 Processing helix chain 'E' and resid 412 through 420 Processing helix chain 'E' and resid 439 through 444 removed outlier: 3.790A pdb=" N PHE E 443 " --> pdb=" O PRO E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 468 removed outlier: 3.588A pdb=" N ILE E 465 " --> pdb=" O PRO E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 484 through 494 Processing helix chain 'E' and resid 510 through 514 removed outlier: 4.055A pdb=" N TYR E 513 " --> pdb=" O LEU E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 541 removed outlier: 3.703A pdb=" N ARG E 541 " --> pdb=" O ASP E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 566 removed outlier: 3.788A pdb=" N THR E 563 " --> pdb=" O PRO E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 632 through 638 removed outlier: 3.749A pdb=" N GLN E 636 " --> pdb=" O ILE E 633 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HIS E 637 " --> pdb=" O SER E 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 661 removed outlier: 3.525A pdb=" N LEU E 661 " --> pdb=" O ILE E 658 " (cutoff:3.500A) Processing helix chain 'E' and resid 679 through 684 removed outlier: 3.647A pdb=" N CYS E 684 " --> pdb=" O LEU E 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 701 through 707 removed outlier: 3.953A pdb=" N ILE E 704 " --> pdb=" O PRO E 701 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU E 707 " --> pdb=" O ILE E 704 " (cutoff:3.500A) Processing helix chain 'E' and resid 724 through 730 removed outlier: 3.630A pdb=" N PHE E 728 " --> pdb=" O PRO E 724 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N CYS E 730 " --> pdb=" O GLU E 726 " (cutoff:3.500A) Processing helix chain 'E' and resid 747 through 753 Processing helix chain 'E' and resid 771 through 776 removed outlier: 3.561A pdb=" N CYS E 776 " --> pdb=" O GLU E 772 " (cutoff:3.500A) Processing helix chain 'E' and resid 788 through 793 Processing helix chain 'E' and resid 795 through 808 Processing helix chain 'F' and resid 22 through 49 removed outlier: 3.689A pdb=" N MET F 48 " --> pdb=" O THR F 44 " (cutoff:3.500A) 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: 4.022A pdb=" N ASN F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 148 removed outlier: 4.531A pdb=" N PHE F 148 " --> pdb=" O PHE F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 168 Processing helix chain 'F' and resid 169 through 179 Processing helix chain 'F' and resid 233 through 253 Processing helix chain 'F' and resid 256 through 284 Processing helix chain 'F' and resid 297 through 302 Processing helix chain 'F' and resid 313 through 343 Processing helix chain 'F' and resid 351 through 356 Processing helix chain 'F' and resid 368 through 381 Processing helix chain 'F' and resid 381 through 389 removed outlier: 4.333A 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 393 through 409 removed outlier: 3.982A pdb=" N GLU F 397 " --> pdb=" O SER F 393 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 418 Processing helix chain 'F' and resid 437 through 443 removed outlier: 3.922A pdb=" N PHE F 441 " --> pdb=" O PRO F 437 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE F 443 " --> pdb=" O THR F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 466 removed outlier: 3.946A pdb=" N ILE F 463 " --> pdb=" O PRO F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 492 Processing helix chain 'F' and resid 509 through 513 removed outlier: 3.834A pdb=" N LEU F 513 " --> pdb=" O MET F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 538 removed outlier: 3.801A pdb=" N SER F 537 " --> pdb=" O THR F 534 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 564 removed outlier: 3.711A 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 611 removed outlier: 4.098A pdb=" N PHE F 609 " --> pdb=" O PRO F 605 " (cutoff:3.500A) Processing helix chain 'F' and resid 629 through 636 removed outlier: 3.524A pdb=" N SER F 632 " --> pdb=" O GLU F 629 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN F 634 " --> pdb=" O VAL F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 653 through 659 removed outlier: 3.934A pdb=" N ILE F 656 " --> pdb=" O PRO F 653 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU F 659 " --> pdb=" O ILE F 656 " (cutoff:3.500A) Processing helix chain 'F' and resid 699 through 705 removed outlier: 3.699A pdb=" N ILE F 702 " --> pdb=" O PRO F 699 " (cutoff:3.500A) Processing helix chain 'F' and resid 723 through 728 Processing helix chain 'F' and resid 745 through 749 removed outlier: 3.540A pdb=" N ILE F 748 " --> pdb=" O SER F 745 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLY F 749 " --> pdb=" O PRO F 746 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 745 through 749' Processing helix chain 'F' and resid 768 through 772 removed outlier: 4.126A pdb=" N LEU F 771 " --> pdb=" O PRO F 768 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY F 772 " --> pdb=" O PRO F 769 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 768 through 772' Processing helix chain 'F' and resid 785 through 790 Processing helix chain 'F' and resid 793 through 802 removed outlier: 3.817A pdb=" N ALA F 802 " --> pdb=" O GLU F 798 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 removed outlier: 3.601A pdb=" N VAL A 293 " --> pdb=" O CYS A 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 3.784A pdb=" N VAL A 60 " --> pdb=" O VAL F 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 350 through 351 Processing sheet with id=AA4, first strand: chain 'A' and resid 421 through 422 removed outlier: 6.824A pdb=" N LEU A 474 " --> pdb=" O HIS A 499 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LYS A 501 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU A 521 " --> pdb=" O ARG A 550 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N LYS A 552 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU A 523 " --> pdb=" O LYS A 552 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU A 572 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ILE A 599 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE A 574 " --> pdb=" O ILE A 599 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 618 through 620 Processing sheet with id=AA6, first strand: chain 'A' and resid 666 through 668 removed outlier: 7.012A pdb=" N LEU A 667 " --> pdb=" O ASP A 691 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 735 through 737 removed outlier: 6.818A pdb=" N LEU A 736 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE A 759 " --> pdb=" O VAL A 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA9, first strand: chain 'B' and resid 420 through 422 removed outlier: 6.966A pdb=" N LEU B 451 " --> pdb=" O TRP B 475 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N TYR B 477 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU B 453 " --> pdb=" O TYR B 477 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU B 474 " --> pdb=" O HIS B 499 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N LYS B 501 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU B 476 " --> pdb=" O LYS B 501 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG B 550 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 523 " --> pdb=" O ARG B 550 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS B 552 " --> pdb=" O LEU B 523 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 573 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP B 620 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE B 619 " --> pdb=" O CYS B 643 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N LEU B 644 " --> pdb=" O TYR B 668 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 736 through 737 removed outlier: 6.611A pdb=" N LEU B 736 " --> pdb=" O GLU B 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 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 'C' and resid 421 through 422 removed outlier: 5.953A pdb=" N LEU C 451 " --> pdb=" O TRP C 475 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TYR C 477 " --> pdb=" O LEU C 451 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU C 453 " --> pdb=" O TYR C 477 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N HIS C 522 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER C 573 " --> pdb=" O LEU C 549 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU C 572 " --> pdb=" O GLU C 595 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS C 645 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU C 644 " --> pdb=" O TYR C 668 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 459 through 461 removed outlier: 6.032A pdb=" N VAL C 459 " --> pdb=" O LYS C 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 735 through 736 removed outlier: 8.155A pdb=" N LEU C 736 " --> pdb=" O GLU C 760 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE C 759 " --> pdb=" O VAL C 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AB8, first strand: chain 'E' and resid 53 through 56 removed outlier: 3.636A pdb=" N ILE E 53 " --> pdb=" O ALA E 311 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL E 293 " --> pdb=" O CYS E 310 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 350 through 351 Processing sheet with id=AC1, first strand: chain 'E' and resid 421 through 422 removed outlier: 6.410A pdb=" N LEU E 428 " --> pdb=" O VAL E 450 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LYS E 452 " --> pdb=" O LEU E 428 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LEU E 430 " --> pdb=" O LYS E 452 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLU E 454 " --> pdb=" O LEU E 430 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LEU E 432 " --> pdb=" O GLU E 454 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU E 474 " --> pdb=" O HIS E 499 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LYS E 501 " --> pdb=" O LEU E 474 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU E 476 " --> pdb=" O LYS E 501 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU E 498 " --> pdb=" O HIS E 522 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N THR E 524 " --> pdb=" O LEU E 498 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE E 500 " --> pdb=" O THR E 524 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU E 572 " --> pdb=" O GLU E 597 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE E 599 " --> pdb=" O LEU E 572 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ILE E 574 " --> pdb=" O ILE E 599 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU E 596 " --> pdb=" O GLU E 618 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASP E 620 " --> pdb=" O LEU E 596 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU E 598 " --> pdb=" O ASP E 620 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 459 through 460 removed outlier: 6.483A pdb=" N VAL E 459 " --> pdb=" O LYS E 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 666 through 668 removed outlier: 6.334A pdb=" N TYR E 689 " --> pdb=" O LEU E 667 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU E 690 " --> pdb=" O ALA E 714 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE E 759 " --> pdb=" O VAL E 785 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 52 through 56 Processing sheet with id=AC5, first strand: chain 'F' and resid 419 through 420 removed outlier: 5.701A pdb=" N LEU F 426 " --> pdb=" O SER F 448 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS F 450 " --> pdb=" O LEU F 426 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N LEU F 428 " --> pdb=" O LYS F 450 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLU F 452 " --> pdb=" O LEU F 428 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU F 430 " --> pdb=" O GLU F 452 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU F 449 " --> pdb=" O CYS F 473 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N HIS F 475 " --> pdb=" O LEU F 449 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU F 451 " --> pdb=" O HIS F 475 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU F 472 " --> pdb=" O SER F 497 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N LYS F 499 " --> pdb=" O LEU F 472 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LEU F 474 " --> pdb=" O LYS F 499 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N MET F 570 " --> pdb=" O GLU F 595 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL F 597 " --> pdb=" O MET F 570 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N VAL F 572 " --> pdb=" O VAL F 597 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU F 594 " --> pdb=" O ASP F 618 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LYS F 620 " --> pdb=" O LEU F 594 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LEU F 596 " --> pdb=" O LYS F 620 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU F 617 " --> pdb=" O LYS F 643 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU F 688 " --> pdb=" O SER F 712 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N PHE F 711 " --> pdb=" O LYS F 735 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 457 through 458 removed outlier: 6.568A pdb=" N VAL F 457 " --> pdb=" O LYS F 480 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 1463 hydrogen bonds defined for protein. 4026 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.34 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9007 1.34 - 1.46: 5923 1.46 - 1.58: 17880 1.58 - 1.70: 11 1.70 - 1.82: 222 Bond restraints: 33043 Sorted by residual: bond pdb=" C10 PEE B 902 " pdb=" O4 PEE B 902 " ideal model delta sigma weight residual 1.206 1.359 -0.153 2.00e-02 2.50e+03 5.83e+01 bond pdb=" O4P PEE B 901 " pdb=" P PEE B 901 " ideal model delta sigma weight residual 1.653 1.783 -0.130 2.00e-02 2.50e+03 4.23e+01 bond pdb=" O4P PEE E 901 " pdb=" P PEE E 901 " ideal model delta sigma weight residual 1.653 1.778 -0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" O4P PEE F 901 " pdb=" P PEE F 901 " ideal model delta sigma weight residual 1.653 1.777 -0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" O4P PEE A 901 " pdb=" P PEE A 901 " ideal model delta sigma weight residual 1.653 1.776 -0.123 2.00e-02 2.50e+03 3.76e+01 ... (remaining 33038 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 43883 2.78 - 5.55: 645 5.55 - 8.33: 117 8.33 - 11.11: 25 11.11 - 13.89: 8 Bond angle restraints: 44678 Sorted by residual: angle pdb=" N LEU A 344 " pdb=" CA LEU A 344 " pdb=" C LEU A 344 " ideal model delta sigma weight residual 111.69 118.08 -6.39 1.23e+00 6.61e-01 2.70e+01 angle pdb=" O1P PEE F 901 " pdb=" P PEE F 901 " pdb=" O2P PEE F 901 " ideal model delta sigma weight residual 119.43 133.32 -13.89 3.00e+00 1.11e-01 2.14e+01 angle pdb=" O1P PEE A 901 " pdb=" P PEE A 901 " pdb=" O2P PEE A 901 " ideal model delta sigma weight residual 119.43 133.28 -13.85 3.00e+00 1.11e-01 2.13e+01 angle pdb=" O1P PEE C 901 " pdb=" P PEE C 901 " pdb=" O2P PEE C 901 " ideal model delta sigma weight residual 119.43 133.23 -13.80 3.00e+00 1.11e-01 2.12e+01 angle pdb=" O1P PEE B 901 " pdb=" P PEE B 901 " pdb=" O2P PEE B 901 " ideal model delta sigma weight residual 119.43 133.21 -13.78 3.00e+00 1.11e-01 2.11e+01 ... (remaining 44673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.59: 19413 35.59 - 71.19: 555 71.19 - 106.78: 29 106.78 - 142.38: 2 142.38 - 177.97: 5 Dihedral angle restraints: 20004 sinusoidal: 8434 harmonic: 11570 Sorted by residual: dihedral pdb=" CB CYS A 113 " pdb=" SG CYS A 113 " pdb=" SG CYS A 295 " pdb=" CB CYS A 295 " ideal model delta sinusoidal sigma weight residual 93.00 36.75 56.25 1 1.00e+01 1.00e-02 4.27e+01 dihedral pdb=" CB CYS C 113 " pdb=" SG CYS C 113 " pdb=" SG CYS C 295 " pdb=" CB CYS C 295 " ideal model delta sinusoidal sigma weight residual 93.00 49.47 43.53 1 1.00e+01 1.00e-02 2.64e+01 dihedral pdb=" CA LYS B 589 " pdb=" C LYS B 589 " pdb=" N MET B 590 " pdb=" CA MET B 590 " ideal model delta harmonic sigma weight residual -180.00 -155.49 -24.51 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 20001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 4843 0.098 - 0.195: 234 0.195 - 0.293: 8 0.293 - 0.391: 0 0.391 - 0.488: 3 Chirality restraints: 5088 Sorted by residual: chirality pdb=" CB ILE A 629 " pdb=" CA ILE A 629 " pdb=" CG1 ILE A 629 " pdb=" CG2 ILE A 629 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.96e+00 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 -2.74 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" C2 PEE F 901 " pdb=" C1 PEE F 901 " pdb=" C3 PEE F 901 " pdb=" O2 PEE F 901 " both_signs ideal model delta sigma weight residual False -2.33 -2.73 0.40 2.00e-01 2.50e+01 4.07e+00 ... (remaining 5085 not shown) Planarity restraints: 5505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 475 " -0.032 2.00e-02 2.50e+03 2.92e-02 2.13e+01 pdb=" CG TRP A 475 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP A 475 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP A 475 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 475 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 475 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 475 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 475 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 475 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 475 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 462 " 0.062 5.00e-02 4.00e+02 9.32e-02 1.39e+01 pdb=" N PRO C 463 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO C 463 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 463 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 724 " 0.055 5.00e-02 4.00e+02 8.35e-02 1.12e+01 pdb=" N PRO B 725 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO B 725 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 725 " 0.046 5.00e-02 4.00e+02 ... (remaining 5502 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7407 2.79 - 3.32: 30868 3.32 - 3.85: 55811 3.85 - 4.37: 67062 4.37 - 4.90: 110187 Nonbonded interactions: 271335 Sorted by model distance: nonbonded pdb=" O ILE E 278 " pdb=" OG1 THR E 282 " model vdw 2.263 3.040 nonbonded pdb=" OD1 ASP F 689 " pdb=" OG SER F 691 " model vdw 2.264 3.040 nonbonded pdb=" O GLN C 560 " pdb=" OG1 THR C 563 " model vdw 2.266 3.040 nonbonded pdb=" O ARG B 492 " pdb=" OG1 THR B 517 " model vdw 2.272 3.040 nonbonded pdb=" O VAL E 591 " pdb=" ND2 ASN E 615 " model vdw 2.282 3.120 ... (remaining 271330 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 68 or resid 93 through 175 or resid 232 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 C16 or name C17 or name O2 or name O4 )))) selection = (chain 'B' and (resid 15 through 68 or resid 93 through 175 or resid 232 through \ 808 or (resid 901 and (name N or name C1 or 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 C18 or name C1 \ 9 or name C2 or name C20 or name C4 or name C5 or name O1P or name O2 or name O2 \ P or name O3P or name O4 or name O4P or name P )) or (resid 902 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C1 \ 7 or name O2 or name O4 )))) selection = (chain 'C' and (resid 15 through 808 or (resid 901 and (name N or name C1 or nam \ e C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or \ name C17 or name C18 or name C19 or name C2 or name C20 or name C4 or name C5 o \ r name O1P or name O2 or name O2P or name O3P or name O4 or name O4P or name P ) \ ) or (resid 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 'E' and (resid 15 through 175 or resid 232 through 808 or (resid 901 and \ (name N or name C1 or name C10 or name C11 or name C12 or name C13 or name C14 o \ r name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or name C2 \ 0 or name C4 or name C5 or name O1P or name O2 or name O2P or name O3P or name O \ 4 or name O4P or name P )) or resid 902)) } 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: 5.430 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: 0.030 Extract box with map and model: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 25.810 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.050 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 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 : 0.005 0.153 33060 Z= 0.265 Angle : 0.886 13.885 44712 Z= 0.487 Chirality : 0.047 0.488 5088 Planarity : 0.006 0.093 5505 Dihedral : 16.341 177.974 12417 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.39 % Allowed : 18.62 % Favored : 80.99 % 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 are not related in a simple way. whole: -1.17 (0.13), residues: 3846 helix: -0.04 (0.12), residues: 1858 sheet: -1.47 (0.30), residues: 362 loop : -1.38 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 18 TYR 0.053 0.002 TYR F 687 PHE 0.044 0.002 PHE D 390 TRP 0.080 0.003 TRP A 475 HIS 0.013 0.001 HIS C 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.27 (33043) covalent geometry : angle 0.88583 / 0.49 (44678) SS BOND : bond 0.00308 / 0.20 ( 17) SS BOND : angle 1.43486 / 0.85 ( 34) hydrogen bonds : bond 0.15447 / 10.09 ( 1463) hydrogen bonds : angle 6.62255 / 4.65 ( 4026) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 543 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7808 (tm-30) REVERT: A 430 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7609 (mt) REVERT: A 434 MET cc_start: 0.8085 (mpp) cc_final: 0.7095 (mpp) REVERT: A 518 LEU cc_start: 0.7284 (tp) cc_final: 0.6860 (tp) REVERT: A 616 LEU cc_start: 0.5752 (mp) cc_final: 0.5478 (mt) REVERT: A 690 LEU cc_start: 0.8655 (tp) cc_final: 0.8155 (mp) REVERT: A 713 LEU cc_start: 0.8571 (tp) cc_final: 0.8321 (pt) REVERT: A 738 LEU cc_start: 0.8183 (mt) cc_final: 0.7811 (mt) REVERT: B 29 ASP cc_start: 0.7609 (m-30) cc_final: 0.7288 (m-30) REVERT: C 102 ASP cc_start: 0.8271 (m-30) cc_final: 0.7978 (m-30) REVERT: C 308 TYR cc_start: 0.9028 (m-80) cc_final: 0.8737 (m-80) REVERT: C 523 LEU cc_start: 0.4419 (mt) cc_final: 0.3979 (tt) REVERT: C 726 GLU cc_start: 0.6296 (tt0) cc_final: 0.6093 (tm-30) REVERT: D 142 PHE cc_start: 0.8329 (t80) cc_final: 0.8092 (t80) REVERT: F 510 MET cc_start: -0.0804 (mmp) cc_final: -0.1727 (mtm) REVERT: F 570 MET cc_start: -0.2196 (mmm) cc_final: -0.2460 (ttt) REVERT: F 800 MET cc_start: 0.0369 (tpt) cc_final: -0.2241 (ptm) outliers start: 14 outliers final: 3 residues processed: 555 average time/residue: 0.2131 time to fit residues: 180.6268 Evaluate side-chains 318 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 314 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 281 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.3980 chunk 298 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 GLN A 66 ASN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 HIS A 576 ASN B 105 GLN B 478 HIS B 617 GLN ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 GLN ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 HIS D 288 ASN E 239 GLN E 418 GLN ** E 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4864 r_free = 0.4864 target = 0.222085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.169185 restraints weight = 53475.376| |-----------------------------------------------------------------------------| r_work (start): 0.4258 rms_B_bonded: 2.28 r_work: 0.3741 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 33060 Z= 0.153 Angle : 0.636 12.208 44712 Z= 0.322 Chirality : 0.042 0.305 5088 Planarity : 0.005 0.090 5505 Dihedral : 9.276 177.478 4415 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.49 % Allowed : 18.73 % Favored : 78.78 % 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 are not related in a simple way. whole: -0.78 (0.14), residues: 3846 helix: 0.41 (0.12), residues: 1888 sheet: -1.66 (0.28), residues: 396 loop : -1.27 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 666 TYR 0.022 0.001 TYR B 648 PHE 0.017 0.001 PHE C 433 TRP 0.022 0.002 TRP A 475 HIS 0.007 0.001 HIS F 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (33043) covalent geometry : angle 0.63523 / 0.32 (44678) SS BOND : bond 0.00317 / 0.20 ( 17) SS BOND : angle 1.22000 / 0.70 ( 34) hydrogen bonds : bond 0.04196 / 2.72 ( 1463) hydrogen bonds : angle 5.15555 / 3.67 ( 4026) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 331 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 LYS cc_start: 0.8451 (mtmm) cc_final: 0.8210 (tptp) REVERT: A 616 LEU cc_start: 0.5603 (mp) cc_final: 0.5380 (mt) REVERT: B 396 GLU cc_start: 0.7907 (tp30) cc_final: 0.7462 (tp30) REVERT: B 616 LEU cc_start: 0.2780 (OUTLIER) cc_final: 0.2572 (mm) REVERT: C 245 GLU cc_start: 0.7658 (tp30) cc_final: 0.7433 (tp30) REVERT: C 308 TYR cc_start: 0.8927 (m-80) cc_final: 0.8660 (m-80) REVERT: C 523 LEU cc_start: 0.4899 (mt) cc_final: 0.4238 (tt) REVERT: C 726 GLU cc_start: 0.7085 (tt0) cc_final: 0.6472 (tp30) REVERT: D 142 PHE cc_start: 0.8370 (t80) cc_final: 0.7941 (t80) REVERT: D 154 GLU cc_start: 0.8562 (mm-30) cc_final: 0.7950 (tt0) REVERT: D 250 PHE cc_start: 0.6382 (t80) cc_final: 0.5947 (t80) REVERT: D 375 MET cc_start: 0.7841 (tpp) cc_final: 0.7583 (mpp) REVERT: D 404 GLN cc_start: 0.7401 (tp-100) cc_final: 0.7004 (tp-100) REVERT: E 418 GLN cc_start: 0.4873 (mm-40) cc_final: 0.4289 (tt0) REVERT: F 146 PHE cc_start: 0.6426 (OUTLIER) cc_final: 0.5725 (m-10) REVERT: F 156 GLU cc_start: 0.6410 (OUTLIER) cc_final: 0.5675 (tp30) REVERT: F 510 MET cc_start: 0.2555 (mmp) cc_final: -0.0086 (mtm) REVERT: F 616 GLU cc_start: 0.7527 (pt0) cc_final: 0.6915 (pp20) REVERT: F 800 MET cc_start: -0.0696 (tpt) cc_final: -0.2435 (ptm) outliers start: 90 outliers final: 50 residues processed: 401 average time/residue: 0.2027 time to fit residues: 131.4952 Evaluate side-chains 313 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 260 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 478 HIS Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 235 LYS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 452 LYS Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 157 HIS Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 669 HIS Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 784 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 235 optimal weight: 0.4980 chunk 273 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 260 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 262 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 380 optimal weight: 8.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 GLN A 239 GLN B 105 GLN B 267 GLN ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 GLN E 370 ASN ** E 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 HIS F 404 ASN ** F 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.220778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.144087 restraints weight = 53121.455| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 5.42 r_work: 0.3516 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 33060 Z= 0.212 Angle : 0.634 12.188 44712 Z= 0.321 Chirality : 0.043 0.262 5088 Planarity : 0.004 0.046 5505 Dihedral : 8.546 178.192 4411 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.33 % Allowed : 18.62 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.14), residues: 3846 helix: 0.41 (0.12), residues: 1898 sheet: -1.75 (0.27), residues: 406 loop : -1.21 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 666 TYR 0.021 0.002 TYR F 511 PHE 0.019 0.002 PHE B 374 TRP 0.030 0.002 TRP F 170 HIS 0.018 0.001 HIS B 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.21 (33043) covalent geometry : angle 0.63281 / 0.32 (44678) SS BOND : bond 0.00538 / 0.31 ( 17) SS BOND : angle 1.43436 / 0.83 ( 34) hydrogen bonds : bond 0.04079 / 2.66 ( 1463) hydrogen bonds : angle 5.05402 / 3.60 ( 4026) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 292 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7503 (pt0) REVERT: A 433 PHE cc_start: 0.7565 (OUTLIER) cc_final: 0.7092 (t80) REVERT: A 518 LEU cc_start: 0.7741 (tp) cc_final: 0.7271 (tp) REVERT: A 733 LEU cc_start: 0.7237 (mt) cc_final: 0.6851 (mt) REVERT: B 616 LEU cc_start: 0.3343 (OUTLIER) cc_final: 0.3137 (mm) REVERT: B 684 CYS cc_start: -0.1962 (OUTLIER) cc_final: -0.2579 (t) REVERT: B 694 HIS cc_start: 0.8075 (m-70) cc_final: 0.7723 (t70) REVERT: B 713 LEU cc_start: 0.8635 (mt) cc_final: 0.8354 (pp) REVERT: C 684 CYS cc_start: 0.3196 (OUTLIER) cc_final: 0.2881 (t) REVERT: C 726 GLU cc_start: 0.7343 (tt0) cc_final: 0.6704 (tp30) REVERT: D 144 PHE cc_start: 0.7684 (m-10) cc_final: 0.7427 (m-10) REVERT: D 145 LYS cc_start: 0.8554 (mmmt) cc_final: 0.7008 (pttt) REVERT: D 250 PHE cc_start: 0.6749 (t80) cc_final: 0.6360 (t80) REVERT: D 375 MET cc_start: 0.8156 (tpp) cc_final: 0.7834 (mpp) REVERT: D 404 GLN cc_start: 0.7440 (tp40) cc_final: 0.7192 (tp-100) REVERT: E 418 GLN cc_start: 0.5051 (mm-40) cc_final: 0.4565 (tt0) REVERT: E 581 LEU cc_start: 0.1639 (OUTLIER) cc_final: 0.1335 (tp) REVERT: F 146 PHE cc_start: 0.6551 (OUTLIER) cc_final: 0.5874 (m-10) REVERT: F 170 TRP cc_start: 0.7767 (t60) cc_final: 0.6836 (t-100) REVERT: F 392 LEU cc_start: 0.7422 (tp) cc_final: 0.7087 (tp) REVERT: F 510 MET cc_start: 0.2919 (OUTLIER) cc_final: 0.0534 (mtm) REVERT: F 616 GLU cc_start: 0.7496 (pt0) cc_final: 0.6961 (pp20) REVERT: F 696 ARG cc_start: 0.8143 (mpp80) cc_final: 0.7787 (mmt180) REVERT: F 800 MET cc_start: -0.1362 (tpt) cc_final: -0.2629 (ptm) outliers start: 120 outliers final: 64 residues processed: 387 average time/residue: 0.1899 time to fit residues: 121.2053 Evaluate side-chains 325 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 253 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 684 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 730 CYS Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 684 CYS Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 169 THR 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 E residue 293 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 157 HIS Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain F residue 391 PHE Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 510 MET Chi-restraints excluded: chain F residue 669 HIS Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 784 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 209 optimal weight: 5.9990 chunk 364 optimal weight: 8.9990 chunk 237 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 180 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 199 optimal weight: 20.0000 chunk 314 optimal weight: 0.9990 chunk 370 optimal weight: 10.0000 chunk 361 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 GLN A 239 GLN A 499 HIS A 614 HIS ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 HIS B 494 ASN ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 672 ASN ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 GLN ** E 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 416 GLN ** F 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.217107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.138187 restraints weight = 53067.673| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 5.27 r_work: 0.3473 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 33060 Z= 0.294 Angle : 0.668 12.065 44712 Z= 0.340 Chirality : 0.044 0.214 5088 Planarity : 0.004 0.045 5505 Dihedral : 8.201 178.578 4411 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.60 % Allowed : 19.56 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.14), residues: 3846 helix: 0.22 (0.12), residues: 1907 sheet: -2.01 (0.26), residues: 420 loop : -1.29 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG D 103 TYR 0.020 0.002 TYR F 511 PHE 0.023 0.002 PHE A 146 TRP 0.036 0.002 TRP A 475 HIS 0.010 0.001 HIS E 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00692 / 0.29 (33043) covalent geometry : angle 0.66671 / 0.34 (44678) SS BOND : bond 0.00622 / 0.38 ( 17) SS BOND : angle 1.52574 / 0.90 ( 34) hydrogen bonds : bond 0.04253 / 2.78 ( 1463) hydrogen bonds : angle 5.12865 / 3.65 ( 4026) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 272 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 GLN cc_start: 0.7954 (pt0) cc_final: 0.7707 (pt0) REVERT: A 380 ASP cc_start: 0.8651 (OUTLIER) cc_final: 0.8440 (t0) REVERT: A 433 PHE cc_start: 0.7546 (OUTLIER) cc_final: 0.6907 (t80) REVERT: A 488 LEU cc_start: 0.4503 (OUTLIER) cc_final: 0.4253 (mt) REVERT: A 518 LEU cc_start: 0.7574 (tp) cc_final: 0.7245 (tp) REVERT: A 733 LEU cc_start: 0.7316 (mt) cc_final: 0.6968 (mt) REVERT: B 616 LEU cc_start: 0.3665 (OUTLIER) cc_final: 0.3437 (mm) REVERT: B 684 CYS cc_start: -0.1894 (OUTLIER) cc_final: -0.2527 (t) REVERT: B 690 LEU cc_start: 0.6970 (mp) cc_final: 0.6252 (tt) REVERT: B 694 HIS cc_start: 0.8217 (m-70) cc_final: 0.7838 (t70) REVERT: B 713 LEU cc_start: 0.8598 (mt) cc_final: 0.8228 (pp) REVERT: C 65 CYS cc_start: 0.5242 (OUTLIER) cc_final: 0.3821 (t) REVERT: C 143 TRP cc_start: 0.7944 (OUTLIER) cc_final: 0.7475 (t60) REVERT: C 684 CYS cc_start: 0.2949 (OUTLIER) cc_final: 0.2667 (t) REVERT: C 726 GLU cc_start: 0.7283 (tt0) cc_final: 0.6634 (tp30) REVERT: D 145 LYS cc_start: 0.8616 (mmmt) cc_final: 0.7154 (pttt) REVERT: D 154 GLU cc_start: 0.8535 (mm-30) cc_final: 0.7865 (tt0) REVERT: E 418 GLN cc_start: 0.4862 (mm-40) cc_final: 0.4388 (tt0) REVERT: E 447 GLU cc_start: 0.3314 (pm20) cc_final: 0.2531 (pm20) REVERT: E 448 LEU cc_start: 0.7676 (tp) cc_final: 0.7398 (tt) REVERT: E 581 LEU cc_start: 0.1423 (OUTLIER) cc_final: 0.1210 (tp) REVERT: F 146 PHE cc_start: 0.6828 (OUTLIER) cc_final: 0.6246 (m-10) REVERT: F 173 ARG cc_start: 0.6870 (ttm110) cc_final: 0.6597 (ptm160) REVERT: F 470 GLN cc_start: 0.7351 (tp40) cc_final: 0.7009 (mm-40) REVERT: F 510 MET cc_start: 0.2937 (OUTLIER) cc_final: 0.1057 (mmt) REVERT: F 598 HIS cc_start: 0.5249 (OUTLIER) cc_final: 0.4763 (t70) REVERT: F 701 GLU cc_start: 0.4678 (OUTLIER) cc_final: 0.2599 (tm-30) REVERT: F 800 MET cc_start: -0.1478 (tpt) cc_final: -0.2449 (ptt) outliers start: 130 outliers final: 76 residues processed: 385 average time/residue: 0.2031 time to fit residues: 126.9316 Evaluate side-chains 337 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 248 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 684 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 501 LYS Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 684 CYS Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 169 THR 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 E residue 293 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 157 HIS Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain F residue 391 PHE Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 510 MET Chi-restraints excluded: chain F residue 511 TYR Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 598 HIS Chi-restraints excluded: chain F residue 669 HIS Chi-restraints excluded: chain F residue 701 GLU Chi-restraints excluded: chain F residue 783 VAL Chi-restraints excluded: chain F residue 784 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 207 optimal weight: 8.9990 chunk 311 optimal weight: 10.0000 chunk 183 optimal weight: 4.9990 chunk 313 optimal weight: 9.9990 chunk 298 optimal weight: 20.0000 chunk 260 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 280 optimal weight: 0.5980 chunk 251 optimal weight: 0.8980 chunk 228 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 GLN A 105 GLN A 239 GLN ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 GLN B 467 GLN ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 GLN ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 375 HIS ** F 693 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 = 0.4863 r_free = 0.4863 target = 0.221327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.168446 restraints weight = 53120.137| |-----------------------------------------------------------------------------| r_work (start): 0.4266 rms_B_bonded: 2.35 r_work: 0.3654 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 33060 Z= 0.230 Angle : 0.614 11.156 44712 Z= 0.311 Chirality : 0.042 0.237 5088 Planarity : 0.004 0.042 5505 Dihedral : 7.773 173.541 4411 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.52 % Allowed : 20.45 % Favored : 76.03 % 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 are not related in a simple way. whole: -0.92 (0.14), residues: 3846 helix: 0.29 (0.12), residues: 1908 sheet: -1.85 (0.27), residues: 413 loop : -1.30 (0.16), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 666 TYR 0.041 0.002 TYR A 689 PHE 0.025 0.002 PHE B 682 TRP 0.030 0.002 TRP F 170 HIS 0.008 0.001 HIS F 598 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.23 (33043) covalent geometry : angle 0.61329 / 0.31 (44678) SS BOND : bond 0.00485 / 0.29 ( 17) SS BOND : angle 1.28811 / 0.77 ( 34) hydrogen bonds : bond 0.03926 / 2.55 ( 1463) hydrogen bonds : angle 4.94870 / 3.53 ( 4026) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 270 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8742 (mt) REVERT: A 433 PHE cc_start: 0.7056 (OUTLIER) cc_final: 0.6361 (t80) REVERT: A 488 LEU cc_start: 0.4504 (OUTLIER) cc_final: 0.4203 (mt) REVERT: A 518 LEU cc_start: 0.7498 (tp) cc_final: 0.7120 (tp) REVERT: A 733 LEU cc_start: 0.6854 (mt) cc_final: 0.6401 (mt) REVERT: B 102 ASP cc_start: 0.8290 (m-30) cc_final: 0.8088 (m-30) REVERT: B 236 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7483 (tm-30) REVERT: B 616 LEU cc_start: 0.3671 (OUTLIER) cc_final: 0.3380 (mm) REVERT: B 690 LEU cc_start: 0.7097 (mp) cc_final: 0.6599 (tt) REVERT: B 713 LEU cc_start: 0.8681 (mt) cc_final: 0.8449 (pt) REVERT: C 65 CYS cc_start: 0.5579 (OUTLIER) cc_final: 0.4153 (t) REVERT: C 245 GLU cc_start: 0.7628 (tp30) cc_final: 0.7396 (tp30) REVERT: C 684 CYS cc_start: 0.2598 (OUTLIER) cc_final: 0.2352 (t) REVERT: C 726 GLU cc_start: 0.7278 (tt0) cc_final: 0.6725 (tp30) REVERT: D 144 PHE cc_start: 0.7851 (m-10) cc_final: 0.7509 (m-10) REVERT: D 145 LYS cc_start: 0.8585 (mmmt) cc_final: 0.7315 (pttt) REVERT: D 375 MET cc_start: 0.8232 (tpp) cc_final: 0.7804 (mpp) REVERT: E 103 ARG cc_start: 0.8547 (tpp-160) cc_final: 0.8090 (tpt90) REVERT: E 418 GLN cc_start: 0.4753 (mm-40) cc_final: 0.4334 (tt0) REVERT: E 447 GLU cc_start: 0.2609 (pm20) cc_final: 0.1840 (pm20) REVERT: E 448 LEU cc_start: 0.7118 (tp) cc_final: 0.6820 (tt) REVERT: E 623 ASP cc_start: 0.6425 (OUTLIER) cc_final: 0.6090 (t70) REVERT: F 146 PHE cc_start: 0.6760 (OUTLIER) cc_final: 0.6284 (m-10) REVERT: F 170 TRP cc_start: 0.7363 (t60) cc_final: 0.6684 (t-100) REVERT: F 470 GLN cc_start: 0.6953 (tp40) cc_final: 0.6656 (mm110) REVERT: F 510 MET cc_start: 0.2508 (OUTLIER) cc_final: 0.0216 (ptp) REVERT: F 598 HIS cc_start: 0.5659 (OUTLIER) cc_final: 0.4880 (t70) REVERT: F 800 MET cc_start: -0.1181 (tpt) cc_final: -0.2480 (ptt) outliers start: 127 outliers final: 82 residues processed: 378 average time/residue: 0.2011 time to fit residues: 125.3900 Evaluate side-chains 347 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 254 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 684 CYS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 169 THR 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 E residue 293 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 623 ASP Chi-restraints excluded: chain E residue 753 LEU Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 157 HIS Chi-restraints excluded: chain F residue 166 PHE Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain F residue 391 PHE Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 510 MET Chi-restraints excluded: chain F residue 598 HIS Chi-restraints excluded: chain F residue 669 HIS Chi-restraints excluded: chain F residue 783 VAL Chi-restraints excluded: chain F residue 784 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 231 optimal weight: 2.9990 chunk 372 optimal weight: 30.0000 chunk 185 optimal weight: 30.0000 chunk 196 optimal weight: 30.0000 chunk 251 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 69 optimal weight: 0.1980 chunk 350 optimal weight: 20.0000 chunk 307 optimal weight: 3.9990 chunk 126 optimal weight: 8.9990 chunk 252 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 GLN A 499 HIS A 708 GLN ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN D 404 GLN E 431 HIS E 614 HIS ** F 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 693 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 = 0.4873 r_free = 0.4873 target = 0.222564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.3956 r_free = 0.3956 target = 0.141642 restraints weight = 52998.826| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 5.76 r_work: 0.3581 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33060 Z= 0.157 Angle : 0.570 12.654 44712 Z= 0.286 Chirality : 0.041 0.428 5088 Planarity : 0.004 0.040 5505 Dihedral : 7.202 171.173 4411 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.33 % Allowed : 20.92 % Favored : 75.76 % 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 are not related in a simple way. whole: -0.73 (0.14), residues: 3846 helix: 0.47 (0.12), residues: 1900 sheet: -1.74 (0.28), residues: 396 loop : -1.25 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 666 TYR 0.026 0.001 TYR A 689 PHE 0.016 0.001 PHE D 250 TRP 0.023 0.001 TRP A 475 HIS 0.010 0.001 HIS B 431 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (33043) covalent geometry : angle 0.56901 / 0.29 (44678) SS BOND : bond 0.00322 / 0.19 ( 17) SS BOND : angle 1.12505 / 0.67 ( 34) hydrogen bonds : bond 0.03627 / 2.35 ( 1463) hydrogen bonds : angle 4.76401 / 3.40 ( 4026) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 269 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 PHE cc_start: 0.9107 (OUTLIER) cc_final: 0.8798 (t80) REVERT: A 317 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8399 (mt) REVERT: A 433 PHE cc_start: 0.7463 (OUTLIER) cc_final: 0.7078 (t80) REVERT: A 434 MET cc_start: 0.8195 (mpp) cc_final: 0.7559 (mmp) REVERT: A 488 LEU cc_start: 0.4609 (OUTLIER) cc_final: 0.4329 (mt) REVERT: A 518 LEU cc_start: 0.7620 (tp) cc_final: 0.7289 (tp) REVERT: A 733 LEU cc_start: 0.7156 (mt) cc_final: 0.6762 (mt) REVERT: B 616 LEU cc_start: 0.3702 (mm) cc_final: 0.3440 (mm) REVERT: B 684 CYS cc_start: -0.1964 (OUTLIER) cc_final: -0.2415 (t) REVERT: B 690 LEU cc_start: 0.7096 (mp) cc_final: 0.6694 (tt) REVERT: B 713 LEU cc_start: 0.8610 (mt) cc_final: 0.8393 (pp) REVERT: C 143 TRP cc_start: 0.7717 (OUTLIER) cc_final: 0.7269 (t60) REVERT: C 245 GLU cc_start: 0.7777 (tp30) cc_final: 0.7567 (tp30) REVERT: C 523 LEU cc_start: 0.4177 (mt) cc_final: 0.3336 (tt) REVERT: C 684 CYS cc_start: 0.2979 (OUTLIER) cc_final: 0.2600 (t) REVERT: C 726 GLU cc_start: 0.7484 (tt0) cc_final: 0.6933 (tp30) REVERT: D 144 PHE cc_start: 0.7778 (m-10) cc_final: 0.7477 (m-10) REVERT: D 145 LYS cc_start: 0.8575 (mmmt) cc_final: 0.7249 (pttt) REVERT: D 154 GLU cc_start: 0.8497 (mm-30) cc_final: 0.7829 (tt0) REVERT: D 250 PHE cc_start: 0.6954 (t80) cc_final: 0.6580 (t80) REVERT: D 375 MET cc_start: 0.8245 (tpp) cc_final: 0.7735 (mpp) REVERT: D 379 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7777 (mp) REVERT: E 418 GLN cc_start: 0.4811 (mm-40) cc_final: 0.4393 (tt0) REVERT: E 447 GLU cc_start: 0.3225 (pm20) cc_final: 0.2439 (pm20) REVERT: E 581 LEU cc_start: 0.1787 (OUTLIER) cc_final: 0.1513 (tp) REVERT: F 146 PHE cc_start: 0.6860 (OUTLIER) cc_final: 0.6430 (m-80) REVERT: F 470 GLN cc_start: 0.7287 (tp40) cc_final: 0.6957 (mm-40) REVERT: F 510 MET cc_start: 0.2401 (OUTLIER) cc_final: 0.0120 (ptt) REVERT: F 598 HIS cc_start: 0.5604 (OUTLIER) cc_final: 0.4991 (t70) REVERT: F 696 ARG cc_start: 0.8276 (mpp80) cc_final: 0.7883 (mmt180) REVERT: F 701 GLU cc_start: 0.4408 (OUTLIER) cc_final: 0.4163 (pm20) REVERT: F 800 MET cc_start: -0.1792 (tpt) cc_final: -0.2601 (ptt) outliers start: 120 outliers final: 68 residues processed: 368 average time/residue: 0.2037 time to fit residues: 122.4742 Evaluate side-chains 329 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 248 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 684 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 501 LYS Chi-restraints excluded: chain C residue 684 CYS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 753 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 157 HIS Chi-restraints excluded: chain F residue 166 PHE Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 391 PHE Chi-restraints excluded: chain F residue 510 MET Chi-restraints excluded: chain F residue 598 HIS Chi-restraints excluded: chain F residue 669 HIS Chi-restraints excluded: chain F residue 701 GLU Chi-restraints excluded: chain F residue 783 VAL Chi-restraints excluded: chain F residue 784 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 98 optimal weight: 1.9990 chunk 265 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 293 optimal weight: 20.0000 chunk 27 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 114 optimal weight: 20.0000 chunk 286 optimal weight: 0.2980 chunk 290 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 HIS ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN D 287 HIS D 404 GLN E 729 GLN ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 ASN ** F 693 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 = 0.4871 r_free = 0.4871 target = 0.222316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3999 r_free = 0.3999 target = 0.142260 restraints weight = 53256.818| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 5.42 r_work: 0.3584 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 33060 Z= 0.175 Angle : 0.576 11.645 44712 Z= 0.290 Chirality : 0.041 0.170 5088 Planarity : 0.004 0.046 5505 Dihedral : 6.785 167.728 4411 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.41 % Allowed : 20.81 % Favored : 75.78 % 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 are not related in a simple way. whole: -0.68 (0.14), residues: 3846 helix: 0.48 (0.12), residues: 1901 sheet: -1.73 (0.27), residues: 409 loop : -1.18 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 666 TYR 0.025 0.002 TYR A 689 PHE 0.015 0.001 PHE D 250 TRP 0.042 0.002 TRP E 475 HIS 0.006 0.001 HIS F 598 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (33043) covalent geometry : angle 0.57563 / 0.29 (44678) SS BOND : bond 0.00369 / 0.22 ( 17) SS BOND : angle 1.27467 / 0.73 ( 34) hydrogen bonds : bond 0.03625 / 2.36 ( 1463) hydrogen bonds : angle 4.73932 / 3.38 ( 4026) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 266 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.8801 (t80) REVERT: A 433 PHE cc_start: 0.7447 (OUTLIER) cc_final: 0.7031 (t80) REVERT: A 434 MET cc_start: 0.8024 (mpp) cc_final: 0.7314 (mmp) REVERT: A 488 LEU cc_start: 0.4601 (OUTLIER) cc_final: 0.4301 (mt) REVERT: A 518 LEU cc_start: 0.7629 (tp) cc_final: 0.7295 (tp) REVERT: A 733 LEU cc_start: 0.6955 (mt) cc_final: 0.6522 (mt) REVERT: B 684 CYS cc_start: -0.2121 (OUTLIER) cc_final: -0.2398 (t) REVERT: B 690 LEU cc_start: 0.7107 (mp) cc_final: 0.6726 (tt) REVERT: B 713 LEU cc_start: 0.8681 (mt) cc_final: 0.8454 (pp) REVERT: C 143 TRP cc_start: 0.7716 (OUTLIER) cc_final: 0.7287 (t60) REVERT: C 684 CYS cc_start: 0.3119 (OUTLIER) cc_final: 0.2656 (t) REVERT: C 726 GLU cc_start: 0.7629 (tt0) cc_final: 0.7088 (tp30) REVERT: D 144 PHE cc_start: 0.7897 (m-10) cc_final: 0.7576 (m-10) REVERT: D 145 LYS cc_start: 0.8596 (mmmt) cc_final: 0.7305 (pttt) REVERT: D 154 GLU cc_start: 0.8500 (mm-30) cc_final: 0.7835 (tt0) REVERT: D 375 MET cc_start: 0.8264 (tpp) cc_final: 0.7737 (mpp) REVERT: D 379 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7876 (mp) REVERT: E 418 GLN cc_start: 0.4887 (mm-40) cc_final: 0.4478 (tt0) REVERT: E 447 GLU cc_start: 0.3237 (pm20) cc_final: 0.2396 (pm20) REVERT: E 448 LEU cc_start: 0.7416 (tp) cc_final: 0.7094 (tt) REVERT: E 581 LEU cc_start: 0.1914 (OUTLIER) cc_final: 0.1621 (tp) REVERT: E 623 ASP cc_start: 0.6461 (OUTLIER) cc_final: 0.6137 (t70) REVERT: F 146 PHE cc_start: 0.6943 (OUTLIER) cc_final: 0.6552 (m-80) REVERT: F 470 GLN cc_start: 0.7302 (tp40) cc_final: 0.6928 (mm-40) REVERT: F 504 ARG cc_start: 0.5245 (tpm170) cc_final: 0.4667 (tpm170) REVERT: F 510 MET cc_start: 0.2259 (OUTLIER) cc_final: 0.0258 (ptp) REVERT: F 598 HIS cc_start: 0.5478 (OUTLIER) cc_final: 0.4856 (t70) REVERT: F 701 GLU cc_start: 0.4461 (OUTLIER) cc_final: 0.4146 (pm20) REVERT: F 800 MET cc_start: -0.1724 (tpt) cc_final: -0.2558 (ptt) outliers start: 123 outliers final: 81 residues processed: 372 average time/residue: 0.2023 time to fit residues: 123.5309 Evaluate side-chains 343 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 249 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 684 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 501 LYS Chi-restraints excluded: chain C residue 684 CYS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 235 LYS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 493 GLU Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 623 ASP Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 157 HIS Chi-restraints excluded: chain F residue 166 PHE Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 391 PHE Chi-restraints excluded: chain F residue 510 MET Chi-restraints excluded: chain F residue 598 HIS Chi-restraints excluded: chain F residue 669 HIS Chi-restraints excluded: chain F residue 701 GLU Chi-restraints excluded: chain F residue 783 VAL Chi-restraints excluded: chain F residue 784 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 272 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 42 optimal weight: 0.1980 chunk 99 optimal weight: 0.7980 chunk 257 optimal weight: 2.9990 chunk 226 optimal weight: 0.9980 chunk 326 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 159 optimal weight: 0.5980 chunk 373 optimal weight: 3.9990 chunk 195 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 494 ASN A 650 HIS ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 GLN B 404 GLN C 576 ASN D 105 GLN D 404 GLN F 107 GLN ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.223182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.173685 restraints weight = 53474.480| |-----------------------------------------------------------------------------| r_work (start): 0.4349 rms_B_bonded: 2.23 r_work: 0.3734 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 33060 Z= 0.120 Angle : 0.556 10.811 44712 Z= 0.276 Chirality : 0.040 0.195 5088 Planarity : 0.004 0.039 5505 Dihedral : 6.261 162.677 4411 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.44 % Allowed : 21.92 % Favored : 75.64 % 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 are not related in a simple way. whole: -0.50 (0.14), residues: 3846 helix: 0.64 (0.12), residues: 1893 sheet: -1.61 (0.28), residues: 387 loop : -1.11 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 173 TYR 0.022 0.001 TYR A 689 PHE 0.017 0.001 PHE D 250 TRP 0.070 0.002 TRP E 475 HIS 0.005 0.001 HIS F 598 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (33043) covalent geometry : angle 0.55536 / 0.28 (44678) SS BOND : bond 0.00253 / 0.16 ( 17) SS BOND : angle 1.11262 / 0.64 ( 34) hydrogen bonds : bond 0.03340 / 2.17 ( 1463) hydrogen bonds : angle 4.58586 / 3.28 ( 4026) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 266 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 PHE cc_start: 0.9026 (OUTLIER) cc_final: 0.8751 (t80) REVERT: A 317 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8228 (mt) REVERT: A 433 PHE cc_start: 0.7171 (OUTLIER) cc_final: 0.6791 (t80) REVERT: A 434 MET cc_start: 0.7795 (mpp) cc_final: 0.7068 (mmp) REVERT: A 488 LEU cc_start: 0.4462 (OUTLIER) cc_final: 0.4149 (mt) REVERT: A 733 LEU cc_start: 0.6687 (mt) cc_final: 0.6243 (mt) REVERT: B 434 MET cc_start: 0.6818 (mmm) cc_final: 0.6205 (tpt) REVERT: B 616 LEU cc_start: 0.3681 (OUTLIER) cc_final: 0.3397 (mm) REVERT: B 690 LEU cc_start: 0.7129 (mp) cc_final: 0.6718 (tt) REVERT: B 713 LEU cc_start: 0.8661 (mt) cc_final: 0.8445 (pp) REVERT: C 143 TRP cc_start: 0.7370 (OUTLIER) cc_final: 0.7029 (t60) REVERT: C 684 CYS cc_start: 0.2916 (OUTLIER) cc_final: 0.2153 (t) REVERT: C 707 LEU cc_start: 0.3665 (mm) cc_final: 0.3161 (tp) REVERT: C 726 GLU cc_start: 0.7487 (tt0) cc_final: 0.6983 (tp30) REVERT: D 144 PHE cc_start: 0.7774 (m-10) cc_final: 0.7433 (m-10) REVERT: D 145 LYS cc_start: 0.8537 (mmmt) cc_final: 0.7317 (pttt) REVERT: D 154 GLU cc_start: 0.8459 (mm-30) cc_final: 0.7884 (tt0) REVERT: D 375 MET cc_start: 0.8147 (tpp) cc_final: 0.7584 (mpp) REVERT: D 379 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7802 (mp) REVERT: E 418 GLN cc_start: 0.4800 (mm-40) cc_final: 0.4522 (tt0) REVERT: E 447 GLU cc_start: 0.3042 (pm20) cc_final: 0.2269 (pm20) REVERT: E 448 LEU cc_start: 0.7240 (tp) cc_final: 0.7010 (tt) REVERT: E 581 LEU cc_start: 0.1809 (OUTLIER) cc_final: 0.1534 (tp) REVERT: E 623 ASP cc_start: 0.6318 (OUTLIER) cc_final: 0.6009 (t70) REVERT: F 146 PHE cc_start: 0.6766 (OUTLIER) cc_final: 0.6490 (m-80) REVERT: F 510 MET cc_start: 0.2023 (OUTLIER) cc_final: 0.0040 (ptp) REVERT: F 598 HIS cc_start: 0.5592 (OUTLIER) cc_final: 0.4761 (t70) REVERT: F 701 GLU cc_start: 0.4094 (OUTLIER) cc_final: 0.1289 (tm-30) REVERT: F 800 MET cc_start: -0.1291 (tpt) cc_final: -0.2432 (ptt) outliers start: 88 outliers final: 51 residues processed: 340 average time/residue: 0.1969 time to fit residues: 109.1579 Evaluate side-chains 315 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 250 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 501 LYS Chi-restraints excluded: chain C residue 684 CYS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 493 GLU Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 623 ASP Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 157 HIS Chi-restraints excluded: chain F residue 166 PHE Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 391 PHE Chi-restraints excluded: chain F residue 510 MET Chi-restraints excluded: chain F residue 598 HIS Chi-restraints excluded: chain F residue 669 HIS Chi-restraints excluded: chain F residue 701 GLU Chi-restraints excluded: chain F residue 783 VAL Chi-restraints excluded: chain F residue 784 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 274 optimal weight: 7.9990 chunk 351 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 0.0010 chunk 47 optimal weight: 0.0970 chunk 205 optimal weight: 8.9990 chunk 377 optimal weight: 4.9990 chunk 203 optimal weight: 6.9990 chunk 107 optimal weight: 0.0970 chunk 33 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 overall best weight: 0.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 HIS B 494 ASN ** C 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 HIS D 404 GLN ** F 113 GLN ** 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 = 0.4894 r_free = 0.4894 target = 0.224164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.172771 restraints weight = 53311.640| |-----------------------------------------------------------------------------| r_work (start): 0.4323 rms_B_bonded: 2.20 r_work: 0.3755 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3621 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 33060 Z= 0.104 Angle : 0.540 12.499 44712 Z= 0.268 Chirality : 0.040 0.175 5088 Planarity : 0.004 0.039 5505 Dihedral : 5.790 149.506 4411 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.22 % Allowed : 22.11 % Favored : 75.67 % 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 are not related in a simple way. whole: -0.35 (0.14), residues: 3846 helix: 0.74 (0.12), residues: 1893 sheet: -1.49 (0.28), residues: 403 loop : -1.01 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 801 TYR 0.021 0.001 TYR A 689 PHE 0.014 0.001 PHE C 244 TRP 0.053 0.002 TRP E 475 HIS 0.005 0.001 HIS C 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (33043) covalent geometry : angle 0.53956 / 0.27 (44678) SS BOND : bond 0.00403 / 0.18 ( 17) SS BOND : angle 1.06953 / 0.60 ( 34) hydrogen bonds : bond 0.03193 / 2.08 ( 1463) hydrogen bonds : angle 4.45518 / 3.18 ( 4026) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 268 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.8305 (tm-30) cc_final: 0.7908 (tt0) REVERT: A 275 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.8724 (t80) REVERT: A 411 TRP cc_start: 0.6233 (m100) cc_final: 0.5927 (m-10) REVERT: A 488 LEU cc_start: 0.4335 (OUTLIER) cc_final: 0.4018 (mt) REVERT: A 733 LEU cc_start: 0.6478 (mt) cc_final: 0.6024 (mt) REVERT: B 434 MET cc_start: 0.6787 (mmm) cc_final: 0.6394 (tpt) REVERT: B 592 ASN cc_start: 0.4945 (p0) cc_final: 0.3694 (m110) REVERT: B 616 LEU cc_start: 0.3669 (OUTLIER) cc_final: 0.3387 (mm) REVERT: B 690 LEU cc_start: 0.7127 (mp) cc_final: 0.6735 (tt) REVERT: B 713 LEU cc_start: 0.8663 (mt) cc_final: 0.8445 (pp) REVERT: C 684 CYS cc_start: 0.3064 (OUTLIER) cc_final: 0.2219 (t) REVERT: C 707 LEU cc_start: 0.3428 (mm) cc_final: 0.2784 (tp) REVERT: C 726 GLU cc_start: 0.7452 (tt0) cc_final: 0.6954 (tp30) REVERT: D 144 PHE cc_start: 0.7780 (m-10) cc_final: 0.7415 (m-10) REVERT: D 154 GLU cc_start: 0.8437 (mm-30) cc_final: 0.7797 (tt0) REVERT: D 250 PHE cc_start: 0.7013 (t80) cc_final: 0.6708 (t80) REVERT: D 375 MET cc_start: 0.8084 (tpp) cc_final: 0.7504 (mpp) REVERT: D 379 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7714 (mp) REVERT: E 418 GLN cc_start: 0.4890 (mm-40) cc_final: 0.4689 (tt0) REVERT: E 581 LEU cc_start: 0.1933 (OUTLIER) cc_final: 0.1670 (tp) REVERT: E 623 ASP cc_start: 0.6287 (OUTLIER) cc_final: 0.6039 (t70) REVERT: F 146 PHE cc_start: 0.6772 (OUTLIER) cc_final: 0.6479 (m-80) REVERT: F 504 ARG cc_start: 0.5032 (tpm170) cc_final: 0.4461 (tpm170) REVERT: F 510 MET cc_start: 0.2071 (mmp) cc_final: 0.0073 (ptt) REVERT: F 570 MET cc_start: -0.2408 (ttt) cc_final: -0.2999 (tpt) REVERT: F 598 HIS cc_start: 0.5606 (OUTLIER) cc_final: 0.4741 (t70) REVERT: F 696 ARG cc_start: 0.8202 (mpp80) cc_final: 0.7893 (mmt180) REVERT: F 701 GLU cc_start: 0.4099 (OUTLIER) cc_final: 0.1312 (tm-30) REVERT: F 800 MET cc_start: -0.1343 (tpt) cc_final: -0.2468 (ptt) outliers start: 80 outliers final: 54 residues processed: 336 average time/residue: 0.1910 time to fit residues: 105.9860 Evaluate side-chains 317 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 253 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 501 LYS Chi-restraints excluded: chain C residue 684 CYS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 493 GLU Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 623 ASP Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 157 HIS Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 391 PHE Chi-restraints excluded: chain F residue 598 HIS Chi-restraints excluded: chain F residue 669 HIS Chi-restraints excluded: chain F residue 701 GLU Chi-restraints excluded: chain F residue 783 VAL Chi-restraints excluded: chain F residue 784 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 44 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 332 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 117 optimal weight: 7.9990 chunk 214 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 650 HIS ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN C 253 HIS ** C 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN D 404 GLN F 107 GLN ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 375 HIS F 573 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4872 r_free = 0.4872 target = 0.221521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.163120 restraints weight = 53331.438| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 1.78 r_work: 0.3720 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 33060 Z= 0.200 Angle : 0.601 15.660 44712 Z= 0.300 Chirality : 0.042 0.195 5088 Planarity : 0.004 0.037 5505 Dihedral : 6.030 142.434 4409 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.86 % Allowed : 22.42 % Favored : 75.73 % 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 are not related in a simple way. whole: -0.49 (0.14), residues: 3846 helix: 0.57 (0.12), residues: 1914 sheet: -1.56 (0.28), residues: 400 loop : -1.02 (0.16), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 417 TYR 0.020 0.002 TYR A 689 PHE 0.016 0.002 PHE C 244 TRP 0.046 0.002 TRP E 475 HIS 0.013 0.001 HIS C 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 (33043) covalent geometry : angle 0.59978 / 0.30 (44678) SS BOND : bond 0.00439 / 0.27 ( 17) SS BOND : angle 1.35922 / 0.78 ( 34) hydrogen bonds : bond 0.03599 / 2.35 ( 1463) hydrogen bonds : angle 4.63241 / 3.31 ( 4026) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 258 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.8713 (t80) REVERT: A 488 LEU cc_start: 0.4528 (OUTLIER) cc_final: 0.4209 (mt) REVERT: A 733 LEU cc_start: 0.6525 (mt) cc_final: 0.6056 (mt) REVERT: B 434 MET cc_start: 0.6411 (mmm) cc_final: 0.6024 (tpt) REVERT: B 592 ASN cc_start: 0.5008 (p0) cc_final: 0.3725 (m110) REVERT: B 690 LEU cc_start: 0.7131 (mp) cc_final: 0.6737 (tt) REVERT: B 713 LEU cc_start: 0.8692 (mt) cc_final: 0.8463 (pp) REVERT: C 143 TRP cc_start: 0.7613 (OUTLIER) cc_final: 0.7197 (t60) REVERT: C 245 GLU cc_start: 0.7460 (tp30) cc_final: 0.7255 (tp30) REVERT: C 443 PHE cc_start: 0.7414 (m-80) cc_final: 0.6994 (m-80) REVERT: C 523 LEU cc_start: 0.3639 (OUTLIER) cc_final: 0.2769 (tt) REVERT: C 684 CYS cc_start: 0.3107 (OUTLIER) cc_final: 0.2248 (t) REVERT: C 707 LEU cc_start: 0.3528 (mm) cc_final: 0.2970 (tp) REVERT: C 726 GLU cc_start: 0.7407 (tt0) cc_final: 0.6882 (tp30) REVERT: C 741 ASN cc_start: 0.3386 (OUTLIER) cc_final: 0.2133 (t0) REVERT: D 144 PHE cc_start: 0.8082 (m-10) cc_final: 0.7782 (m-10) REVERT: D 154 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7791 (tt0) REVERT: D 250 PHE cc_start: 0.7062 (t80) cc_final: 0.6746 (t80) REVERT: D 375 MET cc_start: 0.8079 (tpp) cc_final: 0.7798 (mmm) REVERT: D 379 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7780 (mp) REVERT: E 418 GLN cc_start: 0.4858 (mm-40) cc_final: 0.4638 (tt0) REVERT: E 623 ASP cc_start: 0.6221 (OUTLIER) cc_final: 0.5907 (t70) REVERT: F 146 PHE cc_start: 0.6786 (OUTLIER) cc_final: 0.6484 (m-80) REVERT: F 470 GLN cc_start: 0.7159 (tp40) cc_final: 0.6800 (mm110) REVERT: F 504 ARG cc_start: 0.5091 (tpm170) cc_final: 0.4530 (tpm170) REVERT: F 510 MET cc_start: 0.2407 (mmp) cc_final: 0.0351 (ptt) REVERT: F 570 MET cc_start: -0.2244 (ttt) cc_final: -0.2737 (tpt) REVERT: F 598 HIS cc_start: 0.5598 (OUTLIER) cc_final: 0.4743 (t70) REVERT: F 800 MET cc_start: -0.1415 (tpt) cc_final: -0.2464 (ptt) outliers start: 67 outliers final: 54 residues processed: 314 average time/residue: 0.1799 time to fit residues: 93.1363 Evaluate side-chains 315 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 251 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 501 LYS Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 684 CYS Chi-restraints excluded: chain C residue 741 ASN Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 493 GLU Chi-restraints excluded: chain E residue 623 ASP Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 157 HIS Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 391 PHE Chi-restraints excluded: chain F residue 598 HIS Chi-restraints excluded: chain F residue 669 HIS Chi-restraints excluded: chain F residue 783 VAL Chi-restraints excluded: chain F residue 784 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 187 optimal weight: 5.9990 chunk 384 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 144 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 116 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 286 optimal weight: 10.0000 chunk 195 optimal weight: 0.0170 chunk 72 optimal weight: 0.6980 chunk 288 optimal weight: 6.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 HIS ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN C 253 HIS ** C 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 ASN ** C 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN F 107 GLN ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 375 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.223134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.168047 restraints weight = 53387.527| |-----------------------------------------------------------------------------| r_work (start): 0.4234 rms_B_bonded: 1.93 r_work: 0.3735 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33060 Z= 0.119 Angle : 0.563 17.432 44712 Z= 0.278 Chirality : 0.041 0.167 5088 Planarity : 0.003 0.036 5505 Dihedral : 5.754 131.200 4409 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.94 % Allowed : 22.69 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.14), residues: 3846 helix: 0.66 (0.12), residues: 1906 sheet: -1.48 (0.28), residues: 399 loop : -0.96 (0.16), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 801 TYR 0.024 0.001 TYR B 308 PHE 0.012 0.001 PHE C 244 TRP 0.044 0.002 TRP F 170 HIS 0.013 0.001 HIS C 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (33043) covalent geometry : angle 0.56252 / 0.28 (44678) SS BOND : bond 0.00254 / 0.16 ( 17) SS BOND : angle 1.16175 / 0.66 ( 34) hydrogen bonds : bond 0.03319 / 2.16 ( 1463) hydrogen bonds : angle 4.49788 / 3.22 ( 4026) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13227.52 seconds wall clock time: 225 minutes 47.58 seconds (13547.58 seconds total)