Starting phenix.real_space_refine on Sat Jun 28 04:14:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f79_28898/06_2025/8f79_28898.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f79_28898/06_2025/8f79_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8f79_28898/06_2025/8f79_28898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f79_28898/06_2025/8f79_28898.map" model { file = "/net/cci-nas-00/data/ceres_data/8f79_28898/06_2025/8f79_28898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f79_28898/06_2025/8f79_28898.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.060 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): 1.81s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 102 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: 104 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: 64 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: 93 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: 104 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: 92 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: 20.89, per 1000 atoms: 0.65 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: 7.12 Conformation dependent library (CDL) restraints added in 3.6 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: 4.18 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: 13.68 Time building geometry restraints manager: 8.46 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 - 35.76: 19437 35.76 - 71.52: 555 71.52 - 107.28: 39 107.28 - 143.04: 8 143.04 - 178.80: 9 Dihedral angle restraints: 20048 sinusoidal: 8478 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 20045 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 \ 808 or resid 901 or (resid 902 and (name C10 or name C11 or name C12 or name C1 \ 3 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: 4.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 1.460 Check model and map are aligned: 0.300 Set scattering table: 0.370 Process input model: 71.930 Find NCS groups from input model: 1.890 Set up NCS constraints: 0.160 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: 0.020 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 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 : 17.081 178.800 12461 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 11.61 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (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 TRP 0.080 0.003 TRP A 475 HIS 0.013 0.001 HIS C 155 PHE 0.044 0.002 PHE D 390 TYR 0.053 0.002 TYR F 687 ARG 0.012 0.001 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.15447 ( 1463) hydrogen bonds : angle 6.62255 ( 4026) SS BOND : bond 0.00308 ( 17) SS BOND : angle 1.43486 ( 34) covalent geometry : bond 0.00495 (33043) covalent geometry : angle 0.88583 (44678) *********************** 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 : 3.339 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: A 46 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7808 (tm-30) 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: 0.6861 (tp) REVERT: A 616 LEU cc_start: 0.5752 (mp) cc_final: 0.5480 (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: 0.8320 (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: 0.6092 (tm-30) REVERT: D 142 PHE cc_start: 0.8329 (t80) cc_final: 0.8091 (t80) REVERT: D 385 LEU cc_start: 0.8196 (tp) cc_final: 0.7871 (tt) REVERT: F 510 MET cc_start: -0.0804 (mmp) cc_final: -0.1697 (mtm) REVERT: F 570 MET cc_start: -0.2196 (mmm) cc_final: -0.2462 (ttt) REVERT: F 800 MET cc_start: 0.0369 (tpt) cc_final: -0.2242 (ptm) outliers start: 14 outliers final: 3 residues processed: 555 average time/residue: 0.5003 time to fit residues: 421.4719 Evaluate side-chains 319 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 316 time to evaluate : 3.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 325 optimal weight: 0.8980 chunk 291 optimal weight: 30.0000 chunk 161 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 196 optimal weight: 4.9990 chunk 155 optimal weight: 0.6980 chunk 301 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 183 optimal weight: 0.3980 chunk 224 optimal weight: 0.9990 chunk 349 optimal weight: 7.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 66 ASN A 105 GLN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 HIS A 576 ASN A 650 HIS B 105 GLN B 467 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 C 744 GLN 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** F 407 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4876 r_free = 0.4876 target = 0.223292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.169238 restraints weight = 52118.555| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 2.04 r_work: 0.3761 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33060 Z= 0.142 Angle : 0.626 12.174 44712 Z= 0.317 Chirality : 0.042 0.317 5088 Planarity : 0.005 0.074 5505 Dihedral : 10.772 176.572 4457 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.47 % Allowed : 19.04 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.14), residues: 3846 helix: 0.45 (0.12), residues: 1892 sheet: -1.65 (0.28), residues: 392 loop : -1.30 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 475 HIS 0.007 0.001 HIS F 606 PHE 0.017 0.001 PHE B 682 TYR 0.027 0.001 TYR B 648 ARG 0.022 0.001 ARG A 666 Details of bonding type rmsd hydrogen bonds : bond 0.04157 ( 1463) hydrogen bonds : angle 5.12732 ( 4026) SS BOND : bond 0.00261 ( 17) SS BOND : angle 1.17085 ( 34) covalent geometry : bond 0.00320 (33043) covalent geometry : angle 0.62574 (44678) *********************** 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 430 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 341 time to evaluate : 3.648 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: A 104 HIS cc_start: 0.8538 (OUTLIER) cc_final: 0.8271 (m90) REVERT: A 235 LYS cc_start: 0.8417 (mtmm) cc_final: 0.8213 (tptp) REVERT: A 616 LEU cc_start: 0.5668 (mp) cc_final: 0.5447 (mt) REVERT: B 396 GLU cc_start: 0.7801 (tp30) cc_final: 0.7313 (tp30) REVERT: B 434 MET cc_start: 0.8178 (mmm) cc_final: 0.7971 (mmm) REVERT: B 616 LEU cc_start: 0.2769 (OUTLIER) cc_final: 0.2561 (mm) REVERT: C 245 GLU cc_start: 0.7540 (tp30) cc_final: 0.7317 (tp30) REVERT: C 308 TYR cc_start: 0.8877 (m-80) cc_final: 0.8620 (m-80) REVERT: C 523 LEU cc_start: 0.4888 (mt) cc_final: 0.4236 (tt) REVERT: C 726 GLU cc_start: 0.7064 (tt0) cc_final: 0.6520 (tp30) REVERT: D 142 PHE cc_start: 0.8319 (t80) cc_final: 0.8025 (t80) REVERT: D 154 GLU cc_start: 0.8464 (mm-30) cc_final: 0.7903 (tt0) REVERT: D 250 PHE cc_start: 0.6325 (t80) cc_final: 0.5950 (t80) REVERT: D 306 ARG cc_start: 0.8562 (mmm160) cc_final: 0.8337 (mmm-85) REVERT: D 375 MET cc_start: 0.7734 (tpp) cc_final: 0.7478 (mpp) REVERT: E 418 GLN cc_start: 0.4836 (mm-40) cc_final: 0.4276 (tt0) REVERT: F 146 PHE cc_start: 0.6376 (OUTLIER) cc_final: 0.5670 (m-10) REVERT: F 156 GLU cc_start: 0.6426 (OUTLIER) cc_final: 0.5727 (tp30) REVERT: F 173 ARG cc_start: 0.7597 (ttm110) cc_final: 0.7091 (ttp-110) REVERT: F 510 MET cc_start: 0.2515 (mmp) cc_final: -0.0096 (mtm) REVERT: F 570 MET cc_start: -0.1571 (mmm) cc_final: -0.1814 (ttt) REVERT: F 616 GLU cc_start: 0.7556 (pt0) cc_final: 0.6960 (pp20) REVERT: F 800 MET cc_start: -0.0827 (tpt) cc_final: -0.2450 (ptm) outliers start: 89 outliers final: 45 residues processed: 409 average time/residue: 0.4621 time to fit residues: 302.4495 Evaluate side-chains 318 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 269 time to evaluate : 3.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS 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 279 ILE Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 438 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 95 THR Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 442 VAL 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 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 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 390 VAL 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 231 optimal weight: 3.9990 chunk 61 optimal weight: 0.0970 chunk 267 optimal weight: 0.5980 chunk 237 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 360 optimal weight: 6.9990 chunk 234 optimal weight: 0.9990 chunk 240 optimal weight: 8.9990 chunk 98 optimal weight: 0.5980 chunk 122 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 GLN A 239 GLN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 614 HIS A 650 HIS B 478 HIS ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 HIS C 576 ASN D 404 GLN ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4864 r_free = 0.4864 target = 0.221860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.169276 restraints weight = 53273.527| |-----------------------------------------------------------------------------| r_work (start): 0.4270 rms_B_bonded: 2.16 r_work: 0.3765 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33060 Z= 0.120 Angle : 0.577 12.419 44712 Z= 0.289 Chirality : 0.040 0.244 5088 Planarity : 0.004 0.049 5505 Dihedral : 9.380 174.122 4455 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.58 % Allowed : 19.17 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.14), residues: 3846 helix: 0.58 (0.12), residues: 1900 sheet: -1.67 (0.27), residues: 403 loop : -1.19 (0.16), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 170 HIS 0.010 0.001 HIS C 253 PHE 0.013 0.001 PHE F 667 TYR 0.020 0.001 TYR F 511 ARG 0.011 0.000 ARG A 666 Details of bonding type rmsd hydrogen bonds : bond 0.03678 ( 1463) hydrogen bonds : angle 4.85550 ( 4026) SS BOND : bond 0.00216 ( 17) SS BOND : angle 1.03032 ( 34) covalent geometry : bond 0.00268 (33043) covalent geometry : angle 0.57665 (44678) *********************** 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 401 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 308 time to evaluate : 3.519 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: A 46 GLN cc_start: 0.8082 (tm-30) cc_final: 0.7633 (tt0) REVERT: A 239 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.7112 (pt0) REVERT: A 317 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8238 (tp) REVERT: A 433 PHE cc_start: 0.7398 (OUTLIER) cc_final: 0.6857 (t80) REVERT: A 471 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7583 (mm) REVERT: A 518 LEU cc_start: 0.7595 (tp) cc_final: 0.6994 (tp) REVERT: A 733 LEU cc_start: 0.7024 (mt) cc_final: 0.6610 (mt) REVERT: B 434 MET cc_start: 0.8287 (mmm) cc_final: 0.8074 (mmm) REVERT: B 616 LEU cc_start: 0.3267 (OUTLIER) cc_final: 0.3019 (mm) REVERT: C 684 CYS cc_start: 0.2852 (OUTLIER) cc_final: 0.2629 (t) REVERT: C 726 GLU cc_start: 0.7105 (tt0) cc_final: 0.6526 (tp30) REVERT: D 142 PHE cc_start: 0.8399 (t80) cc_final: 0.7962 (t80) REVERT: D 250 PHE cc_start: 0.6545 (t80) cc_final: 0.6109 (t80) REVERT: D 308 TYR cc_start: 0.9155 (m-80) cc_final: 0.8859 (m-80) REVERT: D 375 MET cc_start: 0.7728 (tpp) cc_final: 0.7429 (mpp) REVERT: E 418 GLN cc_start: 0.4867 (mm-40) cc_final: 0.4530 (tt0) REVERT: F 146 PHE cc_start: 0.6341 (OUTLIER) cc_final: 0.5674 (m-10) REVERT: F 156 GLU cc_start: 0.6324 (OUTLIER) cc_final: 0.5582 (tp30) REVERT: F 170 TRP cc_start: 0.7491 (t60) cc_final: 0.6531 (t-100) REVERT: F 470 GLN cc_start: 0.6960 (tp40) cc_final: 0.6675 (mm-40) REVERT: F 510 MET cc_start: 0.2460 (OUTLIER) cc_final: -0.0020 (mtm) REVERT: F 570 MET cc_start: -0.1716 (mmm) cc_final: -0.1931 (ttt) REVERT: F 581 MET cc_start: 0.5494 (tpt) cc_final: 0.5216 (tpt) REVERT: F 616 GLU cc_start: 0.7470 (pt0) cc_final: 0.6889 (pp20) REVERT: F 696 ARG cc_start: 0.8173 (mpp80) cc_final: 0.7698 (mmt180) REVERT: F 800 MET cc_start: -0.0774 (tpt) cc_final: -0.2432 (ptm) outliers start: 93 outliers final: 44 residues processed: 376 average time/residue: 0.4320 time to fit residues: 263.6670 Evaluate side-chains 323 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 270 time to evaluate : 3.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 239 GLN 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 471 LEU Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 279 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 448 LEU Chi-restraints excluded: chain B residue 451 LEU 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 B residue 727 LEU Chi-restraints excluded: chain B residue 730 CYS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 684 CYS 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 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 275 PHE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 139 MET 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 300 MET 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 510 MET Chi-restraints excluded: chain F residue 669 HIS 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 155 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 368 optimal weight: 6.9990 chunk 244 optimal weight: 4.9990 chunk 367 optimal weight: 0.8980 chunk 107 optimal weight: 8.9990 chunk 191 optimal weight: 20.0000 chunk 305 optimal weight: 20.0000 chunk 340 optimal weight: 3.9990 chunk 292 optimal weight: 9.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 239 GLN A 499 HIS ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 GLN B 267 GLN B 494 ASN ** B 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 672 ASN D 404 GLN ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 GLN E 370 ASN ** E 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN F 112 ASN ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 416 GLN ** F 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.216324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.135875 restraints weight = 53297.840| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 5.13 r_work: 0.3444 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.097 33060 Z= 0.378 Angle : 0.755 12.614 44712 Z= 0.382 Chirality : 0.047 0.301 5088 Planarity : 0.005 0.065 5505 Dihedral : 9.184 157.518 4455 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.41 % Allowed : 19.95 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.13), residues: 3846 helix: 0.01 (0.12), residues: 1928 sheet: -1.98 (0.27), residues: 402 loop : -1.37 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 475 HIS 0.013 0.002 HIS E 312 PHE 0.033 0.003 PHE A 146 TYR 0.025 0.003 TYR F 330 ARG 0.008 0.001 ARG D 403 Details of bonding type rmsd hydrogen bonds : bond 0.04665 ( 1463) hydrogen bonds : angle 5.28298 ( 4026) SS BOND : bond 0.01387 ( 17) SS BOND : angle 1.90860 ( 34) covalent geometry : bond 0.00894 (33043) covalent geometry : angle 0.75325 (44678) *********************** 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 389 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 266 time to evaluate : 3.688 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 433 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.7107 (t80) REVERT: A 488 LEU cc_start: 0.4410 (OUTLIER) cc_final: 0.4171 (mt) REVERT: A 518 LEU cc_start: 0.7559 (tp) cc_final: 0.7259 (tp) REVERT: A 733 LEU cc_start: 0.7287 (mt) cc_final: 0.6932 (mt) REVERT: B 434 MET cc_start: 0.8362 (mmm) cc_final: 0.7991 (mmm) REVERT: B 616 LEU cc_start: 0.3446 (OUTLIER) cc_final: 0.3217 (mm) REVERT: B 684 CYS cc_start: -0.2344 (OUTLIER) cc_final: -0.2985 (t) REVERT: B 690 LEU cc_start: 0.7091 (mp) cc_final: 0.6578 (tt) REVERT: B 694 HIS cc_start: 0.8212 (m-70) cc_final: 0.7830 (t70) REVERT: B 713 LEU cc_start: 0.8616 (mt) cc_final: 0.8378 (pp) REVERT: C 65 CYS cc_start: 0.5592 (OUTLIER) cc_final: 0.4251 (t) REVERT: C 143 TRP cc_start: 0.8131 (OUTLIER) cc_final: 0.7656 (t60) REVERT: C 684 CYS cc_start: 0.2919 (OUTLIER) cc_final: 0.2627 (t) REVERT: C 726 GLU cc_start: 0.7228 (tt0) cc_final: 0.6561 (tp30) REVERT: D 145 LYS cc_start: 0.8604 (mmmt) cc_final: 0.7223 (pttt) REVERT: D 375 MET cc_start: 0.8321 (tpp) cc_final: 0.7903 (mpp) REVERT: E 49 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8225 (pt0) REVERT: E 103 ARG cc_start: 0.8686 (tpp-160) cc_final: 0.8133 (tpt90) REVERT: E 265 MET cc_start: 0.7716 (tmm) cc_final: 0.7514 (tmm) REVERT: E 418 GLN cc_start: 0.4824 (mm-40) cc_final: 0.4372 (tt0) REVERT: E 447 GLU cc_start: 0.2880 (pm20) cc_final: 0.2066 (pm20) REVERT: E 448 LEU cc_start: 0.7751 (tp) cc_final: 0.7484 (tt) REVERT: E 581 LEU cc_start: 0.1614 (OUTLIER) cc_final: 0.1395 (tp) REVERT: F 146 PHE cc_start: 0.6872 (OUTLIER) cc_final: 0.6300 (m-10) REVERT: F 470 GLN cc_start: 0.7274 (tp40) cc_final: 0.6935 (mm-40) REVERT: F 598 HIS cc_start: 0.5269 (OUTLIER) cc_final: 0.4820 (t70) REVERT: F 800 MET cc_start: -0.1370 (tpt) cc_final: -0.2398 (ptt) outliers start: 123 outliers final: 72 residues processed: 376 average time/residue: 0.4305 time to fit residues: 267.5880 Evaluate side-chains 321 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 238 time to evaluate : 3.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 297 VAL 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 B residue 38 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 104 HIS 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 444 ASP 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 104 HIS Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 309 ARG 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 D residue 392 VAL Chi-restraints excluded: chain E residue 49 GLN 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 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 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 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 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 675 LEU 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 50 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 321 optimal weight: 0.5980 chunk 93 optimal weight: 0.5980 chunk 176 optimal weight: 10.0000 chunk 179 optimal weight: 7.9990 chunk 54 optimal weight: 20.0000 chunk 244 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 105 GLN ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 GLN ** B 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN D 287 HIS D 404 GLN E 614 HIS F 107 GLN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.219501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.146158 restraints weight = 52898.058| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 5.95 r_work: 0.3541 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 33060 Z= 0.127 Angle : 0.578 13.012 44712 Z= 0.287 Chirality : 0.041 0.319 5088 Planarity : 0.004 0.042 5505 Dihedral : 7.848 148.786 4455 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.44 % Allowed : 21.11 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.14), residues: 3846 helix: 0.45 (0.12), residues: 1899 sheet: -1.76 (0.27), residues: 402 loop : -1.24 (0.15), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP F 170 HIS 0.007 0.001 HIS F 598 PHE 0.030 0.001 PHE B 682 TYR 0.037 0.001 TYR A 689 ARG 0.013 0.000 ARG B 666 Details of bonding type rmsd hydrogen bonds : bond 0.03639 ( 1463) hydrogen bonds : angle 4.82520 ( 4026) SS BOND : bond 0.00257 ( 17) SS BOND : angle 1.23834 ( 34) covalent geometry : bond 0.00288 (33043) covalent geometry : angle 0.57739 (44678) *********************** 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 362 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 274 time to evaluate : 3.735 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 129 VAL cc_start: 0.9160 (t) cc_final: 0.8942 (p) REVERT: A 317 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8339 (mt) REVERT: A 433 PHE cc_start: 0.7504 (OUTLIER) cc_final: 0.7257 (t80) REVERT: A 434 MET cc_start: 0.8060 (mpp) cc_final: 0.7528 (mmp) REVERT: A 733 LEU cc_start: 0.7143 (mt) cc_final: 0.6719 (mt) REVERT: B 434 MET cc_start: 0.7930 (mmm) cc_final: 0.7528 (mmm) REVERT: B 616 LEU cc_start: 0.3651 (mm) cc_final: 0.3408 (mm) REVERT: B 684 CYS cc_start: -0.1910 (OUTLIER) cc_final: -0.2507 (t) REVERT: B 690 LEU cc_start: 0.7062 (mp) cc_final: 0.6486 (tt) REVERT: B 694 HIS cc_start: 0.8200 (m-70) cc_final: 0.7832 (t70) REVERT: B 713 LEU cc_start: 0.8669 (mt) cc_final: 0.8364 (pp) REVERT: C 684 CYS cc_start: 0.2821 (OUTLIER) cc_final: 0.2481 (t) REVERT: C 726 GLU cc_start: 0.7165 (tt0) cc_final: 0.6572 (tp30) REVERT: D 145 LYS cc_start: 0.8530 (mmmt) cc_final: 0.7182 (pttt) REVERT: D 154 GLU cc_start: 0.8503 (mm-30) cc_final: 0.7849 (tt0) REVERT: D 404 GLN cc_start: 0.7424 (tp40) cc_final: 0.7219 (mt0) REVERT: E 418 GLN cc_start: 0.4764 (mm-40) cc_final: 0.4408 (tt0) REVERT: E 447 GLU cc_start: 0.3083 (pm20) cc_final: 0.2297 (pm20) REVERT: E 448 LEU cc_start: 0.7531 (tp) cc_final: 0.7247 (tt) REVERT: E 581 LEU cc_start: 0.1763 (OUTLIER) cc_final: 0.1470 (tp) REVERT: F 146 PHE cc_start: 0.6790 (OUTLIER) cc_final: 0.6243 (m-10) REVERT: F 300 MET cc_start: 0.8724 (mmp) cc_final: 0.8414 (mmp) REVERT: F 470 GLN cc_start: 0.7358 (tp40) cc_final: 0.7072 (mm-40) REVERT: F 510 MET cc_start: 0.2224 (mmt) cc_final: -0.0430 (ptp) REVERT: F 598 HIS cc_start: 0.5485 (OUTLIER) cc_final: 0.4938 (t70) REVERT: F 701 GLU cc_start: 0.4646 (OUTLIER) cc_final: 0.2476 (tm-30) REVERT: F 800 MET cc_start: -0.1412 (tpt) cc_final: -0.2420 (ptt) outliers start: 88 outliers final: 55 residues processed: 349 average time/residue: 0.4263 time to fit residues: 246.0216 Evaluate side-chains 309 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 246 time to evaluate : 3.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 163 CYS 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 433 PHE Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain B residue 47 VAL 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 432 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 451 LEU 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 19 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 501 LYS Chi-restraints excluded: chain C residue 684 CYS Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 49 GLN 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 283 VAL Chi-restraints excluded: chain E residue 293 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 715 VAL 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 59 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 146 PHE 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 511 TYR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 112 optimal weight: 0.2980 chunk 375 optimal weight: 0.6980 chunk 198 optimal weight: 20.0000 chunk 197 optimal weight: 8.9990 chunk 239 optimal weight: 9.9990 chunk 190 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 300 optimal weight: 0.9990 chunk 227 optimal weight: 6.9990 chunk 314 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 105 GLN ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4872 r_free = 0.4872 target = 0.222391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.162645 restraints weight = 53098.654| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 2.18 r_work: 0.3678 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 33060 Z= 0.188 Angle : 0.592 12.642 44712 Z= 0.295 Chirality : 0.041 0.203 5088 Planarity : 0.004 0.040 5505 Dihedral : 7.257 150.566 4455 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.94 % Allowed : 20.84 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.14), residues: 3846 helix: 0.44 (0.12), residues: 1907 sheet: -1.67 (0.28), residues: 404 loop : -1.23 (0.16), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP F 170 HIS 0.007 0.001 HIS F 598 PHE 0.016 0.002 PHE B 682 TYR 0.027 0.002 TYR A 689 ARG 0.006 0.000 ARG A 666 Details of bonding type rmsd hydrogen bonds : bond 0.03705 ( 1463) hydrogen bonds : angle 4.80146 ( 4026) SS BOND : bond 0.00445 ( 17) SS BOND : angle 1.36243 ( 34) covalent geometry : bond 0.00441 (33043) covalent geometry : angle 0.59084 (44678) *********************** 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 364 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 258 time to evaluate : 3.540 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: A 317 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8355 (mt) REVERT: A 433 PHE cc_start: 0.7424 (OUTLIER) cc_final: 0.7173 (t80) REVERT: A 434 MET cc_start: 0.8074 (mpp) cc_final: 0.7504 (mmp) REVERT: A 488 LEU cc_start: 0.4518 (OUTLIER) cc_final: 0.4227 (mt) REVERT: A 518 LEU cc_start: 0.7542 (tp) cc_final: 0.6986 (tp) REVERT: A 733 LEU cc_start: 0.6996 (mt) cc_final: 0.6598 (mt) REVERT: B 434 MET cc_start: 0.7698 (mmm) cc_final: 0.7436 (mmp) REVERT: B 455 LEU cc_start: 0.8182 (tt) cc_final: 0.7892 (pp) REVERT: B 592 ASN cc_start: 0.4956 (p0) cc_final: 0.3675 (m110) REVERT: B 616 LEU cc_start: 0.3594 (OUTLIER) cc_final: 0.3331 (mm) REVERT: B 684 CYS cc_start: -0.2548 (OUTLIER) cc_final: -0.2755 (t) REVERT: B 690 LEU cc_start: 0.7156 (mp) cc_final: 0.6726 (tt) REVERT: B 694 HIS cc_start: 0.8069 (m-70) cc_final: 0.7773 (t70) REVERT: C 371 ASP cc_start: 0.7747 (OUTLIER) cc_final: 0.7100 (m-30) REVERT: C 684 CYS cc_start: 0.2677 (OUTLIER) cc_final: 0.2361 (t) REVERT: C 726 GLU cc_start: 0.7141 (tt0) cc_final: 0.6569 (tp30) REVERT: D 144 PHE cc_start: 0.7745 (m-10) cc_final: 0.7479 (m-10) REVERT: D 145 LYS cc_start: 0.8607 (mmmt) cc_final: 0.7301 (pttt) REVERT: D 154 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7851 (tt0) REVERT: D 250 PHE cc_start: 0.6708 (t80) cc_final: 0.6314 (t80) REVERT: D 375 MET cc_start: 0.8124 (tpp) cc_final: 0.7690 (mpp) REVERT: D 379 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7798 (mp) REVERT: D 404 GLN cc_start: 0.7443 (tp40) cc_final: 0.7225 (mt0) REVERT: E 418 GLN cc_start: 0.4705 (mm-40) cc_final: 0.4390 (tt0) REVERT: E 447 GLU cc_start: 0.2708 (pm20) cc_final: 0.1934 (pm20) REVERT: E 581 LEU cc_start: 0.1806 (OUTLIER) cc_final: 0.1499 (tp) REVERT: F 146 PHE cc_start: 0.6684 (OUTLIER) cc_final: 0.6258 (m-80) REVERT: F 470 GLN cc_start: 0.7157 (tp40) cc_final: 0.6904 (mm110) REVERT: F 510 MET cc_start: 0.2012 (mmt) cc_final: -0.0474 (ptp) REVERT: F 598 HIS cc_start: 0.5701 (OUTLIER) cc_final: 0.4994 (t70) REVERT: F 696 ARG cc_start: 0.8237 (mpp80) cc_final: 0.7802 (mmt180) REVERT: F 701 GLU cc_start: 0.4191 (OUTLIER) cc_final: 0.1644 (tm-30) REVERT: F 800 MET cc_start: -0.1533 (tpt) cc_final: -0.2526 (ptt) outliers start: 106 outliers final: 71 residues processed: 347 average time/residue: 0.4274 time to fit residues: 242.2259 Evaluate side-chains 327 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 244 time to evaluate : 3.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 163 CYS 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 379 ILE Chi-restraints excluded: chain A residue 433 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 738 LEU Chi-restraints excluded: chain B residue 33 ILE 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 451 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 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 37 MET 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 371 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 501 LYS Chi-restraints excluded: chain C residue 684 CYS 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 361 SER Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 129 VAL 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 753 LEU 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 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 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 556 ILE 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 130 optimal weight: 20.0000 chunk 93 optimal weight: 0.5980 chunk 126 optimal weight: 8.9990 chunk 293 optimal weight: 0.6980 chunk 342 optimal weight: 4.9990 chunk 358 optimal weight: 0.0870 chunk 313 optimal weight: 7.9990 chunk 276 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 168 optimal weight: 5.9990 chunk 336 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 105 GLN A 494 ASN A 499 HIS ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 GLN B 467 GLN ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4884 r_free = 0.4884 target = 0.223922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.169345 restraints weight = 53374.398| |-----------------------------------------------------------------------------| r_work (start): 0.4281 rms_B_bonded: 2.18 r_work: 0.3737 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33060 Z= 0.119 Angle : 0.552 11.645 44712 Z= 0.274 Chirality : 0.040 0.279 5088 Planarity : 0.003 0.039 5505 Dihedral : 6.624 138.651 4455 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.52 % Allowed : 21.56 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.14), residues: 3846 helix: 0.59 (0.12), residues: 1906 sheet: -1.62 (0.27), residues: 410 loop : -1.10 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP F 170 HIS 0.006 0.001 HIS B 431 PHE 0.019 0.001 PHE C 244 TYR 0.024 0.001 TYR A 689 ARG 0.006 0.000 ARG A 666 Details of bonding type rmsd hydrogen bonds : bond 0.03385 ( 1463) hydrogen bonds : angle 4.59013 ( 4026) SS BOND : bond 0.00251 ( 17) SS BOND : angle 1.14734 ( 34) covalent geometry : bond 0.00271 (33043) covalent geometry : angle 0.55088 (44678) *********************** 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 360 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 269 time to evaluate : 3.395 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: A 275 PHE cc_start: 0.9026 (OUTLIER) cc_final: 0.8728 (t80) REVERT: A 317 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8224 (mt) REVERT: A 433 PHE cc_start: 0.7238 (OUTLIER) cc_final: 0.6967 (t80) REVERT: A 434 MET cc_start: 0.7899 (mpp) cc_final: 0.7277 (mmp) REVERT: A 488 LEU cc_start: 0.4406 (OUTLIER) cc_final: 0.4105 (mt) REVERT: A 733 LEU cc_start: 0.6767 (mt) cc_final: 0.6352 (mt) REVERT: B 428 LEU cc_start: 0.7082 (tt) cc_final: 0.6047 (mt) REVERT: B 434 MET cc_start: 0.7376 (mmm) cc_final: 0.6804 (tpp) REVERT: B 592 ASN cc_start: 0.4890 (p0) cc_final: 0.3712 (m110) REVERT: B 616 LEU cc_start: 0.3479 (OUTLIER) cc_final: 0.3203 (mm) REVERT: C 371 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.6875 (m-30) REVERT: C 523 LEU cc_start: 0.4211 (mt) cc_final: 0.3392 (tt) REVERT: C 684 CYS cc_start: 0.2569 (OUTLIER) cc_final: 0.2286 (t) REVERT: C 726 GLU cc_start: 0.7151 (tt0) cc_final: 0.6659 (tp30) REVERT: D 144 PHE cc_start: 0.7558 (m-10) cc_final: 0.7319 (m-10) REVERT: D 145 LYS cc_start: 0.8549 (mmmt) cc_final: 0.7274 (pttt) REVERT: D 154 GLU cc_start: 0.8435 (mm-30) cc_final: 0.7862 (tt0) REVERT: D 250 PHE cc_start: 0.6950 (t80) cc_final: 0.6540 (t80) REVERT: D 375 MET cc_start: 0.8111 (tpp) cc_final: 0.7674 (mpp) REVERT: D 379 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7907 (mp) REVERT: E 418 GLN cc_start: 0.4778 (mm-40) cc_final: 0.4535 (tt0) REVERT: E 447 GLU cc_start: 0.2767 (pm20) cc_final: 0.1973 (pm20) REVERT: E 448 LEU cc_start: 0.6910 (tp) cc_final: 0.6539 (tt) REVERT: E 581 LEU cc_start: 0.1817 (OUTLIER) cc_final: 0.1535 (tp) REVERT: F 146 PHE cc_start: 0.6743 (OUTLIER) cc_final: 0.6379 (m-80) REVERT: F 510 MET cc_start: 0.1844 (mmt) cc_final: -0.0412 (ptp) REVERT: F 598 HIS cc_start: 0.5811 (OUTLIER) cc_final: 0.4956 (t70) REVERT: F 696 ARG cc_start: 0.8271 (mpp80) cc_final: 0.7811 (mmt180) REVERT: F 701 GLU cc_start: 0.4224 (OUTLIER) cc_final: 0.1706 (tm-30) REVERT: F 800 MET cc_start: -0.1383 (tpt) cc_final: -0.2478 (ptt) outliers start: 91 outliers final: 51 residues processed: 349 average time/residue: 0.4242 time to fit residues: 242.7165 Evaluate side-chains 310 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 247 time to evaluate : 3.940 ------------------------------------------------------------------------------- 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 433 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 738 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 253 HIS 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 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 19 ILE Chi-restraints excluded: chain C residue 95 THR 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 371 ASP 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 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 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 753 LEU 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 146 PHE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 212 optimal weight: 7.9990 chunk 156 optimal weight: 0.9990 chunk 210 optimal weight: 3.9990 chunk 368 optimal weight: 20.0000 chunk 67 optimal weight: 30.0000 chunk 384 optimal weight: 2.9990 chunk 283 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 chunk 171 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN A 431 HIS ** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 708 GLN ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 GLN C 46 GLN C 253 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN D 404 GLN ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 470 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4868 r_free = 0.4868 target = 0.221980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.166930 restraints weight = 53107.509| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 1.90 r_work: 0.3756 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 33060 Z= 0.200 Angle : 0.599 15.167 44712 Z= 0.299 Chirality : 0.042 0.181 5088 Planarity : 0.004 0.039 5505 Dihedral : 6.776 137.884 4455 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.72 % Allowed : 21.58 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.14), residues: 3846 helix: 0.50 (0.12), residues: 1914 sheet: -1.53 (0.28), residues: 389 loop : -1.15 (0.16), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 475 HIS 0.013 0.001 HIS C 253 PHE 0.021 0.002 PHE C 244 TYR 0.023 0.002 TYR A 689 ARG 0.006 0.000 ARG B 801 Details of bonding type rmsd hydrogen bonds : bond 0.03682 ( 1463) hydrogen bonds : angle 4.69246 ( 4026) SS BOND : bond 0.00476 ( 17) SS BOND : angle 1.30386 ( 34) covalent geometry : bond 0.00469 (33043) covalent geometry : angle 0.59780 (44678) *********************** 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 351 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 253 time to evaluate : 3.653 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 275 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.8681 (t80) REVERT: A 433 PHE cc_start: 0.7045 (OUTLIER) cc_final: 0.6741 (t80) REVERT: A 434 MET cc_start: 0.7858 (mpp) cc_final: 0.7192 (mmp) REVERT: A 488 LEU cc_start: 0.4520 (OUTLIER) cc_final: 0.4211 (mt) REVERT: A 733 LEU cc_start: 0.6504 (mt) cc_final: 0.6071 (mt) REVERT: B 592 ASN cc_start: 0.4697 (p0) cc_final: 0.3472 (m110) REVERT: C 371 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7058 (m-30) REVERT: C 523 LEU cc_start: 0.4136 (mt) cc_final: 0.3197 (tt) REVERT: C 684 CYS cc_start: 0.2512 (OUTLIER) cc_final: 0.2213 (t) REVERT: C 726 GLU cc_start: 0.7261 (tt0) cc_final: 0.6828 (tp30) REVERT: D 144 PHE cc_start: 0.7901 (m-10) cc_final: 0.7593 (m-10) REVERT: D 145 LYS cc_start: 0.8560 (mmmt) cc_final: 0.7386 (pttt) REVERT: D 154 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7851 (tt0) REVERT: D 250 PHE cc_start: 0.7040 (t80) cc_final: 0.6734 (t80) REVERT: D 375 MET cc_start: 0.8109 (tpp) cc_final: 0.7638 (mpp) REVERT: D 379 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7740 (mp) REVERT: E 418 GLN cc_start: 0.4757 (mm-40) cc_final: 0.4501 (tt0) REVERT: E 447 GLU cc_start: 0.2675 (pm20) cc_final: 0.1881 (pm20) REVERT: E 448 LEU cc_start: 0.6733 (tp) cc_final: 0.6420 (tt) REVERT: E 623 ASP cc_start: 0.6256 (OUTLIER) cc_final: 0.5949 (t70) REVERT: F 146 PHE cc_start: 0.6702 (OUTLIER) cc_final: 0.6389 (m-80) REVERT: F 504 ARG cc_start: 0.5731 (tpm170) cc_final: 0.5132 (tpm170) REVERT: F 510 MET cc_start: 0.2001 (mmt) cc_final: -0.0516 (ptp) REVERT: F 570 MET cc_start: -0.2265 (ttt) cc_final: -0.3030 (tpt) REVERT: F 581 MET cc_start: 0.4655 (tpt) cc_final: 0.4446 (tpt) REVERT: F 588 MET cc_start: -0.4441 (ttt) cc_final: -0.5059 (ttp) REVERT: F 598 HIS cc_start: 0.5832 (OUTLIER) cc_final: 0.4926 (t70) REVERT: F 696 ARG cc_start: 0.8197 (mpp80) cc_final: 0.7750 (mmt180) REVERT: F 701 GLU cc_start: 0.3990 (OUTLIER) cc_final: 0.1244 (tm-30) REVERT: F 800 MET cc_start: -0.1243 (tpt) cc_final: -0.2435 (ptt) outliers start: 98 outliers final: 67 residues processed: 337 average time/residue: 0.4334 time to fit residues: 237.5477 Evaluate side-chains 317 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 240 time to evaluate : 3.329 ------------------------------------------------------------------------------- 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 379 ILE Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 657 GLN Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 742 VAL 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 385 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 451 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 716 THR Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 95 THR 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 371 ASP 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 D residue 380 ASP Chi-restraints excluded: chain E residue 129 VAL 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 623 ASP Chi-restraints excluded: chain E residue 753 LEU 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 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 274 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 362 optimal weight: 0.9990 chunk 179 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 171 optimal weight: 2.9990 chunk 339 optimal weight: 0.8980 chunk 128 optimal weight: 20.0000 chunk 262 optimal weight: 0.5980 chunk 67 optimal weight: 30.0000 chunk 104 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN A 614 HIS ** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 GLN ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 GLN D 105 GLN ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.222949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.173081 restraints weight = 53316.565| |-----------------------------------------------------------------------------| r_work (start): 0.4345 rms_B_bonded: 2.26 r_work: 0.3778 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 33060 Z= 0.131 Angle : 0.561 14.062 44712 Z= 0.278 Chirality : 0.040 0.176 5088 Planarity : 0.003 0.039 5505 Dihedral : 6.425 122.910 4455 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.22 % Allowed : 22.22 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.14), residues: 3846 helix: 0.63 (0.12), residues: 1899 sheet: -1.46 (0.28), residues: 392 loop : -1.10 (0.16), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP F 170 HIS 0.006 0.001 HIS F 598 PHE 0.016 0.001 PHE C 244 TYR 0.024 0.001 TYR B 308 ARG 0.006 0.000 ARG A 666 Details of bonding type rmsd hydrogen bonds : bond 0.03401 ( 1463) hydrogen bonds : angle 4.55356 ( 4026) SS BOND : bond 0.00288 ( 17) SS BOND : angle 1.16928 ( 34) covalent geometry : bond 0.00303 (33043) covalent geometry : angle 0.56000 (44678) *********************** 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 337 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 257 time to evaluate : 3.510 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: 0.9003 (OUTLIER) cc_final: 0.8728 (t80) REVERT: A 433 PHE cc_start: 0.7017 (OUTLIER) cc_final: 0.6753 (t80) REVERT: A 434 MET cc_start: 0.7759 (mpp) cc_final: 0.7066 (mmp) REVERT: A 488 LEU cc_start: 0.4424 (OUTLIER) cc_final: 0.4104 (mt) REVERT: A 733 LEU cc_start: 0.6550 (mt) cc_final: 0.6130 (mt) REVERT: B 419 ARG cc_start: 0.6594 (ttt180) cc_final: 0.6002 (mtm180) REVERT: B 428 LEU cc_start: 0.7164 (tt) cc_final: 0.6145 (mt) REVERT: B 590 MET cc_start: 0.0875 (tmm) cc_final: 0.0599 (tmm) REVERT: B 592 ASN cc_start: 0.5067 (p0) cc_final: 0.3878 (m110) REVERT: B 616 LEU cc_start: 0.3700 (mm) cc_final: 0.3384 (mm) REVERT: C 371 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7103 (m-30) REVERT: C 684 CYS cc_start: 0.2705 (OUTLIER) cc_final: 0.2216 (t) REVERT: C 726 GLU cc_start: 0.7252 (tt0) cc_final: 0.6825 (tp30) REVERT: D 46 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7599 (tt0) REVERT: D 144 PHE cc_start: 0.7849 (m-10) cc_final: 0.7556 (m-10) REVERT: D 145 LYS cc_start: 0.8488 (mmmt) cc_final: 0.7357 (pttt) REVERT: D 154 GLU cc_start: 0.8417 (mm-30) cc_final: 0.7895 (tt0) REVERT: D 250 PHE cc_start: 0.6925 (t80) cc_final: 0.6684 (t80) REVERT: D 375 MET cc_start: 0.8170 (tpp) cc_final: 0.7703 (mpp) REVERT: D 379 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7848 (mp) REVERT: E 418 GLN cc_start: 0.4735 (mm-40) cc_final: 0.4510 (tt0) REVERT: E 447 GLU cc_start: 0.2722 (pm20) cc_final: 0.1968 (pm20) REVERT: E 448 LEU cc_start: 0.6761 (tp) cc_final: 0.6443 (tt) REVERT: E 623 ASP cc_start: 0.6229 (OUTLIER) cc_final: 0.5969 (t70) REVERT: F 146 PHE cc_start: 0.6700 (OUTLIER) cc_final: 0.6409 (m-80) REVERT: F 300 MET cc_start: 0.8499 (mmp) cc_final: 0.8227 (mmp) REVERT: F 504 ARG cc_start: 0.6030 (tpm170) cc_final: 0.5557 (tpm170) REVERT: F 510 MET cc_start: 0.1165 (mmt) cc_final: -0.0723 (ptp) REVERT: F 570 MET cc_start: -0.1836 (ttt) cc_final: -0.2643 (tpt) REVERT: F 581 MET cc_start: 0.4677 (tpt) cc_final: 0.4449 (tpt) REVERT: F 598 HIS cc_start: 0.5608 (OUTLIER) cc_final: 0.4783 (t70) REVERT: F 696 ARG cc_start: 0.8205 (mpp80) cc_final: 0.7775 (mmt180) REVERT: F 701 GLU cc_start: 0.3991 (OUTLIER) cc_final: 0.1164 (tm-30) REVERT: F 800 MET cc_start: -0.1277 (tpt) cc_final: -0.2433 (ptt) outliers start: 80 outliers final: 56 residues processed: 326 average time/residue: 0.4469 time to fit residues: 236.8843 Evaluate side-chains 315 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 248 time to evaluate : 3.651 ------------------------------------------------------------------------------- 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 433 PHE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 657 GLN Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain B residue 95 THR 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 451 LEU 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 716 THR Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 684 CYS Chi-restraints excluded: chain D residue 46 GLN 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 380 ASP Chi-restraints excluded: chain E residue 129 VAL 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 430 LEU Chi-restraints excluded: chain E residue 493 GLU Chi-restraints excluded: chain E residue 623 ASP Chi-restraints excluded: chain E residue 753 LEU 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 146 PHE 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 443 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 350 optimal weight: 7.9990 chunk 323 optimal weight: 1.9990 chunk 230 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 276 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 chunk 328 optimal weight: 1.9990 chunk 332 optimal weight: 0.6980 chunk 360 optimal weight: 3.9990 chunk 201 optimal weight: 30.0000 chunk 288 optimal weight: 0.0570 overall best weight: 0.8902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 GLN D 105 GLN ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.222984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.167247 restraints weight = 53212.269| |-----------------------------------------------------------------------------| r_work (start): 0.4258 rms_B_bonded: 2.17 r_work: 0.3768 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33060 Z= 0.132 Angle : 0.563 14.639 44712 Z= 0.278 Chirality : 0.041 0.204 5088 Planarity : 0.004 0.042 5505 Dihedral : 6.240 107.891 4455 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.05 % Allowed : 22.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.14), residues: 3846 helix: 0.67 (0.12), residues: 1903 sheet: -1.44 (0.28), residues: 394 loop : -1.08 (0.16), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP F 170 HIS 0.006 0.001 HIS C 522 PHE 0.016 0.001 PHE C 502 TYR 0.024 0.001 TYR D 127 ARG 0.007 0.000 ARG A 666 Details of bonding type rmsd hydrogen bonds : bond 0.03378 ( 1463) hydrogen bonds : angle 4.52243 ( 4026) SS BOND : bond 0.00300 ( 17) SS BOND : angle 1.17568 ( 34) covalent geometry : bond 0.00306 (33043) covalent geometry : angle 0.56220 (44678) ********************** 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 332 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 258 time to evaluate : 3.375 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: A 46 GLN cc_start: 0.8312 (tm-30) cc_final: 0.7840 (tt0) REVERT: A 275 PHE cc_start: 0.9008 (OUTLIER) cc_final: 0.8717 (t80) REVERT: A 434 MET cc_start: 0.7850 (mpp) cc_final: 0.7430 (mmp) REVERT: A 488 LEU cc_start: 0.4437 (OUTLIER) cc_final: 0.4117 (mt) REVERT: A 733 LEU cc_start: 0.6450 (mt) cc_final: 0.6015 (mt) REVERT: B 419 ARG cc_start: 0.6620 (ttt180) cc_final: 0.6020 (mtm180) REVERT: B 428 LEU cc_start: 0.7144 (tt) cc_final: 0.6192 (mt) REVERT: B 590 MET cc_start: 0.0726 (tmm) cc_final: 0.0454 (tmm) REVERT: B 592 ASN cc_start: 0.5060 (p0) cc_final: 0.3954 (m110) REVERT: B 713 LEU cc_start: 0.8816 (mt) cc_final: 0.8552 (pp) REVERT: C 371 ASP cc_start: 0.7648 (OUTLIER) cc_final: 0.7086 (m-30) REVERT: C 684 CYS cc_start: 0.2709 (OUTLIER) cc_final: 0.2177 (t) REVERT: C 726 GLU cc_start: 0.7418 (tt0) cc_final: 0.7065 (tp30) REVERT: D 46 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7528 (tt0) REVERT: D 144 PHE cc_start: 0.7874 (m-10) cc_final: 0.7573 (m-10) REVERT: D 145 LYS cc_start: 0.8522 (mmmt) cc_final: 0.7366 (pttt) REVERT: D 154 GLU cc_start: 0.8449 (mm-30) cc_final: 0.7866 (tt0) REVERT: D 375 MET cc_start: 0.8191 (tpp) cc_final: 0.7672 (mpp) REVERT: D 379 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7892 (mp) REVERT: E 447 GLU cc_start: 0.3029 (pm20) cc_final: 0.2096 (pm20) REVERT: E 448 LEU cc_start: 0.6721 (tp) cc_final: 0.6387 (tt) REVERT: E 623 ASP cc_start: 0.6333 (OUTLIER) cc_final: 0.6076 (t70) REVERT: F 146 PHE cc_start: 0.6679 (OUTLIER) cc_final: 0.6407 (m-80) REVERT: F 300 MET cc_start: 0.8495 (mmp) cc_final: 0.8257 (mmp) REVERT: F 504 ARG cc_start: 0.6018 (tpm170) cc_final: 0.5468 (tpm170) REVERT: F 510 MET cc_start: 0.0739 (mmt) cc_final: -0.1028 (ptp) REVERT: F 570 MET cc_start: -0.1751 (ttt) cc_final: -0.2476 (tpt) REVERT: F 588 MET cc_start: -0.4620 (ttt) cc_final: -0.4836 (ttt) REVERT: F 598 HIS cc_start: 0.5626 (OUTLIER) cc_final: 0.4761 (t70) REVERT: F 696 ARG cc_start: 0.8203 (mpp80) cc_final: 0.7784 (mmt180) REVERT: F 701 GLU cc_start: 0.4026 (OUTLIER) cc_final: 0.1200 (tm-30) REVERT: F 800 MET cc_start: -0.1315 (tpt) cc_final: -0.2449 (ptt) outliers start: 74 outliers final: 55 residues processed: 323 average time/residue: 0.4386 time to fit residues: 229.5409 Evaluate side-chains 310 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 245 time to evaluate : 3.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 657 GLN Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 292 ASP 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 632 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 244 PHE 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 371 ASP Chi-restraints excluded: chain C residue 684 CYS Chi-restraints excluded: chain D residue 46 GLN 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 380 ASP Chi-restraints excluded: chain E residue 129 VAL 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 430 LEU Chi-restraints excluded: chain E residue 493 GLU Chi-restraints excluded: chain E residue 623 ASP 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 146 PHE Chi-restraints excluded: chain F residue 157 HIS 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 443 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 155 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 292 optimal weight: 8.9990 chunk 295 optimal weight: 0.0070 chunk 16 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 168 optimal weight: 9.9990 chunk 346 optimal weight: 5.9990 chunk 283 optimal weight: 30.0000 chunk 221 optimal weight: 0.1980 chunk 38 optimal weight: 2.9990 overall best weight: 1.8404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 105 GLN ** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 HIS B 105 GLN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 ASN ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 ASN F 107 GLN ** F 113 GLN ** 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 = 0.221299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.170813 restraints weight = 53015.298| |-----------------------------------------------------------------------------| r_work (start): 0.4330 rms_B_bonded: 2.25 r_work: 0.3751 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3600 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 33060 Z= 0.209 Angle : 0.612 14.463 44712 Z= 0.306 Chirality : 0.042 0.246 5088 Planarity : 0.004 0.041 5505 Dihedral : 6.495 100.319 4453 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.19 % Allowed : 22.33 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.14), residues: 3846 helix: 0.52 (0.12), residues: 1914 sheet: -1.50 (0.28), residues: 407 loop : -1.09 (0.16), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP F 170 HIS 0.006 0.001 HIS F 598 PHE 0.027 0.002 PHE A 433 TYR 0.020 0.002 TYR D 127 ARG 0.007 0.000 ARG A 666 Details of bonding type rmsd hydrogen bonds : bond 0.03689 ( 1463) hydrogen bonds : angle 4.67138 ( 4026) SS BOND : bond 0.00472 ( 17) SS BOND : angle 1.33300 ( 34) covalent geometry : bond 0.00494 (33043) covalent geometry : angle 0.61106 (44678) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28126.35 seconds wall clock time: 485 minutes 4.27 seconds (29104.27 seconds total)