Starting phenix.real_space_refine on Wed May 21 18:42:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v6n_42997/05_2025/8v6n_42997.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v6n_42997/05_2025/8v6n_42997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v6n_42997/05_2025/8v6n_42997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v6n_42997/05_2025/8v6n_42997.map" model { file = "/net/cci-nas-00/data/ceres_data/8v6n_42997/05_2025/8v6n_42997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v6n_42997/05_2025/8v6n_42997.cif" } resolution = 2.59 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= 0.074 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: 7 Type Number sf(0) Gaussians P 20 5.49 5 S 132 5.16 5 Na 1 4.78 5 B 8 2.79 5 C 14500 2.51 5 N 3460 2.21 5 O 4064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 22185 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5184 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 14, 'TRANS': 621} Chain breaks: 2 Chain: "B" Number of atoms: 5184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5184 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 14, 'TRANS': 621} Chain breaks: 2 Chain: "C" Number of atoms: 5184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5184 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 14, 'TRANS': 621} Chain breaks: 2 Chain: "D" Number of atoms: 5184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5184 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 14, 'TRANS': 621} Chain breaks: 2 Chain: "A" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 369 Unusual residues: {' NA': 1, 'ACD': 1, 'FZ4': 2, 'POV': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 316 Unusual residues: {'ACD': 1, 'FZ4': 2, 'POV': 5} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 316 Unusual residues: {'ACD': 1, 'FZ4': 2, 'POV': 5} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 264 Unusual residues: {'ACD': 1, 'FZ4': 2, 'POV': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Time building chain proxies: 12.51, per 1000 atoms: 0.56 Number of scatterers: 22185 At special positions: 0 Unit cell: (152.8, 152.8, 125.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 132 16.00 P 20 15.00 Na 1 11.00 O 4064 8.00 N 3460 7.00 C 14500 6.00 B 8 5.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 619 " distance=2.03 Simple disulfide: pdb=" SG CYS A 721 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 619 " distance=2.03 Simple disulfide: pdb=" SG CYS B 721 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 721 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 619 " distance=2.03 Simple disulfide: pdb=" SG CYS D 721 " - pdb=" SG CYS D 731 " 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: 5.21 Conformation dependent library (CDL) restraints added in 2.5 seconds 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4872 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 7 sheets defined 62.3% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 119 through 128 removed outlier: 3.802A pdb=" N ILE A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 144 removed outlier: 3.639A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 141 " --> pdb=" O GLU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 161 removed outlier: 4.048A pdb=" N MET A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS A 161 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.501A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 197 removed outlier: 3.621A pdb=" N ILE A 189 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASN A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 removed outlier: 3.566A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.515A pdb=" N ILE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 236 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 283 removed outlier: 3.517A pdb=" N GLU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 removed outlier: 3.726A pdb=" N LEU A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 329 removed outlier: 3.514A pdb=" N ARG A 319 " --> pdb=" O ASP A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 352 removed outlier: 3.537A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 362 Processing helix chain 'A' and resid 370 through 374 removed outlier: 3.624A pdb=" N LEU A 373 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 removed outlier: 3.503A pdb=" N VAL A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 424 through 434 removed outlier: 3.733A pdb=" N TRP A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 460 removed outlier: 3.560A pdb=" N TYR A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 507 removed outlier: 3.829A pdb=" N MET A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 504 " --> pdb=" O LYS A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 542 removed outlier: 3.593A pdb=" N VAL A 525 " --> pdb=" O TRP A 521 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A 538 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A 542 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.609A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 Processing helix chain 'A' and resid 574 through 586 Processing helix chain 'A' and resid 587 through 609 removed outlier: 4.371A pdb=" N PHE A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE A 597 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 638 removed outlier: 3.822A pdb=" N LEU A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 666 Processing helix chain 'A' and resid 668 through 687 removed outlier: 3.547A pdb=" N THR A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 706 removed outlier: 3.899A pdb=" N TRP A 692 " --> pdb=" O SER A 688 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 694 " --> pdb=" O ARG A 690 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 697 " --> pdb=" O ARG A 693 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG A 698 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 713 Processing helix chain 'A' and resid 738 through 748 removed outlier: 3.554A pdb=" N HIS A 745 " --> pdb=" O GLU A 741 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER A 747 " --> pdb=" O LYS A 743 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE A 748 " --> pdb=" O THR A 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 128 removed outlier: 3.801A pdb=" N ILE B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER B 128 " --> pdb=" O PHE B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 144 removed outlier: 3.639A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 161 removed outlier: 4.048A pdb=" N MET B 159 " --> pdb=" O PRO B 155 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS B 161 " --> pdb=" O PHE B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.501A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 197 removed outlier: 3.621A pdb=" N ILE B 189 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN B 197 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 204 removed outlier: 3.567A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.515A pdb=" N ILE B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU B 224 " --> pdb=" O ASN B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 236 Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 283 removed outlier: 3.517A pdb=" N GLU B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 removed outlier: 3.726A pdb=" N LEU B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 329 removed outlier: 3.515A pdb=" N ARG B 319 " --> pdb=" O ASP B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 352 removed outlier: 3.537A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 362 Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.625A pdb=" N LEU B 373 " --> pdb=" O LEU B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 removed outlier: 3.503A pdb=" N VAL B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 424 through 434 removed outlier: 3.733A pdb=" N TRP B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 460 removed outlier: 3.558A pdb=" N TYR B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 507 removed outlier: 3.829A pdb=" N MET B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 504 " --> pdb=" O LYS B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 542 removed outlier: 3.594A pdb=" N VAL B 525 " --> pdb=" O TRP B 521 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 538 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE B 542 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 3.609A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 567 Processing helix chain 'B' and resid 574 through 586 Processing helix chain 'B' and resid 587 through 609 removed outlier: 4.371A pdb=" N PHE B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE B 597 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE B 609 " --> pdb=" O LEU B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 638 removed outlier: 3.822A pdb=" N LEU B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 666 Processing helix chain 'B' and resid 668 through 687 removed outlier: 3.547A pdb=" N THR B 680 " --> pdb=" O LEU B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 706 removed outlier: 3.899A pdb=" N TRP B 692 " --> pdb=" O SER B 688 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG B 693 " --> pdb=" O GLU B 689 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU B 694 " --> pdb=" O ARG B 690 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 697 " --> pdb=" O ARG B 693 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG B 698 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 713 Processing helix chain 'B' and resid 738 through 748 removed outlier: 3.554A pdb=" N HIS B 745 " --> pdb=" O GLU B 741 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER B 747 " --> pdb=" O LYS B 743 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 128 removed outlier: 3.801A pdb=" N ILE C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER C 128 " --> pdb=" O PHE C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 144 removed outlier: 3.639A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 161 removed outlier: 4.048A pdb=" N MET C 159 " --> pdb=" O PRO C 155 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS C 161 " --> pdb=" O PHE C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.501A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 197 removed outlier: 3.621A pdb=" N ILE C 189 " --> pdb=" O GLU C 185 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 204 removed outlier: 3.567A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.515A pdb=" N ILE C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU C 224 " --> pdb=" O ASN C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 236 Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 283 removed outlier: 3.516A pdb=" N GLU C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 removed outlier: 3.725A pdb=" N LEU C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 329 removed outlier: 3.514A pdb=" N ARG C 319 " --> pdb=" O ASP C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 352 removed outlier: 3.537A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 362 Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.625A pdb=" N LEU C 373 " --> pdb=" O LEU C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 409 removed outlier: 3.503A pdb=" N VAL C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 424 through 434 removed outlier: 3.733A pdb=" N TRP C 433 " --> pdb=" O LEU C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 460 removed outlier: 3.559A pdb=" N TYR C 448 " --> pdb=" O SER C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 507 removed outlier: 3.828A pdb=" N MET C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA C 504 " --> pdb=" O LYS C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 542 removed outlier: 3.594A pdb=" N VAL C 525 " --> pdb=" O TRP C 521 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE C 538 " --> pdb=" O ILE C 534 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE C 542 " --> pdb=" O PHE C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 561 removed outlier: 3.609A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 567 Processing helix chain 'C' and resid 574 through 586 Processing helix chain 'C' and resid 587 through 609 removed outlier: 4.371A pdb=" N PHE C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE C 597 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU C 608 " --> pdb=" O ALA C 604 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE C 609 " --> pdb=" O LEU C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 638 removed outlier: 3.823A pdb=" N LEU C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 666 Processing helix chain 'C' and resid 668 through 687 removed outlier: 3.547A pdb=" N THR C 680 " --> pdb=" O LEU C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 706 removed outlier: 3.899A pdb=" N TRP C 692 " --> pdb=" O SER C 688 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG C 693 " --> pdb=" O GLU C 689 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU C 694 " --> pdb=" O ARG C 690 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C 697 " --> pdb=" O ARG C 693 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG C 698 " --> pdb=" O LEU C 694 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET C 706 " --> pdb=" O GLU C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 713 Processing helix chain 'C' and resid 738 through 748 removed outlier: 3.554A pdb=" N HIS C 745 " --> pdb=" O GLU C 741 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER C 747 " --> pdb=" O LYS C 743 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE C 748 " --> pdb=" O THR C 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 128 removed outlier: 3.801A pdb=" N ILE D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER D 128 " --> pdb=" O PHE D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 144 removed outlier: 3.639A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 161 removed outlier: 4.048A pdb=" N MET D 159 " --> pdb=" O PRO D 155 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS D 161 " --> pdb=" O PHE D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.501A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 197 removed outlier: 3.621A pdb=" N ILE D 189 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU D 195 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 204 removed outlier: 3.567A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 225 removed outlier: 3.515A pdb=" N ILE D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 236 Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 283 removed outlier: 3.517A pdb=" N GLU D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 removed outlier: 3.726A pdb=" N LEU D 303 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 329 removed outlier: 3.515A pdb=" N ARG D 319 " --> pdb=" O ASP D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 352 removed outlier: 3.537A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 362 Processing helix chain 'D' and resid 370 through 374 removed outlier: 3.626A pdb=" N LEU D 373 " --> pdb=" O LEU D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 409 removed outlier: 3.504A pdb=" N VAL D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 424 through 434 removed outlier: 3.732A pdb=" N TRP D 433 " --> pdb=" O LEU D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 460 removed outlier: 3.559A pdb=" N TYR D 448 " --> pdb=" O SER D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 507 removed outlier: 3.828A pdb=" N MET D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA D 504 " --> pdb=" O LYS D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 542 removed outlier: 3.593A pdb=" N VAL D 525 " --> pdb=" O TRP D 521 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE D 538 " --> pdb=" O ILE D 534 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE D 542 " --> pdb=" O PHE D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 561 removed outlier: 3.609A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 567 Processing helix chain 'D' and resid 574 through 586 Processing helix chain 'D' and resid 587 through 609 removed outlier: 4.371A pdb=" N PHE D 592 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE D 597 " --> pdb=" O VAL D 593 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE D 609 " --> pdb=" O LEU D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 638 removed outlier: 3.822A pdb=" N LEU D 630 " --> pdb=" O SER D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 666 Processing helix chain 'D' and resid 668 through 687 removed outlier: 3.546A pdb=" N THR D 680 " --> pdb=" O LEU D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 706 removed outlier: 3.899A pdb=" N TRP D 692 " --> pdb=" O SER D 688 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG D 693 " --> pdb=" O GLU D 689 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU D 694 " --> pdb=" O ARG D 690 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA D 697 " --> pdb=" O ARG D 693 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG D 698 " --> pdb=" O LEU D 694 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET D 706 " --> pdb=" O GLU D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 713 Processing helix chain 'D' and resid 738 through 748 removed outlier: 3.554A pdb=" N HIS D 745 " --> pdb=" O GLU D 741 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER D 747 " --> pdb=" O LYS D 743 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE D 748 " --> pdb=" O THR D 744 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 74 removed outlier: 4.315A pdb=" N ARG A 73 " --> pdb=" O LYS D 722 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 376 through 382 removed outlier: 6.845A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ALA A 381 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 376 through 382 removed outlier: 6.845A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ALA B 381 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 721 through 722 removed outlier: 4.286A pdb=" N ARG C 73 " --> pdb=" O LYS B 722 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 376 through 382 removed outlier: 6.846A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ALA C 381 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 721 through 722 removed outlier: 4.333A pdb=" N ARG D 73 " --> pdb=" O LYS C 722 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 376 through 382 removed outlier: 6.845A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ALA D 381 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) 919 hydrogen bonds defined for protein. 2709 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: 5.82 Time building geometry restraints manager: 5.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3392 1.31 - 1.44: 5996 1.44 - 1.56: 12764 1.56 - 1.69: 60 1.69 - 1.81: 216 Bond restraints: 22428 Sorted by residual: bond pdb=" C21 POV A 901 " pdb=" O21 POV A 901 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.28e+01 bond pdb=" C21 POV A 908 " pdb=" O21 POV A 908 " ideal model delta sigma weight residual 1.330 1.425 -0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" C21 POV B 902 " pdb=" O21 POV B 902 " ideal model delta sigma weight residual 1.330 1.425 -0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" C31 POV A 903 " pdb=" O31 POV A 903 " ideal model delta sigma weight residual 1.327 1.422 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C21 POV C 902 " pdb=" O21 POV C 902 " ideal model delta sigma weight residual 1.330 1.425 -0.095 2.00e-02 2.50e+03 2.25e+01 ... (remaining 22423 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 28988 2.60 - 5.20: 733 5.20 - 7.80: 215 7.80 - 10.40: 89 10.40 - 13.00: 43 Bond angle restraints: 30068 Sorted by residual: angle pdb=" N LEU A 513 " pdb=" CA LEU A 513 " pdb=" C LEU A 513 " ideal model delta sigma weight residual 114.56 106.69 7.87 1.27e+00 6.20e-01 3.84e+01 angle pdb=" N LEU C 513 " pdb=" CA LEU C 513 " pdb=" C LEU C 513 " ideal model delta sigma weight residual 114.56 106.70 7.86 1.27e+00 6.20e-01 3.83e+01 angle pdb=" N LEU B 513 " pdb=" CA LEU B 513 " pdb=" C LEU B 513 " ideal model delta sigma weight residual 114.56 106.70 7.86 1.27e+00 6.20e-01 3.83e+01 angle pdb=" N LEU D 513 " pdb=" CA LEU D 513 " pdb=" C LEU D 513 " ideal model delta sigma weight residual 114.56 106.71 7.85 1.27e+00 6.20e-01 3.82e+01 angle pdb=" N ILE C 644 " pdb=" CA ILE C 644 " pdb=" C ILE C 644 " ideal model delta sigma weight residual 113.10 108.24 4.86 9.70e-01 1.06e+00 2.51e+01 ... (remaining 30063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 13147 35.82 - 71.63: 411 71.63 - 107.45: 66 107.45 - 143.26: 13 143.26 - 179.08: 3 Dihedral angle restraints: 13640 sinusoidal: 6144 harmonic: 7496 Sorted by residual: dihedral pdb=" CB CYS A 612 " pdb=" SG CYS A 612 " pdb=" SG CYS A 619 " pdb=" CB CYS A 619 " ideal model delta sinusoidal sigma weight residual -86.00 -165.67 79.67 1 1.00e+01 1.00e-02 7.88e+01 dihedral pdb=" CB CYS D 612 " pdb=" SG CYS D 612 " pdb=" SG CYS D 619 " pdb=" CB CYS D 619 " ideal model delta sinusoidal sigma weight residual -86.00 -165.66 79.66 1 1.00e+01 1.00e-02 7.88e+01 dihedral pdb=" CB CYS B 612 " pdb=" SG CYS B 612 " pdb=" SG CYS B 619 " pdb=" CB CYS B 619 " ideal model delta sinusoidal sigma weight residual -86.00 -165.63 79.63 1 1.00e+01 1.00e-02 7.87e+01 ... (remaining 13637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2714 0.058 - 0.116: 503 0.116 - 0.173: 43 0.173 - 0.231: 0 0.231 - 0.289: 12 Chirality restraints: 3272 Sorted by residual: chirality pdb=" CA GLU A 423 " pdb=" N GLU A 423 " pdb=" C GLU A 423 " pdb=" CB GLU A 423 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA GLU B 423 " pdb=" N GLU B 423 " pdb=" C GLU B 423 " pdb=" CB GLU B 423 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA GLU D 423 " pdb=" N GLU D 423 " pdb=" C GLU D 423 " pdb=" CB GLU D 423 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 3269 not shown) Planarity restraints: 3668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 509 " 0.040 5.00e-02 4.00e+02 6.16e-02 6.07e+00 pdb=" N PRO D 510 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO D 510 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 510 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 509 " 0.040 5.00e-02 4.00e+02 6.12e-02 6.00e+00 pdb=" N PRO C 510 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO C 510 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 510 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 509 " 0.040 5.00e-02 4.00e+02 6.11e-02 5.98e+00 pdb=" N PRO A 510 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 510 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 510 " 0.034 5.00e-02 4.00e+02 ... (remaining 3665 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5819 2.80 - 3.32: 18051 3.32 - 3.85: 35570 3.85 - 4.37: 43892 4.37 - 4.90: 73625 Nonbonded interactions: 176957 Sorted by model distance: nonbonded pdb=" O GLU C 308 " pdb=" O HOH C1001 " model vdw 2.274 3.040 nonbonded pdb=" O GLU B 308 " pdb=" O HOH B1001 " model vdw 2.274 3.040 nonbonded pdb=" O GLU D 308 " pdb=" O HOH D1001 " model vdw 2.276 3.040 nonbonded pdb=" O GLU A 308 " pdb=" O HOH A1001 " model vdw 2.311 3.040 nonbonded pdb=" O HIS D 417 " pdb=" OG1 THR D 421 " model vdw 2.314 3.040 ... (remaining 176952 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 62 through 751 or resid 901 or resid 904 or resid 906)) selection = (chain 'B' and (resid 62 through 751 or resid 901 or resid 904 or resid 906)) selection = (chain 'C' and (resid 62 through 751 or resid 901 or resid 904 or resid 906)) selection = (chain 'D' and (resid 62 through 751 or resid 901 or resid 904 or resid 906)) } 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=0.45 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: 0.010 Normalize map: mean=0, sd=1: 0.740 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: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 43.770 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 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 : 0.008 0.096 22436 Z= 0.398 Angle : 1.216 12.999 30084 Z= 0.593 Chirality : 0.046 0.289 3272 Planarity : 0.005 0.062 3668 Dihedral : 16.896 179.078 8744 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -6.02 (0.11), residues: 2520 helix: -4.67 (0.04), residues: 1544 sheet: -0.30 (0.62), residues: 88 loop : -2.61 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 559 HIS 0.006 0.001 HIS D 160 PHE 0.018 0.002 PHE B 447 TYR 0.010 0.001 TYR C 451 ARG 0.003 0.001 ARG D 714 Details of bonding type rmsd hydrogen bonds : bond 0.33698 ( 919) hydrogen bonds : angle 9.74203 ( 2709) SS BOND : bond 0.00395 ( 8) SS BOND : angle 1.36488 ( 16) covalent geometry : bond 0.00781 (22428) covalent geometry : angle 1.21613 (30068) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 561 time to evaluate : 2.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 GLU cc_start: 0.6801 (tt0) cc_final: 0.6466 (tp30) REVERT: A 332 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6845 (mt-10) REVERT: A 488 MET cc_start: 0.6624 (mtp) cc_final: 0.6061 (mmm) REVERT: A 501 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7633 (mm-30) REVERT: B 207 GLU cc_start: 0.7614 (pt0) cc_final: 0.7373 (pt0) REVERT: B 214 GLU cc_start: 0.6787 (tt0) cc_final: 0.6364 (tp30) REVERT: B 351 MET cc_start: 0.8730 (mtp) cc_final: 0.8510 (mtp) REVERT: B 488 MET cc_start: 0.6618 (mtp) cc_final: 0.5996 (mmm) REVERT: C 129 GLU cc_start: 0.6840 (mp0) cc_final: 0.6595 (mp0) REVERT: C 207 GLU cc_start: 0.7738 (pt0) cc_final: 0.7523 (pt0) REVERT: C 332 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6798 (mt-10) REVERT: C 488 MET cc_start: 0.6628 (mtp) cc_final: 0.5994 (mmm) REVERT: D 129 GLU cc_start: 0.6827 (mp0) cc_final: 0.6605 (mp0) REVERT: D 207 GLU cc_start: 0.7572 (pt0) cc_final: 0.7367 (pt0) REVERT: D 488 MET cc_start: 0.6630 (mtp) cc_final: 0.6107 (mmp) outliers start: 0 outliers final: 0 residues processed: 561 average time/residue: 1.2294 time to fit residues: 790.0774 Evaluate side-chains 339 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 5.9990 chunk 191 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 chunk 65 optimal weight: 20.0000 chunk 128 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 chunk 197 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 120 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 228 optimal weight: 0.6980 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN A 205 ASN A 242 ASN A 251 ASN A 274 GLN A 410 ASN A 412 ASN A 643 ASN A 646 GLN A 671 ASN B 71 ASN B 182 ASN B 205 ASN B 227 GLN B 242 ASN B 251 ASN B 412 ASN B 643 ASN B 646 GLN B 671 ASN C 71 ASN C 205 ASN C 220 ASN C 242 ASN C 251 ASN C 274 GLN C 412 ASN C 643 ASN C 646 GLN C 671 ASN D 71 ASN D 205 ASN D 242 ASN D 251 ASN D 274 GLN D 412 ASN D 643 ASN D 646 GLN D 671 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.183541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.131632 restraints weight = 22214.169| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.08 r_work: 0.3251 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 22436 Z= 0.234 Angle : 0.734 10.958 30084 Z= 0.361 Chirality : 0.045 0.221 3272 Planarity : 0.006 0.052 3668 Dihedral : 19.174 137.846 3724 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 4.33 % Allowed : 9.72 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.73 (0.14), residues: 2520 helix: -1.57 (0.11), residues: 1524 sheet: 0.42 (0.64), residues: 84 loop : -2.24 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 559 HIS 0.005 0.002 HIS B 244 PHE 0.028 0.002 PHE B 259 TYR 0.016 0.002 TYR A 451 ARG 0.007 0.001 ARG B 225 Details of bonding type rmsd hydrogen bonds : bond 0.06557 ( 919) hydrogen bonds : angle 4.25449 ( 2709) SS BOND : bond 0.00529 ( 8) SS BOND : angle 1.22887 ( 16) covalent geometry : bond 0.00559 (22428) covalent geometry : angle 0.73342 (30068) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 362 time to evaluate : 2.320 Fit side-chains REVERT: A 121 LYS cc_start: 0.7817 (mptt) cc_final: 0.7523 (tttm) REVERT: A 289 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7689 (mm) REVERT: A 332 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7789 (mt-10) REVERT: A 488 MET cc_start: 0.7141 (mtp) cc_final: 0.6138 (mpm) REVERT: A 574 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.7737 (ptm) REVERT: A 717 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7655 (mmm) REVERT: A 719 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7241 (pm20) REVERT: B 145 LEU cc_start: 0.6857 (OUTLIER) cc_final: 0.6597 (mt) REVERT: B 229 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7346 (p0) REVERT: B 289 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7676 (mm) REVERT: B 309 ASP cc_start: 0.6992 (m-30) cc_final: 0.6677 (m-30) REVERT: B 320 MET cc_start: 0.8834 (mmt) cc_final: 0.8593 (mmt) REVERT: B 332 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7751 (mt-10) REVERT: B 412 ASN cc_start: 0.8072 (m-40) cc_final: 0.7861 (m-40) REVERT: B 418 GLU cc_start: 0.8427 (tt0) cc_final: 0.8101 (mp0) REVERT: B 488 MET cc_start: 0.7185 (mtp) cc_final: 0.6205 (mpm) REVERT: B 717 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7613 (mmm) REVERT: C 145 LEU cc_start: 0.7050 (OUTLIER) cc_final: 0.6719 (mt) REVERT: C 229 ASP cc_start: 0.7772 (OUTLIER) cc_final: 0.7409 (p0) REVERT: C 289 ILE cc_start: 0.8003 (OUTLIER) cc_final: 0.7685 (mm) REVERT: C 320 MET cc_start: 0.8836 (mmt) cc_final: 0.8611 (mmt) REVERT: C 332 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7754 (mt-10) REVERT: C 418 GLU cc_start: 0.8461 (tt0) cc_final: 0.8127 (mp0) REVERT: C 488 MET cc_start: 0.7060 (mtp) cc_final: 0.6108 (mpm) REVERT: C 717 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7654 (mmm) REVERT: D 145 LEU cc_start: 0.7001 (OUTLIER) cc_final: 0.6679 (mt) REVERT: D 289 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7682 (mm) REVERT: D 320 MET cc_start: 0.8825 (mmt) cc_final: 0.8576 (mmt) REVERT: D 332 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7770 (mt-10) REVERT: D 355 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7166 (pm20) REVERT: D 418 GLU cc_start: 0.8497 (tt0) cc_final: 0.8109 (mp0) REVERT: D 488 MET cc_start: 0.7106 (mtp) cc_final: 0.6140 (mpm) REVERT: D 717 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7651 (mmm) REVERT: D 719 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7300 (pm20) outliers start: 98 outliers final: 27 residues processed: 424 average time/residue: 1.2351 time to fit residues: 599.9546 Evaluate side-chains 357 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 314 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 717 MET Chi-restraints excluded: chain D residue 719 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 102 optimal weight: 20.0000 chunk 136 optimal weight: 9.9990 chunk 157 optimal weight: 0.0470 chunk 112 optimal weight: 4.9990 chunk 144 optimal weight: 20.0000 chunk 110 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 171 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 152 optimal weight: 7.9990 chunk 198 optimal weight: 20.0000 overall best weight: 4.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 410 ASN B 160 HIS D 750 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.178129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.129897 restraints weight = 22032.041| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.88 r_work: 0.3177 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 22436 Z= 0.234 Angle : 0.693 10.088 30084 Z= 0.342 Chirality : 0.045 0.261 3272 Planarity : 0.005 0.049 3668 Dihedral : 18.263 120.447 3724 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.64 % Allowed : 11.93 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.33 (0.16), residues: 2520 helix: -0.22 (0.12), residues: 1584 sheet: 0.63 (0.63), residues: 84 loop : -2.21 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 521 HIS 0.006 0.002 HIS D 301 PHE 0.021 0.002 PHE A 259 TYR 0.018 0.002 TYR C 451 ARG 0.008 0.001 ARG A 225 Details of bonding type rmsd hydrogen bonds : bond 0.06204 ( 919) hydrogen bonds : angle 3.93659 ( 2709) SS BOND : bond 0.00566 ( 8) SS BOND : angle 1.20161 ( 16) covalent geometry : bond 0.00567 (22428) covalent geometry : angle 0.69266 (30068) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 330 time to evaluate : 2.193 Fit side-chains REVERT: A 121 LYS cc_start: 0.7989 (mptt) cc_final: 0.7495 (tttm) REVERT: A 289 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7829 (mm) REVERT: A 488 MET cc_start: 0.7220 (mtp) cc_final: 0.6279 (mpm) REVERT: A 546 GLU cc_start: 0.7361 (mp0) cc_final: 0.7062 (mp0) REVERT: A 655 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8345 (tm) REVERT: A 702 GLU cc_start: 0.8422 (mm-30) cc_final: 0.7945 (mt-10) REVERT: A 717 MET cc_start: 0.8423 (mpp) cc_final: 0.7769 (OUTLIER) REVERT: A 719 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7288 (pm20) REVERT: B 129 GLU cc_start: 0.6594 (mp0) cc_final: 0.6325 (mp0) REVERT: B 145 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6753 (mt) REVERT: B 289 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7834 (mm) REVERT: B 309 ASP cc_start: 0.7110 (m-30) cc_final: 0.6759 (m-30) REVERT: B 320 MET cc_start: 0.8940 (mmt) cc_final: 0.8608 (mmt) REVERT: B 418 GLU cc_start: 0.8472 (tt0) cc_final: 0.8149 (mp0) REVERT: B 488 MET cc_start: 0.7204 (mtp) cc_final: 0.6250 (mpm) REVERT: B 546 GLU cc_start: 0.7464 (mp0) cc_final: 0.7129 (mp0) REVERT: B 717 MET cc_start: 0.8430 (mpp) cc_final: 0.7746 (OUTLIER) REVERT: B 719 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7421 (pm20) REVERT: C 145 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.6766 (mt) REVERT: C 289 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7815 (mm) REVERT: C 320 MET cc_start: 0.8941 (mmt) cc_final: 0.8654 (mmt) REVERT: C 418 GLU cc_start: 0.8482 (tt0) cc_final: 0.8165 (mp0) REVERT: C 488 MET cc_start: 0.7265 (mtp) cc_final: 0.6332 (mpm) REVERT: C 717 MET cc_start: 0.8430 (mpp) cc_final: 0.7772 (OUTLIER) REVERT: C 738 LYS cc_start: 0.8843 (mttt) cc_final: 0.8359 (mtmm) REVERT: D 145 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6810 (mt) REVERT: D 289 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7814 (mm) REVERT: D 320 MET cc_start: 0.8948 (mmt) cc_final: 0.8643 (mmt) REVERT: D 355 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7266 (pm20) REVERT: D 418 GLU cc_start: 0.8523 (tt0) cc_final: 0.8146 (mp0) REVERT: D 488 MET cc_start: 0.7199 (mtp) cc_final: 0.6238 (mpm) REVERT: D 546 GLU cc_start: 0.7459 (mp0) cc_final: 0.7102 (mp0) REVERT: D 548 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7995 (tp) REVERT: D 702 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8215 (mm-30) REVERT: D 717 MET cc_start: 0.8436 (mpp) cc_final: 0.7768 (OUTLIER) REVERT: D 719 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7346 (pm20) outliers start: 105 outliers final: 51 residues processed: 397 average time/residue: 1.3887 time to fit residues: 632.1570 Evaluate side-chains 373 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 314 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 255 GLN Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 719 GLU Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 76 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 210 optimal weight: 2.9990 chunk 245 optimal weight: 2.9990 chunk 251 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 144 optimal weight: 20.0000 chunk 54 optimal weight: 0.7980 chunk 206 optimal weight: 1.9990 chunk 229 optimal weight: 9.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 645 GLN A 750 ASN B 750 ASN C 160 HIS C 750 ASN D 160 HIS D 750 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.181852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.132366 restraints weight = 22440.541| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.00 r_work: 0.3234 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22436 Z= 0.113 Angle : 0.522 7.850 30084 Z= 0.263 Chirality : 0.038 0.239 3272 Planarity : 0.003 0.044 3668 Dihedral : 16.893 111.516 3724 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.20 % Allowed : 13.74 % Favored : 82.07 % 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: -0.34 (0.17), residues: 2520 helix: 0.66 (0.13), residues: 1576 sheet: 0.96 (0.62), residues: 84 loop : -2.00 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 521 HIS 0.003 0.001 HIS D 523 PHE 0.012 0.001 PHE D 748 TYR 0.014 0.001 TYR C 451 ARG 0.003 0.000 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.04264 ( 919) hydrogen bonds : angle 3.62415 ( 2709) SS BOND : bond 0.00211 ( 8) SS BOND : angle 0.59628 ( 16) covalent geometry : bond 0.00257 (22428) covalent geometry : angle 0.52178 (30068) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 350 time to evaluate : 2.487 Fit side-chains REVERT: A 121 LYS cc_start: 0.7917 (mptt) cc_final: 0.7410 (tttm) REVERT: A 289 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7850 (mm) REVERT: A 488 MET cc_start: 0.7127 (mtp) cc_final: 0.6178 (mpm) REVERT: A 655 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8373 (tp) REVERT: A 702 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7853 (mt-10) REVERT: A 717 MET cc_start: 0.8312 (mpp) cc_final: 0.7725 (mmm) REVERT: A 719 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7304 (pm20) REVERT: B 129 GLU cc_start: 0.6736 (mp0) cc_final: 0.6448 (mp0) REVERT: B 254 TYR cc_start: 0.7916 (m-80) cc_final: 0.7660 (m-80) REVERT: B 289 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7830 (mm) REVERT: B 309 ASP cc_start: 0.6865 (m-30) cc_final: 0.6539 (m-30) REVERT: B 320 MET cc_start: 0.8932 (mmt) cc_final: 0.8660 (mmt) REVERT: B 412 ASN cc_start: 0.8226 (m-40) cc_final: 0.7963 (m-40) REVERT: B 418 GLU cc_start: 0.8438 (tt0) cc_final: 0.8122 (mp0) REVERT: B 488 MET cc_start: 0.7111 (mtp) cc_final: 0.6198 (mpm) REVERT: B 717 MET cc_start: 0.8342 (mpp) cc_final: 0.7706 (mmm) REVERT: C 289 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7835 (mm) REVERT: C 320 MET cc_start: 0.8937 (mmt) cc_final: 0.8667 (mmt) REVERT: C 418 GLU cc_start: 0.8444 (tt0) cc_final: 0.8123 (mp0) REVERT: C 488 MET cc_start: 0.7173 (mtp) cc_final: 0.6273 (mpm) REVERT: C 519 ASP cc_start: 0.6427 (m-30) cc_final: 0.6186 (m-30) REVERT: C 717 MET cc_start: 0.8324 (mpp) cc_final: 0.7733 (mmm) REVERT: C 738 LYS cc_start: 0.8807 (mttt) cc_final: 0.8371 (mtmp) REVERT: D 289 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7835 (mm) REVERT: D 320 MET cc_start: 0.8945 (mmt) cc_final: 0.8664 (mmt) REVERT: D 355 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7159 (pm20) REVERT: D 418 GLU cc_start: 0.8497 (tt0) cc_final: 0.8124 (mp0) REVERT: D 488 MET cc_start: 0.7119 (mtp) cc_final: 0.6219 (mpm) REVERT: D 702 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7857 (mt-10) REVERT: D 717 MET cc_start: 0.8253 (mpp) cc_final: 0.7738 (mmm) REVERT: D 719 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7314 (pm20) outliers start: 95 outliers final: 37 residues processed: 402 average time/residue: 1.3337 time to fit residues: 610.4906 Evaluate side-chains 377 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 333 time to evaluate : 2.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 369 ARG Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 369 ARG Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 369 ARG Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 369 ARG Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 719 GLU Chi-restraints excluded: chain D residue 750 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 0 optimal weight: 20.0000 chunk 74 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 239 optimal weight: 0.3980 chunk 112 optimal weight: 0.0770 chunk 206 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 149 optimal weight: 0.0980 chunk 10 optimal weight: 8.9990 overall best weight: 1.0940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 750 ASN B 645 GLN C 227 GLN C 645 GLN D 645 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.183510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.133724 restraints weight = 22369.750| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.95 r_work: 0.3264 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22436 Z= 0.098 Angle : 0.517 10.621 30084 Z= 0.253 Chirality : 0.038 0.229 3272 Planarity : 0.003 0.043 3668 Dihedral : 15.978 102.837 3724 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.14 % Allowed : 15.11 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.14 (0.17), residues: 2520 helix: 1.10 (0.13), residues: 1584 sheet: 0.73 (0.62), residues: 88 loop : -1.94 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 692 HIS 0.004 0.001 HIS C 439 PHE 0.010 0.001 PHE C 748 TYR 0.013 0.001 TYR A 451 ARG 0.004 0.000 ARG A 226 Details of bonding type rmsd hydrogen bonds : bond 0.03873 ( 919) hydrogen bonds : angle 3.50934 ( 2709) SS BOND : bond 0.00334 ( 8) SS BOND : angle 0.71563 ( 16) covalent geometry : bond 0.00218 (22428) covalent geometry : angle 0.51735 (30068) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 348 time to evaluate : 2.198 Fit side-chains REVERT: A 121 LYS cc_start: 0.7809 (mptt) cc_final: 0.7296 (tttm) REVERT: A 129 GLU cc_start: 0.6811 (mm-30) cc_final: 0.6401 (pt0) REVERT: A 289 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7855 (mm) REVERT: A 431 MET cc_start: 0.8355 (mmm) cc_final: 0.7777 (mtp) REVERT: A 488 MET cc_start: 0.6991 (mtp) cc_final: 0.6103 (mpm) REVERT: A 546 GLU cc_start: 0.7250 (mp0) cc_final: 0.6978 (mp0) REVERT: A 655 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8295 (tp) REVERT: A 702 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7735 (mt-10) REVERT: A 719 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7170 (pm20) REVERT: B 254 TYR cc_start: 0.7874 (m-80) cc_final: 0.7646 (m-80) REVERT: B 286 GLN cc_start: 0.7939 (mm110) cc_final: 0.7634 (mm110) REVERT: B 289 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7839 (mm) REVERT: B 309 ASP cc_start: 0.6855 (m-30) cc_final: 0.6558 (m-30) REVERT: B 320 MET cc_start: 0.8919 (mmt) cc_final: 0.8626 (mmt) REVERT: B 412 ASN cc_start: 0.8163 (m-40) cc_final: 0.7931 (m-40) REVERT: B 418 GLU cc_start: 0.8399 (tt0) cc_final: 0.7989 (mp0) REVERT: B 423 GLU cc_start: 0.6554 (OUTLIER) cc_final: 0.6252 (pm20) REVERT: B 488 MET cc_start: 0.7012 (mtp) cc_final: 0.6075 (mpm) REVERT: B 546 GLU cc_start: 0.7253 (mp0) cc_final: 0.6958 (mp0) REVERT: B 581 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8410 (mttm) REVERT: B 702 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7724 (mt-10) REVERT: B 717 MET cc_start: 0.8194 (mpp) cc_final: 0.7581 (mmm) REVERT: C 286 GLN cc_start: 0.7952 (mm110) cc_final: 0.7659 (mm110) REVERT: C 289 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7830 (mm) REVERT: C 320 MET cc_start: 0.8921 (mmt) cc_final: 0.8660 (mmt) REVERT: C 418 GLU cc_start: 0.8423 (tt0) cc_final: 0.8009 (mp0) REVERT: C 423 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.6248 (pm20) REVERT: C 488 MET cc_start: 0.7049 (mtp) cc_final: 0.6128 (mpm) REVERT: C 519 ASP cc_start: 0.6313 (m-30) cc_final: 0.6095 (m-30) REVERT: C 702 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7724 (mt-10) REVERT: C 717 MET cc_start: 0.8142 (mpp) cc_final: 0.7628 (mmm) REVERT: C 738 LYS cc_start: 0.8764 (mttt) cc_final: 0.8309 (mtmp) REVERT: D 320 MET cc_start: 0.8930 (mmt) cc_final: 0.8664 (mmt) REVERT: D 355 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7046 (pm20) REVERT: D 418 GLU cc_start: 0.8439 (tt0) cc_final: 0.7994 (mp0) REVERT: D 423 GLU cc_start: 0.6539 (OUTLIER) cc_final: 0.6234 (pm20) REVERT: D 488 MET cc_start: 0.7032 (mtp) cc_final: 0.6096 (mpm) REVERT: D 546 GLU cc_start: 0.7269 (mp0) cc_final: 0.6947 (mp0) REVERT: D 702 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7746 (mt-10) REVERT: D 717 MET cc_start: 0.8130 (mpp) cc_final: 0.7628 (mmm) outliers start: 71 outliers final: 36 residues processed: 391 average time/residue: 1.3460 time to fit residues: 599.0876 Evaluate side-chains 377 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 332 time to evaluate : 2.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 369 ARG Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 369 ARG Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 255 GLN Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 369 ARG Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 620 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 171 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 229 optimal weight: 10.0000 chunk 198 optimal weight: 20.0000 chunk 142 optimal weight: 0.6980 chunk 226 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 122 optimal weight: 0.7980 chunk 99 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 645 GLN B 279 GLN B 645 GLN C 523 HIS C 645 GLN D 523 HIS D 645 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.179666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.130489 restraints weight = 22146.775| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.86 r_work: 0.3203 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 22436 Z= 0.173 Angle : 0.604 10.016 30084 Z= 0.296 Chirality : 0.042 0.241 3272 Planarity : 0.004 0.041 3668 Dihedral : 16.398 107.879 3724 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.93 % Allowed : 14.89 % Favored : 81.18 % 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: 0.12 (0.17), residues: 2520 helix: 1.06 (0.13), residues: 1584 sheet: 0.96 (0.62), residues: 84 loop : -1.94 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 521 HIS 0.005 0.001 HIS C 301 PHE 0.016 0.002 PHE C 569 TYR 0.017 0.002 TYR C 451 ARG 0.004 0.000 ARG A 225 Details of bonding type rmsd hydrogen bonds : bond 0.05107 ( 919) hydrogen bonds : angle 3.67116 ( 2709) SS BOND : bond 0.00281 ( 8) SS BOND : angle 2.10471 ( 16) covalent geometry : bond 0.00414 (22428) covalent geometry : angle 0.60239 (30068) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 329 time to evaluate : 2.245 Fit side-chains REVERT: A 129 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6639 (pt0) REVERT: A 289 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7877 (mm) REVERT: A 431 MET cc_start: 0.8384 (mmm) cc_final: 0.7789 (mtp) REVERT: A 488 MET cc_start: 0.7075 (mtp) cc_final: 0.6169 (mpm) REVERT: A 546 GLU cc_start: 0.7317 (mp0) cc_final: 0.7013 (mp0) REVERT: A 655 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8318 (tp) REVERT: A 682 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8360 (pt0) REVERT: A 702 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7846 (mt-10) REVERT: A 719 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7184 (pm20) REVERT: B 254 TYR cc_start: 0.7993 (m-80) cc_final: 0.7564 (m-80) REVERT: B 289 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7838 (mm) REVERT: B 309 ASP cc_start: 0.6983 (m-30) cc_final: 0.6677 (m-30) REVERT: B 320 MET cc_start: 0.8910 (mmt) cc_final: 0.8588 (mmt) REVERT: B 418 GLU cc_start: 0.8449 (tt0) cc_final: 0.8102 (mp0) REVERT: B 423 GLU cc_start: 0.6566 (OUTLIER) cc_final: 0.6333 (pm20) REVERT: B 488 MET cc_start: 0.7110 (mtp) cc_final: 0.6141 (mpm) REVERT: B 546 GLU cc_start: 0.7292 (mp0) cc_final: 0.7000 (mp0) REVERT: B 717 MET cc_start: 0.8267 (mpp) cc_final: 0.7604 (mmm) REVERT: C 320 MET cc_start: 0.8929 (mmt) cc_final: 0.8635 (mmt) REVERT: C 418 GLU cc_start: 0.8468 (tt0) cc_final: 0.8117 (mp0) REVERT: C 423 GLU cc_start: 0.6574 (OUTLIER) cc_final: 0.6343 (pm20) REVERT: C 431 MET cc_start: 0.8325 (mmm) cc_final: 0.7749 (mtp) REVERT: C 488 MET cc_start: 0.7100 (mtp) cc_final: 0.6182 (mpm) REVERT: C 546 GLU cc_start: 0.7289 (mp0) cc_final: 0.6969 (mp0) REVERT: D 320 MET cc_start: 0.8945 (mmt) cc_final: 0.8653 (mmt) REVERT: D 355 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7189 (pm20) REVERT: D 418 GLU cc_start: 0.8502 (tt0) cc_final: 0.8115 (mp0) REVERT: D 423 GLU cc_start: 0.6548 (OUTLIER) cc_final: 0.6316 (pm20) REVERT: D 431 MET cc_start: 0.8310 (mmm) cc_final: 0.7731 (mtp) REVERT: D 488 MET cc_start: 0.7093 (mtp) cc_final: 0.6152 (mpm) REVERT: D 546 GLU cc_start: 0.7302 (mp0) cc_final: 0.7007 (mp0) REVERT: D 702 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7851 (mt-10) outliers start: 89 outliers final: 46 residues processed: 387 average time/residue: 1.3975 time to fit residues: 616.0032 Evaluate side-chains 369 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 315 time to evaluate : 2.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 369 ARG Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 255 GLN Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 369 ARG Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 46 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 207 optimal weight: 0.0040 chunk 244 optimal weight: 5.9990 chunk 247 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 113 optimal weight: 0.0270 chunk 49 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 overall best weight: 0.8056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN A 410 ASN A 645 GLN A 750 ASN B 279 GLN B 645 GLN C 439 HIS C 645 GLN D 645 GLN D 750 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.184344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.134710 restraints weight = 22377.232| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.07 r_work: 0.3283 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22436 Z= 0.090 Angle : 0.501 9.458 30084 Z= 0.247 Chirality : 0.038 0.207 3272 Planarity : 0.003 0.042 3668 Dihedral : 15.091 95.405 3724 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.03 % Allowed : 17.62 % Favored : 80.34 % 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: 0.57 (0.17), residues: 2520 helix: 1.47 (0.13), residues: 1580 sheet: 0.85 (0.64), residues: 88 loop : -1.83 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 692 HIS 0.004 0.001 HIS C 439 PHE 0.011 0.001 PHE D 748 TYR 0.012 0.001 TYR A 451 ARG 0.004 0.000 ARG C 698 Details of bonding type rmsd hydrogen bonds : bond 0.03567 ( 919) hydrogen bonds : angle 3.40359 ( 2709) SS BOND : bond 0.00094 ( 8) SS BOND : angle 1.15107 ( 16) covalent geometry : bond 0.00199 (22428) covalent geometry : angle 0.50011 (30068) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 344 time to evaluate : 2.360 Fit side-chains REVERT: A 121 LYS cc_start: 0.7860 (mptt) cc_final: 0.7268 (tttm) REVERT: A 129 GLU cc_start: 0.7078 (mm-30) cc_final: 0.6577 (pt0) REVERT: A 431 MET cc_start: 0.8361 (mmm) cc_final: 0.7760 (mtp) REVERT: A 488 MET cc_start: 0.6991 (mtp) cc_final: 0.6093 (mpm) REVERT: A 555 MET cc_start: 0.8181 (tmm) cc_final: 0.7908 (ttm) REVERT: A 702 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7728 (mt-10) REVERT: A 719 GLU cc_start: 0.7487 (pt0) cc_final: 0.7205 (pm20) REVERT: B 320 MET cc_start: 0.8927 (mmt) cc_final: 0.8621 (mmt) REVERT: B 418 GLU cc_start: 0.8377 (tt0) cc_final: 0.7950 (mp0) REVERT: B 431 MET cc_start: 0.8307 (mmm) cc_final: 0.7707 (mtp) REVERT: B 488 MET cc_start: 0.6992 (mtp) cc_final: 0.6047 (mpm) REVERT: B 555 MET cc_start: 0.8187 (tmm) cc_final: 0.7920 (ttm) REVERT: B 581 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8407 (mttm) REVERT: B 702 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7748 (mt-10) REVERT: C 320 MET cc_start: 0.8917 (mmt) cc_final: 0.8632 (mmt) REVERT: C 418 GLU cc_start: 0.8383 (tt0) cc_final: 0.7949 (mp0) REVERT: C 488 MET cc_start: 0.6983 (mtp) cc_final: 0.6078 (mpm) REVERT: C 546 GLU cc_start: 0.7121 (mp0) cc_final: 0.6908 (mp0) REVERT: C 555 MET cc_start: 0.8167 (tmm) cc_final: 0.7919 (ttm) REVERT: C 702 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7766 (mt-10) REVERT: C 717 MET cc_start: 0.8168 (mpp) cc_final: 0.7556 (mmm) REVERT: C 738 LYS cc_start: 0.8739 (mttt) cc_final: 0.8311 (mtmp) REVERT: D 320 MET cc_start: 0.8923 (mmt) cc_final: 0.8639 (mmt) REVERT: D 355 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7041 (pm20) REVERT: D 418 GLU cc_start: 0.8432 (tt0) cc_final: 0.8018 (mp0) REVERT: D 488 MET cc_start: 0.7026 (mtp) cc_final: 0.6079 (mpm) REVERT: D 546 GLU cc_start: 0.7190 (mp0) cc_final: 0.6947 (mp0) REVERT: D 555 MET cc_start: 0.8183 (tmm) cc_final: 0.7935 (ttm) REVERT: D 702 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7726 (mt-10) REVERT: D 717 MET cc_start: 0.8186 (mpp) cc_final: 0.7554 (mmm) outliers start: 46 outliers final: 34 residues processed: 365 average time/residue: 1.3994 time to fit residues: 579.5374 Evaluate side-chains 356 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 321 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 750 ASN Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 369 ARG Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 369 ARG Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 750 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 71 optimal weight: 8.9990 chunk 170 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 89 optimal weight: 0.5980 chunk 201 optimal weight: 8.9990 chunk 228 optimal weight: 20.0000 chunk 44 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.181664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.133285 restraints weight = 22280.224| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.96 r_work: 0.3229 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22436 Z= 0.123 Angle : 0.542 9.273 30084 Z= 0.268 Chirality : 0.039 0.218 3272 Planarity : 0.003 0.041 3668 Dihedral : 15.106 90.204 3724 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.03 % Allowed : 17.14 % Favored : 80.83 % 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 (0.17), residues: 2520 helix: 1.48 (0.13), residues: 1584 sheet: 0.81 (0.64), residues: 88 loop : -1.87 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 559 HIS 0.003 0.001 HIS D 301 PHE 0.011 0.001 PHE C 569 TYR 0.015 0.001 TYR C 451 ARG 0.003 0.000 ARG A 225 Details of bonding type rmsd hydrogen bonds : bond 0.04331 ( 919) hydrogen bonds : angle 3.48387 ( 2709) SS BOND : bond 0.00100 ( 8) SS BOND : angle 1.38204 ( 16) covalent geometry : bond 0.00286 (22428) covalent geometry : angle 0.54081 (30068) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 326 time to evaluate : 2.359 Fit side-chains REVERT: A 121 LYS cc_start: 0.7902 (mptt) cc_final: 0.7261 (tttm) REVERT: A 129 GLU cc_start: 0.7094 (mm-30) cc_final: 0.6572 (pt0) REVERT: A 431 MET cc_start: 0.8400 (mmm) cc_final: 0.7824 (mtp) REVERT: A 488 MET cc_start: 0.7021 (mtp) cc_final: 0.6115 (mpm) REVERT: A 702 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7841 (mt-10) REVERT: A 719 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7271 (pm20) REVERT: A 750 ASN cc_start: 0.7307 (t0) cc_final: 0.6707 (t0) REVERT: B 254 TYR cc_start: 0.8044 (m-80) cc_final: 0.7571 (m-80) REVERT: B 320 MET cc_start: 0.8941 (mmt) cc_final: 0.8649 (mmt) REVERT: B 418 GLU cc_start: 0.8419 (tt0) cc_final: 0.8024 (mp0) REVERT: B 488 MET cc_start: 0.7049 (mtp) cc_final: 0.6230 (mmp) REVERT: B 717 MET cc_start: 0.8246 (mpp) cc_final: 0.7628 (mmm) REVERT: C 320 MET cc_start: 0.8937 (mmt) cc_final: 0.8651 (mmt) REVERT: C 418 GLU cc_start: 0.8436 (tt0) cc_final: 0.8031 (mp0) REVERT: C 431 MET cc_start: 0.8251 (mmm) cc_final: 0.7697 (mtp) REVERT: C 488 MET cc_start: 0.7052 (mtp) cc_final: 0.6125 (mpm) REVERT: C 546 GLU cc_start: 0.7156 (mp0) cc_final: 0.6936 (mp0) REVERT: C 738 LYS cc_start: 0.8781 (mttt) cc_final: 0.8353 (mtmp) REVERT: D 320 MET cc_start: 0.8956 (mmt) cc_final: 0.8670 (mmt) REVERT: D 355 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7150 (pm20) REVERT: D 418 GLU cc_start: 0.8502 (tt0) cc_final: 0.8091 (mp0) REVERT: D 431 MET cc_start: 0.8358 (mmm) cc_final: 0.7774 (mtp) REVERT: D 488 MET cc_start: 0.7049 (mtp) cc_final: 0.6126 (mpm) REVERT: D 546 GLU cc_start: 0.7243 (mp0) cc_final: 0.7001 (mp0) REVERT: D 702 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7832 (mt-10) outliers start: 46 outliers final: 39 residues processed: 344 average time/residue: 1.3054 time to fit residues: 511.6461 Evaluate side-chains 359 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 319 time to evaluate : 2.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 369 ARG Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 171 CYS Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 243 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 235 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 209 optimal weight: 5.9990 chunk 232 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 125 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 645 GLN B 279 GLN B 645 GLN B 735 ASN C 645 GLN C 735 ASN D 645 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.178144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.129263 restraints weight = 22147.971| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.85 r_work: 0.3186 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 22436 Z= 0.217 Angle : 0.651 9.575 30084 Z= 0.321 Chirality : 0.045 0.238 3272 Planarity : 0.004 0.040 3668 Dihedral : 16.267 92.523 3724 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.56 % Allowed : 16.52 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.26 (0.17), residues: 2520 helix: 1.17 (0.13), residues: 1592 sheet: 0.96 (0.64), residues: 84 loop : -1.88 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 521 HIS 0.007 0.002 HIS A 301 PHE 0.017 0.002 PHE B 569 TYR 0.017 0.002 TYR C 451 ARG 0.006 0.001 ARG B 225 Details of bonding type rmsd hydrogen bonds : bond 0.05592 ( 919) hydrogen bonds : angle 3.69491 ( 2709) SS BOND : bond 0.00313 ( 8) SS BOND : angle 2.21563 ( 16) covalent geometry : bond 0.00527 (22428) covalent geometry : angle 0.64915 (30068) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 325 time to evaluate : 2.200 Fit side-chains REVERT: A 129 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6719 (pt0) REVERT: A 184 LYS cc_start: 0.7311 (ttpt) cc_final: 0.7016 (tptm) REVERT: A 289 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7905 (mm) REVERT: A 431 MET cc_start: 0.8373 (mmm) cc_final: 0.7830 (mtp) REVERT: A 488 MET cc_start: 0.7080 (mtp) cc_final: 0.6188 (mpm) REVERT: A 555 MET cc_start: 0.8430 (tmm) cc_final: 0.8087 (ttm) REVERT: A 702 GLU cc_start: 0.8424 (mm-30) cc_final: 0.7924 (mt-10) REVERT: A 719 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7229 (pm20) REVERT: B 254 TYR cc_start: 0.8189 (m-80) cc_final: 0.7706 (m-80) REVERT: B 320 MET cc_start: 0.8928 (mmt) cc_final: 0.8569 (mmt) REVERT: B 418 GLU cc_start: 0.8453 (tt0) cc_final: 0.8088 (mp0) REVERT: B 488 MET cc_start: 0.7147 (mtp) cc_final: 0.6297 (mmp) REVERT: B 555 MET cc_start: 0.8431 (tmm) cc_final: 0.8089 (ttm) REVERT: B 717 MET cc_start: 0.8279 (mpp) cc_final: 0.7619 (mmm) REVERT: C 320 MET cc_start: 0.8941 (mmt) cc_final: 0.8615 (mmt) REVERT: C 418 GLU cc_start: 0.8492 (tt0) cc_final: 0.8111 (mp0) REVERT: C 423 GLU cc_start: 0.6393 (OUTLIER) cc_final: 0.6138 (OUTLIER) REVERT: C 431 MET cc_start: 0.8315 (mmm) cc_final: 0.7741 (mtp) REVERT: C 488 MET cc_start: 0.7139 (mtp) cc_final: 0.6211 (mpm) REVERT: C 546 GLU cc_start: 0.7333 (mp0) cc_final: 0.7048 (mp0) REVERT: C 555 MET cc_start: 0.8421 (tmm) cc_final: 0.8079 (ttm) REVERT: D 289 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7894 (mm) REVERT: D 320 MET cc_start: 0.8961 (mmt) cc_final: 0.8630 (mmt) REVERT: D 355 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7279 (pm20) REVERT: D 418 GLU cc_start: 0.8502 (tt0) cc_final: 0.8129 (mp0) REVERT: D 423 GLU cc_start: 0.6387 (OUTLIER) cc_final: 0.6132 (OUTLIER) REVERT: D 488 MET cc_start: 0.7125 (mtp) cc_final: 0.6290 (mmp) REVERT: D 546 GLU cc_start: 0.7312 (mp0) cc_final: 0.7073 (mp0) REVERT: D 555 MET cc_start: 0.8424 (tmm) cc_final: 0.8082 (ttm) REVERT: D 702 GLU cc_start: 0.8400 (mm-30) cc_final: 0.7906 (mt-10) REVERT: D 717 MET cc_start: 0.8323 (mpp) cc_final: 0.7700 (mmm) outliers start: 58 outliers final: 48 residues processed: 357 average time/residue: 1.2847 time to fit residues: 523.7166 Evaluate side-chains 364 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 313 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 369 ARG Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 171 CYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 369 ARG Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 171 CYS Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 27 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 197 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 229 optimal weight: 0.8980 chunk 187 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 135 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 GLN B 750 ASN C 750 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.180558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.133145 restraints weight = 22323.651| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.93 r_work: 0.3216 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22436 Z= 0.131 Angle : 0.560 9.710 30084 Z= 0.278 Chirality : 0.040 0.223 3272 Planarity : 0.003 0.040 3668 Dihedral : 15.510 88.613 3724 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.86 % Allowed : 17.54 % Favored : 80.61 % 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: 0.51 (0.17), residues: 2520 helix: 1.39 (0.13), residues: 1584 sheet: 0.70 (0.63), residues: 88 loop : -1.79 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 692 HIS 0.003 0.001 HIS A 301 PHE 0.012 0.001 PHE C 569 TYR 0.015 0.002 TYR C 451 ARG 0.003 0.000 ARG A 225 Details of bonding type rmsd hydrogen bonds : bond 0.04482 ( 919) hydrogen bonds : angle 3.51743 ( 2709) SS BOND : bond 0.00120 ( 8) SS BOND : angle 1.44348 ( 16) covalent geometry : bond 0.00309 (22428) covalent geometry : angle 0.55884 (30068) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 315 time to evaluate : 2.225 Fit side-chains REVERT: A 129 GLU cc_start: 0.7101 (mm-30) cc_final: 0.6695 (pt0) REVERT: A 184 LYS cc_start: 0.7234 (ttpt) cc_final: 0.6931 (tptm) REVERT: A 431 MET cc_start: 0.8387 (mmm) cc_final: 0.7818 (mtp) REVERT: A 488 MET cc_start: 0.7046 (mtp) cc_final: 0.6163 (mpm) REVERT: A 555 MET cc_start: 0.8314 (tmm) cc_final: 0.7992 (ttm) REVERT: A 702 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7865 (mt-10) REVERT: A 719 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7338 (pm20) REVERT: B 254 TYR cc_start: 0.8206 (m-80) cc_final: 0.7724 (m-80) REVERT: B 320 MET cc_start: 0.8959 (mmt) cc_final: 0.8623 (mmt) REVERT: B 418 GLU cc_start: 0.8468 (tt0) cc_final: 0.8074 (mp0) REVERT: B 488 MET cc_start: 0.7076 (mtp) cc_final: 0.6147 (mpm) REVERT: B 555 MET cc_start: 0.8321 (tmm) cc_final: 0.8006 (ttm) REVERT: B 717 MET cc_start: 0.8247 (mpp) cc_final: 0.7661 (mmm) REVERT: C 320 MET cc_start: 0.8959 (mmt) cc_final: 0.8637 (mmt) REVERT: C 418 GLU cc_start: 0.8485 (tt0) cc_final: 0.8082 (mp0) REVERT: C 431 MET cc_start: 0.8289 (mmm) cc_final: 0.7724 (mtp) REVERT: C 488 MET cc_start: 0.7059 (mtp) cc_final: 0.6157 (mpm) REVERT: C 546 GLU cc_start: 0.7216 (mp0) cc_final: 0.6965 (mp0) REVERT: C 555 MET cc_start: 0.8315 (tmm) cc_final: 0.8012 (ttm) REVERT: C 738 LYS cc_start: 0.8769 (mttt) cc_final: 0.8332 (mtmp) REVERT: D 184 LYS cc_start: 0.7219 (ttpt) cc_final: 0.6902 (tptm) REVERT: D 320 MET cc_start: 0.8975 (mmt) cc_final: 0.8651 (mmt) REVERT: D 355 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7214 (pm20) REVERT: D 418 GLU cc_start: 0.8536 (tt0) cc_final: 0.8113 (mp0) REVERT: D 488 MET cc_start: 0.7051 (mtp) cc_final: 0.6138 (mpm) REVERT: D 546 GLU cc_start: 0.7262 (mp0) cc_final: 0.7027 (mp0) REVERT: D 555 MET cc_start: 0.8335 (tmm) cc_final: 0.8032 (ttm) REVERT: D 702 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7859 (mt-10) REVERT: D 717 MET cc_start: 0.8313 (mpp) cc_final: 0.7671 (mmm) outliers start: 42 outliers final: 38 residues processed: 334 average time/residue: 1.3322 time to fit residues: 505.8833 Evaluate side-chains 348 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 309 time to evaluate : 2.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 369 ARG Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 171 CYS Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 214 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 202 optimal weight: 10.0000 chunk 123 optimal weight: 0.0470 chunk 169 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 153 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 GLN B 750 ASN C 750 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.179520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.132284 restraints weight = 22231.903| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.89 r_work: 0.3195 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22436 Z= 0.156 Angle : 0.586 9.659 30084 Z= 0.290 Chirality : 0.042 0.230 3272 Planarity : 0.003 0.040 3668 Dihedral : 15.564 89.431 3724 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.61 % Allowed : 16.74 % Favored : 80.65 % 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: 0.46 (0.17), residues: 2520 helix: 1.37 (0.13), residues: 1588 sheet: 1.00 (0.64), residues: 84 loop : -1.87 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 692 HIS 0.005 0.001 HIS A 301 PHE 0.014 0.001 PHE A 569 TYR 0.016 0.002 TYR C 451 ARG 0.004 0.000 ARG A 225 Details of bonding type rmsd hydrogen bonds : bond 0.04868 ( 919) hydrogen bonds : angle 3.56445 ( 2709) SS BOND : bond 0.00139 ( 8) SS BOND : angle 1.62963 ( 16) covalent geometry : bond 0.00374 (22428) covalent geometry : angle 0.58453 (30068) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21830.54 seconds wall clock time: 376 minutes 25.77 seconds (22585.77 seconds total)