Starting phenix.real_space_refine on Sat Jul 4 05:04:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/30jv_57833/07_2026/30jv_57833.cif Found real_map, /net/cci-nas-00/data/ceres_data/30jv_57833/07_2026/30jv_57833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/30jv_57833/07_2026/30jv_57833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/30jv_57833/07_2026/30jv_57833.map" model { file = "/net/cci-nas-00/data/ceres_data/30jv_57833/07_2026/30jv_57833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/30jv_57833/07_2026/30jv_57833.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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: 6 Type Number sf(0) Gaussians Mn 4 7.51 5 P 120 5.49 5 S 56 5.16 5 C 11142 2.51 5 N 3056 2.21 5 O 3562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17940 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4943 Classifications: {'peptide': 608} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 574} Chain breaks: 3 Chain: "B" Number of atoms: 4943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4943 Classifications: {'peptide': 608} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 574} Chain breaks: 3 Chain: "C" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2775 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 19, 'TRANS': 316} Chain breaks: 2 Chain: "D" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2775 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 19, 'TRANS': 316} Chain breaks: 2 Chain: "E" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 592 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "F" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 658 Classifications: {'DNA': 33} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 32} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA%5*END:plan': 1, ' DA%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 592 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "H" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 658 Classifications: {'DNA': 33} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 32} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA%5*END:plan': 1, ' DA%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Time building chain proxies: 3.56, per 1000 atoms: 0.20 Number of scatterers: 17940 At special positions: 0 Unit cell: (154.05, 105.3, 117.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 4 24.99 S 56 16.00 P 120 15.00 O 3562 8.00 N 3056 7.00 C 11142 6.00 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: 1.64 Conformation dependent library (CDL) restraints added in 708.0 milliseconds 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3620 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 18 sheets defined 47.7% alpha, 14.2% beta 56 base pairs and 96 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'A' and resid 31 through 43 removed outlier: 3.586A pdb=" N PHE A 39 " --> pdb=" O PHE A 35 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS A 40 " --> pdb=" O ASP A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 92 removed outlier: 3.608A pdb=" N ILE A 92 " --> pdb=" O TYR A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 111 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 127 through 138 removed outlier: 3.612A pdb=" N TYR A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 159 Processing helix chain 'A' and resid 163 through 170 Processing helix chain 'A' and resid 173 through 187 Processing helix chain 'A' and resid 258 through 262 removed outlier: 3.733A pdb=" N VAL A 262 " --> pdb=" O THR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 277 Processing helix chain 'A' and resid 278 through 299 Processing helix chain 'A' and resid 304 through 316 Proline residue: A 310 - end of helix Processing helix chain 'A' and resid 325 through 339 Processing helix chain 'A' and resid 342 through 347 removed outlier: 3.501A pdb=" N ALA A 347 " --> pdb=" O ALA A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 375 removed outlier: 3.787A pdb=" N LYS A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 399 removed outlier: 4.033A pdb=" N SER A 399 " --> pdb=" O ILE A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 419 Processing helix chain 'A' and resid 421 through 430 removed outlier: 3.537A pdb=" N VAL A 425 " --> pdb=" O PRO A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 440 Processing helix chain 'A' and resid 502 through 515 Processing helix chain 'A' and resid 518 through 522 removed outlier: 4.197A pdb=" N ALA A 521 " --> pdb=" O SER A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 560 Processing helix chain 'A' and resid 572 through 584 removed outlier: 3.503A pdb=" N GLU A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG A 579 " --> pdb=" O PRO A 575 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE A 580 " --> pdb=" O PHE A 576 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET A 584 " --> pdb=" O PHE A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 630 Processing helix chain 'A' and resid 642 through 652 Processing helix chain 'A' and resid 660 through 671 Processing helix chain 'B' and resid 31 through 43 removed outlier: 3.586A pdb=" N PHE B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS B 40 " --> pdb=" O ASP B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 92 removed outlier: 3.608A pdb=" N ILE B 92 " --> pdb=" O TYR B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 111 Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 127 through 138 removed outlier: 3.611A pdb=" N TYR B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 159 Processing helix chain 'B' and resid 163 through 170 Processing helix chain 'B' and resid 173 through 187 Processing helix chain 'B' and resid 258 through 262 removed outlier: 3.734A pdb=" N VAL B 262 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 277 Processing helix chain 'B' and resid 278 through 299 Processing helix chain 'B' and resid 304 through 316 Proline residue: B 310 - end of helix Processing helix chain 'B' and resid 325 through 339 Processing helix chain 'B' and resid 342 through 347 removed outlier: 3.501A pdb=" N ALA B 347 " --> pdb=" O ALA B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 375 removed outlier: 3.787A pdb=" N LYS B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 399 removed outlier: 4.033A pdb=" N SER B 399 " --> pdb=" O ILE B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 419 Processing helix chain 'B' and resid 421 through 430 removed outlier: 3.537A pdb=" N VAL B 425 " --> pdb=" O PRO B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 440 Processing helix chain 'B' and resid 502 through 515 Processing helix chain 'B' and resid 518 through 522 removed outlier: 4.198A pdb=" N ALA B 521 " --> pdb=" O SER B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 560 Processing helix chain 'B' and resid 572 through 584 removed outlier: 3.502A pdb=" N GLU B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG B 579 " --> pdb=" O PRO B 575 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE B 580 " --> pdb=" O PHE B 576 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET B 584 " --> pdb=" O PHE B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 630 Processing helix chain 'B' and resid 642 through 652 Processing helix chain 'B' and resid 660 through 671 Processing helix chain 'C' and resid 501 through 515 removed outlier: 3.879A pdb=" N SER C 505 " --> pdb=" O PRO C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 522 Processing helix chain 'C' and resid 549 through 559 removed outlier: 3.588A pdb=" N ALA C 559 " --> pdb=" O ALA C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 583 removed outlier: 3.820A pdb=" N GLU C 578 " --> pdb=" O LYS C 574 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ARG C 579 " --> pdb=" O PRO C 575 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE C 580 " --> pdb=" O PHE C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 588 Processing helix chain 'C' and resid 615 through 630 Processing helix chain 'C' and resid 642 through 654 Processing helix chain 'C' and resid 660 through 669 removed outlier: 3.767A pdb=" N ARG C 666 " --> pdb=" O GLU C 662 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE C 667 " --> pdb=" O GLU C 663 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER C 668 " --> pdb=" O GLU C 664 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N MET C 669 " --> pdb=" O THR C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 672 No H-bonds generated for 'chain 'C' and resid 670 through 672' Processing helix chain 'C' and resid 693 through 703 Processing helix chain 'C' and resid 750 through 769 Processing helix chain 'C' and resid 770 through 795 Processing helix chain 'D' and resid 501 through 515 removed outlier: 3.877A pdb=" N SER D 505 " --> pdb=" O PRO D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 522 Processing helix chain 'D' and resid 549 through 559 removed outlier: 3.585A pdb=" N ALA D 559 " --> pdb=" O ALA D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 577 Processing helix chain 'D' and resid 577 through 585 Processing helix chain 'D' and resid 586 through 588 No H-bonds generated for 'chain 'D' and resid 586 through 588' Processing helix chain 'D' and resid 615 through 630 Processing helix chain 'D' and resid 642 through 654 Processing helix chain 'D' and resid 660 through 669 removed outlier: 3.772A pdb=" N ARG D 666 " --> pdb=" O GLU D 662 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N PHE D 667 " --> pdb=" O GLU D 663 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER D 668 " --> pdb=" O GLU D 664 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N MET D 669 " --> pdb=" O THR D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 672 No H-bonds generated for 'chain 'D' and resid 670 through 672' Processing helix chain 'D' and resid 693 through 703 Processing helix chain 'D' and resid 750 through 769 Processing helix chain 'D' and resid 770 through 795 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 29 removed outlier: 4.026A pdb=" N VAL A 15 " --> pdb=" O TYR A 565 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N LEU A 539 " --> pdb=" O GLN A 564 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASN A 566 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N VAL A 541 " --> pdb=" O ASN A 566 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL A 455 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N ASP A 542 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 9.146A pdb=" N ILE A 457 " --> pdb=" O ASP A 542 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY A 493 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ASP A 485 " --> pdb=" O VAL A 491 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL A 491 " --> pdb=" O ASP A 485 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 52 removed outlier: 6.456A pdb=" N TYR A 83 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N VAL A 118 " --> pdb=" O TYR A 83 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N GLU A 85 " --> pdb=" O VAL A 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 57 through 61 Processing sheet with id=AA4, first strand: chain 'A' and resid 161 through 162 Processing sheet with id=AA5, first strand: chain 'A' and resid 270 through 271 removed outlier: 7.050A pdb=" N LYS C 723 " --> pdb=" O ASP C 717 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ASP C 717 " --> pdb=" O LYS C 723 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LEU C 713 " --> pdb=" O TYR C 727 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 474 through 476 removed outlier: 3.761A pdb=" N GLY A 476 " --> pdb=" O LEU A 466 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 26 through 29 removed outlier: 4.025A pdb=" N VAL B 15 " --> pdb=" O TYR B 565 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N LEU B 539 " --> pdb=" O GLN B 564 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASN B 566 " --> pdb=" O LEU B 539 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N VAL B 541 " --> pdb=" O ASN B 566 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL B 455 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N ASP B 542 " --> pdb=" O VAL B 455 " (cutoff:3.500A) removed outlier: 9.146A pdb=" N ILE B 457 " --> pdb=" O ASP B 542 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY B 493 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ASP B 485 " --> pdb=" O VAL B 491 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL B 491 " --> pdb=" O ASP B 485 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.456A pdb=" N TYR B 83 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N VAL B 118 " --> pdb=" O TYR B 83 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N GLU B 85 " --> pdb=" O VAL B 118 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 57 through 61 Processing sheet with id=AB1, first strand: chain 'B' and resid 161 through 162 Processing sheet with id=AB2, first strand: chain 'B' and resid 270 through 271 removed outlier: 7.050A pdb=" N LYS D 723 " --> pdb=" O ASP D 717 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ASP D 717 " --> pdb=" O LYS D 723 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU D 713 " --> pdb=" O TYR D 727 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 474 through 476 removed outlier: 3.761A pdb=" N GLY B 476 " --> pdb=" O LEU B 466 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 491 through 497 removed outlier: 6.442A pdb=" N VAL C 491 " --> pdb=" O ASP C 485 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASP C 485 " --> pdb=" O VAL C 491 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY C 493 " --> pdb=" O LEU C 483 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL C 455 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N ASP C 542 " --> pdb=" O VAL C 455 " (cutoff:3.500A) removed outlier: 9.406A pdb=" N ILE C 457 " --> pdb=" O ASP C 542 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU C 539 " --> pdb=" O GLN C 564 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ASN C 566 " --> pdb=" O LEU C 539 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL C 541 " --> pdb=" O ASN C 566 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 474 through 476 removed outlier: 3.993A pdb=" N GLY C 476 " --> pdb=" O LEU C 466 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET C 614 " --> pdb=" O ILE C 465 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 684 through 686 Processing sheet with id=AB7, first strand: chain 'D' and resid 491 through 497 removed outlier: 6.453A pdb=" N VAL D 491 " --> pdb=" O ASP D 485 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP D 485 " --> pdb=" O VAL D 491 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY D 493 " --> pdb=" O LEU D 483 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL D 455 " --> pdb=" O VAL D 540 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N ASP D 542 " --> pdb=" O VAL D 455 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N ILE D 457 " --> pdb=" O ASP D 542 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU D 539 " --> pdb=" O GLN D 564 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ASN D 566 " --> pdb=" O LEU D 539 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL D 541 " --> pdb=" O ASN D 566 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 474 through 476 removed outlier: 4.000A pdb=" N GLY D 476 " --> pdb=" O LEU D 466 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET D 614 " --> pdb=" O ILE D 465 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 684 through 686 704 hydrogen bonds defined for protein. 1986 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 136 hydrogen bonds 272 hydrogen bond angles 0 basepair planarities 56 basepair parallelities 96 stacking parallelities Total time for adding SS restraints: 4.09 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4403 1.33 - 1.45: 4246 1.45 - 1.57: 9647 1.57 - 1.69: 240 1.69 - 1.81: 90 Bond restraints: 18626 Sorted by residual: bond pdb=" C3' DG E -6 " pdb=" C2' DG E -6 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.18e+01 bond pdb=" C3' DG G -6 " pdb=" C2' DG G -6 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.18e+01 bond pdb=" C3' DC G -17 " pdb=" C2' DC G -17 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DC E -17 " pdb=" C2' DC E -17 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+01 bond pdb=" C3' DT E -26 " pdb=" C2' DT E -26 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.31e+00 ... (remaining 18621 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 25218 2.12 - 4.24: 461 4.24 - 6.37: 38 6.37 - 8.49: 13 8.49 - 10.61: 2 Bond angle restraints: 25732 Sorted by residual: angle pdb=" N ARG B 569 " pdb=" CA ARG B 569 " pdb=" C ARG B 569 " ideal model delta sigma weight residual 111.52 118.30 -6.78 1.40e+00 5.10e-01 2.34e+01 angle pdb=" N ARG A 569 " pdb=" CA ARG A 569 " pdb=" C ARG A 569 " ideal model delta sigma weight residual 111.52 118.26 -6.74 1.40e+00 5.10e-01 2.32e+01 angle pdb=" N3 DT G -22 " pdb=" C4 DT G -22 " pdb=" O4 DT G -22 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" N3 DT G -16 " pdb=" C4 DT G -16 " pdb=" O4 DT G -16 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" N3 DT E -26 " pdb=" C4 DT E -26 " pdb=" O4 DT E -26 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 ... (remaining 25727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.94: 10034 34.94 - 69.88: 839 69.88 - 104.82: 33 104.82 - 139.76: 6 139.76 - 174.71: 2 Dihedral angle restraints: 10914 sinusoidal: 5338 harmonic: 5576 Sorted by residual: dihedral pdb=" CA GLU D 604 " pdb=" C GLU D 604 " pdb=" N GLU D 605 " pdb=" CA GLU D 605 " ideal model delta harmonic sigma weight residual 180.00 158.24 21.76 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA GLU C 604 " pdb=" C GLU C 604 " pdb=" N GLU C 605 " pdb=" CA GLU C 605 " ideal model delta harmonic sigma weight residual 180.00 158.52 21.48 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" C4' DT G -26 " pdb=" C3' DT G -26 " pdb=" O3' DT G -26 " pdb=" P DA G -25 " ideal model delta sinusoidal sigma weight residual 220.00 45.29 174.71 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 10911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2340 0.058 - 0.116: 412 0.116 - 0.174: 46 0.174 - 0.232: 4 0.232 - 0.290: 2 Chirality restraints: 2804 Sorted by residual: chirality pdb=" CA ARG B 569 " pdb=" N ARG B 569 " pdb=" C ARG B 569 " pdb=" CB ARG B 569 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA ARG A 569 " pdb=" N ARG A 569 " pdb=" C ARG A 569 " pdb=" CB ARG A 569 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA VAL A 541 " pdb=" N VAL A 541 " pdb=" C VAL A 541 " pdb=" CB VAL A 541 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 2801 not shown) Planarity restraints: 2862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 567 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.08e+00 pdb=" C PRO A 567 " -0.035 2.00e-02 2.50e+03 pdb=" O PRO A 567 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL A 568 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 567 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.08e+00 pdb=" C PRO B 567 " 0.035 2.00e-02 2.50e+03 pdb=" O PRO B 567 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL B 568 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 570 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.96e+00 pdb=" N PRO B 571 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 571 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 571 " 0.029 5.00e-02 4.00e+02 ... (remaining 2859 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 50 2.63 - 3.20: 15664 3.20 - 3.77: 30659 3.77 - 4.33: 41546 4.33 - 4.90: 64350 Nonbonded interactions: 152269 Sorted by model distance: nonbonded pdb=" OP2 DT H -2 " pdb="MN MN B1000 " model vdw 2.064 3.060 nonbonded pdb=" OD2 ASP B 71 " pdb="MN MN B1000 " model vdw 2.076 3.060 nonbonded pdb=" OD2 ASP A 71 " pdb="MN MN A1000 " model vdw 2.076 3.060 nonbonded pdb=" OP2 DT F -2 " pdb="MN MN A1000 " model vdw 2.078 3.060 nonbonded pdb=" O TYR B 86 " pdb="MN MN B1000 " model vdw 2.101 3.060 ... (remaining 152264 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } 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: 10.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 19.200 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:7.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 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 : 0.004 0.055 18626 Z= 0.298 Angle : 0.629 10.610 25732 Z= 0.441 Chirality : 0.045 0.290 2804 Planarity : 0.004 0.050 2862 Dihedral : 21.437 174.705 7294 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.99 % Favored : 97.90 % Rotamer: Outliers : 2.12 % Allowed : 26.86 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.19), residues: 1860 helix: 1.96 (0.19), residues: 782 sheet: 0.14 (0.34), residues: 252 loop : -0.34 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 121 TYR 0.021 0.001 TYR B 389 PHE 0.010 0.001 PHE A 97 TRP 0.030 0.001 TRP B 572 HIS 0.003 0.001 HIS D 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.30 (18626) covalent geometry : angle 0.62882 / 0.44 (25732) hydrogen bonds : bond 0.13595 / 8.95 ( 840) hydrogen bonds : angle 5.72758 / 4.13 ( 2258) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 98 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 TYR cc_start: 0.7979 (m-80) cc_final: 0.7722 (m-80) REVERT: A 62 MET cc_start: 0.8593 (ppp) cc_final: 0.8215 (ppp) REVERT: A 490 CYS cc_start: 0.8643 (m) cc_final: 0.8404 (m) REVERT: A 498 TYR cc_start: 0.7860 (m-80) cc_final: 0.7475 (m-80) REVERT: A 557 GLN cc_start: 0.8975 (tm130) cc_final: 0.8754 (tm-30) REVERT: A 569 ARG cc_start: 0.6712 (OUTLIER) cc_final: 0.5557 (tmt170) REVERT: B 43 TYR cc_start: 0.7977 (m-80) cc_final: 0.7721 (m-80) REVERT: B 62 MET cc_start: 0.8605 (ppp) cc_final: 0.8230 (ppp) REVERT: B 490 CYS cc_start: 0.8646 (m) cc_final: 0.8407 (m) REVERT: B 498 TYR cc_start: 0.7845 (m-80) cc_final: 0.7459 (m-80) REVERT: B 557 GLN cc_start: 0.8977 (tm130) cc_final: 0.8758 (tm-30) REVERT: B 569 ARG cc_start: 0.6611 (OUTLIER) cc_final: 0.5494 (tmt170) REVERT: C 584 MET cc_start: 0.8895 (tpp) cc_final: 0.8587 (tpp) REVERT: C 705 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8081 (mp10) REVERT: C 787 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7725 (pp30) REVERT: D 614 MET cc_start: 0.8161 (ppp) cc_final: 0.7667 (pmt) REVERT: D 705 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8080 (mp10) REVERT: D 787 GLN cc_start: 0.7819 (pt0) cc_final: 0.7605 (pp30) outliers start: 36 outliers final: 15 residues processed: 126 average time/residue: 0.6088 time to fit residues: 86.2316 Evaluate side-chains 115 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 569 ARG Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 569 ARG Chi-restraints excluded: chain C residue 553 GLU Chi-restraints excluded: chain C residue 705 GLN Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 781 ILE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain D residue 705 GLN Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 781 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 HIS A 562 ASN B 495 HIS B 562 ASN C 761 ASN D 585 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.108550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.077205 restraints weight = 41740.666| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.88 r_work: 0.3199 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.0587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 18626 Z= 0.184 Angle : 0.561 7.460 25732 Z= 0.310 Chirality : 0.042 0.253 2804 Planarity : 0.004 0.040 2862 Dihedral : 22.351 177.297 3451 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.12 % Allowed : 24.56 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.20), residues: 1860 helix: 2.08 (0.19), residues: 790 sheet: -0.03 (0.30), residues: 288 loop : -0.25 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 579 TYR 0.029 0.001 TYR B 389 PHE 0.010 0.001 PHE B 97 TRP 0.014 0.001 TRP B 572 HIS 0.004 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (18626) covalent geometry : angle 0.56148 / 0.31 (25732) hydrogen bonds : bond 0.04368 / 2.95 ( 840) hydrogen bonds : angle 4.87101 / 3.50 ( 2258) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 104 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8625 (ppp) cc_final: 0.8234 (ppp) REVERT: A 121 ARG cc_start: 0.9336 (ptp-170) cc_final: 0.9088 (pmm-80) REVERT: A 498 TYR cc_start: 0.7851 (m-80) cc_final: 0.7550 (m-80) REVERT: A 557 GLN cc_start: 0.8992 (tm130) cc_final: 0.8788 (tm-30) REVERT: A 569 ARG cc_start: 0.6709 (OUTLIER) cc_final: 0.5771 (tmt170) REVERT: B 62 MET cc_start: 0.8641 (ppp) cc_final: 0.8254 (ppp) REVERT: B 121 ARG cc_start: 0.9333 (ptp-170) cc_final: 0.9082 (pmm-80) REVERT: B 498 TYR cc_start: 0.7844 (m-80) cc_final: 0.7545 (m-80) REVERT: B 557 GLN cc_start: 0.8991 (tm130) cc_final: 0.8787 (tm-30) REVERT: B 569 ARG cc_start: 0.6574 (OUTLIER) cc_final: 0.5696 (tmt170) REVERT: C 497 SER cc_start: 0.8783 (p) cc_final: 0.8374 (m) REVERT: C 705 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8023 (mp10) REVERT: C 787 GLN cc_start: 0.8132 (pt0) cc_final: 0.7701 (pp30) REVERT: D 497 SER cc_start: 0.8754 (p) cc_final: 0.8339 (m) REVERT: D 705 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8020 (mp10) REVERT: D 787 GLN cc_start: 0.7839 (pt0) cc_final: 0.7634 (pp30) outliers start: 70 outliers final: 20 residues processed: 164 average time/residue: 0.5510 time to fit residues: 101.6354 Evaluate side-chains 118 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 569 ARG Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 569 ARG Chi-restraints excluded: chain C residue 553 GLU Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain C residue 705 GLN Chi-restraints excluded: chain C residue 723 LYS Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain C residue 781 ILE Chi-restraints excluded: chain D residue 553 GLU Chi-restraints excluded: chain D residue 705 GLN Chi-restraints excluded: chain D residue 723 LYS Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain D residue 781 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 125 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 140 optimal weight: 0.0970 chunk 152 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 chunk 40 optimal weight: 0.0050 chunk 137 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 160 optimal weight: 0.6980 chunk 123 optimal weight: 8.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 HIS A 256 GLN A 495 HIS A 562 ASN B 136 HIS B 495 HIS B 562 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.110006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.079032 restraints weight = 42017.367| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.91 r_work: 0.3235 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.0746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 18626 Z= 0.116 Angle : 0.535 7.581 25732 Z= 0.296 Chirality : 0.040 0.256 2804 Planarity : 0.004 0.037 2862 Dihedral : 22.206 178.130 3437 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.18 % Allowed : 25.15 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.20), residues: 1860 helix: 2.11 (0.19), residues: 792 sheet: 0.05 (0.30), residues: 288 loop : -0.21 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 569 TYR 0.027 0.001 TYR A 389 PHE 0.015 0.001 PHE C 536 TRP 0.016 0.001 TRP A 206 HIS 0.003 0.001 HIS C 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.12 (18626) covalent geometry : angle 0.53486 / 0.30 (25732) hydrogen bonds : bond 0.03930 / 2.65 ( 840) hydrogen bonds : angle 4.60933 / 3.31 ( 2258) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 105 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8651 (ppp) cc_final: 0.8281 (ppp) REVERT: A 557 GLN cc_start: 0.8936 (tm130) cc_final: 0.8726 (tm-30) REVERT: A 613 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7317 (mp) REVERT: B 62 MET cc_start: 0.8656 (ppp) cc_final: 0.8286 (ppp) REVERT: B 498 TYR cc_start: 0.7827 (m-80) cc_final: 0.7522 (m-80) REVERT: B 557 GLN cc_start: 0.8938 (tm130) cc_final: 0.8730 (tm-30) REVERT: C 492 LEU cc_start: 0.8973 (mp) cc_final: 0.8677 (mp) REVERT: C 497 SER cc_start: 0.8691 (p) cc_final: 0.8325 (m) REVERT: C 584 MET cc_start: 0.8942 (tpt) cc_final: 0.8618 (tpp) REVERT: C 705 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.7988 (mp10) REVERT: C 723 LYS cc_start: 0.9381 (OUTLIER) cc_final: 0.8906 (pttm) REVERT: C 787 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7698 (pp30) REVERT: D 492 LEU cc_start: 0.8973 (mp) cc_final: 0.8691 (mp) REVERT: D 497 SER cc_start: 0.8733 (p) cc_final: 0.8407 (m) REVERT: D 584 MET cc_start: 0.9015 (tpp) cc_final: 0.8773 (tpp) REVERT: D 705 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.7987 (mp10) REVERT: D 723 LYS cc_start: 0.9381 (OUTLIER) cc_final: 0.8906 (pttm) REVERT: D 787 GLN cc_start: 0.7838 (pt0) cc_final: 0.7625 (pp30) outliers start: 54 outliers final: 10 residues processed: 150 average time/residue: 0.5299 time to fit residues: 90.1167 Evaluate side-chains 113 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain C residue 705 GLN Chi-restraints excluded: chain C residue 723 LYS Chi-restraints excluded: chain C residue 781 ILE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain D residue 553 GLU Chi-restraints excluded: chain D residue 705 GLN Chi-restraints excluded: chain D residue 723 LYS Chi-restraints excluded: chain D residue 781 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 60 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 167 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 191 optimal weight: 30.0000 chunk 33 optimal weight: 0.6980 chunk 81 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 75 optimal weight: 0.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 HIS B 136 HIS B 256 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.107254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.075754 restraints weight = 41981.944| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.88 r_work: 0.3157 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 18626 Z= 0.234 Angle : 0.593 8.497 25732 Z= 0.319 Chirality : 0.043 0.257 2804 Planarity : 0.004 0.036 2862 Dihedral : 22.305 177.754 3426 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.06 % Allowed : 25.09 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.19), residues: 1860 helix: 2.04 (0.19), residues: 792 sheet: -0.01 (0.30), residues: 290 loop : -0.32 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 359 TYR 0.028 0.002 TYR B 389 PHE 0.013 0.002 PHE A 367 TRP 0.019 0.002 TRP B 206 HIS 0.005 0.001 HIS C 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.23 (18626) covalent geometry : angle 0.59297 / 0.32 (25732) hydrogen bonds : bond 0.04320 / 2.95 ( 840) hydrogen bonds : angle 4.60772 / 3.31 ( 2258) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 100 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8683 (ppp) cc_final: 0.8291 (ppp) REVERT: A 471 LEU cc_start: 0.8868 (mt) cc_final: 0.8640 (mm) REVERT: A 557 GLN cc_start: 0.8998 (tm130) cc_final: 0.8765 (tm-30) REVERT: A 613 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.7231 (mp) REVERT: A 646 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.8160 (tpt-90) REVERT: B 62 MET cc_start: 0.8686 (ppp) cc_final: 0.8281 (ppp) REVERT: B 471 LEU cc_start: 0.8875 (mt) cc_final: 0.8646 (mm) REVERT: B 557 GLN cc_start: 0.9005 (tm130) cc_final: 0.8776 (tm-30) REVERT: B 646 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8166 (tpt-90) REVERT: C 584 MET cc_start: 0.8931 (tpt) cc_final: 0.8669 (tpp) REVERT: C 705 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8071 (mp10) REVERT: C 787 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7703 (pp30) REVERT: D 584 MET cc_start: 0.8974 (tpp) cc_final: 0.8766 (tpp) REVERT: D 705 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8065 (mp10) REVERT: D 787 GLN cc_start: 0.7855 (pt0) cc_final: 0.7644 (pp30) outliers start: 69 outliers final: 24 residues processed: 158 average time/residue: 0.5490 time to fit residues: 98.4712 Evaluate side-chains 118 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 553 GLU Chi-restraints excluded: chain C residue 705 GLN Chi-restraints excluded: chain C residue 723 LYS Chi-restraints excluded: chain C residue 781 ILE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 553 GLU Chi-restraints excluded: chain D residue 705 GLN Chi-restraints excluded: chain D residue 723 LYS Chi-restraints excluded: chain D residue 781 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 50 optimal weight: 7.9990 chunk 169 optimal weight: 6.9990 chunk 185 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 194 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 chunk 132 optimal weight: 10.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 562 ASN B 562 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.107778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.076504 restraints weight = 41793.502| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.88 r_work: 0.3182 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 18626 Z= 0.182 Angle : 0.560 7.144 25732 Z= 0.305 Chirality : 0.041 0.257 2804 Planarity : 0.004 0.037 2862 Dihedral : 22.318 178.537 3426 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.65 % Allowed : 25.09 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.20), residues: 1860 helix: 2.08 (0.19), residues: 790 sheet: -0.17 (0.30), residues: 300 loop : -0.26 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 359 TYR 0.027 0.001 TYR B 389 PHE 0.010 0.001 PHE A 536 TRP 0.016 0.001 TRP C 572 HIS 0.004 0.001 HIS C 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 (18626) covalent geometry : angle 0.55980 / 0.30 (25732) hydrogen bonds : bond 0.03897 / 2.65 ( 840) hydrogen bonds : angle 4.50438 / 3.23 ( 2258) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 96 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8707 (ppp) cc_final: 0.8305 (ppp) REVERT: A 165 ASP cc_start: 0.8461 (m-30) cc_final: 0.8095 (m-30) REVERT: A 471 LEU cc_start: 0.8875 (mt) cc_final: 0.8651 (mm) REVERT: A 613 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7063 (mp) REVERT: A 646 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.8087 (tpt-90) REVERT: B 62 MET cc_start: 0.8693 (ppp) cc_final: 0.8292 (ppp) REVERT: B 165 ASP cc_start: 0.8456 (m-30) cc_final: 0.8087 (m-30) REVERT: B 471 LEU cc_start: 0.8862 (mt) cc_final: 0.8633 (mm) REVERT: B 498 TYR cc_start: 0.8398 (OUTLIER) cc_final: 0.8114 (m-80) REVERT: B 646 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.8085 (tpt-90) REVERT: C 465 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8339 (mp) REVERT: C 584 MET cc_start: 0.8867 (tpt) cc_final: 0.8640 (tpp) REVERT: C 787 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7696 (pp30) REVERT: D 465 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8343 (mp) REVERT: D 787 GLN cc_start: 0.7827 (pt0) cc_final: 0.7622 (pp30) outliers start: 62 outliers final: 25 residues processed: 146 average time/residue: 0.5696 time to fit residues: 94.5041 Evaluate side-chains 121 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 553 GLU Chi-restraints excluded: chain C residue 673 ILE Chi-restraints excluded: chain C residue 723 LYS Chi-restraints excluded: chain C residue 781 ILE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 553 GLU Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 723 LYS Chi-restraints excluded: chain D residue 781 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 27 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 29 optimal weight: 0.0270 chunk 145 optimal weight: 2.9990 chunk 188 optimal weight: 10.0000 overall best weight: 1.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 585 ASN C 705 GLN D 705 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.107555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.076247 restraints weight = 41690.707| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.88 r_work: 0.3180 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 18626 Z= 0.191 Angle : 0.572 8.781 25732 Z= 0.307 Chirality : 0.041 0.257 2804 Planarity : 0.004 0.036 2862 Dihedral : 22.280 178.787 3420 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.53 % Allowed : 25.56 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.20), residues: 1860 helix: 2.09 (0.19), residues: 790 sheet: -0.18 (0.30), residues: 300 loop : -0.27 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 359 TYR 0.028 0.001 TYR A 389 PHE 0.010 0.001 PHE B 97 TRP 0.017 0.001 TRP C 572 HIS 0.004 0.001 HIS C 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 (18626) covalent geometry : angle 0.57239 / 0.31 (25732) hydrogen bonds : bond 0.03905 / 2.66 ( 840) hydrogen bonds : angle 4.48479 / 3.22 ( 2258) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 94 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8738 (ppp) cc_final: 0.8323 (ppp) REVERT: A 165 ASP cc_start: 0.8460 (m-30) cc_final: 0.8089 (m-30) REVERT: A 471 LEU cc_start: 0.8880 (mt) cc_final: 0.8656 (mm) REVERT: A 613 ILE cc_start: 0.7767 (OUTLIER) cc_final: 0.7000 (mp) REVERT: A 646 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.8090 (tpt-90) REVERT: B 62 MET cc_start: 0.8720 (ppp) cc_final: 0.8316 (ppp) REVERT: B 165 ASP cc_start: 0.8446 (m-30) cc_final: 0.8074 (m-30) REVERT: B 471 LEU cc_start: 0.8886 (mt) cc_final: 0.8660 (mm) REVERT: B 646 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.8086 (tpt-90) REVERT: C 465 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8326 (mp) REVERT: C 648 GLN cc_start: 0.9518 (tp40) cc_final: 0.9299 (tp-100) REVERT: C 787 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7676 (pp30) REVERT: D 465 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8334 (mp) REVERT: D 648 GLN cc_start: 0.9513 (tp40) cc_final: 0.9301 (tp-100) REVERT: D 787 GLN cc_start: 0.7832 (pt0) cc_final: 0.7630 (pp30) outliers start: 60 outliers final: 24 residues processed: 143 average time/residue: 0.6052 time to fit residues: 97.5495 Evaluate side-chains 120 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 553 GLU Chi-restraints excluded: chain C residue 673 ILE Chi-restraints excluded: chain C residue 723 LYS Chi-restraints excluded: chain C residue 781 ILE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 553 GLU Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 723 LYS Chi-restraints excluded: chain D residue 781 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 142 optimal weight: 0.4980 chunk 137 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 108 optimal weight: 0.6980 chunk 5 optimal weight: 0.0000 chunk 181 optimal weight: 2.9990 chunk 189 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 chunk 147 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 256 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.108599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.077414 restraints weight = 42031.879| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.89 r_work: 0.3206 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 18626 Z= 0.127 Angle : 0.551 9.171 25732 Z= 0.298 Chirality : 0.040 0.259 2804 Planarity : 0.004 0.042 2862 Dihedral : 22.209 179.760 3420 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.65 % Allowed : 26.38 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.20), residues: 1860 helix: 2.15 (0.19), residues: 792 sheet: -0.06 (0.30), residues: 300 loop : -0.23 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 121 TYR 0.027 0.001 TYR B 389 PHE 0.012 0.001 PHE A 97 TRP 0.018 0.001 TRP B 572 HIS 0.003 0.001 HIS C 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (18626) covalent geometry : angle 0.55136 / 0.30 (25732) hydrogen bonds : bond 0.03640 / 2.47 ( 840) hydrogen bonds : angle 4.38251 / 3.14 ( 2258) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 109 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8749 (ppp) cc_final: 0.8338 (ppp) REVERT: A 165 ASP cc_start: 0.8417 (m-30) cc_final: 0.8048 (m-30) REVERT: A 556 CYS cc_start: 0.9167 (m) cc_final: 0.8739 (p) REVERT: A 613 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.6906 (mp) REVERT: A 661 GLU cc_start: 0.9264 (mp0) cc_final: 0.8998 (tp30) REVERT: B 62 MET cc_start: 0.8727 (ppp) cc_final: 0.8316 (ppp) REVERT: B 165 ASP cc_start: 0.8419 (m-30) cc_final: 0.8049 (m-30) REVERT: B 556 CYS cc_start: 0.9169 (m) cc_final: 0.8742 (p) REVERT: B 661 GLU cc_start: 0.9270 (mp0) cc_final: 0.9001 (tp30) REVERT: C 584 MET cc_start: 0.8808 (tpp) cc_final: 0.8547 (tpp) REVERT: C 648 GLN cc_start: 0.9547 (tp40) cc_final: 0.9338 (tp-100) REVERT: C 723 LYS cc_start: 0.9366 (OUTLIER) cc_final: 0.9027 (pttm) REVERT: C 787 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7667 (pp30) REVERT: D 584 MET cc_start: 0.9120 (tpp) cc_final: 0.8882 (tpp) REVERT: D 648 GLN cc_start: 0.9542 (tp40) cc_final: 0.9341 (tp-100) REVERT: D 723 LYS cc_start: 0.9367 (OUTLIER) cc_final: 0.9025 (pttm) outliers start: 45 outliers final: 20 residues processed: 146 average time/residue: 0.5085 time to fit residues: 84.5261 Evaluate side-chains 119 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 553 GLU Chi-restraints excluded: chain C residue 723 LYS Chi-restraints excluded: chain C residue 781 ILE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain D residue 553 GLU Chi-restraints excluded: chain D residue 723 LYS Chi-restraints excluded: chain D residue 781 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 166 optimal weight: 0.9990 chunk 142 optimal weight: 0.6980 chunk 43 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 139 optimal weight: 10.0000 chunk 97 optimal weight: 0.3980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 256 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.108787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.077554 restraints weight = 42057.917| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.90 r_work: 0.3210 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 18626 Z= 0.133 Angle : 0.565 9.700 25732 Z= 0.304 Chirality : 0.041 0.260 2804 Planarity : 0.004 0.060 2862 Dihedral : 22.153 179.814 3420 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.41 % Allowed : 27.09 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.20), residues: 1860 helix: 2.16 (0.19), residues: 792 sheet: -0.00 (0.30), residues: 300 loop : -0.22 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 646 TYR 0.027 0.001 TYR B 389 PHE 0.013 0.001 PHE A 97 TRP 0.026 0.002 TRP A 206 HIS 0.003 0.001 HIS C 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (18626) covalent geometry : angle 0.56496 / 0.30 (25732) hydrogen bonds : bond 0.03613 / 2.46 ( 840) hydrogen bonds : angle 4.34626 / 3.13 ( 2258) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 107 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8735 (ppp) cc_final: 0.8321 (ppp) REVERT: A 556 CYS cc_start: 0.9174 (m) cc_final: 0.8766 (p) REVERT: A 613 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.6794 (mp) REVERT: A 661 GLU cc_start: 0.9249 (mp0) cc_final: 0.9007 (tp30) REVERT: B 62 MET cc_start: 0.8747 (ppp) cc_final: 0.8339 (ppp) REVERT: B 556 CYS cc_start: 0.9175 (m) cc_final: 0.8768 (p) REVERT: B 661 GLU cc_start: 0.9247 (mp0) cc_final: 0.9001 (tp30) REVERT: C 584 MET cc_start: 0.8829 (tpp) cc_final: 0.8584 (tpp) REVERT: C 723 LYS cc_start: 0.9379 (OUTLIER) cc_final: 0.8947 (pttm) REVERT: C 787 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7685 (pp30) REVERT: D 648 GLN cc_start: 0.9554 (tp40) cc_final: 0.9340 (tp-100) REVERT: D 723 LYS cc_start: 0.9377 (OUTLIER) cc_final: 0.8944 (pttm) outliers start: 41 outliers final: 21 residues processed: 134 average time/residue: 0.5403 time to fit residues: 82.4077 Evaluate side-chains 114 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 553 GLU Chi-restraints excluded: chain C residue 723 LYS Chi-restraints excluded: chain C residue 781 ILE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain D residue 553 GLU Chi-restraints excluded: chain D residue 723 LYS Chi-restraints excluded: chain D residue 781 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 120 optimal weight: 0.0870 chunk 38 optimal weight: 5.9990 chunk 36 optimal weight: 0.0970 chunk 39 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 158 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 256 GLN B 459 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.109401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.078279 restraints weight = 41624.526| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.87 r_work: 0.3217 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 18626 Z= 0.120 Angle : 0.571 11.418 25732 Z= 0.303 Chirality : 0.041 0.261 2804 Planarity : 0.004 0.038 2862 Dihedral : 22.098 179.615 3420 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.12 % Allowed : 27.62 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.20), residues: 1860 helix: 2.17 (0.19), residues: 800 sheet: 0.01 (0.30), residues: 300 loop : -0.16 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 646 TYR 0.027 0.001 TYR A 389 PHE 0.016 0.001 PHE C 619 TRP 0.022 0.001 TRP B 572 HIS 0.004 0.001 HIS B 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (18626) covalent geometry : angle 0.57115 / 0.30 (25732) hydrogen bonds : bond 0.03517 / 2.39 ( 840) hydrogen bonds : angle 4.30362 / 3.09 ( 2258) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 95 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8752 (ppp) cc_final: 0.8340 (ppp) REVERT: A 556 CYS cc_start: 0.9170 (m) cc_final: 0.8770 (p) REVERT: A 613 ILE cc_start: 0.7604 (OUTLIER) cc_final: 0.6769 (mp) REVERT: A 661 GLU cc_start: 0.9241 (mp0) cc_final: 0.8994 (tp30) REVERT: B 62 MET cc_start: 0.8743 (ppp) cc_final: 0.8329 (ppp) REVERT: B 556 CYS cc_start: 0.9173 (m) cc_final: 0.8775 (p) REVERT: B 661 GLU cc_start: 0.9245 (mp0) cc_final: 0.8996 (tp30) REVERT: C 574 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8735 (mppt) REVERT: C 584 MET cc_start: 0.8839 (tpp) cc_final: 0.8604 (tpp) REVERT: C 648 GLN cc_start: 0.9512 (tp40) cc_final: 0.9292 (tp-100) REVERT: C 723 LYS cc_start: 0.9375 (OUTLIER) cc_final: 0.8913 (pttm) REVERT: C 787 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7695 (pp30) REVERT: D 648 GLN cc_start: 0.9573 (tp40) cc_final: 0.9372 (tp-100) REVERT: D 723 LYS cc_start: 0.9376 (OUTLIER) cc_final: 0.8915 (pttm) REVERT: D 787 GLN cc_start: 0.8008 (pt0) cc_final: 0.7689 (pp30) outliers start: 36 outliers final: 23 residues processed: 122 average time/residue: 0.5624 time to fit residues: 78.4391 Evaluate side-chains 121 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 553 GLU Chi-restraints excluded: chain C residue 574 LYS Chi-restraints excluded: chain C residue 723 LYS Chi-restraints excluded: chain C residue 781 ILE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain D residue 553 GLU Chi-restraints excluded: chain D residue 723 LYS Chi-restraints excluded: chain D residue 781 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 24 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 151 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 170 optimal weight: 9.9990 chunk 96 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 256 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.107310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.075970 restraints weight = 41754.707| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.87 r_work: 0.3173 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 18626 Z= 0.213 Angle : 0.596 9.972 25732 Z= 0.318 Chirality : 0.043 0.260 2804 Planarity : 0.004 0.041 2862 Dihedral : 22.262 179.855 3420 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.94 % Allowed : 27.86 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.20), residues: 1860 helix: 2.14 (0.19), residues: 798 sheet: -0.06 (0.30), residues: 300 loop : -0.22 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 666 TYR 0.027 0.002 TYR B 389 PHE 0.019 0.002 PHE C 619 TRP 0.025 0.002 TRP B 572 HIS 0.004 0.001 HIS B 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 (18626) covalent geometry : angle 0.59614 / 0.32 (25732) hydrogen bonds : bond 0.03960 / 2.70 ( 840) hydrogen bonds : angle 4.39775 / 3.16 ( 2258) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 91 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8785 (ppp) cc_final: 0.8362 (ppp) REVERT: A 165 ASP cc_start: 0.8445 (m-30) cc_final: 0.8075 (m-30) REVERT: A 613 ILE cc_start: 0.7647 (OUTLIER) cc_final: 0.6803 (mp) REVERT: A 661 GLU cc_start: 0.9265 (mp0) cc_final: 0.8983 (tp30) REVERT: B 62 MET cc_start: 0.8772 (ppp) cc_final: 0.8352 (ppp) REVERT: B 165 ASP cc_start: 0.8437 (m-30) cc_final: 0.8064 (m-30) REVERT: B 556 CYS cc_start: 0.9135 (m) cc_final: 0.8695 (p) REVERT: B 661 GLU cc_start: 0.9269 (mp0) cc_final: 0.8986 (tp30) REVERT: C 584 MET cc_start: 0.8841 (tpp) cc_final: 0.8608 (tpp) REVERT: C 648 GLN cc_start: 0.9540 (tp40) cc_final: 0.9320 (tp-100) REVERT: C 787 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7700 (pp30) REVERT: D 787 GLN cc_start: 0.8039 (pt0) cc_final: 0.7715 (pp30) outliers start: 33 outliers final: 23 residues processed: 117 average time/residue: 0.5724 time to fit residues: 76.2822 Evaluate side-chains 114 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 553 GLU Chi-restraints excluded: chain C residue 723 LYS Chi-restraints excluded: chain C residue 781 ILE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain D residue 553 GLU Chi-restraints excluded: chain D residue 723 LYS Chi-restraints excluded: chain D residue 781 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 121 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 149 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 169 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 191 optimal weight: 30.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 256 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.107235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.075963 restraints weight = 42081.675| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.86 r_work: 0.3167 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 18626 Z= 0.198 Angle : 0.608 13.708 25732 Z= 0.321 Chirality : 0.042 0.259 2804 Planarity : 0.004 0.039 2862 Dihedral : 22.325 179.943 3420 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.77 % Allowed : 28.09 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.20), residues: 1860 helix: 2.06 (0.19), residues: 790 sheet: -0.10 (0.31), residues: 300 loop : -0.31 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 666 TYR 0.026 0.001 TYR B 389 PHE 0.017 0.001 PHE C 619 TRP 0.030 0.002 TRP B 572 HIS 0.004 0.001 HIS D 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 (18626) covalent geometry : angle 0.60790 / 0.32 (25732) hydrogen bonds : bond 0.03801 / 2.57 ( 840) hydrogen bonds : angle 4.42270 / 3.18 ( 2258) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5085.04 seconds wall clock time: 87 minutes 46.99 seconds (5266.99 seconds total)