Starting phenix.real_space_refine on Mon Jan 13 13:11:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w2h_43748/01_2025/8w2h_43748_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w2h_43748/01_2025/8w2h_43748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w2h_43748/01_2025/8w2h_43748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w2h_43748/01_2025/8w2h_43748.map" model { file = "/net/cci-nas-00/data/ceres_data/8w2h_43748/01_2025/8w2h_43748_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w2h_43748/01_2025/8w2h_43748_trim.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.246 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 44 5.49 5 Mg 4 5.21 5 S 152 5.16 5 C 14752 2.51 5 N 4180 2.21 5 O 4572 1.98 5 H 23240 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 46944 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 11622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 11622 Classifications: {'peptide': 761} Link IDs: {'PTRANS': 20, 'TRANS': 740} Chain: "B" Number of atoms: 11622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 11622 Classifications: {'peptide': 761} Link IDs: {'PTRANS': 20, 'TRANS': 740} Chain: "C" Number of atoms: 11622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 11622 Classifications: {'peptide': 761} Link IDs: {'PTRANS': 20, 'TRANS': 740} Chain: "D" Number of atoms: 11622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 11622 Classifications: {'peptide': 761} Link IDs: {'PTRANS': 20, 'TRANS': 740} Chain: "A" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 114 Unusual residues: {' MG': 1, 'ATP': 3, 'FBP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 114 Unusual residues: {' MG': 1, 'ATP': 3, 'FBP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 114 Unusual residues: {' MG': 1, 'ATP': 3, 'FBP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 114 Unusual residues: {' MG': 1, 'ATP': 3, 'FBP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 16.27, per 1000 atoms: 0.35 Number of scatterers: 46944 At special positions: 0 Unit cell: (158.55, 131.25, 129.15, 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 152 16.00 P 44 15.00 Mg 4 11.99 O 4572 8.00 N 4180 7.00 C 14752 6.00 H 23240 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 9.05 Conformation dependent library (CDL) restraints added in 2.8 seconds 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5440 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 25 sheets defined 50.1% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.32 Creating SS restraints... Processing helix chain 'A' and resid 29 through 44 Processing helix chain 'A' and resid 54 through 61 Processing helix chain 'A' and resid 69 through 74 removed outlier: 3.792A pdb=" N VAL A 73 " --> pdb=" O TRP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 93 Processing helix chain 'A' and resid 94 through 108 removed outlier: 3.621A pdb=" N ALA A 100 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS A 108 " --> pdb=" O ASN A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 131 Processing helix chain 'A' and resid 131 through 143 Processing helix chain 'A' and resid 177 through 194 removed outlier: 3.597A pdb=" N ILE A 192 " --> pdb=" O VAL A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 224 Processing helix chain 'A' and resid 238 through 254 removed outlier: 3.565A pdb=" N GLY A 254 " --> pdb=" O THR A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 288 Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 306 through 326 Processing helix chain 'A' and resid 348 through 363 Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 369 through 374 removed outlier: 4.132A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 390 removed outlier: 3.649A pdb=" N HIS A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 428 Processing helix chain 'A' and resid 438 through 444 Processing helix chain 'A' and resid 452 through 456 removed outlier: 3.608A pdb=" N VAL A 455 " --> pdb=" O TRP A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 475 removed outlier: 3.934A pdb=" N GLY A 475 " --> pdb=" O LEU A 472 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 472 through 475' Processing helix chain 'A' and resid 476 through 488 Processing helix chain 'A' and resid 497 through 511 Processing helix chain 'A' and resid 512 through 513 No H-bonds generated for 'chain 'A' and resid 512 through 513' Processing helix chain 'A' and resid 514 through 518 Processing helix chain 'A' and resid 540 through 557 Processing helix chain 'A' and resid 577 through 588 Processing helix chain 'A' and resid 600 through 616 Processing helix chain 'A' and resid 635 through 647 Processing helix chain 'A' and resid 659 through 663 removed outlier: 3.680A pdb=" N GLN A 662 " --> pdb=" O GLY A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 693 Processing helix chain 'A' and resid 703 through 705 No H-bonds generated for 'chain 'A' and resid 703 through 705' Processing helix chain 'A' and resid 722 through 726 Processing helix chain 'A' and resid 739 through 742 removed outlier: 3.648A pdb=" N LEU A 742 " --> pdb=" O GLN A 739 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 739 through 742' Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.805A pdb=" N MET A 747 " --> pdb=" O SER A 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 44 Processing helix chain 'B' and resid 54 through 61 Processing helix chain 'B' and resid 69 through 74 removed outlier: 3.741A pdb=" N VAL B 73 " --> pdb=" O TRP B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 93 Processing helix chain 'B' and resid 94 through 108 removed outlier: 3.624A pdb=" N ALA B 100 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HIS B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 131 Processing helix chain 'B' and resid 131 through 143 Processing helix chain 'B' and resid 177 through 194 removed outlier: 3.566A pdb=" N ILE B 192 " --> pdb=" O VAL B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 224 Processing helix chain 'B' and resid 238 through 254 removed outlier: 3.567A pdb=" N GLY B 254 " --> pdb=" O THR B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 288 Processing helix chain 'B' and resid 297 through 302 Processing helix chain 'B' and resid 306 through 326 Processing helix chain 'B' and resid 348 through 363 Processing helix chain 'B' and resid 366 through 368 No H-bonds generated for 'chain 'B' and resid 366 through 368' Processing helix chain 'B' and resid 369 through 374 removed outlier: 4.132A pdb=" N LEU B 373 " --> pdb=" O GLU B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 390 removed outlier: 3.649A pdb=" N HIS B 390 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 428 Processing helix chain 'B' and resid 438 through 445 Processing helix chain 'B' and resid 452 through 456 removed outlier: 3.588A pdb=" N VAL B 455 " --> pdb=" O TRP B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 488 Processing helix chain 'B' and resid 497 through 510 Processing helix chain 'B' and resid 511 through 513 No H-bonds generated for 'chain 'B' and resid 511 through 513' Processing helix chain 'B' and resid 540 through 559 removed outlier: 4.299A pdb=" N ALA B 559 " --> pdb=" O ILE B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 588 Processing helix chain 'B' and resid 600 through 617 Processing helix chain 'B' and resid 635 through 647 Processing helix chain 'B' and resid 659 through 663 removed outlier: 3.696A pdb=" N GLN B 662 " --> pdb=" O GLY B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 693 Processing helix chain 'B' and resid 703 through 705 No H-bonds generated for 'chain 'B' and resid 703 through 705' Processing helix chain 'B' and resid 722 through 726 Processing helix chain 'B' and resid 739 through 742 removed outlier: 3.627A pdb=" N LEU B 742 " --> pdb=" O GLN B 739 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 739 through 742' Processing helix chain 'B' and resid 743 through 751 removed outlier: 3.835A pdb=" N MET B 747 " --> pdb=" O SER B 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 54 through 61 Processing helix chain 'C' and resid 69 through 74 removed outlier: 3.727A pdb=" N VAL C 73 " --> pdb=" O TRP C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 93 Processing helix chain 'C' and resid 94 through 108 removed outlier: 3.620A pdb=" N ALA C 100 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS C 108 " --> pdb=" O ASN C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 131 Processing helix chain 'C' and resid 131 through 143 Processing helix chain 'C' and resid 177 through 194 removed outlier: 3.604A pdb=" N ILE C 192 " --> pdb=" O VAL C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 224 Processing helix chain 'C' and resid 238 through 254 removed outlier: 3.562A pdb=" N GLY C 254 " --> pdb=" O THR C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 288 Processing helix chain 'C' and resid 297 through 302 Processing helix chain 'C' and resid 306 through 326 Processing helix chain 'C' and resid 348 through 363 Processing helix chain 'C' and resid 366 through 368 No H-bonds generated for 'chain 'C' and resid 366 through 368' Processing helix chain 'C' and resid 369 through 374 removed outlier: 4.130A pdb=" N LEU C 373 " --> pdb=" O GLU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 390 removed outlier: 3.648A pdb=" N HIS C 390 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 428 Processing helix chain 'C' and resid 438 through 445 Processing helix chain 'C' and resid 452 through 456 removed outlier: 3.603A pdb=" N VAL C 455 " --> pdb=" O TRP C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 488 Processing helix chain 'C' and resid 497 through 510 Processing helix chain 'C' and resid 511 through 513 No H-bonds generated for 'chain 'C' and resid 511 through 513' Processing helix chain 'C' and resid 540 through 557 Processing helix chain 'C' and resid 558 through 560 No H-bonds generated for 'chain 'C' and resid 558 through 560' Processing helix chain 'C' and resid 577 through 588 Processing helix chain 'C' and resid 600 through 617 removed outlier: 3.660A pdb=" N THR C 617 " --> pdb=" O GLU C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 647 Processing helix chain 'C' and resid 659 through 663 removed outlier: 3.628A pdb=" N GLN C 662 " --> pdb=" O GLY C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 693 Processing helix chain 'C' and resid 703 through 705 No H-bonds generated for 'chain 'C' and resid 703 through 705' Processing helix chain 'C' and resid 722 through 726 Processing helix chain 'C' and resid 739 through 742 removed outlier: 3.629A pdb=" N LEU C 742 " --> pdb=" O GLN C 739 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 739 through 742' Processing helix chain 'C' and resid 743 through 752 removed outlier: 3.855A pdb=" N MET C 747 " --> pdb=" O SER C 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'D' and resid 54 through 61 Processing helix chain 'D' and resid 69 through 74 removed outlier: 3.719A pdb=" N VAL D 73 " --> pdb=" O TRP D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 93 Processing helix chain 'D' and resid 94 through 108 removed outlier: 3.623A pdb=" N ALA D 100 " --> pdb=" O GLU D 96 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HIS D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 131 Processing helix chain 'D' and resid 131 through 143 Processing helix chain 'D' and resid 177 through 194 removed outlier: 3.538A pdb=" N ILE D 192 " --> pdb=" O VAL D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 224 Processing helix chain 'D' and resid 238 through 254 removed outlier: 3.570A pdb=" N GLY D 254 " --> pdb=" O THR D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 288 Processing helix chain 'D' and resid 297 through 302 Processing helix chain 'D' and resid 306 through 326 Processing helix chain 'D' and resid 348 through 363 Processing helix chain 'D' and resid 366 through 368 No H-bonds generated for 'chain 'D' and resid 366 through 368' Processing helix chain 'D' and resid 369 through 374 removed outlier: 4.131A pdb=" N LEU D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 390 removed outlier: 3.649A pdb=" N HIS D 390 " --> pdb=" O LYS D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 428 Processing helix chain 'D' and resid 438 through 445 Processing helix chain 'D' and resid 452 through 456 removed outlier: 3.589A pdb=" N VAL D 455 " --> pdb=" O TRP D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 488 Processing helix chain 'D' and resid 497 through 510 Processing helix chain 'D' and resid 511 through 513 No H-bonds generated for 'chain 'D' and resid 511 through 513' Processing helix chain 'D' and resid 540 through 557 Processing helix chain 'D' and resid 558 through 560 No H-bonds generated for 'chain 'D' and resid 558 through 560' Processing helix chain 'D' and resid 577 through 588 Processing helix chain 'D' and resid 600 through 617 removed outlier: 3.595A pdb=" N THR D 617 " --> pdb=" O GLU D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 647 Processing helix chain 'D' and resid 659 through 663 removed outlier: 3.641A pdb=" N GLN D 662 " --> pdb=" O GLY D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 693 Processing helix chain 'D' and resid 703 through 705 No H-bonds generated for 'chain 'D' and resid 703 through 705' Processing helix chain 'D' and resid 722 through 726 Processing helix chain 'D' and resid 739 through 742 removed outlier: 3.619A pdb=" N LEU D 742 " --> pdb=" O GLN D 739 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 739 through 742' Processing helix chain 'D' and resid 743 through 752 removed outlier: 3.873A pdb=" N MET D 747 " --> pdb=" O SER D 743 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 67 removed outlier: 4.619A pdb=" N THR A 22 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA A 17 " --> pdb=" O ASN A 112 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N CYS A 114 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLY A 19 " --> pdb=" O CYS A 114 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ILE A 116 " --> pdb=" O GLY A 19 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU A 21 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N VAL A 162 " --> pdb=" O VAL A 336 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N LEU A 338 " --> pdb=" O VAL A 162 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 227 through 229 removed outlier: 6.330A pdb=" N TRP A 227 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ALA A 263 " --> pdb=" O TRP A 227 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N PHE A 229 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR A 202 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N THR A 294 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL A 204 " --> pdb=" O THR A 294 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 447 through 449 removed outlier: 6.311A pdb=" N LEU A 402 " --> pdb=" O TYR A 433 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N VAL A 435 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE A 404 " --> pdb=" O VAL A 435 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 591 through 593 removed outlier: 5.996A pdb=" N ALA A 591 " --> pdb=" O LEU A 625 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ASN A 627 " --> pdb=" O ALA A 591 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N TYR A 593 " --> pdb=" O ASN A 627 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ARG A 565 " --> pdb=" O GLY A 622 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N VAL A 624 " --> pdb=" O ARG A 565 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N PHE A 567 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ARG A 626 " --> pdb=" O PHE A 567 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL A 569 " --> pdb=" O ARG A 626 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 694 through 695 Processing sheet with id=AA6, first strand: chain 'A' and resid 712 through 713 Processing sheet with id=AA7, first strand: chain 'A' and resid 729 through 730 Processing sheet with id=AA8, first strand: chain 'B' and resid 65 through 67 removed outlier: 4.639A pdb=" N THR B 22 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA B 17 " --> pdb=" O ASN B 112 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N CYS B 114 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLY B 19 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE B 116 " --> pdb=" O GLY B 19 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU B 21 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N VAL B 162 " --> pdb=" O VAL B 336 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N LEU B 338 " --> pdb=" O VAL B 162 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 227 through 229 removed outlier: 3.507A pdb=" N TRP B 227 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR B 202 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N THR B 294 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL B 204 " --> pdb=" O THR B 294 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 447 through 449 removed outlier: 6.266A pdb=" N LEU B 402 " --> pdb=" O TYR B 433 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL B 435 " --> pdb=" O LEU B 402 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE B 404 " --> pdb=" O VAL B 435 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 591 through 593 removed outlier: 6.048A pdb=" N ALA B 591 " --> pdb=" O LEU B 625 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ASN B 627 " --> pdb=" O ALA B 591 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N TYR B 593 " --> pdb=" O ASN B 627 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ARG B 565 " --> pdb=" O GLY B 622 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N VAL B 624 " --> pdb=" O ARG B 565 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N PHE B 567 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ARG B 626 " --> pdb=" O PHE B 567 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL B 569 " --> pdb=" O ARG B 626 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 694 through 695 Processing sheet with id=AB4, first strand: chain 'B' and resid 729 through 730 Processing sheet with id=AB5, first strand: chain 'C' and resid 65 through 67 removed outlier: 4.642A pdb=" N THR C 22 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA C 17 " --> pdb=" O ASN C 112 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N CYS C 114 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLY C 19 " --> pdb=" O CYS C 114 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ILE C 116 " --> pdb=" O GLY C 19 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU C 21 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N VAL C 162 " --> pdb=" O VAL C 336 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N LEU C 338 " --> pdb=" O VAL C 162 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 227 through 229 removed outlier: 6.496A pdb=" N TRP C 227 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ALA C 263 " --> pdb=" O TRP C 227 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N PHE C 229 " --> pdb=" O ALA C 263 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR C 202 " --> pdb=" O ARG C 292 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N THR C 294 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL C 204 " --> pdb=" O THR C 294 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 447 through 449 removed outlier: 6.264A pdb=" N LEU C 402 " --> pdb=" O TYR C 433 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL C 435 " --> pdb=" O LEU C 402 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ILE C 404 " --> pdb=" O VAL C 435 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 591 through 593 removed outlier: 5.966A pdb=" N ALA C 591 " --> pdb=" O LEU C 625 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ASN C 627 " --> pdb=" O ALA C 591 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N TYR C 593 " --> pdb=" O ASN C 627 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 694 through 695 Processing sheet with id=AC1, first strand: chain 'C' and resid 729 through 730 Processing sheet with id=AC2, first strand: chain 'D' and resid 65 through 67 removed outlier: 4.639A pdb=" N THR D 22 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA D 17 " --> pdb=" O ASN D 112 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N CYS D 114 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLY D 19 " --> pdb=" O CYS D 114 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ILE D 116 " --> pdb=" O GLY D 19 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU D 21 " --> pdb=" O ILE D 116 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N VAL D 162 " --> pdb=" O VAL D 336 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N LEU D 338 " --> pdb=" O VAL D 162 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 227 through 229 removed outlier: 6.596A pdb=" N THR D 202 " --> pdb=" O ARG D 292 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N THR D 294 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL D 204 " --> pdb=" O THR D 294 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 447 through 449 removed outlier: 6.266A pdb=" N LEU D 402 " --> pdb=" O TYR D 433 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL D 435 " --> pdb=" O LEU D 402 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE D 404 " --> pdb=" O VAL D 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 591 through 593 removed outlier: 5.897A pdb=" N ALA D 591 " --> pdb=" O LEU D 625 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ASN D 627 " --> pdb=" O ALA D 591 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR D 593 " --> pdb=" O ASN D 627 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ARG D 565 " --> pdb=" O GLY D 622 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL D 624 " --> pdb=" O ARG D 565 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N PHE D 567 " --> pdb=" O VAL D 624 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ARG D 626 " --> pdb=" O PHE D 567 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL D 569 " --> pdb=" O ARG D 626 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 694 through 695 Processing sheet with id=AC7, first strand: chain 'D' and resid 729 through 730 1201 hydrogen bonds defined for protein. 3432 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: 16.07 Time building geometry restraints manager: 10.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 23184 1.03 - 1.22: 56 1.22 - 1.42: 9960 1.42 - 1.62: 13864 1.62 - 1.81: 316 Bond restraints: 47380 Sorted by residual: bond pdb=" C6 ATP A 804 " pdb=" N6 ATP A 804 " ideal model delta sigma weight residual 1.337 1.452 -0.115 1.10e-02 8.26e+03 1.09e+02 bond pdb=" C6 ATP C 803 " pdb=" N6 ATP C 803 " ideal model delta sigma weight residual 1.337 1.452 -0.115 1.10e-02 8.26e+03 1.09e+02 bond pdb=" C6 ATP C 804 " pdb=" N6 ATP C 804 " ideal model delta sigma weight residual 1.337 1.452 -0.115 1.10e-02 8.26e+03 1.09e+02 bond pdb=" C6 ATP B 803 " pdb=" N6 ATP B 803 " ideal model delta sigma weight residual 1.337 1.452 -0.115 1.10e-02 8.26e+03 1.09e+02 bond pdb=" C6 ATP B 804 " pdb=" N6 ATP B 804 " ideal model delta sigma weight residual 1.337 1.452 -0.115 1.10e-02 8.26e+03 1.09e+02 ... (remaining 47375 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 84380 3.33 - 6.65: 782 6.65 - 9.98: 124 9.98 - 13.30: 54 13.30 - 16.63: 32 Bond angle restraints: 85372 Sorted by residual: angle pdb=" PB ATP C 803 " pdb=" O3B ATP C 803 " pdb=" PG ATP C 803 " ideal model delta sigma weight residual 139.87 123.24 16.63 1.00e+00 1.00e+00 2.76e+02 angle pdb=" PB ATP B 803 " pdb=" O3B ATP B 803 " pdb=" PG ATP B 803 " ideal model delta sigma weight residual 139.87 123.31 16.56 1.00e+00 1.00e+00 2.74e+02 angle pdb=" PB ATP D 803 " pdb=" O3B ATP D 803 " pdb=" PG ATP D 803 " ideal model delta sigma weight residual 139.87 123.36 16.51 1.00e+00 1.00e+00 2.73e+02 angle pdb=" PB ATP A 803 " pdb=" O3B ATP A 803 " pdb=" PG ATP A 803 " ideal model delta sigma weight residual 139.87 123.36 16.51 1.00e+00 1.00e+00 2.73e+02 angle pdb=" PB ATP D 802 " pdb=" O3B ATP D 802 " pdb=" PG ATP D 802 " ideal model delta sigma weight residual 139.87 123.51 16.36 1.00e+00 1.00e+00 2.68e+02 ... (remaining 85367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 19886 17.65 - 35.29: 1650 35.29 - 52.94: 583 52.94 - 70.58: 250 70.58 - 88.23: 51 Dihedral angle restraints: 22420 sinusoidal: 12540 harmonic: 9880 Sorted by residual: dihedral pdb=" CA GLY C 711 " pdb=" C GLY C 711 " pdb=" N LEU C 712 " pdb=" CA LEU C 712 " ideal model delta harmonic sigma weight residual -180.00 -153.43 -26.57 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA GLY B 711 " pdb=" C GLY B 711 " pdb=" N LEU B 712 " pdb=" CA LEU B 712 " ideal model delta harmonic sigma weight residual -180.00 -153.48 -26.52 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA GLY D 711 " pdb=" C GLY D 711 " pdb=" N LEU D 712 " pdb=" CA LEU D 712 " ideal model delta harmonic sigma weight residual -180.00 -153.52 -26.48 0 5.00e+00 4.00e-02 2.81e+01 ... (remaining 22417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2633 0.044 - 0.089: 735 0.089 - 0.133: 210 0.133 - 0.177: 66 0.177 - 0.222: 16 Chirality restraints: 3660 Sorted by residual: chirality pdb=" CB VAL B 587 " pdb=" CA VAL B 587 " pdb=" CG1 VAL B 587 " pdb=" CG2 VAL B 587 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" C2' ATP D 803 " pdb=" C1' ATP D 803 " pdb=" C3' ATP D 803 " pdb=" O2' ATP D 803 " both_signs ideal model delta sigma weight residual False -2.68 -2.47 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" C2' ATP A 803 " pdb=" C1' ATP A 803 " pdb=" C3' ATP A 803 " pdb=" O2' ATP A 803 " both_signs ideal model delta sigma weight residual False -2.68 -2.47 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 3657 not shown) Planarity restraints: 7108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 328 " 0.052 5.00e-02 4.00e+02 7.91e-02 1.00e+01 pdb=" N PRO D 329 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO D 329 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 329 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 328 " -0.052 5.00e-02 4.00e+02 7.91e-02 1.00e+01 pdb=" N PRO C 329 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO C 329 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 329 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 328 " 0.052 5.00e-02 4.00e+02 7.90e-02 9.99e+00 pdb=" N PRO B 329 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 329 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 329 " 0.043 5.00e-02 4.00e+02 ... (remaining 7105 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 7409 2.28 - 2.86: 108737 2.86 - 3.44: 131368 3.44 - 4.02: 183180 4.02 - 4.60: 277822 Nonbonded interactions: 708516 Sorted by model distance: nonbonded pdb=" HG SER B 464 " pdb=" O LEU B 466 " model vdw 1.700 2.450 nonbonded pdb=" HG SER D 464 " pdb=" O LEU D 466 " model vdw 1.704 2.450 nonbonded pdb=" OD1 ASP B 590 " pdb=" HH TYR B 754 " model vdw 1.710 2.450 nonbonded pdb=" O LEU A 725 " pdb=" HG1 THR A 729 " model vdw 1.710 2.450 nonbonded pdb=" HG SER C 464 " pdb=" O LEU C 466 " model vdw 1.711 2.450 ... (remaining 708511 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.590 Extract box with map and model: 1.230 Check model and map are aligned: 0.260 Set scattering table: 0.310 Process input model: 74.400 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.120 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: 0.010 Load rotamer database and sin/cos tables:8.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 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 : 0.009 0.175 24140 Z= 0.629 Angle : 1.217 16.626 32736 Z= 0.839 Chirality : 0.049 0.222 3660 Planarity : 0.006 0.079 4148 Dihedral : 14.683 88.229 9160 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.29 % Favored : 96.64 % Rotamer: Outliers : 0.53 % Allowed : 3.23 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.14), residues: 3036 helix: 0.19 (0.13), residues: 1324 sheet: -0.03 (0.23), residues: 436 loop : -0.08 (0.18), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 685 HIS 0.006 0.001 HIS B 453 PHE 0.020 0.003 PHE A 203 TYR 0.015 0.002 TYR A 674 ARG 0.007 0.001 ARG D 564 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 621 time to evaluate : 2.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.7940 (mttp) cc_final: 0.7712 (mttt) REVERT: A 99 ARG cc_start: 0.8149 (ttm110) cc_final: 0.7817 (ttm-80) REVERT: A 444 LYS cc_start: 0.8178 (mtpp) cc_final: 0.7954 (mttm) REVERT: A 597 ASP cc_start: 0.8125 (t0) cc_final: 0.7835 (t0) REVERT: B 66 LYS cc_start: 0.7942 (mttp) cc_final: 0.7725 (mttt) REVERT: B 99 ARG cc_start: 0.8145 (ttm110) cc_final: 0.7812 (ttm-80) REVERT: B 318 MET cc_start: 0.8513 (ttp) cc_final: 0.8311 (ttm) REVERT: B 362 MET cc_start: 0.7415 (mmm) cc_final: 0.7048 (mmm) REVERT: B 597 ASP cc_start: 0.8245 (t0) cc_final: 0.7888 (t70) REVERT: C 66 LYS cc_start: 0.7949 (mttp) cc_final: 0.7732 (mttt) REVERT: C 597 ASP cc_start: 0.8058 (t0) cc_final: 0.7635 (t0) REVERT: D 362 MET cc_start: 0.7510 (mmm) cc_final: 0.7135 (mmm) REVERT: D 597 ASP cc_start: 0.8229 (t0) cc_final: 0.7889 (t0) outliers start: 13 outliers final: 14 residues processed: 630 average time/residue: 2.4860 time to fit residues: 1795.7053 Evaluate side-chains 464 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 450 time to evaluate : 2.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 621 ARG Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 621 ARG Chi-restraints excluded: chain D residue 678 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 0.9990 chunk 230 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 238 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 144 optimal weight: 0.6980 chunk 177 optimal weight: 0.8980 chunk 276 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 HIS A 483 ASN B 342 GLN B 453 HIS B 483 ASN C 342 GLN C 453 HIS C 483 ASN D 342 GLN D 453 HIS D 483 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.137213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.107170 restraints weight = 72316.664| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.75 r_work: 0.2982 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24140 Z= 0.289 Angle : 0.597 8.394 32736 Z= 0.314 Chirality : 0.042 0.170 3660 Planarity : 0.005 0.053 4148 Dihedral : 11.614 89.990 3867 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.80 % Allowed : 11.97 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.15), residues: 3036 helix: 1.23 (0.14), residues: 1348 sheet: 0.00 (0.22), residues: 464 loop : -0.05 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 685 HIS 0.006 0.001 HIS C 660 PHE 0.015 0.002 PHE C 670 TYR 0.012 0.002 TYR A 385 ARG 0.006 0.001 ARG A 210 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 475 time to evaluate : 2.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8183 (mttp) cc_final: 0.7907 (mttt) REVERT: A 84 ILE cc_start: 0.8544 (mm) cc_final: 0.8337 (mt) REVERT: A 272 LYS cc_start: 0.7572 (mtpp) cc_final: 0.7311 (mtmt) REVERT: A 360 LYS cc_start: 0.7239 (tppt) cc_final: 0.6921 (tppp) REVERT: A 440 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7575 (mt-10) REVERT: A 444 LYS cc_start: 0.8191 (mtpp) cc_final: 0.7672 (mttp) REVERT: A 476 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7410 (mt0) REVERT: A 513 ARG cc_start: 0.7065 (tpt90) cc_final: 0.6604 (ttm-80) REVERT: A 542 ASP cc_start: 0.8721 (t70) cc_final: 0.8361 (t70) REVERT: A 597 ASP cc_start: 0.8624 (t0) cc_final: 0.8251 (t0) REVERT: A 681 LYS cc_start: 0.8149 (mmtt) cc_final: 0.7864 (mtmt) REVERT: A 714 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7790 (mttt) REVERT: B 66 LYS cc_start: 0.8151 (mttp) cc_final: 0.7876 (mttt) REVERT: B 251 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.6978 (ttm110) REVERT: B 344 VAL cc_start: 0.8659 (p) cc_final: 0.8352 (m) REVERT: B 349 MET cc_start: 0.7979 (mmt) cc_final: 0.7750 (tpt) REVERT: B 362 MET cc_start: 0.7332 (mmm) cc_final: 0.6786 (mmm) REVERT: B 444 LYS cc_start: 0.8213 (mtpp) cc_final: 0.7863 (mttm) REVERT: B 448 GLN cc_start: 0.8238 (tt0) cc_final: 0.7953 (tt0) REVERT: B 469 LYS cc_start: 0.8326 (mmtt) cc_final: 0.8074 (mmtt) REVERT: B 515 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7046 (tp30) REVERT: B 542 ASP cc_start: 0.8745 (t70) cc_final: 0.8402 (t70) REVERT: B 597 ASP cc_start: 0.8704 (t0) cc_final: 0.8396 (t0) REVERT: B 693 VAL cc_start: 0.8595 (t) cc_final: 0.8303 (p) REVERT: B 700 PHE cc_start: 0.8399 (t80) cc_final: 0.8067 (t80) REVERT: B 702 ASN cc_start: 0.6838 (p0) cc_final: 0.6562 (t0) REVERT: C 66 LYS cc_start: 0.8254 (mttp) cc_final: 0.7966 (mttt) REVERT: C 344 VAL cc_start: 0.8661 (p) cc_final: 0.8357 (m) REVERT: C 515 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7111 (tp30) REVERT: C 542 ASP cc_start: 0.8723 (t70) cc_final: 0.8360 (t70) REVERT: C 597 ASP cc_start: 0.8528 (t0) cc_final: 0.8079 (t0) REVERT: C 678 LEU cc_start: 0.8378 (pp) cc_final: 0.7873 (mt) REVERT: C 693 VAL cc_start: 0.8588 (t) cc_final: 0.8300 (p) REVERT: C 702 ASN cc_start: 0.6846 (p0) cc_final: 0.6592 (t0) REVERT: D 344 VAL cc_start: 0.8655 (p) cc_final: 0.8358 (m) REVERT: D 362 MET cc_start: 0.7380 (mmm) cc_final: 0.6874 (mmm) REVERT: D 444 LYS cc_start: 0.8215 (mtpp) cc_final: 0.7860 (mttm) REVERT: D 448 GLN cc_start: 0.8248 (tt0) cc_final: 0.7964 (tt0) REVERT: D 515 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.7011 (tp30) REVERT: D 542 ASP cc_start: 0.8766 (t70) cc_final: 0.8401 (t70) REVERT: D 597 ASP cc_start: 0.8671 (t0) cc_final: 0.8319 (t0) REVERT: D 613 GLU cc_start: 0.8027 (tp30) cc_final: 0.7714 (mm-30) REVERT: D 693 VAL cc_start: 0.8592 (t) cc_final: 0.8309 (p) REVERT: D 702 ASN cc_start: 0.6838 (p0) cc_final: 0.6579 (t0) outliers start: 44 outliers final: 24 residues processed: 502 average time/residue: 2.4436 time to fit residues: 1410.8219 Evaluate side-chains 470 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 440 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 714 LYS Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 621 ARG Chi-restraints excluded: chain C residue 714 LYS Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 515 GLU Chi-restraints excluded: chain D residue 621 ARG Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 714 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 75 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 288 optimal weight: 0.4980 chunk 172 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 258 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 chunk 231 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN A 453 HIS A 483 ASN A 702 ASN B 107 GLN B 453 HIS B 483 ASN C 107 GLN C 453 HIS C 483 ASN D 107 GLN D 453 HIS D 483 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.134845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.104535 restraints weight = 72962.148| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.76 r_work: 0.2951 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 24140 Z= 0.315 Angle : 0.579 7.926 32736 Z= 0.303 Chirality : 0.043 0.147 3660 Planarity : 0.004 0.056 4148 Dihedral : 11.379 86.915 3857 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.61 % Allowed : 12.95 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.15), residues: 3036 helix: 1.40 (0.14), residues: 1344 sheet: 0.19 (0.22), residues: 476 loop : 0.07 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 685 HIS 0.010 0.001 HIS B 660 PHE 0.015 0.002 PHE A 498 TYR 0.013 0.002 TYR D 674 ARG 0.007 0.001 ARG B 513 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 493 time to evaluate : 2.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8235 (mttp) cc_final: 0.7957 (mttt) REVERT: A 84 ILE cc_start: 0.8614 (mm) cc_final: 0.8387 (mt) REVERT: A 440 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7676 (mt-10) REVERT: A 444 LYS cc_start: 0.8235 (mtpp) cc_final: 0.7730 (mttm) REVERT: A 513 ARG cc_start: 0.7115 (tpt90) cc_final: 0.6891 (ttp-110) REVERT: A 542 ASP cc_start: 0.8814 (t70) cc_final: 0.8482 (t70) REVERT: A 597 ASP cc_start: 0.8742 (t0) cc_final: 0.8414 (t0) REVERT: A 681 LYS cc_start: 0.8194 (mmtt) cc_final: 0.7968 (mtmt) REVERT: A 714 LYS cc_start: 0.8399 (mtmt) cc_final: 0.7870 (mttt) REVERT: A 715 LYS cc_start: 0.8878 (mttm) cc_final: 0.8656 (mmtp) REVERT: B 66 LYS cc_start: 0.8234 (mttp) cc_final: 0.7954 (mttt) REVERT: B 84 ILE cc_start: 0.8614 (mm) cc_final: 0.8397 (mt) REVERT: B 127 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8323 (mp) REVERT: B 242 PHE cc_start: 0.8503 (t80) cc_final: 0.8298 (t80) REVERT: B 344 VAL cc_start: 0.8705 (p) cc_final: 0.8443 (m) REVERT: B 444 LYS cc_start: 0.8175 (mtpp) cc_final: 0.7788 (mttm) REVERT: B 469 LYS cc_start: 0.8443 (mmtt) cc_final: 0.8216 (mmtt) REVERT: B 515 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7190 (tp30) REVERT: B 542 ASP cc_start: 0.8876 (t70) cc_final: 0.8562 (t70) REVERT: B 564 ARG cc_start: 0.8175 (mtm-85) cc_final: 0.7868 (mtm-85) REVERT: C 66 LYS cc_start: 0.8295 (mttp) cc_final: 0.7998 (mttt) REVERT: C 84 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7992 (mp) REVERT: C 237 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7567 (m-30) REVERT: C 256 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7510 (mtm-85) REVERT: C 344 VAL cc_start: 0.8692 (p) cc_final: 0.8432 (m) REVERT: C 515 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7112 (tp30) REVERT: C 542 ASP cc_start: 0.8823 (t70) cc_final: 0.8494 (t70) REVERT: C 597 ASP cc_start: 0.8713 (t0) cc_final: 0.8364 (t0) REVERT: C 678 LEU cc_start: 0.8377 (pp) cc_final: 0.7951 (mt) REVERT: D 344 VAL cc_start: 0.8697 (p) cc_final: 0.8442 (m) REVERT: D 515 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7095 (tp30) REVERT: D 542 ASP cc_start: 0.8844 (t70) cc_final: 0.8498 (t70) REVERT: D 597 ASP cc_start: 0.8698 (t0) cc_final: 0.8343 (t0) REVERT: D 613 GLU cc_start: 0.8039 (tp30) cc_final: 0.7752 (mm-30) outliers start: 64 outliers final: 29 residues processed: 515 average time/residue: 2.4786 time to fit residues: 1475.4303 Evaluate side-chains 499 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 463 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 714 LYS Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 621 ARG Chi-restraints excluded: chain C residue 714 LYS Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 515 GLU Chi-restraints excluded: chain D residue 621 ARG Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 714 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 265 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 215 optimal weight: 0.5980 chunk 227 optimal weight: 3.9990 chunk 269 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 chunk 262 optimal weight: 0.8980 chunk 137 optimal weight: 0.4980 chunk 169 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 296 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 107 GLN A 453 HIS A 483 ASN A 620 GLN A 702 ASN B 104 ASN B 107 GLN B 453 HIS B 483 ASN B 702 ASN C 104 ASN C 107 GLN C 453 HIS C 483 ASN C 620 GLN C 702 ASN D 104 ASN D 107 GLN D 453 HIS D 483 ASN D 702 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.135553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.106417 restraints weight = 73336.370| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.71 r_work: 0.2966 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24140 Z= 0.240 Angle : 0.536 8.172 32736 Z= 0.281 Chirality : 0.041 0.147 3660 Planarity : 0.004 0.050 4148 Dihedral : 11.053 89.298 3857 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.45 % Allowed : 14.01 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.15), residues: 3036 helix: 1.52 (0.14), residues: 1372 sheet: 0.16 (0.22), residues: 476 loop : 0.05 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 740 HIS 0.006 0.001 HIS D 660 PHE 0.013 0.001 PHE A 203 TYR 0.010 0.001 TYR A 385 ARG 0.005 0.000 ARG B 513 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 482 time to evaluate : 2.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8200 (mttp) cc_final: 0.7909 (mttt) REVERT: A 84 ILE cc_start: 0.8587 (mm) cc_final: 0.8338 (mt) REVERT: A 440 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7571 (mt-10) REVERT: A 444 LYS cc_start: 0.8115 (mtpp) cc_final: 0.7592 (mttm) REVERT: A 469 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.7305 (mptm) REVERT: A 476 GLN cc_start: 0.7693 (mt0) cc_final: 0.7457 (mp10) REVERT: A 597 ASP cc_start: 0.8800 (t0) cc_final: 0.8528 (t0) REVERT: A 681 LYS cc_start: 0.8148 (mmtt) cc_final: 0.7898 (mtmt) REVERT: A 714 LYS cc_start: 0.8345 (mtmt) cc_final: 0.7805 (mttt) REVERT: A 715 LYS cc_start: 0.8867 (mttm) cc_final: 0.8614 (mmtp) REVERT: A 755 ARG cc_start: 0.8142 (mmt180) cc_final: 0.7630 (mmt180) REVERT: B 66 LYS cc_start: 0.8213 (mttp) cc_final: 0.7922 (mttt) REVERT: B 84 ILE cc_start: 0.8574 (mm) cc_final: 0.8347 (mt) REVERT: B 127 ILE cc_start: 0.8501 (mt) cc_final: 0.8293 (mp) REVERT: B 245 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7359 (mp0) REVERT: B 344 VAL cc_start: 0.8666 (p) cc_final: 0.8414 (m) REVERT: B 444 LYS cc_start: 0.8122 (mtpp) cc_final: 0.7710 (mttm) REVERT: B 469 LYS cc_start: 0.8399 (mmtt) cc_final: 0.8183 (mmtt) REVERT: B 513 ARG cc_start: 0.7405 (ttt90) cc_final: 0.7101 (ttp-110) REVERT: B 515 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7186 (tp30) REVERT: C 66 LYS cc_start: 0.8245 (mttp) cc_final: 0.7919 (mttt) REVERT: C 84 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.7980 (mp) REVERT: C 256 ARG cc_start: 0.7706 (mtm180) cc_final: 0.7412 (mtm-85) REVERT: C 344 VAL cc_start: 0.8654 (p) cc_final: 0.8399 (m) REVERT: C 515 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7155 (tp30) REVERT: C 542 ASP cc_start: 0.8829 (t70) cc_final: 0.8473 (t70) REVERT: C 597 ASP cc_start: 0.8678 (t0) cc_final: 0.8365 (t0) REVERT: C 605 LYS cc_start: 0.8584 (ttmm) cc_final: 0.8275 (tttp) REVERT: C 678 LEU cc_start: 0.8315 (pp) cc_final: 0.7962 (mt) REVERT: D 344 VAL cc_start: 0.8636 (p) cc_final: 0.8381 (m) REVERT: D 515 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.7055 (tp30) REVERT: D 564 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7435 (ptt180) REVERT: D 597 ASP cc_start: 0.8694 (t0) cc_final: 0.8089 (t0) REVERT: D 613 GLU cc_start: 0.8023 (tp30) cc_final: 0.7732 (mm-30) outliers start: 60 outliers final: 31 residues processed: 509 average time/residue: 2.5269 time to fit residues: 1474.1320 Evaluate side-chains 506 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 469 time to evaluate : 2.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 469 LYS Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 621 ARG Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 515 GLU Chi-restraints excluded: chain D residue 564 ARG Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 621 ARG Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 655 THR Chi-restraints excluded: chain D residue 678 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 226 optimal weight: 1.9990 chunk 60 optimal weight: 0.1980 chunk 3 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 143 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 238 optimal weight: 1.9990 chunk 274 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 107 GLN A 453 HIS A 483 ASN A 702 ASN B 104 ASN B 107 GLN B 453 HIS B 483 ASN B 702 ASN C 104 ASN C 107 GLN C 157 ASN C 453 HIS C 483 ASN C 702 ASN D 104 ASN D 107 GLN D 453 HIS D 483 ASN D 702 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.135566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.106575 restraints weight = 73381.967| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.70 r_work: 0.2977 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24140 Z= 0.204 Angle : 0.515 8.199 32736 Z= 0.270 Chirality : 0.040 0.144 3660 Planarity : 0.004 0.051 4148 Dihedral : 10.803 85.549 3857 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.21 % Allowed : 15.16 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.15), residues: 3036 helix: 1.71 (0.14), residues: 1372 sheet: 0.08 (0.22), residues: 476 loop : 0.06 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 740 HIS 0.005 0.001 HIS A 660 PHE 0.011 0.001 PHE D 203 TYR 0.009 0.001 TYR A 674 ARG 0.005 0.000 ARG B 564 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 494 time to evaluate : 2.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8279 (mttp) cc_final: 0.8003 (mttt) REVERT: A 84 ILE cc_start: 0.8564 (mm) cc_final: 0.8351 (mt) REVERT: A 93 THR cc_start: 0.8683 (m) cc_final: 0.8446 (p) REVERT: A 245 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6660 (mp0) REVERT: A 440 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7615 (mt-10) REVERT: A 444 LYS cc_start: 0.8150 (mtpp) cc_final: 0.7633 (mttp) REVERT: A 469 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.7358 (mptm) REVERT: A 476 GLN cc_start: 0.7656 (mt0) cc_final: 0.7442 (mp10) REVERT: A 681 LYS cc_start: 0.8199 (mmtt) cc_final: 0.7965 (mtmt) REVERT: A 714 LYS cc_start: 0.8354 (mtmt) cc_final: 0.7859 (mttt) REVERT: A 715 LYS cc_start: 0.8846 (mttm) cc_final: 0.8585 (mmtp) REVERT: B 66 LYS cc_start: 0.8269 (mttp) cc_final: 0.7994 (mttt) REVERT: B 84 ILE cc_start: 0.8575 (mm) cc_final: 0.8370 (mt) REVERT: B 93 THR cc_start: 0.8688 (m) cc_final: 0.8455 (p) REVERT: B 245 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7150 (mp0) REVERT: B 256 ARG cc_start: 0.7729 (mtm-85) cc_final: 0.7372 (mtm-85) REVERT: B 344 VAL cc_start: 0.8687 (p) cc_final: 0.8450 (m) REVERT: B 444 LYS cc_start: 0.8145 (mtpp) cc_final: 0.7729 (mttm) REVERT: B 469 LYS cc_start: 0.8407 (mmtt) cc_final: 0.8191 (mmtt) REVERT: B 513 ARG cc_start: 0.7398 (ttt90) cc_final: 0.7176 (ttp-110) REVERT: B 515 GLU cc_start: 0.7341 (tp30) cc_final: 0.7059 (tp30) REVERT: B 605 LYS cc_start: 0.8613 (ttmm) cc_final: 0.8329 (tttp) REVERT: C 66 LYS cc_start: 0.8304 (mttp) cc_final: 0.7968 (mttt) REVERT: C 256 ARG cc_start: 0.7759 (mtm180) cc_final: 0.7400 (mtm-85) REVERT: C 344 VAL cc_start: 0.8688 (p) cc_final: 0.8451 (m) REVERT: C 542 ASP cc_start: 0.8829 (t70) cc_final: 0.8497 (t70) REVERT: C 597 ASP cc_start: 0.8686 (t0) cc_final: 0.8378 (t0) REVERT: C 678 LEU cc_start: 0.8277 (pp) cc_final: 0.8012 (mt) REVERT: C 692 GLU cc_start: 0.7584 (tt0) cc_final: 0.7175 (tm-30) REVERT: D 245 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6729 (mp0) REVERT: D 344 VAL cc_start: 0.8678 (p) cc_final: 0.8436 (m) REVERT: D 564 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7434 (ptt180) REVERT: D 597 ASP cc_start: 0.8704 (t0) cc_final: 0.8438 (t0) REVERT: D 613 GLU cc_start: 0.8104 (tp30) cc_final: 0.7834 (mm-30) outliers start: 54 outliers final: 31 residues processed: 516 average time/residue: 2.4470 time to fit residues: 1457.0976 Evaluate side-chains 508 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 473 time to evaluate : 2.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 469 LYS Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 621 ARG Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 564 ARG Chi-restraints excluded: chain D residue 621 ARG Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 655 THR Chi-restraints excluded: chain D residue 678 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 59 optimal weight: 1.9990 chunk 278 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 chunk 161 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 282 optimal weight: 1.9990 chunk 267 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 165 optimal weight: 3.9990 chunk 232 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 107 GLN A 453 HIS A 483 ASN A 702 ASN B 104 ASN B 107 GLN B 157 ASN B 483 ASN B 702 ASN C 104 ASN C 107 GLN C 483 ASN C 702 ASN D 104 ASN D 107 GLN D 157 ASN D 483 ASN D 702 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.132650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.103273 restraints weight = 73445.358| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.69 r_work: 0.2940 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 24140 Z= 0.350 Angle : 0.578 7.531 32736 Z= 0.304 Chirality : 0.043 0.139 3660 Planarity : 0.004 0.056 4148 Dihedral : 11.238 85.867 3857 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.15 % Allowed : 14.71 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.15), residues: 3036 helix: 1.55 (0.14), residues: 1380 sheet: 0.11 (0.22), residues: 476 loop : 0.04 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 685 HIS 0.011 0.001 HIS D 660 PHE 0.013 0.002 PHE D 203 TYR 0.012 0.002 TYR A 385 ARG 0.006 0.001 ARG A 210 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 496 time to evaluate : 2.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8299 (mttp) cc_final: 0.8012 (mttt) REVERT: A 84 ILE cc_start: 0.8582 (mm) cc_final: 0.8378 (mt) REVERT: A 93 THR cc_start: 0.8714 (m) cc_final: 0.8491 (p) REVERT: A 245 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6663 (mp0) REVERT: A 440 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7630 (mt-10) REVERT: A 444 LYS cc_start: 0.8260 (mtpp) cc_final: 0.7740 (mttm) REVERT: A 469 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.7466 (mptm) REVERT: A 476 GLN cc_start: 0.7731 (mt0) cc_final: 0.7496 (mp10) REVERT: A 681 LYS cc_start: 0.8228 (mmtt) cc_final: 0.7984 (mtmt) REVERT: A 692 GLU cc_start: 0.7545 (tt0) cc_final: 0.7152 (tm-30) REVERT: A 714 LYS cc_start: 0.8386 (mtmt) cc_final: 0.7887 (mttt) REVERT: A 715 LYS cc_start: 0.8931 (mttm) cc_final: 0.8707 (mmtp) REVERT: B 56 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7767 (tt0) REVERT: B 66 LYS cc_start: 0.8298 (mttp) cc_final: 0.8012 (mttt) REVERT: B 93 THR cc_start: 0.8709 (m) cc_final: 0.8495 (p) REVERT: B 142 GLU cc_start: 0.7334 (tm-30) cc_final: 0.7132 (tm-30) REVERT: B 245 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7373 (mp0) REVERT: B 344 VAL cc_start: 0.8725 (p) cc_final: 0.8489 (m) REVERT: B 444 LYS cc_start: 0.8185 (mtpp) cc_final: 0.7773 (mttm) REVERT: B 469 LYS cc_start: 0.8486 (mmtt) cc_final: 0.8284 (mmtt) REVERT: B 476 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7487 (mt0) REVERT: B 513 ARG cc_start: 0.7447 (ttt90) cc_final: 0.7204 (ttp-110) REVERT: B 515 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6903 (tp30) REVERT: C 66 LYS cc_start: 0.8314 (mttp) cc_final: 0.7982 (mttt) REVERT: C 208 MET cc_start: 0.8179 (mtm) cc_final: 0.7915 (mtm) REVERT: C 245 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6759 (mp0) REVERT: C 344 VAL cc_start: 0.8733 (p) cc_final: 0.8490 (m) REVERT: C 476 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7526 (mt0) REVERT: C 678 LEU cc_start: 0.8371 (pp) cc_final: 0.7965 (mp) REVERT: D 93 THR cc_start: 0.8712 (m) cc_final: 0.8495 (p) REVERT: D 245 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6744 (mp0) REVERT: D 286 ARG cc_start: 0.8186 (mtt180) cc_final: 0.7976 (mmm-85) REVERT: D 344 VAL cc_start: 0.8723 (p) cc_final: 0.8481 (m) REVERT: D 444 LYS cc_start: 0.8185 (mtpp) cc_final: 0.7778 (mttm) REVERT: D 476 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7484 (mt0) REVERT: D 564 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7562 (ptt180) REVERT: D 597 ASP cc_start: 0.8773 (t0) cc_final: 0.8509 (t0) REVERT: D 613 GLU cc_start: 0.8119 (tp30) cc_final: 0.7857 (mm-30) REVERT: D 692 GLU cc_start: 0.7606 (tt0) cc_final: 0.7182 (tm-30) outliers start: 77 outliers final: 45 residues processed: 536 average time/residue: 2.4898 time to fit residues: 1546.2816 Evaluate side-chains 535 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 481 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 469 LYS Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 476 GLN Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 621 ARG Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 476 GLN Chi-restraints excluded: chain D residue 564 ARG Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 621 ARG Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 655 THR Chi-restraints excluded: chain D residue 678 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 121 optimal weight: 1.9990 chunk 299 optimal weight: 0.6980 chunk 197 optimal weight: 0.7980 chunk 199 optimal weight: 0.0980 chunk 215 optimal weight: 1.9990 chunk 268 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 301 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 246 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 107 GLN A 483 ASN B 104 ASN B 107 GLN B 483 ASN B 702 ASN C 104 ASN C 107 GLN C 483 ASN C 702 ASN D 104 ASN D 107 GLN D 199 HIS D 483 ASN D 702 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.135513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.105102 restraints weight = 72070.409| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.75 r_work: 0.2963 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24140 Z= 0.209 Angle : 0.529 8.158 32736 Z= 0.277 Chirality : 0.041 0.154 3660 Planarity : 0.004 0.054 4148 Dihedral : 10.811 86.511 3857 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.21 % Favored : 97.76 % Rotamer: Outliers : 2.57 % Allowed : 16.34 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.15), residues: 3036 helix: 1.70 (0.14), residues: 1380 sheet: 0.06 (0.22), residues: 476 loop : -0.06 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 685 HIS 0.005 0.001 HIS D 660 PHE 0.011 0.001 PHE A 203 TYR 0.009 0.001 TYR A 385 ARG 0.008 0.000 ARG B 210 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 484 time to evaluate : 2.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7738 (tt0) REVERT: A 66 LYS cc_start: 0.8258 (mttp) cc_final: 0.7968 (mttt) REVERT: A 84 ILE cc_start: 0.8543 (mm) cc_final: 0.8340 (mt) REVERT: A 93 THR cc_start: 0.8717 (m) cc_final: 0.8486 (p) REVERT: A 245 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6518 (mp0) REVERT: A 440 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7562 (mt-10) REVERT: A 444 LYS cc_start: 0.8224 (mtpp) cc_final: 0.7687 (mttm) REVERT: A 469 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.7321 (mptm) REVERT: A 476 GLN cc_start: 0.7620 (mt0) cc_final: 0.7408 (mp10) REVERT: A 681 LYS cc_start: 0.8185 (mmtt) cc_final: 0.7922 (mtmt) REVERT: A 698 ARG cc_start: 0.6285 (ptt-90) cc_final: 0.5972 (ptp-170) REVERT: A 714 LYS cc_start: 0.8332 (mtmt) cc_final: 0.7826 (mttt) REVERT: A 715 LYS cc_start: 0.8902 (mttm) cc_final: 0.8669 (mmtp) REVERT: B 56 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7742 (tt0) REVERT: B 66 LYS cc_start: 0.8260 (mttp) cc_final: 0.7967 (mttt) REVERT: B 93 THR cc_start: 0.8711 (m) cc_final: 0.8490 (p) REVERT: B 245 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7146 (mp0) REVERT: B 344 VAL cc_start: 0.8683 (p) cc_final: 0.8433 (m) REVERT: B 444 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7697 (mttm) REVERT: B 469 LYS cc_start: 0.8392 (mmtt) cc_final: 0.8184 (mmtt) REVERT: B 513 ARG cc_start: 0.7406 (ttt90) cc_final: 0.7165 (ttp-110) REVERT: B 605 LYS cc_start: 0.8581 (ttmm) cc_final: 0.8245 (tttp) REVERT: B 692 GLU cc_start: 0.7725 (tt0) cc_final: 0.6980 (tm-30) REVERT: C 66 LYS cc_start: 0.8274 (mttp) cc_final: 0.7931 (mttt) REVERT: C 93 THR cc_start: 0.8709 (m) cc_final: 0.8475 (p) REVERT: C 245 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6624 (mp0) REVERT: C 344 VAL cc_start: 0.8687 (p) cc_final: 0.8431 (m) REVERT: C 678 LEU cc_start: 0.8306 (pp) cc_final: 0.7995 (mt) REVERT: C 692 GLU cc_start: 0.7741 (tt0) cc_final: 0.7005 (tm-30) REVERT: D 56 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7767 (tt0) REVERT: D 93 THR cc_start: 0.8714 (m) cc_final: 0.8488 (p) REVERT: D 245 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6693 (mp0) REVERT: D 344 VAL cc_start: 0.8663 (p) cc_final: 0.8412 (m) REVERT: D 444 LYS cc_start: 0.8110 (mtpp) cc_final: 0.7698 (mttm) REVERT: D 564 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7509 (ptt180) REVERT: D 597 ASP cc_start: 0.8712 (t0) cc_final: 0.8124 (t0) REVERT: D 613 GLU cc_start: 0.8101 (tp30) cc_final: 0.7825 (mm-30) REVERT: D 619 ILE cc_start: 0.6878 (OUTLIER) cc_final: 0.6019 (pp) REVERT: D 692 GLU cc_start: 0.7571 (tt0) cc_final: 0.7130 (tm-30) outliers start: 63 outliers final: 39 residues processed: 520 average time/residue: 2.4340 time to fit residues: 1456.9654 Evaluate side-chains 529 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 484 time to evaluate : 2.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 469 LYS Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 621 ARG Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 564 ARG Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 621 ARG Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 655 THR Chi-restraints excluded: chain D residue 678 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 216 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 158 optimal weight: 0.0980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 107 GLN A 483 ASN B 104 ASN B 107 GLN B 483 ASN B 702 ASN C 104 ASN C 107 GLN C 157 ASN C 483 ASN D 104 ASN D 107 GLN D 199 HIS D 483 ASN D 702 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.134417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.104539 restraints weight = 72997.756| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.75 r_work: 0.2959 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24140 Z= 0.253 Angle : 0.537 7.927 32736 Z= 0.281 Chirality : 0.041 0.139 3660 Planarity : 0.004 0.056 4148 Dihedral : 10.827 85.812 3857 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.98 % Favored : 97.99 % Rotamer: Outliers : 2.57 % Allowed : 16.58 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.15), residues: 3036 helix: 1.73 (0.14), residues: 1380 sheet: 0.04 (0.22), residues: 476 loop : -0.10 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 740 HIS 0.007 0.001 HIS D 660 PHE 0.011 0.001 PHE A 203 TYR 0.010 0.001 TYR A 385 ARG 0.008 0.000 ARG B 210 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 494 time to evaluate : 2.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7750 (tt0) REVERT: A 66 LYS cc_start: 0.8263 (mttp) cc_final: 0.7977 (mttt) REVERT: A 245 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6552 (mp0) REVERT: A 440 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7563 (mt-10) REVERT: A 444 LYS cc_start: 0.8235 (mtpp) cc_final: 0.7700 (mttm) REVERT: A 469 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.7356 (mptm) REVERT: A 476 GLN cc_start: 0.7717 (mt0) cc_final: 0.7474 (mp10) REVERT: A 681 LYS cc_start: 0.8206 (mmtt) cc_final: 0.7931 (mtmt) REVERT: A 692 GLU cc_start: 0.7570 (tt0) cc_final: 0.7138 (tm-30) REVERT: A 698 ARG cc_start: 0.6302 (ptt-90) cc_final: 0.5990 (ptp-170) REVERT: A 714 LYS cc_start: 0.8382 (mtmt) cc_final: 0.7870 (mttt) REVERT: A 715 LYS cc_start: 0.8882 (mttm) cc_final: 0.8637 (mmtp) REVERT: B 56 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7738 (tt0) REVERT: B 66 LYS cc_start: 0.8245 (mttp) cc_final: 0.7945 (mttt) REVERT: B 93 THR cc_start: 0.8732 (m) cc_final: 0.8517 (p) REVERT: B 245 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7160 (mp0) REVERT: B 344 VAL cc_start: 0.8691 (p) cc_final: 0.8448 (m) REVERT: B 444 LYS cc_start: 0.8129 (mtpp) cc_final: 0.7710 (mttm) REVERT: B 469 LYS cc_start: 0.8406 (mmtt) cc_final: 0.8206 (mmtt) REVERT: B 513 ARG cc_start: 0.7410 (ttt90) cc_final: 0.7166 (ttp-110) REVERT: B 692 GLU cc_start: 0.7757 (tt0) cc_final: 0.7004 (tm-30) REVERT: C 56 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7797 (tt0) REVERT: C 66 LYS cc_start: 0.8265 (mttp) cc_final: 0.7922 (mttt) REVERT: C 93 THR cc_start: 0.8718 (m) cc_final: 0.8495 (p) REVERT: C 344 VAL cc_start: 0.8694 (p) cc_final: 0.8443 (m) REVERT: C 444 LYS cc_start: 0.8103 (mtpp) cc_final: 0.7667 (mttp) REVERT: C 476 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7474 (mt0) REVERT: C 597 ASP cc_start: 0.8712 (t0) cc_final: 0.8208 (t0) REVERT: C 678 LEU cc_start: 0.8317 (pp) cc_final: 0.8023 (mt) REVERT: C 692 GLU cc_start: 0.7769 (tt0) cc_final: 0.7023 (tm-30) REVERT: D 56 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7747 (tt0) REVERT: D 245 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6606 (mp0) REVERT: D 344 VAL cc_start: 0.8677 (p) cc_final: 0.8430 (m) REVERT: D 444 LYS cc_start: 0.8124 (mtpp) cc_final: 0.7705 (mttm) REVERT: D 564 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7547 (ptt180) REVERT: D 597 ASP cc_start: 0.8724 (t0) cc_final: 0.8154 (t0) REVERT: D 613 GLU cc_start: 0.8109 (tp30) cc_final: 0.7832 (mm-30) REVERT: D 692 GLU cc_start: 0.7582 (tt0) cc_final: 0.7159 (tm-30) outliers start: 63 outliers final: 42 residues processed: 529 average time/residue: 2.5443 time to fit residues: 1550.7189 Evaluate side-chains 526 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 479 time to evaluate : 2.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 469 LYS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 621 ARG Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain D residue 564 ARG Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 621 ARG Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 655 THR Chi-restraints excluded: chain D residue 678 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 303 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 222 optimal weight: 0.9990 chunk 178 optimal weight: 0.6980 chunk 212 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 239 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 107 GLN A 483 ASN B 104 ASN B 107 GLN B 483 ASN B 702 ASN C 104 ASN C 107 GLN C 483 ASN D 104 ASN D 107 GLN D 199 HIS D 483 ASN D 702 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.134204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.104212 restraints weight = 73220.076| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.76 r_work: 0.2953 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24140 Z= 0.268 Angle : 0.545 7.913 32736 Z= 0.285 Chirality : 0.041 0.138 3660 Planarity : 0.004 0.063 4148 Dihedral : 10.854 85.630 3857 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.17 % Favored : 97.79 % Rotamer: Outliers : 2.53 % Allowed : 16.99 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.15), residues: 3036 helix: 1.62 (0.14), residues: 1404 sheet: 0.02 (0.22), residues: 476 loop : -0.05 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 740 HIS 0.008 0.001 HIS A 660 PHE 0.011 0.001 PHE D 203 TYR 0.010 0.001 TYR A 385 ARG 0.010 0.001 ARG B 210 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 476 time to evaluate : 2.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7749 (tt0) REVERT: A 66 LYS cc_start: 0.8273 (mttp) cc_final: 0.7981 (mttt) REVERT: A 245 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6561 (mp0) REVERT: A 440 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7554 (mt-10) REVERT: A 444 LYS cc_start: 0.8232 (mtpp) cc_final: 0.7689 (mttm) REVERT: A 469 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.7351 (mptm) REVERT: A 476 GLN cc_start: 0.7728 (mt0) cc_final: 0.7486 (mp10) REVERT: A 681 LYS cc_start: 0.8214 (mmtt) cc_final: 0.7933 (mtmt) REVERT: A 688 GLU cc_start: 0.7969 (tt0) cc_final: 0.7668 (mt-10) REVERT: A 692 GLU cc_start: 0.7584 (tt0) cc_final: 0.7149 (tm-30) REVERT: A 698 ARG cc_start: 0.6296 (ptt-90) cc_final: 0.6000 (ptp-170) REVERT: A 714 LYS cc_start: 0.8370 (mtmt) cc_final: 0.7867 (mttt) REVERT: A 715 LYS cc_start: 0.8885 (mttm) cc_final: 0.8641 (mmtp) REVERT: B 56 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7738 (tt0) REVERT: B 66 LYS cc_start: 0.8264 (mttp) cc_final: 0.7968 (mttt) REVERT: B 245 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7367 (mp0) REVERT: B 272 LYS cc_start: 0.7382 (mtmt) cc_final: 0.7127 (mtpp) REVERT: B 286 ARG cc_start: 0.8197 (mtt180) cc_final: 0.7969 (mtt180) REVERT: B 344 VAL cc_start: 0.8692 (p) cc_final: 0.8458 (m) REVERT: B 444 LYS cc_start: 0.8099 (mtpp) cc_final: 0.7677 (mttm) REVERT: B 469 LYS cc_start: 0.8415 (mmtt) cc_final: 0.8213 (mmtt) REVERT: B 513 ARG cc_start: 0.7398 (ttt90) cc_final: 0.7174 (ttp-110) REVERT: B 692 GLU cc_start: 0.7771 (tt0) cc_final: 0.7017 (tm-30) REVERT: C 56 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7821 (tt0) REVERT: C 66 LYS cc_start: 0.8259 (mttp) cc_final: 0.7920 (mttt) REVERT: C 208 MET cc_start: 0.8160 (mtp) cc_final: 0.7955 (mtm) REVERT: C 272 LYS cc_start: 0.7371 (mtmt) cc_final: 0.7093 (mtpp) REVERT: C 344 VAL cc_start: 0.8701 (p) cc_final: 0.8455 (m) REVERT: C 444 LYS cc_start: 0.8133 (mtpp) cc_final: 0.7708 (mttm) REVERT: C 597 ASP cc_start: 0.8733 (t0) cc_final: 0.8217 (t0) REVERT: C 678 LEU cc_start: 0.8317 (pp) cc_final: 0.8016 (mt) REVERT: C 692 GLU cc_start: 0.7786 (tt0) cc_final: 0.7039 (tm-30) REVERT: D 56 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7756 (tt0) REVERT: D 245 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6640 (mp0) REVERT: D 344 VAL cc_start: 0.8677 (p) cc_final: 0.8434 (m) REVERT: D 444 LYS cc_start: 0.8135 (mtpp) cc_final: 0.7718 (mttm) REVERT: D 564 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7505 (ptt180) REVERT: D 597 ASP cc_start: 0.8734 (t0) cc_final: 0.8421 (t0) REVERT: D 613 GLU cc_start: 0.8103 (tp30) cc_final: 0.7847 (mm-30) REVERT: D 616 LYS cc_start: 0.8221 (mttt) cc_final: 0.7917 (mttm) REVERT: D 619 ILE cc_start: 0.6947 (OUTLIER) cc_final: 0.6095 (pp) REVERT: D 692 GLU cc_start: 0.7574 (tt0) cc_final: 0.7172 (tm-30) outliers start: 62 outliers final: 44 residues processed: 511 average time/residue: 2.5348 time to fit residues: 1510.2314 Evaluate side-chains 520 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 471 time to evaluate : 2.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 469 LYS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 621 ARG Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain D residue 564 ARG Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 621 ARG Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 655 THR Chi-restraints excluded: chain D residue 678 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 78 optimal weight: 0.9980 chunk 271 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 284 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 266 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 107 GLN A 483 ASN B 104 ASN B 107 GLN B 483 ASN C 104 ASN C 107 GLN C 483 ASN D 104 ASN D 107 GLN D 199 HIS D 483 ASN D 702 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.135048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.104483 restraints weight = 71836.101| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.76 r_work: 0.2949 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24140 Z= 0.272 Angle : 0.546 7.874 32736 Z= 0.286 Chirality : 0.041 0.138 3660 Planarity : 0.004 0.061 4148 Dihedral : 10.859 85.576 3857 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.27 % Favored : 97.69 % Rotamer: Outliers : 2.45 % Allowed : 17.32 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.15), residues: 3036 helix: 1.72 (0.14), residues: 1380 sheet: -0.18 (0.22), residues: 444 loop : -0.12 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 740 HIS 0.008 0.001 HIS D 660 PHE 0.012 0.001 PHE A 203 TYR 0.010 0.002 TYR A 385 ARG 0.008 0.000 ARG B 210 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 480 time to evaluate : 2.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7739 (tt0) REVERT: A 66 LYS cc_start: 0.8271 (mttp) cc_final: 0.7962 (mttt) REVERT: A 245 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6574 (mp0) REVERT: A 440 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7551 (mt-10) REVERT: A 444 LYS cc_start: 0.8234 (mtpp) cc_final: 0.7693 (mttm) REVERT: A 469 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.7341 (mptm) REVERT: A 476 GLN cc_start: 0.7713 (mt0) cc_final: 0.7479 (mp10) REVERT: A 681 LYS cc_start: 0.8210 (mmtt) cc_final: 0.7925 (mtmt) REVERT: A 688 GLU cc_start: 0.7867 (tt0) cc_final: 0.7555 (mt-10) REVERT: A 692 GLU cc_start: 0.7577 (tt0) cc_final: 0.7153 (tm-30) REVERT: A 698 ARG cc_start: 0.6298 (ptt-90) cc_final: 0.6006 (ptp-170) REVERT: A 714 LYS cc_start: 0.8322 (mtmt) cc_final: 0.7833 (mttt) REVERT: A 715 LYS cc_start: 0.8880 (mttm) cc_final: 0.8635 (mmtp) REVERT: B 56 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7740 (tt0) REVERT: B 66 LYS cc_start: 0.8267 (mttp) cc_final: 0.7947 (mttt) REVERT: B 245 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7352 (mp0) REVERT: B 272 LYS cc_start: 0.7364 (mtmt) cc_final: 0.7095 (mtpp) REVERT: B 286 ARG cc_start: 0.8179 (mtt180) cc_final: 0.7978 (mtt180) REVERT: B 344 VAL cc_start: 0.8690 (p) cc_final: 0.8456 (m) REVERT: B 444 LYS cc_start: 0.8126 (mtpp) cc_final: 0.7701 (mttm) REVERT: B 469 LYS cc_start: 0.8423 (mmtt) cc_final: 0.8223 (mmtt) REVERT: B 513 ARG cc_start: 0.7383 (ttt90) cc_final: 0.7147 (ttp-110) REVERT: C 56 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7859 (tt0) REVERT: C 66 LYS cc_start: 0.8248 (mttp) cc_final: 0.7894 (mttt) REVERT: C 272 LYS cc_start: 0.7347 (mtmt) cc_final: 0.7075 (mtpp) REVERT: C 344 VAL cc_start: 0.8749 (p) cc_final: 0.8507 (m) REVERT: C 444 LYS cc_start: 0.8138 (mtpp) cc_final: 0.7710 (mttm) REVERT: C 476 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7414 (mt0) REVERT: C 597 ASP cc_start: 0.8737 (t0) cc_final: 0.8222 (t0) REVERT: C 678 LEU cc_start: 0.8325 (pp) cc_final: 0.8007 (mt) REVERT: C 767 GLU cc_start: 0.6929 (mm-30) cc_final: 0.6536 (mm-30) REVERT: D 56 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7760 (tt0) REVERT: D 245 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6635 (mp0) REVERT: D 272 LYS cc_start: 0.7398 (mtmt) cc_final: 0.7125 (mtpp) REVERT: D 444 LYS cc_start: 0.8133 (mtpp) cc_final: 0.7707 (mttm) REVERT: D 564 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7516 (ptt180) REVERT: D 597 ASP cc_start: 0.8737 (t0) cc_final: 0.8428 (t0) REVERT: D 613 GLU cc_start: 0.8088 (tp30) cc_final: 0.7831 (mm-30) REVERT: D 616 LYS cc_start: 0.8223 (mttt) cc_final: 0.7933 (mttm) REVERT: D 619 ILE cc_start: 0.6886 (OUTLIER) cc_final: 0.6030 (pp) REVERT: D 692 GLU cc_start: 0.7552 (tt0) cc_final: 0.7100 (tm-30) REVERT: D 710 ILE cc_start: 0.8763 (tt) cc_final: 0.8246 (tt) REVERT: D 767 GLU cc_start: 0.6929 (mm-30) cc_final: 0.6530 (mm-30) outliers start: 60 outliers final: 43 residues processed: 514 average time/residue: 2.4847 time to fit residues: 1470.9101 Evaluate side-chains 521 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 472 time to evaluate : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 469 LYS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 621 ARG Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain D residue 564 ARG Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 621 ARG Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 655 THR Chi-restraints excluded: chain D residue 678 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 235 optimal weight: 1.9990 chunk 273 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 73 optimal weight: 0.2980 chunk 183 optimal weight: 0.6980 chunk 234 optimal weight: 0.5980 chunk 122 optimal weight: 0.0040 chunk 62 optimal weight: 0.9990 chunk 143 optimal weight: 0.9990 chunk 190 optimal weight: 0.0970 chunk 65 optimal weight: 0.0970 overall best weight: 0.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 107 GLN A 483 ASN B 104 ASN B 107 GLN B 483 ASN C 104 ASN C 107 GLN C 483 ASN C 702 ASN D 104 ASN D 107 GLN D 199 HIS D 483 ASN D 702 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.138689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.108559 restraints weight = 71560.873| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.75 r_work: 0.3008 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24140 Z= 0.144 Angle : 0.493 8.737 32736 Z= 0.259 Chirality : 0.040 0.145 3660 Planarity : 0.004 0.063 4148 Dihedral : 10.119 84.284 3857 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.88 % Allowed : 17.93 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.15), residues: 3036 helix: 2.09 (0.14), residues: 1372 sheet: -0.28 (0.23), residues: 444 loop : -0.01 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 685 HIS 0.003 0.001 HIS A 199 PHE 0.011 0.001 PHE A 203 TYR 0.008 0.001 TYR C 433 ARG 0.010 0.000 ARG B 210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31791.33 seconds wall clock time: 539 minutes 38.58 seconds (32378.58 seconds total)