Starting phenix.real_space_refine on Sun Aug 24 17:56:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v6n_42997/08_2025/8v6n_42997.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v6n_42997/08_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_42997/08_2025/8v6n_42997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v6n_42997/08_2025/8v6n_42997.map" model { file = "/net/cci-nas-00/data/ceres_data/8v6n_42997/08_2025/8v6n_42997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v6n_42997/08_2025/8v6n_42997.cif" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.074 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.12, per 1000 atoms: 0.19 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: 1.50 Conformation dependent library (CDL) restraints added in 852.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.51 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: 3.10 Time building geometry restraints manager: 1.97 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 901 or resid 904 or resid 906)) selection = (chain 'B' and (resid 62 through 901 or resid 904 or resid 906)) selection = (chain 'C' and (resid 62 through 901 or resid 904 or resid 906)) selection = (chain 'D' and (resid 62 through 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: 0.000 Normalize map: mean=0, sd=1: 0.880 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: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.420 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.740 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.003 0.001 ARG D 714 TYR 0.010 0.001 TYR C 451 PHE 0.018 0.002 PHE B 447 TRP 0.008 0.001 TRP A 559 HIS 0.006 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.00781 (22428) covalent geometry : angle 1.21613 (30068) SS BOND : bond 0.00395 ( 8) SS BOND : angle 1.36488 ( 16) hydrogen bonds : bond 0.33698 ( 919) hydrogen bonds : angle 9.74203 ( 2709) *********************** 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 : 0.544 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: 0.5486 time to fit residues: 351.1331 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 : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 247 optimal weight: 4.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.4091 r_free = 0.4091 target = 0.189616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.137956 restraints weight = 22335.287| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.17 r_work: 0.3314 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22436 Z= 0.151 Angle : 0.617 8.479 30084 Z= 0.307 Chirality : 0.040 0.201 3272 Planarity : 0.005 0.050 3668 Dihedral : 18.564 133.677 3724 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.02 % Allowed : 10.20 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.76 (0.14), residues: 2520 helix: -1.58 (0.11), residues: 1532 sheet: 0.22 (0.65), residues: 88 loop : -2.26 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 712 TYR 0.015 0.002 TYR A 451 PHE 0.021 0.002 PHE B 259 TRP 0.016 0.001 TRP C 559 HIS 0.004 0.001 HIS A 523 Details of bonding type rmsd covalent geometry : bond 0.00347 (22428) covalent geometry : angle 0.61643 (30068) SS BOND : bond 0.00248 ( 8) SS BOND : angle 0.94397 ( 16) hydrogen bonds : bond 0.04966 ( 919) hydrogen bonds : angle 4.14800 ( 2709) *********************** 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 455 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 364 time to evaluate : 0.642 Fit side-chains REVERT: A 309 ASP cc_start: 0.6874 (m-30) cc_final: 0.6593 (m-30) REVERT: A 332 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7723 (mt-10) REVERT: A 488 MET cc_start: 0.7111 (mtp) cc_final: 0.6086 (mmp) REVERT: A 717 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7574 (mmm) REVERT: B 145 LEU cc_start: 0.6795 (OUTLIER) cc_final: 0.6553 (mt) REVERT: B 214 GLU cc_start: 0.7836 (tt0) cc_final: 0.7262 (tp30) REVERT: B 229 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.7169 (p0) REVERT: B 254 TYR cc_start: 0.7917 (m-80) cc_final: 0.7624 (m-80) REVERT: B 309 ASP cc_start: 0.6832 (m-30) cc_final: 0.6566 (m-30) REVERT: B 315 ASP cc_start: 0.6614 (p0) cc_final: 0.6411 (p0) REVERT: B 332 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7635 (mt-10) REVERT: B 350 LYS cc_start: 0.8632 (tppt) cc_final: 0.8347 (tttt) REVERT: B 418 GLU cc_start: 0.8466 (tt0) cc_final: 0.8057 (mp0) REVERT: B 423 GLU cc_start: 0.6126 (OUTLIER) cc_final: 0.5921 (pm20) REVERT: B 488 MET cc_start: 0.7101 (mtp) cc_final: 0.6089 (mpm) REVERT: B 655 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8250 (tt) REVERT: B 717 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7545 (mmm) REVERT: C 129 GLU cc_start: 0.7111 (mp0) cc_final: 0.6465 (pm20) REVERT: C 145 LEU cc_start: 0.6951 (OUTLIER) cc_final: 0.6653 (mt) REVERT: C 229 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.7111 (p0) REVERT: C 289 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7600 (mm) REVERT: C 332 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7669 (mt-10) REVERT: C 418 GLU cc_start: 0.8461 (tt0) cc_final: 0.8117 (mp0) REVERT: C 423 GLU cc_start: 0.6125 (OUTLIER) cc_final: 0.5920 (pm20) REVERT: C 488 MET cc_start: 0.7015 (mtp) cc_final: 0.6068 (mpm) REVERT: C 641 ASP cc_start: 0.7887 (t0) cc_final: 0.7670 (t70) REVERT: C 655 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8231 (tt) REVERT: C 717 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7580 (mmm) REVERT: D 129 GLU cc_start: 0.7121 (mp0) cc_final: 0.6558 (pm20) REVERT: D 145 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6582 (mt) REVERT: D 229 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7298 (p0) REVERT: D 332 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7710 (mt-10) REVERT: D 350 LYS cc_start: 0.8629 (tppt) cc_final: 0.8334 (tttt) REVERT: D 355 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7192 (pm20) REVERT: D 418 GLU cc_start: 0.8498 (tt0) cc_final: 0.8068 (mp0) REVERT: D 488 MET cc_start: 0.7004 (mtp) cc_final: 0.6041 (mpm) REVERT: D 641 ASP cc_start: 0.7840 (t0) cc_final: 0.7625 (t70) REVERT: D 655 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8238 (tt) REVERT: D 717 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7571 (mmm) outliers start: 91 outliers final: 18 residues processed: 421 average time/residue: 0.5522 time to fit residues: 264.9763 Evaluate side-chains 342 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 308 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 423 GLU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain A residue 743 LYS 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 423 GLU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain B residue 743 LYS 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 423 GLU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain C residue 743 LYS Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 162 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 491 LEU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 717 MET Chi-restraints excluded: chain D residue 743 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 143 optimal weight: 7.9990 chunk 166 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 162 optimal weight: 20.0000 chunk 140 optimal weight: 8.9990 chunk 220 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN A 735 ASN D 279 GLN D 439 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.180646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.130827 restraints weight = 22296.615| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.02 r_work: 0.3203 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22436 Z= 0.187 Angle : 0.637 8.490 30084 Z= 0.317 Chirality : 0.043 0.240 3272 Planarity : 0.004 0.045 3668 Dihedral : 17.653 116.176 3724 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 4.46 % Allowed : 12.23 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.16), residues: 2520 helix: 0.02 (0.12), residues: 1548 sheet: 0.67 (0.63), residues: 84 loop : -2.14 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 225 TYR 0.015 0.002 TYR B 451 PHE 0.020 0.002 PHE A 259 TRP 0.009 0.002 TRP C 521 HIS 0.005 0.002 HIS A 523 Details of bonding type rmsd covalent geometry : bond 0.00446 (22428) covalent geometry : angle 0.63683 (30068) SS BOND : bond 0.00397 ( 8) SS BOND : angle 1.15546 ( 16) hydrogen bonds : bond 0.05724 ( 919) hydrogen bonds : angle 3.80801 ( 2709) *********************** 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 438 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 337 time to evaluate : 0.675 Fit side-chains REVERT: A 129 GLU cc_start: 0.6644 (mp0) cc_final: 0.6286 (mp0) REVERT: A 289 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7762 (mm) REVERT: A 488 MET cc_start: 0.7244 (mtp) cc_final: 0.6255 (mpm) REVERT: A 717 MET cc_start: 0.8336 (mpp) cc_final: 0.7711 (mmm) REVERT: B 129 GLU cc_start: 0.6488 (mp0) cc_final: 0.6175 (mp0) REVERT: B 145 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6769 (mt) REVERT: B 229 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7478 (p0) REVERT: B 254 TYR cc_start: 0.7953 (m-80) cc_final: 0.7587 (m-80) REVERT: B 289 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7790 (mm) REVERT: B 320 MET cc_start: 0.8907 (mmt) cc_final: 0.8562 (mmt) REVERT: B 418 GLU cc_start: 0.8455 (tt0) cc_final: 0.8075 (mp0) REVERT: B 488 MET cc_start: 0.7227 (mtp) cc_final: 0.6227 (mpm) REVERT: B 501 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.7062 (mp0) REVERT: B 717 MET cc_start: 0.8358 (mpp) cc_final: 0.7692 (OUTLIER) REVERT: C 145 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6734 (mt) REVERT: C 289 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7745 (mm) REVERT: C 412 ASN cc_start: 0.8094 (m-40) cc_final: 0.7859 (m-40) REVERT: C 418 GLU cc_start: 0.8486 (tt0) cc_final: 0.8147 (mp0) REVERT: C 488 MET cc_start: 0.7175 (mtp) cc_final: 0.6246 (mpm) REVERT: C 501 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.7082 (mp0) REVERT: C 717 MET cc_start: 0.8379 (mpp) cc_final: 0.7729 (OUTLIER) REVERT: D 145 LEU cc_start: 0.7039 (OUTLIER) cc_final: 0.6718 (mt) REVERT: D 289 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7734 (mm) REVERT: D 355 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7293 (pm20) REVERT: D 418 GLU cc_start: 0.8554 (tt0) cc_final: 0.8114 (mp0) REVERT: D 488 MET cc_start: 0.7187 (mtp) cc_final: 0.6255 (mpm) REVERT: D 501 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.6898 (mp0) REVERT: D 717 MET cc_start: 0.8354 (mpp) cc_final: 0.7701 (OUTLIER) outliers start: 101 outliers final: 46 residues processed: 407 average time/residue: 0.5607 time to fit residues: 260.0096 Evaluate side-chains 368 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 314 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 458 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 599 LEU 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 171 CYS Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 501 GLU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 574 MET 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 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 458 VAL Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 501 GLU 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 599 LEU Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 746 VAL 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 289 ILE Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 501 GLU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 599 LEU 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 146 optimal weight: 0.0980 chunk 153 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 244 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 188 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 205 optimal weight: 1.9990 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 750 ASN B 735 ASN B 750 ASN C 735 ASN C 750 ASN D 735 ASN D 750 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.178616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.129244 restraints weight = 22220.776| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.01 r_work: 0.3182 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 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 = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 22436 Z= 0.207 Angle : 0.650 10.700 30084 Z= 0.319 Chirality : 0.044 0.262 3272 Planarity : 0.004 0.043 3668 Dihedral : 17.370 116.383 3724 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.55 % Allowed : 13.74 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.16), residues: 2520 helix: 0.41 (0.13), residues: 1580 sheet: 0.80 (0.63), residues: 84 loop : -2.05 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 225 TYR 0.016 0.002 TYR C 451 PHE 0.017 0.002 PHE A 259 TRP 0.010 0.002 TRP A 521 HIS 0.006 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00501 (22428) covalent geometry : angle 0.64967 (30068) SS BOND : bond 0.00468 ( 8) SS BOND : angle 1.03168 ( 16) hydrogen bonds : bond 0.05572 ( 919) hydrogen bonds : angle 3.76544 ( 2709) *********************** 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 431 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 328 time to evaluate : 0.783 Fit side-chains REVERT: A 129 GLU cc_start: 0.6483 (mp0) cc_final: 0.6177 (mp0) REVERT: A 289 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7829 (mm) REVERT: A 371 ARG cc_start: 0.7980 (tpt170) cc_final: 0.7693 (tpt170) REVERT: A 443 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8563 (tp) REVERT: A 488 MET cc_start: 0.7140 (mtp) cc_final: 0.6200 (mpm) REVERT: A 546 GLU cc_start: 0.7330 (mp0) cc_final: 0.7019 (mp0) REVERT: A 717 MET cc_start: 0.8399 (mpp) cc_final: 0.7757 (mmm) REVERT: A 719 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7377 (pm20) REVERT: B 129 GLU cc_start: 0.6568 (mp0) cc_final: 0.6290 (mp0) REVERT: B 145 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6758 (mt) REVERT: B 289 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7847 (mm) REVERT: B 418 GLU cc_start: 0.8453 (tt0) cc_final: 0.8078 (mp0) REVERT: B 431 MET cc_start: 0.8282 (mmm) cc_final: 0.7738 (mtp) REVERT: B 443 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8574 (tp) REVERT: B 488 MET cc_start: 0.7151 (mtp) cc_final: 0.6206 (mpm) REVERT: B 501 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.6803 (mp0) REVERT: B 546 GLU cc_start: 0.7366 (mp0) cc_final: 0.7075 (mp0) REVERT: B 574 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.8086 (ptt) REVERT: C 145 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6854 (mt) REVERT: C 289 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7841 (mm) REVERT: C 418 GLU cc_start: 0.8471 (tt0) cc_final: 0.8119 (mp0) REVERT: C 443 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8565 (tp) REVERT: C 488 MET cc_start: 0.7134 (mtp) cc_final: 0.6236 (mpm) REVERT: C 501 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.6792 (mp0) REVERT: C 546 GLU cc_start: 0.7372 (mp0) cc_final: 0.7044 (mp0) REVERT: C 574 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8120 (ptt) REVERT: C 655 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8379 (tp) REVERT: C 702 GLU cc_start: 0.8415 (mm-30) cc_final: 0.7939 (mt-10) REVERT: C 717 MET cc_start: 0.8377 (mpp) cc_final: 0.7713 (OUTLIER) REVERT: D 289 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7789 (mm) REVERT: D 355 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7263 (pm20) REVERT: D 418 GLU cc_start: 0.8504 (tt0) cc_final: 0.8126 (mp0) REVERT: D 443 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8569 (tp) REVERT: D 488 MET cc_start: 0.7162 (mtp) cc_final: 0.6213 (mpm) REVERT: D 501 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.6706 (mp0) REVERT: D 546 GLU cc_start: 0.7404 (mp0) cc_final: 0.7103 (mp0) REVERT: D 574 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8101 (ptt) REVERT: D 702 GLU cc_start: 0.8436 (mm-30) cc_final: 0.7944 (mt-10) REVERT: D 717 MET cc_start: 0.8393 (mpp) cc_final: 0.7719 (OUTLIER) REVERT: D 719 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7422 (pm20) outliers start: 103 outliers final: 48 residues processed: 401 average time/residue: 0.5648 time to fit residues: 257.2571 Evaluate side-chains 370 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 305 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 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 596 VAL Chi-restraints excluded: chain A residue 599 LEU 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 171 CYS 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 443 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 501 GLU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 574 MET 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 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 257 GLU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 501 GLU 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 599 LEU 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 229 ASP 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 289 ILE 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 501 GLU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 599 LEU Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 719 GLU Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 25 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 245 optimal weight: 1.9990 chunk 165 optimal weight: 20.0000 chunk 160 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 195 optimal weight: 20.0000 chunk 148 optimal weight: 9.9990 chunk 149 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 410 ASN A 750 ASN B 750 ASN C 750 ASN D 750 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.180393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.129406 restraints weight = 22103.708| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.15 r_work: 0.3210 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 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 = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.4680 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= 0.148 Angle : 0.574 10.238 30084 Z= 0.282 Chirality : 0.041 0.248 3272 Planarity : 0.004 0.044 3668 Dihedral : 16.687 108.525 3724 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.64 % Allowed : 13.96 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.17), residues: 2520 helix: 0.83 (0.13), residues: 1580 sheet: 1.05 (0.62), residues: 84 loop : -1.97 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 225 TYR 0.015 0.002 TYR C 451 PHE 0.012 0.001 PHE B 569 TRP 0.009 0.001 TRP C 521 HIS 0.004 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00352 (22428) covalent geometry : angle 0.57426 (30068) SS BOND : bond 0.00341 ( 8) SS BOND : angle 0.65244 ( 16) hydrogen bonds : bond 0.04788 ( 919) hydrogen bonds : angle 3.62440 ( 2709) *********************** 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 434 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 329 time to evaluate : 0.548 Fit side-chains REVERT: A 129 GLU cc_start: 0.6651 (OUTLIER) cc_final: 0.6343 (mp0) REVERT: A 289 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7864 (mm) REVERT: A 431 MET cc_start: 0.8368 (mmm) cc_final: 0.7769 (mtp) REVERT: A 443 LEU cc_start: 0.8853 (mt) cc_final: 0.8549 (tp) REVERT: A 488 MET cc_start: 0.7054 (mtp) cc_final: 0.6094 (mpm) REVERT: A 546 GLU cc_start: 0.7294 (mp0) cc_final: 0.6971 (mp0) REVERT: B 129 GLU cc_start: 0.6620 (mp0) cc_final: 0.6278 (mp0) REVERT: B 254 TYR cc_start: 0.7921 (m-80) cc_final: 0.7583 (m-80) REVERT: B 289 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7823 (mm) REVERT: B 320 MET cc_start: 0.8867 (mmt) cc_final: 0.8475 (mmt) REVERT: B 418 GLU cc_start: 0.8437 (tt0) cc_final: 0.8028 (mp0) REVERT: B 431 MET cc_start: 0.8294 (mmm) cc_final: 0.8042 (mtp) REVERT: B 434 LYS cc_start: 0.8377 (tptt) cc_final: 0.7676 (ttpt) REVERT: B 443 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8561 (tp) REVERT: B 488 MET cc_start: 0.7033 (mtp) cc_final: 0.6123 (mpm) REVERT: B 501 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.6845 (mp0) REVERT: B 546 GLU cc_start: 0.7315 (mp0) cc_final: 0.7010 (mp0) REVERT: C 289 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7827 (mm) REVERT: C 418 GLU cc_start: 0.8478 (tt0) cc_final: 0.8065 (mp0) REVERT: C 443 LEU cc_start: 0.8856 (mt) cc_final: 0.8544 (tp) REVERT: C 488 MET cc_start: 0.7090 (mtp) cc_final: 0.6173 (mpm) REVERT: C 501 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.6834 (mp0) REVERT: C 546 GLU cc_start: 0.7279 (mp0) cc_final: 0.6947 (mp0) REVERT: C 702 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7825 (mt-10) REVERT: C 717 MET cc_start: 0.8278 (mpp) cc_final: 0.7663 (mmm) REVERT: C 738 LYS cc_start: 0.8776 (mttt) cc_final: 0.8321 (mtmp) REVERT: D 289 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7816 (mm) REVERT: D 355 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7177 (pm20) REVERT: D 418 GLU cc_start: 0.8492 (tt0) cc_final: 0.8070 (mp0) REVERT: D 443 LEU cc_start: 0.8834 (mt) cc_final: 0.8548 (tp) REVERT: D 488 MET cc_start: 0.7032 (mtp) cc_final: 0.6105 (mpm) REVERT: D 501 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.6672 (mp0) REVERT: D 546 GLU cc_start: 0.7318 (mp0) cc_final: 0.6984 (mp0) REVERT: D 702 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7834 (mt-10) REVERT: D 717 MET cc_start: 0.8311 (mpp) cc_final: 0.7696 (mmm) outliers start: 105 outliers final: 55 residues processed: 403 average time/residue: 0.5767 time to fit residues: 263.2388 Evaluate side-chains 397 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 333 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLU 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 369 ARG 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 599 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 750 ASN Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 289 ILE 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 501 GLU Chi-restraints excluded: chain B residue 552 VAL 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 730 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 233 LEU 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 289 ILE Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 501 GLU 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 599 LEU Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 746 VAL 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 255 GLN 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 458 VAL Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 501 GLU 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 599 LEU Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 6 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 59 optimal weight: 5.9990 chunk 235 optimal weight: 0.7980 chunk 119 optimal weight: 0.7980 chunk 76 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 168 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 202 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 overall best weight: 3.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.178828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.130919 restraints weight = 22277.907| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.73 r_work: 0.3200 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 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 = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.4829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 22436 Z= 0.193 Angle : 0.633 10.427 30084 Z= 0.309 Chirality : 0.044 0.247 3272 Planarity : 0.004 0.041 3668 Dihedral : 16.826 109.111 3724 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.51 % Allowed : 14.53 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.17), residues: 2520 helix: 0.93 (0.13), residues: 1584 sheet: 0.91 (0.63), residues: 84 loop : -1.97 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 225 TYR 0.016 0.002 TYR C 451 PHE 0.016 0.002 PHE A 569 TRP 0.010 0.002 TRP C 521 HIS 0.005 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00465 (22428) covalent geometry : angle 0.63181 (30068) SS BOND : bond 0.00235 ( 8) SS BOND : angle 1.73979 ( 16) hydrogen bonds : bond 0.05392 ( 919) hydrogen bonds : angle 3.69500 ( 2709) *********************** 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 434 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 332 time to evaluate : 0.687 Fit side-chains REVERT: A 129 GLU cc_start: 0.6618 (OUTLIER) cc_final: 0.6413 (mp0) REVERT: A 184 LYS cc_start: 0.7167 (ttmt) cc_final: 0.6955 (tppt) REVERT: A 289 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7867 (mm) REVERT: A 443 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8601 (tp) REVERT: A 488 MET cc_start: 0.7096 (mtp) cc_final: 0.6161 (mpm) REVERT: A 546 GLU cc_start: 0.7318 (mp0) cc_final: 0.7046 (mp0) REVERT: A 682 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8366 (pt0) REVERT: A 717 MET cc_start: 0.8231 (mpp) cc_final: 0.7674 (mmm) REVERT: A 750 ASN cc_start: 0.7333 (t0) cc_final: 0.6461 (t0) REVERT: B 129 GLU cc_start: 0.6592 (mp0) cc_final: 0.6260 (mp0) REVERT: B 254 TYR cc_start: 0.7976 (m-80) cc_final: 0.7530 (m-80) REVERT: B 276 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6223 (mp0) REVERT: B 289 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7867 (mm) REVERT: B 320 MET cc_start: 0.8936 (mmt) cc_final: 0.8582 (mmt) REVERT: B 361 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.7525 (mp) REVERT: B 418 GLU cc_start: 0.8430 (tt0) cc_final: 0.8056 (mp0) REVERT: B 423 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.6394 (pm20) REVERT: B 431 MET cc_start: 0.8276 (mmm) cc_final: 0.7670 (mtp) REVERT: B 443 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8595 (tp) REVERT: B 488 MET cc_start: 0.7089 (mtp) cc_final: 0.6154 (mpm) REVERT: B 501 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.6819 (mp0) REVERT: B 546 GLU cc_start: 0.7316 (mp0) cc_final: 0.7042 (mp0) REVERT: B 682 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8367 (pt0) REVERT: C 129 GLU cc_start: 0.7322 (mm-30) cc_final: 0.7109 (mm-30) REVERT: C 289 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7852 (mm) REVERT: C 361 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.7528 (mp) REVERT: C 418 GLU cc_start: 0.8478 (tt0) cc_final: 0.8095 (mp0) REVERT: C 423 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.6339 (pm20) REVERT: C 443 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8595 (tp) REVERT: C 488 MET cc_start: 0.7144 (mtp) cc_final: 0.6238 (mpm) REVERT: C 501 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.6800 (mp0) REVERT: C 546 GLU cc_start: 0.7289 (mp0) cc_final: 0.6988 (mp0) REVERT: C 702 GLU cc_start: 0.8374 (mm-30) cc_final: 0.7897 (mt-10) REVERT: C 717 MET cc_start: 0.8243 (mpp) cc_final: 0.7637 (mmm) REVERT: D 289 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7828 (mm) REVERT: D 355 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7240 (pm20) REVERT: D 361 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.7530 (mp) REVERT: D 418 GLU cc_start: 0.8485 (tt0) cc_final: 0.8111 (mp0) REVERT: D 443 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8605 (tp) REVERT: D 488 MET cc_start: 0.7086 (mtp) cc_final: 0.6161 (mpm) REVERT: D 501 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.6742 (mp0) REVERT: D 546 GLU cc_start: 0.7322 (mp0) cc_final: 0.7028 (mp0) REVERT: D 702 GLU cc_start: 0.8379 (mm-30) cc_final: 0.7892 (mt-10) REVERT: D 717 MET cc_start: 0.8223 (mpp) cc_final: 0.7631 (mmm) outliers start: 102 outliers final: 48 residues processed: 403 average time/residue: 0.5629 time to fit residues: 258.1501 Evaluate side-chains 389 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 321 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLU 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 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 596 VAL Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 361 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 501 GLU Chi-restraints excluded: chain B residue 552 VAL 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 682 GLU Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 66 LYS 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 289 ILE Chi-restraints excluded: chain C residue 361 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 498 SER Chi-restraints excluded: chain C residue 501 GLU 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 66 LYS 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 255 GLN Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 361 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 501 GLU 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 26 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 157 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 129 optimal weight: 20.0000 chunk 185 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 750 ASN C 439 HIS C 750 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.180416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.132852 restraints weight = 22218.927| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.92 r_work: 0.3209 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 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 = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22436 Z= 0.140 Angle : 0.570 9.872 30084 Z= 0.280 Chirality : 0.041 0.243 3272 Planarity : 0.004 0.043 3668 Dihedral : 16.229 103.961 3724 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.62 % Allowed : 15.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.17), residues: 2520 helix: 1.19 (0.13), residues: 1580 sheet: 1.03 (0.63), residues: 84 loop : -1.89 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 698 TYR 0.015 0.002 TYR C 451 PHE 0.013 0.001 PHE D 748 TRP 0.009 0.001 TRP B 692 HIS 0.004 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00333 (22428) covalent geometry : angle 0.56868 (30068) SS BOND : bond 0.00157 ( 8) SS BOND : angle 1.81293 ( 16) hydrogen bonds : bond 0.04629 ( 919) hydrogen bonds : angle 3.56789 ( 2709) *********************** 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 418 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 336 time to evaluate : 0.878 Fit side-chains REVERT: A 184 LYS cc_start: 0.7138 (ttmt) cc_final: 0.6914 (tppt) REVERT: A 289 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7886 (mm) REVERT: A 431 MET cc_start: 0.8389 (mmm) cc_final: 0.7816 (mtp) REVERT: A 443 LEU cc_start: 0.8880 (mt) cc_final: 0.8586 (tp) REVERT: A 488 MET cc_start: 0.7065 (mtp) cc_final: 0.6150 (mpm) REVERT: A 546 GLU cc_start: 0.7332 (mp0) cc_final: 0.7040 (mp0) REVERT: A 555 MET cc_start: 0.8372 (tmm) cc_final: 0.8070 (ttm) REVERT: B 129 GLU cc_start: 0.6580 (mp0) cc_final: 0.6318 (mp0) REVERT: B 134 GLU cc_start: 0.6927 (mp0) cc_final: 0.6671 (tt0) REVERT: B 254 TYR cc_start: 0.7961 (m-80) cc_final: 0.7612 (m-80) REVERT: B 289 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7900 (mm) REVERT: B 418 GLU cc_start: 0.8462 (tt0) cc_final: 0.8072 (mp0) REVERT: B 431 MET cc_start: 0.8307 (mmm) cc_final: 0.7721 (mtp) REVERT: B 443 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8596 (tp) REVERT: B 488 MET cc_start: 0.7057 (mtp) cc_final: 0.6144 (mpm) REVERT: B 501 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.6824 (mp0) REVERT: B 546 GLU cc_start: 0.7279 (mp0) cc_final: 0.7001 (mp0) REVERT: B 555 MET cc_start: 0.8383 (tmm) cc_final: 0.8092 (ttm) REVERT: C 289 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7868 (mm) REVERT: C 418 GLU cc_start: 0.8510 (tt0) cc_final: 0.8083 (mp0) REVERT: C 443 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8584 (tp) REVERT: C 488 MET cc_start: 0.7091 (mtp) cc_final: 0.6204 (mpm) REVERT: C 501 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.6816 (mp0) REVERT: C 546 GLU cc_start: 0.7285 (mp0) cc_final: 0.6977 (mp0) REVERT: C 555 MET cc_start: 0.8357 (tmm) cc_final: 0.8051 (ttm) REVERT: C 702 GLU cc_start: 0.8371 (mm-30) cc_final: 0.7879 (mt-10) REVERT: C 717 MET cc_start: 0.8230 (mpp) cc_final: 0.7664 (mmm) REVERT: C 738 LYS cc_start: 0.8782 (mttt) cc_final: 0.8352 (mtmp) REVERT: D 289 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7854 (mm) REVERT: D 355 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7265 (pm20) REVERT: D 418 GLU cc_start: 0.8536 (tt0) cc_final: 0.8060 (mp0) REVERT: D 443 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8589 (tp) REVERT: D 488 MET cc_start: 0.7059 (mtp) cc_final: 0.6138 (mpm) REVERT: D 501 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.6700 (mp0) REVERT: D 546 GLU cc_start: 0.7296 (mp0) cc_final: 0.7000 (mp0) REVERT: D 555 MET cc_start: 0.8374 (tmm) cc_final: 0.8072 (ttm) REVERT: D 702 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7911 (mt-10) REVERT: D 717 MET cc_start: 0.8261 (mpp) cc_final: 0.7669 (mmm) outliers start: 82 outliers final: 52 residues processed: 388 average time/residue: 0.5928 time to fit residues: 261.8378 Evaluate side-chains 381 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 319 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 369 ARG Chi-restraints excluded: chain A residue 423 GLU 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 720 LEU Chi-restraints excluded: chain A residue 746 VAL 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 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 501 GLU Chi-restraints excluded: chain B residue 552 VAL 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 66 LYS Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 233 LEU 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 289 ILE 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 498 SER Chi-restraints excluded: chain C residue 501 GLU 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 C residue 750 ASN Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 229 ASP 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 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 501 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 119 optimal weight: 0.9990 chunk 188 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 222 optimal weight: 9.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN C 750 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.180487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.132789 restraints weight = 22077.491| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.74 r_work: 0.3226 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 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 = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22436 Z= 0.138 Angle : 0.561 9.791 30084 Z= 0.276 Chirality : 0.040 0.230 3272 Planarity : 0.003 0.040 3668 Dihedral : 15.947 99.611 3724 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.92 % Allowed : 16.12 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.17), residues: 2520 helix: 1.31 (0.13), residues: 1584 sheet: 1.10 (0.63), residues: 84 loop : -1.88 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 225 TYR 0.015 0.002 TYR C 451 PHE 0.013 0.001 PHE D 748 TRP 0.009 0.001 TRP B 692 HIS 0.004 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00326 (22428) covalent geometry : angle 0.55967 (30068) SS BOND : bond 0.00118 ( 8) SS BOND : angle 1.62302 ( 16) hydrogen bonds : bond 0.04638 ( 919) hydrogen bonds : angle 3.51429 ( 2709) *********************** 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 395 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 329 time to evaluate : 0.725 Fit side-chains REVERT: A 184 LYS cc_start: 0.7154 (ttmt) cc_final: 0.6934 (tppt) REVERT: A 289 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7904 (mm) REVERT: A 431 MET cc_start: 0.8346 (mmm) cc_final: 0.7764 (mtp) REVERT: A 443 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8559 (tp) REVERT: A 488 MET cc_start: 0.7062 (mtp) cc_final: 0.6144 (mpm) REVERT: A 546 GLU cc_start: 0.7307 (mp0) cc_final: 0.7032 (mp0) REVERT: B 129 GLU cc_start: 0.6625 (mp0) cc_final: 0.6383 (mp0) REVERT: B 289 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7897 (mm) REVERT: B 320 MET cc_start: 0.8911 (mmt) cc_final: 0.8520 (mmt) REVERT: B 418 GLU cc_start: 0.8428 (tt0) cc_final: 0.8050 (mp0) REVERT: B 431 MET cc_start: 0.8261 (mmm) cc_final: 0.7661 (mtp) REVERT: B 443 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8577 (tp) REVERT: B 488 MET cc_start: 0.7074 (mtp) cc_final: 0.6149 (mpm) REVERT: B 501 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.6778 (mp0) REVERT: B 546 GLU cc_start: 0.7302 (mp0) cc_final: 0.7025 (mp0) REVERT: C 289 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7876 (mm) REVERT: C 418 GLU cc_start: 0.8463 (tt0) cc_final: 0.8070 (mp0) REVERT: C 443 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8566 (tp) REVERT: C 488 MET cc_start: 0.7071 (mtp) cc_final: 0.6167 (mpm) REVERT: C 501 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.6758 (mp0) REVERT: C 546 GLU cc_start: 0.7260 (mp0) cc_final: 0.6964 (mp0) REVERT: C 702 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7821 (mt-10) REVERT: C 717 MET cc_start: 0.8191 (mpp) cc_final: 0.7624 (mmm) REVERT: C 738 LYS cc_start: 0.8764 (mttt) cc_final: 0.8333 (mtmp) REVERT: C 750 ASN cc_start: 0.7425 (OUTLIER) cc_final: 0.6722 (t0) REVERT: D 289 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7843 (mm) REVERT: D 355 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7204 (pm20) REVERT: D 418 GLU cc_start: 0.8501 (tt0) cc_final: 0.8044 (mp0) REVERT: D 423 GLU cc_start: 0.6075 (OUTLIER) cc_final: 0.5753 (pm20) REVERT: D 443 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8573 (tp) REVERT: D 488 MET cc_start: 0.7039 (mtp) cc_final: 0.6138 (mpm) REVERT: D 501 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.6646 (mp0) REVERT: D 546 GLU cc_start: 0.7277 (mp0) cc_final: 0.7007 (mp0) REVERT: D 702 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7824 (mt-10) REVERT: D 717 MET cc_start: 0.8221 (mpp) cc_final: 0.7640 (mmm) outliers start: 66 outliers final: 50 residues processed: 369 average time/residue: 0.5740 time to fit residues: 239.9204 Evaluate side-chains 382 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 319 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 369 ARG 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 720 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain B residue 171 CYS 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 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 501 GLU Chi-restraints excluded: chain B residue 552 VAL 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 66 LYS Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 233 LEU 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 289 ILE 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 498 SER Chi-restraints excluded: chain C residue 501 GLU 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 C residue 750 ASN Chi-restraints excluded: chain D residue 66 LYS 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 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 501 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 184 optimal weight: 2.9990 chunk 165 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 50 optimal weight: 0.0570 chunk 123 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 chunk 157 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 overall best weight: 1.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN A 279 GLN A 410 ASN A 750 ASN C 227 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.180993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.133569 restraints weight = 22256.292| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.94 r_work: 0.3221 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 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 = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22436 Z= 0.126 Angle : 0.551 9.508 30084 Z= 0.272 Chirality : 0.040 0.222 3272 Planarity : 0.003 0.042 3668 Dihedral : 15.582 93.953 3724 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.69 % Allowed : 16.34 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.17), residues: 2520 helix: 1.43 (0.13), residues: 1580 sheet: 1.16 (0.64), residues: 84 loop : -1.80 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 225 TYR 0.015 0.001 TYR C 451 PHE 0.015 0.001 PHE C 748 TRP 0.009 0.001 TRP B 692 HIS 0.004 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00294 (22428) covalent geometry : angle 0.55023 (30068) SS BOND : bond 0.00094 ( 8) SS BOND : angle 1.45542 ( 16) hydrogen bonds : bond 0.04391 ( 919) hydrogen bonds : angle 3.48023 ( 2709) *********************** 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 388 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 327 time to evaluate : 0.764 Fit side-chains REVERT: A 129 GLU cc_start: 0.6687 (mp0) cc_final: 0.6061 (mm-30) REVERT: A 184 LYS cc_start: 0.7148 (ttmt) cc_final: 0.6921 (tppt) REVERT: A 289 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7898 (mm) REVERT: A 431 MET cc_start: 0.8384 (mmm) cc_final: 0.7809 (mtp) REVERT: A 443 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8611 (tp) REVERT: A 488 MET cc_start: 0.7066 (mtp) cc_final: 0.6183 (mpm) REVERT: A 546 GLU cc_start: 0.7266 (mp0) cc_final: 0.7007 (mp0) REVERT: A 555 MET cc_start: 0.8301 (tmm) cc_final: 0.7986 (ttm) REVERT: B 254 TYR cc_start: 0.8052 (m-80) cc_final: 0.7596 (m-80) REVERT: B 289 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7931 (mm) REVERT: B 320 MET cc_start: 0.8926 (mmt) cc_final: 0.8540 (mmt) REVERT: B 418 GLU cc_start: 0.8458 (tt0) cc_final: 0.8066 (mp0) REVERT: B 431 MET cc_start: 0.8313 (mmm) cc_final: 0.7718 (mtp) REVERT: B 443 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8585 (tp) REVERT: B 488 MET cc_start: 0.7029 (mtp) cc_final: 0.6126 (mpm) REVERT: B 501 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.6739 (mp0) REVERT: B 546 GLU cc_start: 0.7226 (mp0) cc_final: 0.6994 (mp0) REVERT: B 555 MET cc_start: 0.8307 (tmm) cc_final: 0.7998 (ttm) REVERT: C 418 GLU cc_start: 0.8497 (tt0) cc_final: 0.8090 (mp0) REVERT: C 431 MET cc_start: 0.8352 (mmm) cc_final: 0.7779 (mtp) REVERT: C 443 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8580 (tp) REVERT: C 488 MET cc_start: 0.7089 (mtp) cc_final: 0.6178 (mpm) REVERT: C 501 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.6744 (mp0) REVERT: C 546 GLU cc_start: 0.7271 (mp0) cc_final: 0.6956 (mp0) REVERT: C 555 MET cc_start: 0.8294 (tmm) cc_final: 0.7979 (ttm) REVERT: C 702 GLU cc_start: 0.8353 (mm-30) cc_final: 0.7836 (mt-10) REVERT: C 738 LYS cc_start: 0.8773 (mttt) cc_final: 0.8352 (mtmp) REVERT: C 750 ASN cc_start: 0.7408 (t0) cc_final: 0.6729 (t0) REVERT: D 355 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7216 (pm20) REVERT: D 418 GLU cc_start: 0.8540 (tt0) cc_final: 0.8084 (mp0) REVERT: D 443 LEU cc_start: 0.8850 (mt) cc_final: 0.8586 (tp) REVERT: D 488 MET cc_start: 0.7052 (mtp) cc_final: 0.6139 (mpm) REVERT: D 501 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.6618 (mp0) REVERT: D 546 GLU cc_start: 0.7334 (mp0) cc_final: 0.7046 (mp0) REVERT: D 555 MET cc_start: 0.8304 (tmm) cc_final: 0.7995 (ttm) REVERT: D 702 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7843 (mt-10) REVERT: D 717 MET cc_start: 0.8228 (mpp) cc_final: 0.7648 (mmm) outliers start: 61 outliers final: 44 residues processed: 361 average time/residue: 0.5964 time to fit residues: 243.4874 Evaluate side-chains 369 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 317 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 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 720 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 750 ASN Chi-restraints excluded: chain B residue 171 CYS 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 423 GLU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 501 GLU Chi-restraints excluded: chain B residue 552 VAL 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 66 LYS Chi-restraints excluded: chain C residue 233 LEU 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 423 GLU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 501 GLU 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 66 LYS Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 501 GLU 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 105 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 111 optimal weight: 0.9980 chunk 143 optimal weight: 3.9990 chunk 206 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 131 optimal weight: 10.0000 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN C 750 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.181273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.133755 restraints weight = 22280.545| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.95 r_work: 0.3223 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 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 = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22436 Z= 0.122 Angle : 0.542 9.633 30084 Z= 0.268 Chirality : 0.040 0.255 3272 Planarity : 0.003 0.041 3668 Dihedral : 15.327 88.336 3724 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.43 % Allowed : 16.21 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.17), residues: 2520 helix: 1.50 (0.13), residues: 1580 sheet: 1.16 (0.64), residues: 84 loop : -1.79 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 225 TYR 0.015 0.001 TYR C 451 PHE 0.016 0.001 PHE A 748 TRP 0.009 0.001 TRP C 692 HIS 0.003 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00283 (22428) covalent geometry : angle 0.54147 (30068) SS BOND : bond 0.00080 ( 8) SS BOND : angle 1.36331 ( 16) hydrogen bonds : bond 0.04354 ( 919) hydrogen bonds : angle 3.44833 ( 2709) ********************** 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 376 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 321 time to evaluate : 0.703 Fit side-chains REVERT: A 184 LYS cc_start: 0.7128 (ttmt) cc_final: 0.6741 (tptm) REVERT: A 431 MET cc_start: 0.8406 (mmm) cc_final: 0.7832 (mtp) REVERT: A 443 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8612 (tp) REVERT: A 488 MET cc_start: 0.7041 (mtp) cc_final: 0.6154 (mpm) REVERT: A 546 GLU cc_start: 0.7210 (mp0) cc_final: 0.6976 (mp0) REVERT: A 555 MET cc_start: 0.8300 (tmm) cc_final: 0.8011 (ttm) REVERT: B 254 TYR cc_start: 0.8073 (m-80) cc_final: 0.7608 (m-80) REVERT: B 320 MET cc_start: 0.8931 (mmt) cc_final: 0.8570 (mmt) REVERT: B 418 GLU cc_start: 0.8465 (tt0) cc_final: 0.8068 (mp0) REVERT: B 431 MET cc_start: 0.8325 (mmm) cc_final: 0.7728 (mtp) REVERT: B 443 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8586 (tp) REVERT: B 488 MET cc_start: 0.7019 (mtp) cc_final: 0.6116 (mpm) REVERT: B 501 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.6712 (mp0) REVERT: B 546 GLU cc_start: 0.7181 (mp0) cc_final: 0.6981 (mp0) REVERT: B 555 MET cc_start: 0.8309 (tmm) cc_final: 0.8028 (ttm) REVERT: C 418 GLU cc_start: 0.8480 (tt0) cc_final: 0.8072 (mp0) REVERT: C 443 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8580 (tp) REVERT: C 488 MET cc_start: 0.7061 (mtp) cc_final: 0.6151 (mpm) REVERT: C 501 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.6710 (mp0) REVERT: C 546 GLU cc_start: 0.7205 (mp0) cc_final: 0.6939 (mp0) REVERT: C 555 MET cc_start: 0.8301 (tmm) cc_final: 0.8013 (ttm) REVERT: C 702 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7837 (mt-10) REVERT: C 717 MET cc_start: 0.8252 (mpp) cc_final: 0.7674 (mmm) REVERT: C 738 LYS cc_start: 0.8759 (mttt) cc_final: 0.8342 (mtmp) REVERT: D 355 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7234 (pm20) REVERT: D 418 GLU cc_start: 0.8555 (tt0) cc_final: 0.8085 (mp0) REVERT: D 431 MET cc_start: 0.8354 (mmm) cc_final: 0.7788 (mtp) REVERT: D 443 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8587 (tp) REVERT: D 488 MET cc_start: 0.7050 (mtp) cc_final: 0.6140 (mpm) REVERT: D 546 GLU cc_start: 0.7266 (mp0) cc_final: 0.6998 (mp0) REVERT: D 555 MET cc_start: 0.8310 (tmm) cc_final: 0.8019 (ttm) REVERT: D 702 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7835 (mt-10) outliers start: 55 outliers final: 43 residues processed: 349 average time/residue: 0.6065 time to fit residues: 239.1788 Evaluate side-chains 362 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 313 time to evaluate : 0.836 ------------------------------------------------------------------------------- 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 720 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 241 VAL 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 501 GLU Chi-restraints excluded: chain B residue 552 VAL 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 66 LYS Chi-restraints excluded: chain C residue 233 LEU 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 423 GLU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 501 GLU Chi-restraints excluded: chain C residue 552 VAL 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 66 LYS Chi-restraints excluded: chain D residue 246 LYS 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 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 37 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 189 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 chunk 142 optimal weight: 0.6980 chunk 45 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 92 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.180020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.132199 restraints weight = 22221.112| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.74 r_work: 0.3222 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 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 = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22436 Z= 0.147 Angle : 0.578 9.578 30084 Z= 0.286 Chirality : 0.041 0.244 3272 Planarity : 0.004 0.042 3668 Dihedral : 15.417 89.538 3724 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.61 % Allowed : 16.52 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.17), residues: 2520 helix: 1.40 (0.13), residues: 1588 sheet: 1.07 (0.63), residues: 84 loop : -1.82 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 225 TYR 0.016 0.002 TYR C 451 PHE 0.013 0.001 PHE D 748 TRP 0.009 0.001 TRP C 692 HIS 0.004 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00349 (22428) covalent geometry : angle 0.57665 (30068) SS BOND : bond 0.00113 ( 8) SS BOND : angle 1.54911 ( 16) hydrogen bonds : bond 0.04739 ( 919) hydrogen bonds : angle 3.52626 ( 2709) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9884.96 seconds wall clock time: 167 minutes 59.27 seconds (10079.27 seconds total)