Starting phenix.real_space_refine on Sat Jul 4 07:03:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8act_15353/07_2026/8act_15353.cif Found real_map, /net/cci-nas-00/data/ceres_data/8act_15353/07_2026/8act_15353.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8act_15353/07_2026/8act_15353.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8act_15353/07_2026/8act_15353.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8act_15353/07_2026/8act_15353.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8act_15353/07_2026/8act_15353.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8act_15353/07_2026/8act_15353.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8act_15353/07_2026/8act_15353.map" } resolution = 3.6 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= 0.024 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 P 6 5.49 5 Mg 2 5.21 5 S 111 5.16 5 C 11989 2.51 5 N 3188 2.21 5 O 3547 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s 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: 18843 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7080 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 873, 7071 Classifications: {'peptide': 873} Link IDs: {'PTRANS': 31, 'TRANS': 841} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'M3L:plan-1': 2} Unresolved non-hydrogen planarities: 2 Conformer: "B" Number of residues, atoms: 873, 7071 Classifications: {'peptide': 873} Link IDs: {'PTRANS': 31, 'TRANS': 841} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'M3L:plan-1': 2} Unresolved non-hydrogen planarities: 2 bond proxies already assigned to first conformer: 7203 Chain: "B" Number of atoms: 6956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 857, 6956 Classifications: {'peptide': 857} Link IDs: {'PTRANS': 31, 'TRANS': 825} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'M3L:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1248 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "D" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1248 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "E" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1118 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 6, 'TRANS': 131} Chain breaks: 2 Chain: "F" Number of atoms: 1127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1127 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLN A 163 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 163 " occ=0.50 Time building chain proxies: 6.41, per 1000 atoms: 0.34 Number of scatterers: 18843 At special positions: 0 Unit cell: (94.08, 165.48, 182.28, 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) S 111 16.00 P 6 15.00 Mg 2 11.99 O 3547 8.00 N 3188 7.00 C 11989 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: 1.89 Conformation dependent library (CDL) restraints added in 1.0 seconds 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4378 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 18 sheets defined 61.1% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 9 through 16 Proline residue: A 14 - end of helix Processing helix chain 'A' and resid 19 through 28 Processing helix chain 'A' and resid 74 through 77 Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.547A pdb=" N LEU A 93 " --> pdb=" O MET A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 111 Processing helix chain 'A' and resid 131 through 134 removed outlier: 4.374A pdb=" N TYR A 134 " --> pdb=" O LEU A 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 131 through 134' Processing helix chain 'A' and resid 135 through 142 Processing helix chain 'A' and resid 153 through 169 Processing helix chain 'A' and resid 183 through 202 removed outlier: 4.112A pdb=" N GLY A 202 " --> pdb=" O ILE A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 231 removed outlier: 4.342A pdb=" N ASN A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Proline residue: A 225 - end of helix removed outlier: 3.755A pdb=" N PHE A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 274 Processing helix chain 'A' and resid 283 through 291 removed outlier: 3.978A pdb=" N TYR A 287 " --> pdb=" O TYR A 283 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 289 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 290 " --> pdb=" O PHE A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 301 removed outlier: 3.630A pdb=" N LEU A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 removed outlier: 4.062A pdb=" N TYR A 310 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 339 removed outlier: 3.597A pdb=" N GLU A 328 " --> pdb=" O ASP A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 360 removed outlier: 3.960A pdb=" N GLY A 360 " --> pdb=" O ILE A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 389 Processing helix chain 'A' and resid 391 through 401 Processing helix chain 'A' and resid 416 through 448 Processing helix chain 'A' and resid 475 through 494 removed outlier: 3.752A pdb=" N ASN A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 504 removed outlier: 4.168A pdb=" N LYS A 502 " --> pdb=" O GLN A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 525 Processing helix chain 'A' and resid 529 through 538 Processing helix chain 'A' and resid 544 through 556 Processing helix chain 'A' and resid 568 through 572 removed outlier: 4.453A pdb=" N GLY A 571 " --> pdb=" O ASN A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 599 Processing helix chain 'A' and resid 602 through 611 Processing helix chain 'A' and resid 614 through 621 Processing helix chain 'A' and resid 646 through 664 removed outlier: 3.526A pdb=" N SER A 664 " --> pdb=" O THR A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 697 Processing helix chain 'A' and resid 699 through 707 removed outlier: 3.731A pdb=" N ARG A 703 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE A 704 " --> pdb=" O GLU A 700 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N CYS A 705 " --> pdb=" O GLY A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 722 Processing helix chain 'A' and resid 723 through 726 Processing helix chain 'A' and resid 737 through 748 Processing helix chain 'A' and resid 768 through 825 Processing helix chain 'A' and resid 827 through 840 removed outlier: 3.616A pdb=" N LYS A 831 " --> pdb=" O TRP A 827 " (cutoff:3.500A) Proline residue: A 838 - end of helix Processing helix chain 'A' and resid 841 through 906 removed outlier: 3.980A pdb=" N ASP A 906 " --> pdb=" O GLU A 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 10 Processing helix chain 'B' and resid 12 through 17 Processing helix chain 'B' and resid 19 through 28 removed outlier: 3.516A pdb=" N THR B 28 " --> pdb=" O LEU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 97 through 111 removed outlier: 3.614A pdb=" N LEU B 102 " --> pdb=" O GLU B 98 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER B 111 " --> pdb=" O ASP B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 142 Processing helix chain 'B' and resid 153 through 169 Processing helix chain 'B' and resid 183 through 198 Processing helix chain 'B' and resid 217 through 232 removed outlier: 3.864A pdb=" N ASN B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Proline residue: B 225 - end of helix removed outlier: 3.926A pdb=" N PHE B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 275 removed outlier: 4.499A pdb=" N ILE B 274 " --> pdb=" O LYS B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 289 Processing helix chain 'B' and resid 290 through 292 No H-bonds generated for 'chain 'B' and resid 290 through 292' Processing helix chain 'B' and resid 294 through 302 removed outlier: 3.713A pdb=" N LEU B 298 " --> pdb=" O LYS B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 310 removed outlier: 3.601A pdb=" N ASP B 309 " --> pdb=" O ASN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 340 Processing helix chain 'B' and resid 342 through 361 removed outlier: 3.828A pdb=" N MET B 357 " --> pdb=" O THR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 389 removed outlier: 4.228A pdb=" N ALA B 381 " --> pdb=" O GLY B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 401 Processing helix chain 'B' and resid 416 through 448 removed outlier: 3.914A pdb=" N VAL B 420 " --> pdb=" O ASN B 416 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ILE B 421 " --> pdb=" O VAL B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 494 Processing helix chain 'B' and resid 494 through 504 Processing helix chain 'B' and resid 517 through 525 removed outlier: 4.019A pdb=" N ILE B 524 " --> pdb=" O CYS B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 540 Processing helix chain 'B' and resid 544 through 557 removed outlier: 3.913A pdb=" N ASN B 555 " --> pdb=" O LYS B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 599 Processing helix chain 'B' and resid 602 through 611 removed outlier: 3.538A pdb=" N LYS B 611 " --> pdb=" O GLY B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 622 removed outlier: 3.557A pdb=" N ALA B 622 " --> pdb=" O SER B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 664 removed outlier: 3.744A pdb=" N SER B 664 " --> pdb=" O THR B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 697 Processing helix chain 'B' and resid 697 through 708 Processing helix chain 'B' and resid 715 through 723 Processing helix chain 'B' and resid 738 through 748 Processing helix chain 'B' and resid 768 through 826 removed outlier: 3.625A pdb=" N LEU B 772 " --> pdb=" O GLY B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 835 removed outlier: 4.062A pdb=" N LYS B 831 " --> pdb=" O TRP B 827 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU B 832 " --> pdb=" O PRO B 828 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR B 833 " --> pdb=" O TRP B 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 898 removed outlier: 3.754A pdb=" N ALA B 850 " --> pdb=" O GLU B 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 62 Processing helix chain 'C' and resid 75 through 83 Processing helix chain 'C' and resid 88 through 95 Processing helix chain 'C' and resid 100 through 106 Processing helix chain 'C' and resid 110 through 125 removed outlier: 4.108A pdb=" N PHE C 114 " --> pdb=" O ASP C 110 " (cutoff:3.500A) Proline residue: C 116 - end of helix removed outlier: 4.156A pdb=" N LYS C 125 " --> pdb=" O ILE C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 removed outlier: 3.738A pdb=" N VAL C 139 " --> pdb=" O GLU C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 159 Processing helix chain 'C' and resid 165 through 173 removed outlier: 3.519A pdb=" N VAL C 169 " --> pdb=" O THR C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 195 Processing helix chain 'D' and resid 47 through 62 Processing helix chain 'D' and resid 73 through 83 removed outlier: 4.195A pdb=" N GLY D 77 " --> pdb=" O TYR D 73 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASP D 78 " --> pdb=" O GLY D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 96 Processing helix chain 'D' and resid 100 through 107 Processing helix chain 'D' and resid 111 through 125 Proline residue: D 116 - end of helix removed outlier: 3.565A pdb=" N LYS D 125 " --> pdb=" O ILE D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 removed outlier: 4.178A pdb=" N VAL D 139 " --> pdb=" O GLU D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 160 removed outlier: 3.723A pdb=" N LEU D 160 " --> pdb=" O VAL D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 173 removed outlier: 3.712A pdb=" N MET D 173 " --> pdb=" O VAL D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 195 Processing helix chain 'E' and resid 28 through 37 removed outlier: 3.533A pdb=" N ALA E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 49 through 56 Processing helix chain 'E' and resid 62 through 73 removed outlier: 4.659A pdb=" N MET E 69 " --> pdb=" O GLU E 65 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ILE E 70 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS E 71 " --> pdb=" O ASP E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 88 Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 95 through 107 Processing helix chain 'E' and resid 115 through 127 Processing helix chain 'E' and resid 131 through 142 removed outlier: 4.190A pdb=" N GLN E 137 " --> pdb=" O GLU E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 160 removed outlier: 3.861A pdb=" N LEU E 155 " --> pdb=" O ASP E 151 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR E 160 " --> pdb=" O VAL E 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 37 Processing helix chain 'F' and resid 45 through 57 Processing helix chain 'F' and resid 64 through 73 removed outlier: 3.772A pdb=" N GLU F 68 " --> pdb=" O GLU F 64 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA F 73 " --> pdb=" O MET F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 90 Processing helix chain 'F' and resid 95 through 107 Processing helix chain 'F' and resid 115 through 126 Processing helix chain 'F' and resid 131 through 139 Processing helix chain 'F' and resid 151 through 162 removed outlier: 3.680A pdb=" N ILE F 159 " --> pdb=" O LEU F 155 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 40 removed outlier: 6.866A pdb=" N THR A 60 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ARG A 54 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LYS A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL A 59 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL A 71 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 118 removed outlier: 6.675A pdb=" N SER A 173 " --> pdb=" O HIS A 668 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N VAL A 670 " --> pdb=" O SER A 173 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU A 175 " --> pdb=" O VAL A 670 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N CYS A 672 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N THR A 177 " --> pdb=" O CYS A 672 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLN A 172 " --> pdb=" O GLY A 458 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LEU A 460 " --> pdb=" O GLN A 172 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE A 174 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 232 through 233 Processing sheet with id=AA4, first strand: chain 'A' and resid 363 through 366 removed outlier: 6.976A pdb=" N LYS A 363 " --> pdb=" O ASP A 376 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 403 through 406 Processing sheet with id=AA6, first strand: chain 'A' and resid 563 through 564 Processing sheet with id=AA7, first strand: chain 'A' and resid 712 through 713 Processing sheet with id=AA8, first strand: chain 'B' and resid 46 through 49 removed outlier: 3.883A pdb=" N MET B 77 " --> pdb=" O PHE B 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 55 removed outlier: 3.730A pdb=" N SER B 53 " --> pdb=" O THR B 60 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 115 through 118 removed outlier: 3.889A pdb=" N PHE B 121 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N SER B 173 " --> pdb=" O HIS B 668 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N VAL B 670 " --> pdb=" O SER B 173 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU B 175 " --> pdb=" O VAL B 670 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N CYS B 672 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR B 177 " --> pdb=" O CYS B 672 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN B 172 " --> pdb=" O PHE B 456 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER B 260 " --> pdb=" O HIS B 251 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 363 through 366 removed outlier: 4.424A pdb=" N LYS B 363 " --> pdb=" O ASP B 376 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP B 376 " --> pdb=" O LYS B 363 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 403 through 404 Processing sheet with id=AB4, first strand: chain 'B' and resid 563 through 564 removed outlier: 3.775A pdb=" N PHE B 577 " --> pdb=" O TYR B 588 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 711 through 714 removed outlier: 3.586A pdb=" N ASN B 711 " --> pdb=" O PHE B 765 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 148 through 149 Processing sheet with id=AB8, first strand: chain 'D' and resid 70 through 72 Processing sheet with id=AB9, first strand: chain 'D' and resid 147 through 149 1031 hydrogen bonds defined for protein. 3010 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.17 Time building geometry restraints manager: 2.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6183 1.34 - 1.46: 4054 1.46 - 1.58: 8763 1.58 - 1.70: 6 1.70 - 1.82: 199 Bond restraints: 19205 Sorted by residual: bond pdb=" C4 ADP A1001 " pdb=" C5 ADP A1001 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C4 ADP B1001 " pdb=" C5 ADP B1001 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C5 ADP B1001 " pdb=" C6 ADP B1001 " ideal model delta sigma weight residual 1.490 1.404 0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C5 ADP A1001 " pdb=" C6 ADP A1001 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" O3 PO4 A1002 " pdb=" P PO4 A1002 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.05e+00 ... (remaining 19200 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 25405 2.04 - 4.07: 361 4.07 - 6.11: 58 6.11 - 8.14: 18 8.14 - 10.18: 12 Bond angle restraints: 25854 Sorted by residual: angle pdb=" C GLN A 454 " pdb=" CA GLN A 454 " pdb=" CB GLN A 454 " ideal model delta sigma weight residual 115.89 109.70 6.19 1.32e+00 5.74e-01 2.20e+01 angle pdb=" N VAL B 133 " pdb=" CA VAL B 133 " pdb=" C VAL B 133 " ideal model delta sigma weight residual 113.71 109.76 3.95 9.50e-01 1.11e+00 1.73e+01 angle pdb=" N LEU B 881 " pdb=" CA LEU B 881 " pdb=" C LEU B 881 " ideal model delta sigma weight residual 111.07 107.06 4.01 1.07e+00 8.73e-01 1.40e+01 angle pdb=" C ILE B 356 " pdb=" N MET B 357 " pdb=" CA MET B 357 " ideal model delta sigma weight residual 121.14 115.16 5.98 1.75e+00 3.27e-01 1.17e+01 angle pdb=" C1' ADP A1001 " pdb=" C2' ADP A1001 " pdb=" C3' ADP A1001 " ideal model delta sigma weight residual 111.00 100.82 10.18 3.00e+00 1.11e-01 1.15e+01 ... (remaining 25849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.97: 11218 28.97 - 57.93: 437 57.93 - 86.90: 30 86.90 - 115.86: 2 115.86 - 144.83: 4 Dihedral angle restraints: 11691 sinusoidal: 4928 harmonic: 6763 Sorted by residual: dihedral pdb=" O1B ADP A1001 " pdb=" O3A ADP A1001 " pdb=" PB ADP A1001 " pdb=" PA ADP A1001 " ideal model delta sinusoidal sigma weight residual -60.00 84.83 -144.83 1 2.00e+01 2.50e-03 4.36e+01 dihedral pdb=" O2A ADP A1001 " pdb=" O3A ADP A1001 " pdb=" PA ADP A1001 " pdb=" PB ADP A1001 " ideal model delta sinusoidal sigma weight residual -60.00 75.23 -135.23 1 2.00e+01 2.50e-03 4.10e+01 dihedral pdb=" O2A ADP B1001 " pdb=" O3A ADP B1001 " pdb=" PA ADP B1001 " pdb=" PB ADP B1001 " ideal model delta sinusoidal sigma weight residual -60.00 65.54 -125.54 1 2.00e+01 2.50e-03 3.79e+01 ... (remaining 11688 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2255 0.050 - 0.100: 442 0.100 - 0.150: 90 0.150 - 0.199: 5 0.199 - 0.249: 3 Chirality restraints: 2795 Sorted by residual: chirality pdb=" C3' ADP B1001 " pdb=" C2' ADP B1001 " pdb=" C4' ADP B1001 " pdb=" O3' ADP B1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.76 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA LEU B 881 " pdb=" N LEU B 881 " pdb=" C LEU B 881 " pdb=" CB LEU B 881 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" C3' ADP A1001 " pdb=" C2' ADP A1001 " pdb=" C4' ADP A1001 " pdb=" O3' ADP A1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.73 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 2792 not shown) Planarity restraints: 3346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 47 " -0.053 5.00e-02 4.00e+02 7.88e-02 9.94e+00 pdb=" N PRO D 48 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO D 48 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 48 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 111 " 0.012 2.00e-02 2.50e+03 1.72e-02 5.18e+00 pdb=" CG PHE C 111 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE C 111 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE C 111 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE C 111 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 111 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 111 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 666 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO A 667 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 667 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 667 " -0.030 5.00e-02 4.00e+02 ... (remaining 3343 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 146 2.43 - 3.05: 12458 3.05 - 3.66: 31646 3.66 - 4.28: 44503 4.28 - 4.90: 72133 Nonbonded interactions: 160886 Sorted by model distance: nonbonded pdb=" O2B ADP B1001 " pdb="MG MG B1003 " model vdw 1.812 2.170 nonbonded pdb=" O2B ADP A1001 " pdb="MG MG A1003 " model vdw 1.960 2.170 nonbonded pdb=" OG SER A 242 " pdb="MG MG A1003 " model vdw 2.038 2.170 nonbonded pdb=" O3 PO4 B1002 " pdb="MG MG B1003 " model vdw 2.058 2.170 nonbonded pdb=" OG1 THR B 185 " pdb="MG MG B1003 " model vdw 2.063 2.170 ... (remaining 160881 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 162 or resid 164 through 198 or resid 216 throug \ h 368 or resid 371 through 406 or resid 410 through 898 or resid 1001 through 10 \ 03)) selection = (chain 'B' and (resid 3 through 162 or resid 164 through 624 or resid 645 throug \ h 1003)) } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 20 through 143 or resid 149 through 162)) selection = (chain 'F' and (resid 20 through 56 or resid 60 through 143 or resid 149 through \ 162)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 12.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 22.030 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 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 : 0.003 0.111 19205 Z= 0.161 Angle : 0.639 10.178 25854 Z= 0.321 Chirality : 0.041 0.249 2795 Planarity : 0.004 0.079 3346 Dihedral : 14.828 144.830 7313 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.18), residues: 2283 helix: 1.19 (0.15), residues: 1295 sheet: -0.84 (0.39), residues: 163 loop : -0.54 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 120 TYR 0.017 0.001 TYR E 118 PHE 0.039 0.001 PHE C 111 TRP 0.016 0.001 TRP A 816 HIS 0.003 0.001 HIS B 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.16 (19205) covalent geometry : angle 0.63912 / 0.32 (25854) hydrogen bonds : bond 0.14250 / 9.25 ( 1031) hydrogen bonds : angle 6.05140 / 4.27 ( 3010) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 432 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 TYR cc_start: 0.7931 (m-80) cc_final: 0.7318 (m-80) REVERT: A 413 LYS cc_start: 0.7321 (tptp) cc_final: 0.7010 (tmtt) REVERT: A 690 MET cc_start: 0.7877 (tmm) cc_final: 0.7570 (tmm) REVERT: A 700 GLU cc_start: 0.8677 (mp0) cc_final: 0.8360 (mp0) REVERT: A 811 LEU cc_start: 0.8568 (mt) cc_final: 0.8354 (pp) REVERT: A 849 MET cc_start: 0.7981 (ptp) cc_final: 0.7052 (tpt) REVERT: A 852 MET cc_start: 0.8949 (tpp) cc_final: 0.8540 (tpp) REVERT: A 877 MET cc_start: 0.7447 (mmt) cc_final: 0.6018 (mmt) REVERT: A 889 LEU cc_start: 0.9341 (mt) cc_final: 0.9031 (tt) REVERT: B 6 MET cc_start: 0.5534 (mmt) cc_final: 0.5216 (mmt) REVERT: B 113 MET cc_start: 0.7565 (mtp) cc_final: 0.7180 (mtm) REVERT: B 312 PHE cc_start: 0.6053 (m-10) cc_final: 0.5663 (m-80) REVERT: B 435 MET cc_start: 0.8152 (tmm) cc_final: 0.7713 (tmm) REVERT: B 439 MET cc_start: 0.8376 (mtp) cc_final: 0.7916 (mtp) REVERT: B 531 MET cc_start: 0.7498 (ttt) cc_final: 0.6975 (tpp) REVERT: B 536 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8786 (tm-30) REVERT: B 606 VAL cc_start: 0.8508 (t) cc_final: 0.8178 (t) REVERT: B 799 MET cc_start: 0.7779 (mpp) cc_final: 0.7024 (ppp) REVERT: B 804 LEU cc_start: 0.8984 (tp) cc_final: 0.8674 (mt) REVERT: B 811 LEU cc_start: 0.9192 (mt) cc_final: 0.8974 (tp) REVERT: B 834 PHE cc_start: 0.6558 (t80) cc_final: 0.5843 (t80) REVERT: B 852 MET cc_start: 0.8454 (ppp) cc_final: 0.8139 (ppp) REVERT: C 59 MET cc_start: 0.7710 (mmm) cc_final: 0.6872 (mmm) REVERT: C 69 MET cc_start: 0.6723 (mpp) cc_final: 0.5591 (tpt) REVERT: C 117 MET cc_start: 0.7066 (tpt) cc_final: 0.6851 (tpt) REVERT: D 56 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6455 (tp30) REVERT: D 109 MET cc_start: 0.9027 (mmm) cc_final: 0.8745 (mmt) REVERT: D 140 PHE cc_start: 0.7676 (m-80) cc_final: 0.6989 (m-80) REVERT: D 142 LYS cc_start: 0.3241 (mmtt) cc_final: 0.2702 (mmmt) REVERT: E 36 MET cc_start: 0.8812 (mmp) cc_final: 0.8595 (mmp) REVERT: E 130 PHE cc_start: 0.6949 (m-80) cc_final: 0.6426 (m-80) REVERT: E 139 PHE cc_start: 0.7024 (m-80) cc_final: 0.6538 (m-80) REVERT: F 20 MET cc_start: 0.4415 (ppp) cc_final: 0.1062 (mmm) REVERT: F 26 ILE cc_start: 0.7394 (pt) cc_final: 0.6988 (pt) REVERT: F 34 THR cc_start: 0.8184 (m) cc_final: 0.7440 (m) REVERT: F 40 ARG cc_start: 0.7167 (mmp-170) cc_final: 0.6399 (ptt-90) REVERT: F 69 MET cc_start: 0.0142 (mmt) cc_final: -0.0317 (mmp) REVERT: F 113 VAL cc_start: 0.6650 (m) cc_final: 0.6199 (p) REVERT: F 156 VAL cc_start: 0.9226 (t) cc_final: 0.9019 (m) outliers start: 0 outliers final: 0 residues processed: 432 average time/residue: 0.1661 time to fit residues: 104.4775 Evaluate side-chains 260 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.0470 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 overall best weight: 1.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 418 GLN B 444 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 ASN ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 GLN ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN E 78 ASN E 157 HIS ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.078776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.062201 restraints weight = 223583.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.064346 restraints weight = 95793.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.065770 restraints weight = 55124.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.066636 restraints weight = 37500.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.067256 restraints weight = 29026.973| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3862 r_free = 0.3862 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3862 r_free = 0.3862 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19205 Z= 0.159 Angle : 0.708 13.163 25854 Z= 0.357 Chirality : 0.044 0.180 2795 Planarity : 0.004 0.050 3346 Dihedral : 7.597 154.993 2534 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.74 % Allowed : 10.46 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.18), residues: 2283 helix: 0.96 (0.14), residues: 1314 sheet: -0.61 (0.42), residues: 149 loop : -0.76 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 712 TYR 0.023 0.002 TYR E 118 PHE 0.036 0.002 PHE C 61 TRP 0.013 0.001 TRP B 438 HIS 0.013 0.001 HIS B 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (19205) covalent geometry : angle 0.70800 / 0.36 (25854) hydrogen bonds : bond 0.04556 / 3.01 ( 1031) hydrogen bonds : angle 5.09251 / 3.59 ( 3010) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 286 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.7959 (mmt) cc_final: 0.7646 (mmt) REVERT: A 350 TYR cc_start: 0.7762 (m-80) cc_final: 0.7377 (m-80) REVERT: A 699 LEU cc_start: 0.8866 (tp) cc_final: 0.8635 (tp) REVERT: A 700 GLU cc_start: 0.8427 (mp0) cc_final: 0.8007 (mp0) REVERT: A 807 ARG cc_start: 0.8761 (mmm160) cc_final: 0.8549 (tpt90) REVERT: A 849 MET cc_start: 0.7925 (ptp) cc_final: 0.7022 (tpt) REVERT: A 889 LEU cc_start: 0.9255 (mt) cc_final: 0.8902 (tt) REVERT: B 6 MET cc_start: 0.5449 (mmt) cc_final: 0.5160 (mmt) REVERT: B 418 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.6818 (pp30) REVERT: B 536 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8541 (tm-30) REVERT: B 606 VAL cc_start: 0.8372 (t) cc_final: 0.8137 (t) REVERT: B 811 LEU cc_start: 0.9030 (mt) cc_final: 0.8213 (tp) REVERT: B 817 ASN cc_start: 0.8613 (m-40) cc_final: 0.8242 (m110) REVERT: B 821 PHE cc_start: 0.8086 (t80) cc_final: 0.7553 (t80) REVERT: B 852 MET cc_start: 0.8700 (ppp) cc_final: 0.8319 (ppp) REVERT: C 59 MET cc_start: 0.7671 (mmm) cc_final: 0.6658 (mmm) REVERT: C 69 MET cc_start: 0.6452 (mpp) cc_final: 0.5568 (tpt) REVERT: D 51 ILE cc_start: 0.5253 (mm) cc_final: 0.4959 (mm) REVERT: D 56 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6357 (tp30) REVERT: D 62 ASP cc_start: 0.4918 (OUTLIER) cc_final: 0.4087 (p0) REVERT: D 69 MET cc_start: 0.4944 (tpp) cc_final: 0.4698 (tpp) REVERT: D 140 PHE cc_start: 0.7347 (m-80) cc_final: 0.6829 (m-80) REVERT: D 142 LYS cc_start: 0.3409 (mmtt) cc_final: 0.2671 (mmmt) REVERT: E 85 MET cc_start: 0.6246 (tmm) cc_final: 0.5854 (tmm) REVERT: E 118 TYR cc_start: 0.7773 (t80) cc_final: 0.7353 (t80) REVERT: E 122 MET cc_start: 0.8062 (mtm) cc_final: 0.6394 (tpt) REVERT: E 139 PHE cc_start: 0.6486 (m-80) cc_final: 0.6152 (m-80) REVERT: F 20 MET cc_start: 0.4126 (ppp) cc_final: 0.0446 (mmm) REVERT: F 26 ILE cc_start: 0.7455 (pt) cc_final: 0.6960 (pt) REVERT: F 34 THR cc_start: 0.7933 (m) cc_final: 0.7337 (p) REVERT: F 40 ARG cc_start: 0.6717 (mmp-170) cc_final: 0.6072 (ptt-90) REVERT: F 69 MET cc_start: 0.0738 (mmt) cc_final: 0.0205 (mmp) outliers start: 15 outliers final: 7 residues processed: 293 average time/residue: 0.1481 time to fit residues: 65.8186 Evaluate side-chains 235 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 226 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 833 TYR Chi-restraints excluded: chain B residue 874 GLU Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain E residue 78 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 119 optimal weight: 0.6980 chunk 15 optimal weight: 0.1980 chunk 202 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 88 optimal weight: 0.0980 chunk 94 optimal weight: 9.9990 chunk 13 optimal weight: 0.2980 chunk 64 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 chunk 193 optimal weight: 9.9990 chunk 201 optimal weight: 9.9990 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 ASN B 418 GLN B 444 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 581 HIS ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 GLN ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 39 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.079304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.063611 restraints weight = 159634.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.066145 restraints weight = 80530.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.067045 restraints weight = 41061.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.067162 restraints weight = 34198.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.067433 restraints weight = 29213.359| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3863 r_free = 0.3863 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3863 r_free = 0.3863 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19205 Z= 0.134 Angle : 0.679 14.706 25854 Z= 0.339 Chirality : 0.042 0.171 2795 Planarity : 0.004 0.051 3346 Dihedral : 7.522 160.468 2534 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.48 % Allowed : 11.90 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.18), residues: 2283 helix: 0.85 (0.14), residues: 1326 sheet: -0.82 (0.40), residues: 164 loop : -0.85 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 94 TYR 0.025 0.001 TYR A 609 PHE 0.029 0.001 PHE A 821 TRP 0.009 0.001 TRP A 816 HIS 0.010 0.001 HIS B 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (19205) covalent geometry : angle 0.67943 / 0.34 (25854) hydrogen bonds : bond 0.04182 / 2.75 ( 1031) hydrogen bonds : angle 4.89851 / 3.45 ( 3010) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 250 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.9199 (mt) cc_final: 0.8974 (pp) REVERT: A 77 MET cc_start: 0.7879 (mmt) cc_final: 0.7514 (mmt) REVERT: A 92 MET cc_start: 0.8023 (mmm) cc_final: 0.7790 (mmt) REVERT: A 350 TYR cc_start: 0.7754 (m-80) cc_final: 0.7379 (m-80) REVERT: A 811 LEU cc_start: 0.8335 (mt) cc_final: 0.8134 (mt) REVERT: A 849 MET cc_start: 0.7942 (ptp) cc_final: 0.7040 (tpt) REVERT: A 889 LEU cc_start: 0.9270 (mt) cc_final: 0.8937 (tt) REVERT: B 6 MET cc_start: 0.5461 (mmt) cc_final: 0.5174 (mmt) REVERT: B 817 ASN cc_start: 0.8528 (m-40) cc_final: 0.8183 (m110) REVERT: C 59 MET cc_start: 0.7777 (mmm) cc_final: 0.6981 (mmm) REVERT: C 61 PHE cc_start: 0.6504 (t80) cc_final: 0.6246 (t80) REVERT: C 69 MET cc_start: 0.6654 (mpp) cc_final: 0.5785 (tpt) REVERT: C 94 ARG cc_start: 0.8143 (ptt-90) cc_final: 0.7928 (ptt-90) REVERT: D 56 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6361 (tp30) REVERT: D 140 PHE cc_start: 0.7434 (m-80) cc_final: 0.6841 (m-80) REVERT: D 142 LYS cc_start: 0.3703 (mmtt) cc_final: 0.2969 (mmmt) REVERT: E 85 MET cc_start: 0.6084 (tmm) cc_final: 0.5564 (tmm) REVERT: E 139 PHE cc_start: 0.6620 (m-80) cc_final: 0.6289 (m-80) REVERT: F 20 MET cc_start: 0.4104 (ppp) cc_final: 0.0501 (mmm) REVERT: F 26 ILE cc_start: 0.7335 (pt) cc_final: 0.7036 (pt) REVERT: F 34 THR cc_start: 0.7915 (m) cc_final: 0.7215 (m) REVERT: F 40 ARG cc_start: 0.6729 (mmp-170) cc_final: 0.6286 (ptt-90) REVERT: F 117 ASP cc_start: 0.8927 (p0) cc_final: 0.8011 (m-30) REVERT: F 122 MET cc_start: 0.8561 (tpt) cc_final: 0.8269 (ttm) outliers start: 30 outliers final: 13 residues processed: 268 average time/residue: 0.1528 time to fit residues: 62.6154 Evaluate side-chains 228 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 215 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 833 TYR Chi-restraints excluded: chain B residue 874 GLU Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 85 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 61 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 49 optimal weight: 0.0970 chunk 35 optimal weight: 0.0770 chunk 56 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 154 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 224 optimal weight: 10.0000 overall best weight: 0.5936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 885 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN D 50 GLN ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN F 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.079356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.063297 restraints weight = 176465.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.065293 restraints weight = 80149.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.066596 restraints weight = 47328.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.067440 restraints weight = 32772.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.068017 restraints weight = 25547.358| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3879 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3879 r_free = 0.3879 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3879 r_free = 0.3879 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3879 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19205 Z= 0.131 Angle : 0.689 14.406 25854 Z= 0.340 Chirality : 0.042 0.223 2795 Planarity : 0.004 0.050 3346 Dihedral : 7.477 168.430 2534 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.38 % Allowed : 13.67 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.18), residues: 2283 helix: 0.84 (0.14), residues: 1321 sheet: -0.83 (0.40), residues: 164 loop : -0.88 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 858 TYR 0.021 0.001 TYR B 422 PHE 0.028 0.001 PHE A 821 TRP 0.010 0.001 TRP A 816 HIS 0.004 0.001 HIS B 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (19205) covalent geometry : angle 0.68943 / 0.34 (25854) hydrogen bonds : bond 0.03993 / 2.63 ( 1031) hydrogen bonds : angle 4.83655 / 3.37 ( 3010) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 240 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.7945 (mmt) cc_final: 0.7538 (mmt) REVERT: A 92 MET cc_start: 0.7988 (mmm) cc_final: 0.7753 (mmt) REVERT: A 350 TYR cc_start: 0.7858 (m-80) cc_final: 0.7389 (m-80) REVERT: A 807 ARG cc_start: 0.8753 (mmm160) cc_final: 0.8337 (tpt90) REVERT: A 811 LEU cc_start: 0.8311 (mt) cc_final: 0.7589 (mt) REVERT: A 848 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7706 (mt-10) REVERT: A 849 MET cc_start: 0.7970 (ptp) cc_final: 0.7081 (tpt) REVERT: A 889 LEU cc_start: 0.9211 (mt) cc_final: 0.8863 (tt) REVERT: B 817 ASN cc_start: 0.8546 (m-40) cc_final: 0.8189 (m110) REVERT: B 821 PHE cc_start: 0.8071 (t80) cc_final: 0.7587 (t80) REVERT: B 852 MET cc_start: 0.8844 (ppp) cc_final: 0.8063 (ppp) REVERT: B 872 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8734 (pt0) REVERT: C 59 MET cc_start: 0.7699 (mmm) cc_final: 0.6996 (mmm) REVERT: C 69 MET cc_start: 0.6610 (mpp) cc_final: 0.5720 (tpt) REVERT: D 56 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6442 (tp30) REVERT: D 140 PHE cc_start: 0.7268 (m-80) cc_final: 0.6765 (m-80) REVERT: D 142 LYS cc_start: 0.3553 (mmtt) cc_final: 0.2835 (mmmt) REVERT: E 85 MET cc_start: 0.5985 (tmm) cc_final: 0.5455 (tmm) REVERT: E 139 PHE cc_start: 0.6527 (m-80) cc_final: 0.6169 (m-80) REVERT: F 20 MET cc_start: 0.4099 (ppp) cc_final: 0.0437 (mmm) REVERT: F 26 ILE cc_start: 0.7086 (pt) cc_final: 0.6878 (pt) REVERT: F 34 THR cc_start: 0.7858 (m) cc_final: 0.7164 (m) REVERT: F 40 ARG cc_start: 0.6644 (mmp-170) cc_final: 0.6325 (ptt-90) REVERT: F 56 LEU cc_start: 0.5802 (pp) cc_final: 0.4694 (tt) REVERT: F 117 ASP cc_start: 0.8946 (p0) cc_final: 0.8106 (m-30) REVERT: F 136 ASP cc_start: 0.7891 (m-30) cc_final: 0.7511 (p0) REVERT: F 137 GLN cc_start: 0.6185 (tm-30) cc_final: 0.5984 (pp30) outliers start: 28 outliers final: 13 residues processed: 254 average time/residue: 0.1394 time to fit residues: 55.6733 Evaluate side-chains 232 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 218 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 610 GLN Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 539 MET Chi-restraints excluded: chain B residue 833 TYR Chi-restraints excluded: chain B residue 872 GLU Chi-restraints excluded: chain B residue 874 GLU Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain F residue 85 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 108 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 206 optimal weight: 0.9990 chunk 226 optimal weight: 1.9990 chunk 218 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 chunk 130 optimal weight: 8.9990 chunk 109 optimal weight: 0.9980 chunk 193 optimal weight: 8.9990 chunk 66 optimal weight: 0.0870 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.078665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.062425 restraints weight = 186648.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.064403 restraints weight = 84905.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.065679 restraints weight = 50610.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.066581 restraints weight = 35302.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.067123 restraints weight = 27456.623| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3854 r_free = 0.3854 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3854 r_free = 0.3854 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19205 Z= 0.136 Angle : 0.680 12.169 25854 Z= 0.338 Chirality : 0.042 0.209 2795 Planarity : 0.004 0.049 3346 Dihedral : 7.487 173.602 2534 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.48 % Allowed : 14.36 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.18), residues: 2283 helix: 0.81 (0.14), residues: 1317 sheet: -0.86 (0.40), residues: 164 loop : -0.91 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 858 TYR 0.027 0.001 TYR E 118 PHE 0.027 0.001 PHE B 312 TRP 0.011 0.001 TRP A 816 HIS 0.005 0.001 HIS B 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (19205) covalent geometry : angle 0.68032 / 0.34 (25854) hydrogen bonds : bond 0.03932 / 2.59 ( 1031) hydrogen bonds : angle 4.81216 / 3.35 ( 3010) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 236 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8018 (mmt) cc_final: 0.7553 (mmt) REVERT: A 92 MET cc_start: 0.8041 (mmm) cc_final: 0.7787 (mmt) REVERT: A 350 TYR cc_start: 0.7717 (m-80) cc_final: 0.7383 (m-80) REVERT: A 776 MET cc_start: 0.9102 (mtm) cc_final: 0.8763 (ptp) REVERT: A 807 ARG cc_start: 0.8760 (mmm160) cc_final: 0.8467 (tpt90) REVERT: A 849 MET cc_start: 0.8031 (ptp) cc_final: 0.7149 (tpt) REVERT: A 852 MET cc_start: 0.8603 (ttm) cc_final: 0.7775 (ttm) REVERT: A 856 PHE cc_start: 0.7800 (m-10) cc_final: 0.7353 (m-80) REVERT: A 889 LEU cc_start: 0.9238 (mt) cc_final: 0.8904 (tt) REVERT: B 297 LEU cc_start: 0.8531 (mt) cc_final: 0.8329 (tp) REVERT: B 535 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7230 (mt-10) REVERT: B 809 ASP cc_start: 0.9100 (m-30) cc_final: 0.8853 (p0) REVERT: B 817 ASN cc_start: 0.8583 (m-40) cc_final: 0.8217 (m110) REVERT: B 821 PHE cc_start: 0.8036 (t80) cc_final: 0.7699 (t80) REVERT: B 852 MET cc_start: 0.8586 (ppp) cc_final: 0.7913 (ppp) REVERT: C 59 MET cc_start: 0.7721 (mmm) cc_final: 0.6975 (mmm) REVERT: C 69 MET cc_start: 0.6685 (mpp) cc_final: 0.5771 (tpt) REVERT: D 56 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6483 (tp30) REVERT: D 140 PHE cc_start: 0.7278 (m-80) cc_final: 0.6725 (m-80) REVERT: D 142 LYS cc_start: 0.3514 (mmtt) cc_final: 0.2806 (mmmt) REVERT: E 85 MET cc_start: 0.6075 (tmm) cc_final: 0.5165 (tmm) REVERT: F 20 MET cc_start: 0.4133 (ppp) cc_final: 0.0302 (mmm) REVERT: F 26 ILE cc_start: 0.7417 (pt) cc_final: 0.7184 (pt) REVERT: F 40 ARG cc_start: 0.6579 (mmp-170) cc_final: 0.6366 (ptt-90) REVERT: F 69 MET cc_start: 0.1044 (mmp) cc_final: -0.0214 (mmt) REVERT: F 136 ASP cc_start: 0.7851 (m-30) cc_final: 0.7464 (p0) outliers start: 30 outliers final: 15 residues processed: 253 average time/residue: 0.1465 time to fit residues: 57.5565 Evaluate side-chains 231 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 215 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 610 GLN Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 539 MET Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 610 GLN Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 123 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 70 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 59 optimal weight: 0.0370 chunk 112 optimal weight: 7.9990 chunk 203 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 45 optimal weight: 0.0980 chunk 179 optimal weight: 4.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.078894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.063791 restraints weight = 134955.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.065372 restraints weight = 73578.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.066052 restraints weight = 42119.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.066304 restraints weight = 38055.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.066323 restraints weight = 33432.032| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3823 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3823 r_free = 0.3823 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3823 r_free = 0.3823 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3823 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19205 Z= 0.124 Angle : 0.690 16.023 25854 Z= 0.340 Chirality : 0.042 0.167 2795 Planarity : 0.004 0.072 3346 Dihedral : 7.454 174.589 2534 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.48 % Allowed : 15.30 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.18), residues: 2283 helix: 0.84 (0.14), residues: 1312 sheet: -0.77 (0.41), residues: 161 loop : -0.93 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 434 TYR 0.017 0.001 TYR A 609 PHE 0.028 0.001 PHE C 61 TRP 0.012 0.001 TRP B 593 HIS 0.005 0.001 HIS B 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (19205) covalent geometry : angle 0.68996 / 0.34 (25854) hydrogen bonds : bond 0.03877 / 2.55 ( 1031) hydrogen bonds : angle 4.73740 / 3.29 ( 3010) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 233 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.7993 (mmt) cc_final: 0.7541 (mmt) REVERT: A 92 MET cc_start: 0.8020 (mmm) cc_final: 0.7814 (mmt) REVERT: A 350 TYR cc_start: 0.7709 (m-80) cc_final: 0.7345 (m-80) REVERT: A 807 ARG cc_start: 0.8730 (mmm160) cc_final: 0.8434 (tpt90) REVERT: A 849 MET cc_start: 0.7962 (ptp) cc_final: 0.7674 (tpt) REVERT: A 856 PHE cc_start: 0.7791 (m-10) cc_final: 0.7371 (m-80) REVERT: A 865 LYS cc_start: 0.9248 (tppt) cc_final: 0.9023 (pttp) REVERT: A 889 LEU cc_start: 0.9222 (mt) cc_final: 0.8885 (tt) REVERT: B 312 PHE cc_start: 0.5929 (m-80) cc_final: 0.5727 (m-80) REVERT: B 447 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7266 (mm) REVERT: B 515 MET cc_start: 0.5367 (pmm) cc_final: 0.5132 (pmm) REVERT: B 548 PHE cc_start: 0.6077 (t80) cc_final: 0.5837 (t80) REVERT: B 817 ASN cc_start: 0.8439 (m-40) cc_final: 0.8129 (m110) REVERT: B 852 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8105 (ppp) REVERT: C 59 MET cc_start: 0.7784 (mmm) cc_final: 0.7069 (mmm) REVERT: C 69 MET cc_start: 0.6801 (mpp) cc_final: 0.5860 (tpt) REVERT: D 56 GLU cc_start: 0.7231 (mm-30) cc_final: 0.6507 (tp30) REVERT: D 140 PHE cc_start: 0.7474 (m-80) cc_final: 0.6798 (m-80) REVERT: D 142 LYS cc_start: 0.3780 (mmtt) cc_final: 0.3034 (mmmt) REVERT: E 65 GLU cc_start: 0.6278 (tt0) cc_final: 0.5858 (mp0) REVERT: E 85 MET cc_start: 0.5696 (tmm) cc_final: 0.5342 (tmm) REVERT: F 20 MET cc_start: 0.4150 (ppp) cc_final: 0.0430 (mmm) REVERT: F 26 ILE cc_start: 0.7404 (pt) cc_final: 0.7159 (pt) REVERT: F 117 ASP cc_start: 0.8833 (p0) cc_final: 0.7901 (m-30) outliers start: 30 outliers final: 17 residues processed: 249 average time/residue: 0.1501 time to fit residues: 57.7066 Evaluate side-chains 230 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 211 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 610 GLN Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 539 MET Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 610 GLN Chi-restraints excluded: chain B residue 833 TYR Chi-restraints excluded: chain B residue 852 MET Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 138 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 194 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 219 optimal weight: 0.4980 chunk 113 optimal weight: 0.0770 chunk 51 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 66 optimal weight: 0.0870 chunk 60 optimal weight: 0.9980 chunk 143 optimal weight: 9.9990 overall best weight: 0.9318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.078443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.062418 restraints weight = 176603.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.064368 restraints weight = 81034.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.065622 restraints weight = 48280.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.066466 restraints weight = 33779.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.067008 restraints weight = 26440.769| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3854 r_free = 0.3854 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3854 r_free = 0.3854 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19205 Z= 0.133 Angle : 0.696 14.746 25854 Z= 0.343 Chirality : 0.042 0.184 2795 Planarity : 0.004 0.050 3346 Dihedral : 7.466 178.565 2534 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.53 % Allowed : 16.04 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.18), residues: 2283 helix: 0.88 (0.14), residues: 1307 sheet: -0.81 (0.43), residues: 149 loop : -0.88 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 858 TYR 0.039 0.002 TYR E 118 PHE 0.028 0.001 PHE D 54 TRP 0.012 0.001 TRP A 816 HIS 0.004 0.001 HIS B 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (19205) covalent geometry : angle 0.69559 / 0.34 (25854) hydrogen bonds : bond 0.03829 / 2.53 ( 1031) hydrogen bonds : angle 4.74103 / 3.28 ( 3010) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 225 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8026 (mmt) cc_final: 0.7538 (mmt) REVERT: A 350 TYR cc_start: 0.7796 (m-80) cc_final: 0.7444 (m-80) REVERT: A 807 ARG cc_start: 0.8751 (mmm160) cc_final: 0.8450 (tpt90) REVERT: A 852 MET cc_start: 0.8558 (ttm) cc_final: 0.8029 (ttm) REVERT: A 856 PHE cc_start: 0.7860 (m-10) cc_final: 0.7536 (m-80) REVERT: A 865 LYS cc_start: 0.9268 (tppt) cc_final: 0.8987 (pttp) REVERT: A 889 LEU cc_start: 0.9223 (mt) cc_final: 0.8887 (tt) REVERT: B 165 MET cc_start: 0.8532 (tpp) cc_final: 0.7974 (tpp) REVERT: B 297 LEU cc_start: 0.8295 (tp) cc_final: 0.7948 (pp) REVERT: B 312 PHE cc_start: 0.5776 (m-80) cc_final: 0.5501 (m-80) REVERT: B 362 MET cc_start: 0.6665 (tpt) cc_final: 0.6223 (tpp) REVERT: B 447 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7267 (mm) REVERT: B 515 MET cc_start: 0.5531 (pmm) cc_final: 0.5276 (pmm) REVERT: B 548 PHE cc_start: 0.5947 (t80) cc_final: 0.5669 (t80) REVERT: B 809 ASP cc_start: 0.9077 (m-30) cc_final: 0.8829 (p0) REVERT: B 817 ASN cc_start: 0.8500 (m-40) cc_final: 0.8131 (m110) REVERT: B 821 PHE cc_start: 0.8261 (t80) cc_final: 0.7945 (t80) REVERT: B 852 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8237 (ppp) REVERT: C 59 MET cc_start: 0.7807 (mmm) cc_final: 0.7064 (mmm) REVERT: C 69 MET cc_start: 0.6692 (mpp) cc_final: 0.5800 (tpt) REVERT: D 56 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6539 (tp30) REVERT: D 140 PHE cc_start: 0.7223 (m-80) cc_final: 0.6658 (m-80) REVERT: D 142 LYS cc_start: 0.3622 (mmtt) cc_final: 0.2817 (mmmt) REVERT: E 65 GLU cc_start: 0.6274 (tt0) cc_final: 0.5764 (mp0) REVERT: E 85 MET cc_start: 0.5742 (tmm) cc_final: 0.5363 (tmm) REVERT: E 138 MET cc_start: 0.8146 (mpp) cc_final: 0.7605 (tpt) REVERT: F 20 MET cc_start: 0.4228 (ppp) cc_final: 0.0125 (mmm) REVERT: F 40 ARG cc_start: 0.6328 (ptt-90) cc_final: 0.5915 (ppt170) REVERT: F 117 ASP cc_start: 0.8843 (p0) cc_final: 0.7919 (m-30) outliers start: 31 outliers final: 24 residues processed: 245 average time/residue: 0.1490 time to fit residues: 56.3005 Evaluate side-chains 235 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 610 GLN Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 539 MET Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 610 GLN Chi-restraints excluded: chain B residue 833 TYR Chi-restraints excluded: chain B residue 852 MET Chi-restraints excluded: chain B residue 888 GLN Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain F residue 159 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 5 optimal weight: 0.0970 chunk 77 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 217 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 199 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 174 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 HIS ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.077793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.061105 restraints weight = 220873.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.063241 restraints weight = 94022.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.064607 restraints weight = 54465.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.065500 restraints weight = 37181.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.066094 restraints weight = 28619.296| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3829 r_free = 0.3829 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3829 r_free = 0.3829 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19205 Z= 0.141 Angle : 0.707 13.447 25854 Z= 0.350 Chirality : 0.043 0.304 2795 Planarity : 0.004 0.050 3346 Dihedral : 7.420 176.461 2534 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.33 % Allowed : 16.73 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.18), residues: 2283 helix: 0.91 (0.14), residues: 1309 sheet: -0.58 (0.46), residues: 129 loop : -0.97 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 858 TYR 0.015 0.001 TYR B 422 PHE 0.027 0.001 PHE B 821 TRP 0.013 0.001 TRP A 816 HIS 0.003 0.001 HIS A 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (19205) covalent geometry : angle 0.70666 / 0.35 (25854) hydrogen bonds : bond 0.03826 / 2.54 ( 1031) hydrogen bonds : angle 4.75454 / 3.30 ( 3010) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 222 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8086 (mmt) cc_final: 0.7544 (mmt) REVERT: A 113 MET cc_start: 0.6309 (mmt) cc_final: 0.5818 (mmt) REVERT: A 350 TYR cc_start: 0.7810 (m-80) cc_final: 0.7440 (m-80) REVERT: A 388 MET cc_start: 0.6038 (mpp) cc_final: 0.5448 (mtt) REVERT: A 405 LYS cc_start: 0.9030 (ttmt) cc_final: 0.8743 (tttp) REVERT: A 781 LEU cc_start: 0.7792 (mm) cc_final: 0.7583 (mt) REVERT: A 807 ARG cc_start: 0.8734 (mmm160) cc_final: 0.8443 (tpt90) REVERT: A 847 LYS cc_start: 0.7714 (pptt) cc_final: 0.7436 (pptt) REVERT: A 852 MET cc_start: 0.8586 (ttm) cc_final: 0.8124 (ttm) REVERT: A 856 PHE cc_start: 0.7830 (m-10) cc_final: 0.7490 (m-80) REVERT: A 865 LYS cc_start: 0.9254 (tppt) cc_final: 0.8976 (pttp) REVERT: A 889 LEU cc_start: 0.9218 (mt) cc_final: 0.8884 (tt) REVERT: B 297 LEU cc_start: 0.8352 (tp) cc_final: 0.8010 (pp) REVERT: B 312 PHE cc_start: 0.5935 (m-80) cc_final: 0.5578 (m-80) REVERT: B 447 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7294 (mm) REVERT: B 809 ASP cc_start: 0.9050 (m-30) cc_final: 0.8805 (p0) REVERT: B 817 ASN cc_start: 0.8521 (m-40) cc_final: 0.8095 (m110) REVERT: B 821 PHE cc_start: 0.8159 (t80) cc_final: 0.7892 (t80) REVERT: B 852 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8242 (ppp) REVERT: C 59 MET cc_start: 0.7854 (mmm) cc_final: 0.7088 (mmm) REVERT: C 69 MET cc_start: 0.6693 (mpp) cc_final: 0.5772 (tpt) REVERT: D 56 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6461 (tp30) REVERT: D 140 PHE cc_start: 0.7275 (m-80) cc_final: 0.6242 (m-80) REVERT: D 142 LYS cc_start: 0.3531 (mmtt) cc_final: 0.2727 (mmmt) REVERT: D 193 MET cc_start: 0.6992 (mtm) cc_final: 0.6587 (tpp) REVERT: E 65 GLU cc_start: 0.6382 (tt0) cc_final: 0.6057 (mp0) REVERT: E 85 MET cc_start: 0.5794 (tmm) cc_final: 0.5385 (tmm) REVERT: E 138 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7618 (tpt) REVERT: F 20 MET cc_start: 0.4330 (ppp) cc_final: 0.0131 (mmm) REVERT: F 40 ARG cc_start: 0.6472 (ptt-90) cc_final: 0.5753 (ppt170) REVERT: F 69 MET cc_start: 0.0050 (mmt) cc_final: -0.0876 (mmt) REVERT: F 117 ASP cc_start: 0.8918 (p0) cc_final: 0.8068 (m-30) outliers start: 27 outliers final: 22 residues processed: 239 average time/residue: 0.1537 time to fit residues: 56.5651 Evaluate side-chains 238 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 213 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 610 GLN Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 539 MET Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 610 GLN Chi-restraints excluded: chain B residue 833 TYR Chi-restraints excluded: chain B residue 852 MET Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 138 MET Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 138 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 124 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 49 optimal weight: 0.0770 chunk 172 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.078120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.062161 restraints weight = 164101.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.064021 restraints weight = 77470.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.065235 restraints weight = 47156.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.066043 restraints weight = 33475.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.066562 restraints weight = 26523.582| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3845 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3845 r_free = 0.3845 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3845 r_free = 0.3845 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3845 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19205 Z= 0.127 Angle : 0.720 14.042 25854 Z= 0.354 Chirality : 0.042 0.318 2795 Planarity : 0.004 0.050 3346 Dihedral : 7.291 172.969 2534 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.33 % Allowed : 17.18 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.18), residues: 2283 helix: 0.92 (0.14), residues: 1315 sheet: -0.68 (0.45), residues: 139 loop : -0.99 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 858 TYR 0.047 0.002 TYR E 118 PHE 0.020 0.001 PHE B 821 TRP 0.012 0.001 TRP A 816 HIS 0.003 0.001 HIS B 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (19205) covalent geometry : angle 0.71969 / 0.35 (25854) hydrogen bonds : bond 0.03786 / 2.51 ( 1031) hydrogen bonds : angle 4.71429 / 3.27 ( 3010) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 227 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8069 (mmt) cc_final: 0.7527 (mmt) REVERT: A 113 MET cc_start: 0.6165 (mmt) cc_final: 0.5647 (mmt) REVERT: A 350 TYR cc_start: 0.7815 (m-80) cc_final: 0.7456 (m-80) REVERT: A 388 MET cc_start: 0.5969 (mpp) cc_final: 0.5408 (mtt) REVERT: A 781 LEU cc_start: 0.7756 (mm) cc_final: 0.7544 (mt) REVERT: A 847 LYS cc_start: 0.7851 (pptt) cc_final: 0.7539 (pptt) REVERT: A 856 PHE cc_start: 0.7905 (m-10) cc_final: 0.7670 (m-80) REVERT: A 865 LYS cc_start: 0.9210 (tppt) cc_final: 0.8974 (pttp) REVERT: A 889 LEU cc_start: 0.9206 (mt) cc_final: 0.8874 (tt) REVERT: B 43 LYS cc_start: 0.8088 (mmtp) cc_final: 0.7565 (mmmt) REVERT: B 113 MET cc_start: 0.7394 (ptt) cc_final: 0.6670 (ppp) REVERT: B 297 LEU cc_start: 0.8315 (tp) cc_final: 0.7981 (pp) REVERT: B 312 PHE cc_start: 0.6088 (m-80) cc_final: 0.5666 (m-80) REVERT: B 447 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7305 (mm) REVERT: B 809 ASP cc_start: 0.9047 (m-30) cc_final: 0.8775 (p0) REVERT: B 817 ASN cc_start: 0.8501 (m-40) cc_final: 0.8072 (m110) REVERT: B 852 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8183 (ppp) REVERT: C 59 MET cc_start: 0.7867 (mmm) cc_final: 0.7105 (mmm) REVERT: C 69 MET cc_start: 0.6679 (mpp) cc_final: 0.5781 (tpt) REVERT: D 56 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6433 (tp30) REVERT: D 140 PHE cc_start: 0.7232 (m-80) cc_final: 0.6238 (m-80) REVERT: D 142 LYS cc_start: 0.3588 (mmtt) cc_final: 0.2757 (mmmt) REVERT: D 193 MET cc_start: 0.6933 (mtm) cc_final: 0.6533 (tpp) REVERT: E 65 GLU cc_start: 0.6433 (tt0) cc_final: 0.6115 (mp0) REVERT: E 85 MET cc_start: 0.5807 (tmm) cc_final: 0.5424 (tmm) REVERT: E 138 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7583 (tpt) REVERT: F 20 MET cc_start: 0.4390 (ppp) cc_final: 0.0159 (mmm) REVERT: F 40 ARG cc_start: 0.6458 (ptt-90) cc_final: 0.5763 (ppt170) REVERT: F 69 MET cc_start: 0.0156 (mmt) cc_final: -0.0894 (mmt) outliers start: 27 outliers final: 22 residues processed: 241 average time/residue: 0.1459 time to fit residues: 54.5133 Evaluate side-chains 244 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 219 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 610 GLN Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 539 MET Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 610 GLN Chi-restraints excluded: chain B residue 833 TYR Chi-restraints excluded: chain B residue 852 MET Chi-restraints excluded: chain B residue 888 GLN Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 138 MET Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 138 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 102 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 48 optimal weight: 0.4980 chunk 219 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 171 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.078133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.062196 restraints weight = 174900.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.064148 restraints weight = 78873.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.065410 restraints weight = 46565.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.066248 restraints weight = 32444.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.066789 restraints weight = 25446.524| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3863 r_free = 0.3863 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3863 r_free = 0.3863 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19205 Z= 0.133 Angle : 0.727 14.204 25854 Z= 0.360 Chirality : 0.043 0.311 2795 Planarity : 0.004 0.050 3346 Dihedral : 7.097 165.508 2534 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.58 % Allowed : 17.52 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.18), residues: 2283 helix: 0.91 (0.14), residues: 1312 sheet: -0.73 (0.45), residues: 139 loop : -1.01 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 858 TYR 0.036 0.001 TYR B 422 PHE 0.026 0.001 PHE A 436 TRP 0.014 0.001 TRP A 816 HIS 0.003 0.001 HIS B 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (19205) covalent geometry : angle 0.72695 / 0.36 (25854) hydrogen bonds : bond 0.03829 / 2.53 ( 1031) hydrogen bonds : angle 4.72090 / 3.27 ( 3010) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 223 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TYR cc_start: 0.7847 (m-80) cc_final: 0.7491 (m-10) REVERT: A 77 MET cc_start: 0.8090 (mmt) cc_final: 0.7548 (mmt) REVERT: A 350 TYR cc_start: 0.7701 (m-80) cc_final: 0.7360 (m-80) REVERT: A 388 MET cc_start: 0.6054 (mpp) cc_final: 0.5849 (mtm) REVERT: A 405 LYS cc_start: 0.8827 (tttp) cc_final: 0.8247 (tptm) REVERT: A 776 MET cc_start: 0.8923 (mtm) cc_final: 0.8673 (ptp) REVERT: A 781 LEU cc_start: 0.7723 (mm) cc_final: 0.7463 (mt) REVERT: A 847 LYS cc_start: 0.7803 (pptt) cc_final: 0.7496 (pptt) REVERT: A 856 PHE cc_start: 0.7916 (m-10) cc_final: 0.7690 (m-80) REVERT: A 889 LEU cc_start: 0.9181 (mt) cc_final: 0.8835 (tt) REVERT: B 43 LYS cc_start: 0.8075 (mmtp) cc_final: 0.7594 (mmmt) REVERT: B 113 MET cc_start: 0.7436 (ptt) cc_final: 0.6861 (ppp) REVERT: B 179 GLU cc_start: 0.6145 (tp30) cc_final: 0.4819 (tp30) REVERT: B 297 LEU cc_start: 0.8298 (tp) cc_final: 0.7936 (pp) REVERT: B 312 PHE cc_start: 0.6078 (m-80) cc_final: 0.5591 (m-80) REVERT: B 447 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7247 (mm) REVERT: B 809 ASP cc_start: 0.8997 (m-30) cc_final: 0.8785 (p0) REVERT: B 817 ASN cc_start: 0.8412 (m-40) cc_final: 0.7981 (m110) REVERT: B 852 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8219 (ppp) REVERT: C 59 MET cc_start: 0.7814 (mmm) cc_final: 0.7017 (mmm) REVERT: C 69 MET cc_start: 0.6653 (mpp) cc_final: 0.5794 (tpt) REVERT: D 56 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6378 (tp30) REVERT: D 140 PHE cc_start: 0.7203 (m-80) cc_final: 0.6537 (m-10) REVERT: D 193 MET cc_start: 0.6960 (mtm) cc_final: 0.6567 (tpp) REVERT: E 65 GLU cc_start: 0.6455 (tt0) cc_final: 0.6137 (mp0) REVERT: E 85 MET cc_start: 0.6044 (tmm) cc_final: 0.5669 (tmm) REVERT: E 115 LYS cc_start: 0.7440 (mmmt) cc_final: 0.7196 (mmmt) REVERT: F 20 MET cc_start: 0.4393 (ppp) cc_final: 0.0098 (mmm) REVERT: F 40 ARG cc_start: 0.6395 (ptt-90) cc_final: 0.5703 (ppt170) REVERT: F 69 MET cc_start: 0.0246 (mmt) cc_final: -0.0805 (mmt) REVERT: F 117 ASP cc_start: 0.8712 (p0) cc_final: 0.7814 (m-30) outliers start: 32 outliers final: 25 residues processed: 240 average time/residue: 0.1477 time to fit residues: 54.8949 Evaluate side-chains 243 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 216 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 610 GLN Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 610 GLN Chi-restraints excluded: chain B residue 833 TYR Chi-restraints excluded: chain B residue 852 MET Chi-restraints excluded: chain B residue 888 GLN Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 138 MET Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain F residue 159 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 48 optimal weight: 0.9980 chunk 203 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 198 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 167 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.077942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.062484 restraints weight = 145922.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.064252 restraints weight = 70183.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.065430 restraints weight = 43207.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.066190 restraints weight = 30770.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.066711 restraints weight = 24487.515| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3850 r_free = 0.3850 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3850 r_free = 0.3850 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19205 Z= 0.136 Angle : 0.757 15.977 25854 Z= 0.373 Chirality : 0.043 0.308 2795 Planarity : 0.004 0.050 3346 Dihedral : 6.950 158.440 2534 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.38 % Allowed : 17.82 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.18), residues: 2283 helix: 0.87 (0.15), residues: 1309 sheet: -0.81 (0.45), residues: 141 loop : -0.97 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 858 TYR 0.037 0.001 TYR B 422 PHE 0.024 0.001 PHE A 436 TRP 0.014 0.001 TRP A 816 HIS 0.004 0.001 HIS E 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (19205) covalent geometry : angle 0.75749 / 0.37 (25854) hydrogen bonds : bond 0.03845 / 2.57 ( 1031) hydrogen bonds : angle 4.79373 / 3.32 ( 3010) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5410.15 seconds wall clock time: 93 minutes 52.36 seconds (5632.36 seconds total)