Starting phenix.real_space_refine on Mon May 19 23:01:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8act_15353/05_2025/8act_15353.cif Found real_map, /net/cci-nas-00/data/ceres_data/8act_15353/05_2025/8act_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8act_15353/05_2025/8act_15353.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8act_15353/05_2025/8act_15353.map" model { file = "/net/cci-nas-00/data/ceres_data/8act_15353/05_2025/8act_15353.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8act_15353/05_2025/8act_15353.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.024 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 17.38, per 1000 atoms: 0.92 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: 4.67 Conformation dependent library (CDL) restraints added in 3.7 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: 2.29 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: 7.67 Time building geometry restraints manager: 5.44 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 898 or resid 1001 through 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: 11.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.800 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 53.560 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.100 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (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 TRP 0.016 0.001 TRP A 816 HIS 0.003 0.001 HIS B 556 PHE 0.039 0.001 PHE C 111 TYR 0.017 0.001 TYR E 118 ARG 0.003 0.000 ARG E 120 Details of bonding type rmsd hydrogen bonds : bond 0.14250 ( 1031) hydrogen bonds : angle 6.05140 ( 3010) covalent geometry : bond 0.00327 (19205) covalent geometry : angle 0.63912 (25854) *********************** 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 : 2.263 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: 0.7317 (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: 0.8353 (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: 0.8375 (mtp) cc_final: 0.7915 (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: 0.3240 (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: 0.3539 time to fit residues: 219.4249 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 : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 193 optimal weight: 10.0000 chunk 173 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 133 optimal weight: 8.9990 chunk 207 optimal weight: 0.6980 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 HIS ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.078560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.062300 restraints weight = 198334.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.064324 restraints weight = 89290.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.065644 restraints weight = 52670.326| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3813 r_free = 0.3813 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3813 r_free = 0.3813 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19205 Z= 0.163 Angle : 0.713 13.244 25854 Z= 0.359 Chirality : 0.044 0.196 2795 Planarity : 0.005 0.050 3346 Dihedral : 7.609 155.889 2534 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.64 % Allowed : 10.61 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.18), residues: 2283 helix: 0.95 (0.14), residues: 1310 sheet: -0.62 (0.42), residues: 149 loop : -0.75 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 438 HIS 0.012 0.001 HIS B 581 PHE 0.034 0.002 PHE C 61 TYR 0.024 0.002 TYR E 118 ARG 0.010 0.001 ARG A 712 Details of bonding type rmsd hydrogen bonds : bond 0.04553 ( 1031) hydrogen bonds : angle 5.09529 ( 3010) covalent geometry : bond 0.00363 (19205) covalent geometry : angle 0.71285 (25854) *********************** 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 297 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 284 time to evaluate : 2.131 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: 0.7981 (mmt) cc_final: 0.7656 (mmt) REVERT: A 350 TYR cc_start: 0.7707 (m-80) cc_final: 0.7332 (m-80) REVERT: A 699 LEU cc_start: 0.8884 (tp) cc_final: 0.8653 (tp) REVERT: A 700 GLU cc_start: 0.8513 (mp0) cc_final: 0.8085 (mp0) REVERT: A 807 ARG cc_start: 0.8750 (mmm160) cc_final: 0.8533 (tpt90) REVERT: A 847 LYS cc_start: 0.7938 (pttp) cc_final: 0.7438 (pttt) REVERT: A 849 MET cc_start: 0.7960 (ptp) cc_final: 0.7036 (tpt) REVERT: A 889 LEU cc_start: 0.9284 (mt) cc_final: 0.8948 (tt) REVERT: B 6 MET cc_start: 0.5461 (mmt) cc_final: 0.5178 (mmt) REVERT: B 418 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.6828 (pp30) REVERT: B 536 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8600 (tm-30) REVERT: B 606 VAL cc_start: 0.8377 (t) cc_final: 0.8134 (t) REVERT: B 811 LEU cc_start: 0.8952 (mt) cc_final: 0.8179 (tp) REVERT: B 817 ASN cc_start: 0.8494 (m-40) cc_final: 0.8167 (m110) REVERT: B 821 PHE cc_start: 0.7987 (t80) cc_final: 0.7486 (t80) REVERT: B 852 MET cc_start: 0.8758 (ppp) cc_final: 0.8367 (ppp) REVERT: C 59 MET cc_start: 0.7708 (mmm) cc_final: 0.6727 (mmm) REVERT: C 69 MET cc_start: 0.6519 (mpp) cc_final: 0.5565 (tpt) REVERT: D 51 ILE cc_start: 0.5258 (mm) cc_final: 0.4944 (mm) REVERT: D 56 GLU cc_start: 0.7007 (mm-30) cc_final: 0.6386 (tp30) REVERT: D 62 ASP cc_start: 0.4959 (OUTLIER) cc_final: 0.4130 (p0) REVERT: D 69 MET cc_start: 0.4902 (tpp) cc_final: 0.4654 (tpp) REVERT: D 140 PHE cc_start: 0.7483 (m-80) cc_final: 0.6899 (m-80) REVERT: D 142 LYS cc_start: 0.3505 (mmtt) cc_final: 0.2663 (mmmt) REVERT: E 85 MET cc_start: 0.6281 (tmm) cc_final: 0.5882 (tmm) REVERT: E 118 TYR cc_start: 0.7807 (t80) cc_final: 0.7388 (t80) REVERT: E 122 MET cc_start: 0.8056 (mtm) cc_final: 0.6383 (tpt) REVERT: E 139 PHE cc_start: 0.6513 (m-80) cc_final: 0.6159 (m-80) REVERT: F 20 MET cc_start: 0.4128 (ppp) cc_final: 0.0457 (mmm) REVERT: F 26 ILE cc_start: 0.7461 (pt) cc_final: 0.6970 (pt) REVERT: F 34 THR cc_start: 0.7878 (m) cc_final: 0.7283 (p) REVERT: F 40 ARG cc_start: 0.6696 (mmp-170) cc_final: 0.6055 (ptt-90) REVERT: F 69 MET cc_start: 0.0703 (mmt) cc_final: 0.0164 (mmp) outliers start: 13 outliers final: 4 residues processed: 291 average time/residue: 0.3174 time to fit residues: 139.4666 Evaluate side-chains 230 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 224 time to evaluate : 2.021 ------------------------------------------------------------------------------- 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 896 ASP Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain D residue 62 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 208 optimal weight: 0.9980 chunk 222 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 221 optimal weight: 0.0980 chunk 213 optimal weight: 6.9990 chunk 158 optimal weight: 0.2980 chunk 197 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 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** B 581 HIS ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 GLN ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 HIS F 27 GLN F 39 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.078406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.062660 restraints weight = 165224.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.064793 restraints weight = 82898.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.066326 restraints weight = 44462.594| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3830 r_free = 0.3830 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3830 r_free = 0.3830 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3830 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.2994 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= 0.143 Angle : 0.680 15.099 25854 Z= 0.339 Chirality : 0.042 0.165 2795 Planarity : 0.004 0.050 3346 Dihedral : 7.591 165.436 2534 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.43 % Allowed : 12.54 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.18), residues: 2283 helix: 0.83 (0.14), residues: 1328 sheet: -0.78 (0.40), residues: 163 loop : -0.86 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 816 HIS 0.010 0.001 HIS B 581 PHE 0.027 0.002 PHE A 821 TYR 0.025 0.002 TYR A 609 ARG 0.013 0.001 ARG C 94 Details of bonding type rmsd hydrogen bonds : bond 0.04172 ( 1031) hydrogen bonds : angle 4.92726 ( 3010) covalent geometry : bond 0.00311 (19205) covalent geometry : angle 0.67973 (25854) *********************** 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 275 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 246 time to evaluate : 2.049 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: A 77 MET cc_start: 0.7897 (mmt) cc_final: 0.7487 (mmt) REVERT: A 92 MET cc_start: 0.8065 (mmm) cc_final: 0.7831 (mmt) REVERT: A 350 TYR cc_start: 0.7735 (m-80) cc_final: 0.7363 (m-80) REVERT: A 811 LEU cc_start: 0.8283 (mt) cc_final: 0.8083 (mt) REVERT: A 849 MET cc_start: 0.8039 (ptp) cc_final: 0.7085 (tpt) REVERT: A 869 ARG cc_start: 0.9043 (tpm170) cc_final: 0.8814 (tpm170) REVERT: A 889 LEU cc_start: 0.9263 (mt) cc_final: 0.8927 (tt) REVERT: B 6 MET cc_start: 0.5487 (mmt) cc_final: 0.5190 (mmt) REVERT: B 536 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8674 (tm-30) REVERT: B 811 LEU cc_start: 0.8995 (mt) cc_final: 0.8464 (tp) REVERT: B 817 ASN cc_start: 0.8599 (m-40) cc_final: 0.8249 (m110) REVERT: B 821 PHE cc_start: 0.7986 (t80) cc_final: 0.7560 (t80) REVERT: C 59 MET cc_start: 0.7732 (mmm) cc_final: 0.6934 (mmm) REVERT: C 69 MET cc_start: 0.6547 (mpp) cc_final: 0.5646 (tpt) REVERT: D 56 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6444 (tp30) REVERT: D 69 MET cc_start: 0.5026 (tpp) cc_final: 0.4816 (tpp) REVERT: D 140 PHE cc_start: 0.7465 (m-80) cc_final: 0.6863 (m-80) REVERT: D 142 LYS cc_start: 0.3603 (mmtt) cc_final: 0.2871 (mmmt) REVERT: E 85 MET cc_start: 0.6208 (tmm) cc_final: 0.5666 (tmm) REVERT: E 111 LYS cc_start: 0.8614 (pttm) cc_final: 0.8408 (ptpp) REVERT: E 118 TYR cc_start: 0.7824 (t80) cc_final: 0.7524 (t80) REVERT: E 122 MET cc_start: 0.8014 (mtm) cc_final: 0.6412 (tpt) REVERT: E 130 PHE cc_start: 0.7399 (m-80) cc_final: 0.7116 (m-80) REVERT: F 20 MET cc_start: 0.4228 (ppp) cc_final: 0.0485 (mmm) REVERT: F 26 ILE cc_start: 0.7355 (pt) cc_final: 0.7062 (pt) REVERT: F 34 THR cc_start: 0.7915 (m) cc_final: 0.7201 (m) REVERT: F 40 ARG cc_start: 0.6742 (mmp-170) cc_final: 0.6281 (ptt-90) REVERT: F 122 MET cc_start: 0.8567 (tpt) cc_final: 0.8275 (ttm) outliers start: 29 outliers final: 12 residues processed: 264 average time/residue: 0.3091 time to fit residues: 122.8188 Evaluate side-chains 226 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 214 time to evaluate : 2.007 ------------------------------------------------------------------------------- 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 366 LEU Chi-restraints excluded: chain B residue 581 HIS 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 896 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 169 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 43 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 171 optimal weight: 0.9990 chunk 227 optimal weight: 7.9990 chunk 202 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 168 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 885 ASN ** B 418 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 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.077856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.061653 restraints weight = 185913.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.063575 restraints weight = 84643.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.064831 restraints weight = 50416.589| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3781 r_free = 0.3781 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3781 r_free = 0.3781 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3781 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19205 Z= 0.152 Angle : 0.696 13.451 25854 Z= 0.343 Chirality : 0.043 0.220 2795 Planarity : 0.004 0.059 3346 Dihedral : 7.614 173.126 2534 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.43 % Allowed : 13.92 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.18), residues: 2283 helix: 0.77 (0.14), residues: 1322 sheet: -0.86 (0.39), residues: 163 loop : -0.89 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 816 HIS 0.010 0.001 HIS B 581 PHE 0.035 0.002 PHE B 312 TYR 0.032 0.002 TYR B 422 ARG 0.020 0.001 ARG C 94 Details of bonding type rmsd hydrogen bonds : bond 0.04042 ( 1031) hydrogen bonds : angle 4.92044 ( 3010) covalent geometry : bond 0.00340 (19205) covalent geometry : angle 0.69649 (25854) *********************** 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 262 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 233 time to evaluate : 2.173 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: A 77 MET cc_start: 0.8076 (mmt) cc_final: 0.7574 (mmt) REVERT: A 92 MET cc_start: 0.8083 (mmm) cc_final: 0.7831 (mmt) REVERT: A 350 TYR cc_start: 0.7798 (m-80) cc_final: 0.7352 (m-80) REVERT: A 807 ARG cc_start: 0.8739 (mmm160) cc_final: 0.8111 (tpt90) REVERT: A 811 LEU cc_start: 0.8294 (mt) cc_final: 0.7666 (mt) REVERT: A 848 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7760 (tt0) REVERT: A 849 MET cc_start: 0.8045 (ptp) cc_final: 0.7089 (tpt) REVERT: A 889 LEU cc_start: 0.9250 (mt) cc_final: 0.8922 (tt) REVERT: B 431 VAL cc_start: 0.9396 (t) cc_final: 0.8993 (t) REVERT: B 536 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8639 (tm-30) REVERT: B 811 LEU cc_start: 0.8895 (mt) cc_final: 0.8446 (tp) REVERT: B 817 ASN cc_start: 0.8489 (m-40) cc_final: 0.8179 (m110) REVERT: B 821 PHE cc_start: 0.8053 (t80) cc_final: 0.7597 (t80) REVERT: B 852 MET cc_start: 0.8908 (ppp) cc_final: 0.8127 (ppp) REVERT: B 872 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8796 (pt0) REVERT: B 877 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8698 (tpp) REVERT: C 59 MET cc_start: 0.7787 (mmm) cc_final: 0.7083 (mmm) REVERT: C 69 MET cc_start: 0.6674 (mpp) cc_final: 0.5628 (tpt) REVERT: D 56 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6526 (tp30) REVERT: D 69 MET cc_start: 0.5169 (tpp) cc_final: 0.4908 (tpp) REVERT: D 140 PHE cc_start: 0.7395 (m-80) cc_final: 0.6784 (m-80) REVERT: D 142 LYS cc_start: 0.3611 (mmtt) cc_final: 0.2890 (mmmt) REVERT: E 85 MET cc_start: 0.6136 (tmm) cc_final: 0.5548 (tmm) REVERT: E 111 LYS cc_start: 0.8579 (pttm) cc_final: 0.8350 (pttm) REVERT: E 118 TYR cc_start: 0.7773 (t80) cc_final: 0.7468 (t80) REVERT: E 122 MET cc_start: 0.8035 (mtm) cc_final: 0.6595 (tpt) REVERT: F 20 MET cc_start: 0.4304 (ppp) cc_final: 0.0220 (mmm) REVERT: F 26 ILE cc_start: 0.7258 (pt) cc_final: 0.7036 (pt) REVERT: F 34 THR cc_start: 0.7887 (m) cc_final: 0.7182 (m) REVERT: F 40 ARG cc_start: 0.6714 (mmp-170) cc_final: 0.6369 (ptt-90) REVERT: F 69 MET cc_start: 0.0718 (tpp) cc_final: 0.0468 (tpp) REVERT: F 117 ASP cc_start: 0.8885 (p0) cc_final: 0.7952 (m-30) REVERT: F 122 MET cc_start: 0.8605 (tpt) cc_final: 0.8240 (ttm) outliers start: 29 outliers final: 16 residues processed: 248 average time/residue: 0.2992 time to fit residues: 116.0842 Evaluate side-chains 235 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 217 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 610 GLN Chi-restraints excluded: chain A residue 704 ILE 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 366 LEU Chi-restraints excluded: chain B residue 539 MET Chi-restraints excluded: chain B residue 581 HIS Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 610 GLN Chi-restraints excluded: chain B residue 872 GLU Chi-restraints excluded: chain B residue 877 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 F residue 85 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 111 optimal weight: 5.9990 chunk 206 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 195 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 196 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4118 r_free = 0.4118 target = 0.075182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.058912 restraints weight = 207473.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.060840 restraints weight = 92922.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.062056 restraints weight = 54829.058| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3701 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3701 r_free = 0.3701 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3701 r_free = 0.3701 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 19205 Z= 0.233 Angle : 0.749 10.633 25854 Z= 0.376 Chirality : 0.045 0.203 2795 Planarity : 0.005 0.052 3346 Dihedral : 7.908 179.499 2534 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.83 % Allowed : 15.00 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.17), residues: 2283 helix: 0.52 (0.14), residues: 1312 sheet: -1.00 (0.43), residues: 135 loop : -0.92 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 829 HIS 0.008 0.002 HIS B 581 PHE 0.029 0.002 PHE C 61 TYR 0.039 0.002 TYR B 422 ARG 0.018 0.001 ARG C 94 Details of bonding type rmsd hydrogen bonds : bond 0.04308 ( 1031) hydrogen bonds : angle 5.15815 ( 3010) covalent geometry : bond 0.00519 (19205) covalent geometry : angle 0.74864 (25854) *********************** 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 258 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 221 time to evaluate : 2.099 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: 0.8239 (mmt) cc_final: 0.7928 (mmt) REVERT: A 92 MET cc_start: 0.8191 (mmm) cc_final: 0.7943 (mmt) REVERT: A 350 TYR cc_start: 0.7967 (m-80) cc_final: 0.7569 (m-80) REVERT: A 723 ARG cc_start: 0.5827 (mtm180) cc_final: 0.5217 (mtm180) REVERT: A 776 MET cc_start: 0.8998 (mtm) cc_final: 0.8621 (ptp) REVERT: A 807 ARG cc_start: 0.8801 (mmm160) cc_final: 0.8423 (tpt90) REVERT: A 856 PHE cc_start: 0.7835 (m-10) cc_final: 0.7424 (m-80) REVERT: A 865 LYS cc_start: 0.9179 (pttm) cc_final: 0.8863 (tppt) REVERT: A 889 LEU cc_start: 0.9262 (mt) cc_final: 0.8928 (tt) REVERT: B 43 LYS cc_start: 0.8189 (mmtp) cc_final: 0.7683 (mmmt) REVERT: B 447 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7562 (mm) REVERT: B 821 PHE cc_start: 0.8129 (t80) cc_final: 0.7573 (t80) REVERT: B 852 MET cc_start: 0.8694 (ppp) cc_final: 0.8222 (ppp) REVERT: C 59 MET cc_start: 0.7861 (mmm) cc_final: 0.7122 (mmm) REVERT: C 69 MET cc_start: 0.6747 (mpp) cc_final: 0.5577 (tpt) REVERT: C 94 ARG cc_start: 0.8418 (ptt-90) cc_final: 0.8074 (ptt-90) REVERT: D 56 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6608 (tp30) REVERT: D 69 MET cc_start: 0.5253 (tpp) cc_final: 0.5026 (tpp) REVERT: D 140 PHE cc_start: 0.7452 (m-80) cc_final: 0.6862 (m-80) REVERT: E 65 GLU cc_start: 0.6407 (tt0) cc_final: 0.5853 (mp0) REVERT: F 20 MET cc_start: 0.4579 (ppp) cc_final: 0.0356 (tpt) REVERT: F 26 ILE cc_start: 0.7434 (pt) cc_final: 0.7178 (pt) REVERT: F 34 THR cc_start: 0.7954 (m) cc_final: 0.7284 (m) REVERT: F 40 ARG cc_start: 0.6702 (mmp-170) cc_final: 0.6336 (ptt-90) REVERT: F 69 MET cc_start: 0.0706 (tpp) cc_final: 0.0498 (tpp) outliers start: 37 outliers final: 23 residues processed: 243 average time/residue: 0.3002 time to fit residues: 112.3862 Evaluate side-chains 235 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 211 time to evaluate : 2.195 ------------------------------------------------------------------------------- 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 605 VAL Chi-restraints excluded: chain A residue 610 GLN Chi-restraints excluded: chain A residue 704 ILE 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 366 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 539 MET Chi-restraints excluded: chain B residue 557 LEU 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 795 VAL Chi-restraints excluded: chain B residue 833 TYR 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 E residue 50 ARG Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain F residue 90 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 78 optimal weight: 0.9980 chunk 211 optimal weight: 0.1980 chunk 56 optimal weight: 0.8980 chunk 183 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 49 optimal weight: 0.0470 chunk 4 optimal weight: 3.9990 chunk 164 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 150 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 GLN ** A 482 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** ** B 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 154 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.076775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.060404 restraints weight = 201147.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.062386 restraints weight = 89550.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.063669 restraints weight = 52914.651| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3760 r_free = 0.3760 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3760 r_free = 0.3760 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19205 Z= 0.131 Angle : 0.696 13.047 25854 Z= 0.345 Chirality : 0.043 0.188 2795 Planarity : 0.004 0.050 3346 Dihedral : 7.659 179.756 2534 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.38 % Allowed : 16.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.18), residues: 2283 helix: 0.65 (0.14), residues: 1314 sheet: -0.81 (0.44), residues: 135 loop : -0.92 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 593 HIS 0.005 0.001 HIS B 581 PHE 0.026 0.001 PHE C 114 TYR 0.016 0.002 TYR A 609 ARG 0.011 0.000 ARG A 858 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 1031) hydrogen bonds : angle 4.86873 ( 3010) covalent geometry : bond 0.00285 (19205) covalent geometry : angle 0.69650 (25854) *********************** 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 258 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 230 time to evaluate : 2.308 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: 0.9292 (mt) cc_final: 0.9069 (pp) REVERT: A 77 MET cc_start: 0.8164 (mmt) cc_final: 0.7575 (mmt) REVERT: A 92 MET cc_start: 0.8181 (mmm) cc_final: 0.7932 (mmt) REVERT: A 350 TYR cc_start: 0.7753 (m-80) cc_final: 0.7381 (m-80) REVERT: A 388 MET cc_start: 0.5922 (mpp) cc_final: 0.5519 (mtt) REVERT: A 807 ARG cc_start: 0.8751 (mmm160) cc_final: 0.8446 (tpt90) REVERT: A 849 MET cc_start: 0.8191 (ptp) cc_final: 0.7355 (tpt) REVERT: A 856 PHE cc_start: 0.7847 (m-10) cc_final: 0.7462 (m-80) REVERT: A 889 LEU cc_start: 0.9240 (mt) cc_final: 0.8920 (tt) REVERT: B 43 LYS cc_start: 0.8103 (mmtp) cc_final: 0.7607 (mmmt) REVERT: B 179 GLU cc_start: 0.6985 (mm-30) cc_final: 0.6609 (tp30) REVERT: B 362 MET cc_start: 0.6364 (OUTLIER) cc_final: 0.6116 (tpt) REVERT: B 403 ARG cc_start: 0.8240 (mtp180) cc_final: 0.7705 (ttp-170) REVERT: B 447 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7556 (mm) REVERT: B 821 PHE cc_start: 0.8086 (t80) cc_final: 0.7660 (t80) REVERT: B 852 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8117 (ppp) REVERT: C 59 MET cc_start: 0.7767 (mmm) cc_final: 0.7053 (mmm) REVERT: C 69 MET cc_start: 0.6800 (mpp) cc_final: 0.5715 (tpt) REVERT: C 94 ARG cc_start: 0.8237 (ptt-90) cc_final: 0.7764 (ptt-90) REVERT: D 56 GLU cc_start: 0.7255 (mm-30) cc_final: 0.6465 (tp30) REVERT: D 69 MET cc_start: 0.5239 (tpp) cc_final: 0.4992 (tpp) REVERT: D 109 MET cc_start: 0.8243 (mmm) cc_final: 0.8030 (mmt) REVERT: D 140 PHE cc_start: 0.7428 (m-80) cc_final: 0.6249 (m-80) REVERT: D 142 LYS cc_start: 0.3682 (mmtt) cc_final: 0.2861 (mmmt) REVERT: E 65 GLU cc_start: 0.6310 (tt0) cc_final: 0.5791 (mp0) REVERT: E 85 MET cc_start: 0.6160 (tmm) cc_final: 0.5796 (tmm) REVERT: E 118 TYR cc_start: 0.7501 (t80) cc_final: 0.7106 (t80) REVERT: E 122 MET cc_start: 0.7891 (mtm) cc_final: 0.6627 (tpt) REVERT: F 20 MET cc_start: 0.4577 (ppp) cc_final: 0.0410 (tpt) REVERT: F 26 ILE cc_start: 0.7420 (pt) cc_final: 0.7188 (pt) REVERT: F 40 ARG cc_start: 0.6623 (mmp-170) cc_final: 0.6305 (ptt-90) REVERT: F 69 MET cc_start: 0.0823 (tpp) cc_final: 0.0584 (tpp) REVERT: F 90 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7487 (tp) REVERT: F 117 ASP cc_start: 0.8836 (p0) cc_final: 0.7871 (m-30) REVERT: F 136 ASP cc_start: 0.7921 (m-30) cc_final: 0.7538 (p0) REVERT: F 137 GLN cc_start: 0.6338 (tm-30) cc_final: 0.6034 (pt0) outliers start: 28 outliers final: 16 residues processed: 246 average time/residue: 0.3287 time to fit residues: 125.4093 Evaluate side-chains 239 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 219 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 610 GLN Chi-restraints excluded: chain B residue 31 PHE Chi-restraints excluded: chain B residue 297 LEU 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 447 LEU Chi-restraints excluded: chain B residue 539 MET Chi-restraints excluded: chain B residue 557 LEU 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 C residue 96 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain F residue 90 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 155 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 189 optimal weight: 6.9990 chunk 211 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 208 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.074928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.059559 restraints weight = 146585.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.061154 restraints weight = 74593.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.062215 restraints weight = 47461.096| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 19205 Z= 0.201 Angle : 0.737 14.853 25854 Z= 0.369 Chirality : 0.044 0.172 2795 Planarity : 0.004 0.050 3346 Dihedral : 7.677 171.678 2534 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.83 % Allowed : 16.93 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.17), residues: 2283 helix: 0.59 (0.14), residues: 1308 sheet: -1.12 (0.44), residues: 133 loop : -1.02 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 816 HIS 0.005 0.001 HIS B 581 PHE 0.020 0.002 PHE D 61 TYR 0.016 0.002 TYR A 283 ARG 0.010 0.001 ARG A 858 Details of bonding type rmsd hydrogen bonds : bond 0.04099 ( 1031) hydrogen bonds : angle 5.07767 ( 3010) covalent geometry : bond 0.00453 (19205) covalent geometry : angle 0.73682 (25854) *********************** 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 253 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 216 time to evaluate : 2.733 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: A 77 MET cc_start: 0.8326 (mmt) cc_final: 0.8004 (mmt) REVERT: A 350 TYR cc_start: 0.7809 (m-80) cc_final: 0.7455 (m-80) REVERT: A 405 LYS cc_start: 0.8960 (ttmt) cc_final: 0.8701 (tttp) REVERT: A 723 ARG cc_start: 0.5791 (mtm180) cc_final: 0.5185 (mtm180) REVERT: A 776 MET cc_start: 0.9024 (mtm) cc_final: 0.8747 (ptp) REVERT: A 849 MET cc_start: 0.8172 (ptp) cc_final: 0.7339 (tpt) REVERT: A 856 PHE cc_start: 0.7871 (m-10) cc_final: 0.7440 (m-80) REVERT: A 865 LYS cc_start: 0.9350 (tppt) cc_final: 0.8842 (pttp) REVERT: A 889 LEU cc_start: 0.9267 (mt) cc_final: 0.8942 (tt) REVERT: B 43 LYS cc_start: 0.8093 (mmtp) cc_final: 0.7669 (mmmt) REVERT: B 113 MET cc_start: 0.7618 (ptt) cc_final: 0.6855 (ppp) REVERT: B 179 GLU cc_start: 0.7309 (mm-30) cc_final: 0.6831 (tp30) REVERT: B 447 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7560 (mm) REVERT: B 821 PHE cc_start: 0.8121 (t80) cc_final: 0.7621 (t80) REVERT: B 852 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8159 (ppp) REVERT: C 59 MET cc_start: 0.7718 (mmm) cc_final: 0.6973 (mmm) REVERT: C 69 MET cc_start: 0.6783 (mpp) cc_final: 0.5940 (mmt) REVERT: C 75 GLN cc_start: 0.8307 (tm-30) cc_final: 0.8095 (tm-30) REVERT: D 56 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6444 (tp30) REVERT: D 149 MET cc_start: 0.4663 (OUTLIER) cc_final: 0.4272 (mtt) REVERT: E 26 ILE cc_start: 0.7933 (mt) cc_final: 0.7427 (tt) REVERT: E 65 GLU cc_start: 0.6479 (tt0) cc_final: 0.6013 (mp0) REVERT: F 20 MET cc_start: 0.4649 (ppp) cc_final: 0.0340 (tpt) REVERT: F 40 ARG cc_start: 0.6559 (mmp-170) cc_final: 0.6293 (ptt-90) REVERT: F 90 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7480 (tp) REVERT: F 136 ASP cc_start: 0.7831 (m-30) cc_final: 0.7491 (p0) outliers start: 37 outliers final: 24 residues processed: 234 average time/residue: 0.3049 time to fit residues: 110.0799 Evaluate side-chains 229 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 2.122 ------------------------------------------------------------------------------- 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 605 VAL Chi-restraints excluded: chain A residue 610 GLN Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain B residue 31 PHE Chi-restraints excluded: chain B residue 69 VAL 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 515 MET Chi-restraints excluded: chain B residue 557 LEU 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 795 VAL Chi-restraints excluded: chain B residue 833 TYR Chi-restraints excluded: chain B residue 852 MET Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain F residue 90 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 186 optimal weight: 4.9990 chunk 220 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 chunk 215 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 HIS C 50 GLN ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.076161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.060193 restraints weight = 173294.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.062033 restraints weight = 81882.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.063201 restraints weight = 49811.129| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3748 r_free = 0.3748 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3748 r_free = 0.3748 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.4634 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= 0.137 Angle : 0.724 15.568 25854 Z= 0.358 Chirality : 0.043 0.220 2795 Planarity : 0.004 0.051 3346 Dihedral : 7.506 168.136 2534 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.43 % Allowed : 17.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.17), residues: 2283 helix: 0.65 (0.14), residues: 1311 sheet: -0.94 (0.44), residues: 134 loop : -1.04 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 816 HIS 0.007 0.001 HIS B 581 PHE 0.043 0.001 PHE C 61 TYR 0.033 0.002 TYR E 118 ARG 0.008 0.000 ARG A 858 Details of bonding type rmsd hydrogen bonds : bond 0.04005 ( 1031) hydrogen bonds : angle 4.91796 ( 3010) covalent geometry : bond 0.00301 (19205) covalent geometry : angle 0.72394 (25854) *********************** 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 246 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 217 time to evaluate : 2.064 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: A 77 MET cc_start: 0.8236 (mmt) cc_final: 0.7783 (mmt) REVERT: A 350 TYR cc_start: 0.7758 (m-80) cc_final: 0.7383 (m-80) REVERT: A 405 LYS cc_start: 0.8997 (ttmt) cc_final: 0.8727 (tttp) REVERT: A 410 TYR cc_start: 0.7489 (m-80) cc_final: 0.7270 (m-80) REVERT: A 776 MET cc_start: 0.9007 (mtm) cc_final: 0.8648 (ptp) REVERT: A 848 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7773 (tt0) REVERT: A 849 MET cc_start: 0.8199 (ptp) cc_final: 0.7189 (tpt) REVERT: A 856 PHE cc_start: 0.7949 (m-10) cc_final: 0.7637 (m-80) REVERT: A 889 LEU cc_start: 0.9245 (mt) cc_final: 0.8940 (tt) REVERT: B 43 LYS cc_start: 0.8137 (mmtp) cc_final: 0.7746 (mmmt) REVERT: B 113 MET cc_start: 0.7512 (ptt) cc_final: 0.7121 (ppp) REVERT: B 179 GLU cc_start: 0.7053 (mm-30) cc_final: 0.6739 (tp30) REVERT: B 403 ARG cc_start: 0.8244 (mtp-110) cc_final: 0.7725 (ttp-170) REVERT: B 447 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7559 (mm) REVERT: B 821 PHE cc_start: 0.8044 (t80) cc_final: 0.7813 (t80) REVERT: B 852 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8081 (ppp) REVERT: C 59 MET cc_start: 0.7768 (mmm) cc_final: 0.7067 (mmm) REVERT: C 69 MET cc_start: 0.6762 (mpp) cc_final: 0.5648 (tpt) REVERT: D 56 GLU cc_start: 0.7284 (mm-30) cc_final: 0.6500 (tp30) REVERT: D 142 LYS cc_start: 0.3759 (mmtt) cc_final: 0.2964 (mmmt) REVERT: E 65 GLU cc_start: 0.6430 (tt0) cc_final: 0.6039 (mp0) REVERT: E 118 TYR cc_start: 0.7628 (t80) cc_final: 0.7197 (t80) REVERT: E 122 MET cc_start: 0.8004 (mtm) cc_final: 0.6897 (tpt) REVERT: F 20 MET cc_start: 0.4660 (ppp) cc_final: 0.0348 (tpt) REVERT: F 40 ARG cc_start: 0.6492 (mmp-170) cc_final: 0.6282 (ptt-90) REVERT: F 69 MET cc_start: 0.0801 (tpp) cc_final: -0.0254 (mmt) REVERT: F 90 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7517 (tp) REVERT: F 117 ASP cc_start: 0.8786 (p0) cc_final: 0.7805 (m-30) outliers start: 29 outliers final: 22 residues processed: 237 average time/residue: 0.2846 time to fit residues: 105.6586 Evaluate side-chains 228 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 203 time to evaluate : 2.207 ------------------------------------------------------------------------------- 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 610 GLN Chi-restraints excluded: chain A residue 760 HIS Chi-restraints excluded: chain B residue 31 PHE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 333 ASP 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 557 LEU 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 795 VAL Chi-restraints excluded: chain B residue 833 TYR Chi-restraints excluded: chain B residue 852 MET Chi-restraints excluded: chain C residue 42 ILE 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 117 MET Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain F residue 90 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 130 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 195 optimal weight: 1.9990 chunk 39 optimal weight: 0.0770 chunk 7 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 overall best weight: 0.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.076263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.060409 restraints weight = 180150.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.062297 restraints weight = 82129.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.063544 restraints weight = 49135.261| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3761 r_free = 0.3761 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3761 r_free = 0.3761 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19205 Z= 0.137 Angle : 0.736 17.088 25854 Z= 0.360 Chirality : 0.043 0.213 2795 Planarity : 0.004 0.051 3346 Dihedral : 7.311 160.498 2534 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.58 % Allowed : 17.72 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.17), residues: 2283 helix: 0.65 (0.14), residues: 1317 sheet: -0.99 (0.44), residues: 134 loop : -1.08 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 816 HIS 0.007 0.001 HIS B 581 PHE 0.028 0.001 PHE C 61 TYR 0.029 0.002 TYR E 118 ARG 0.017 0.000 ARG A 858 Details of bonding type rmsd hydrogen bonds : bond 0.03973 ( 1031) hydrogen bonds : angle 4.88514 ( 3010) covalent geometry : bond 0.00304 (19205) covalent geometry : angle 0.73551 (25854) *********************** 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 245 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 213 time to evaluate : 2.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 TYR cc_start: 0.7760 (m-80) cc_final: 0.7424 (m-80) REVERT: A 405 LYS cc_start: 0.9026 (ttmt) cc_final: 0.8780 (tttp) REVERT: A 410 TYR cc_start: 0.7578 (m-80) cc_final: 0.7345 (m-80) REVERT: A 776 MET cc_start: 0.8971 (mtm) cc_final: 0.8621 (ptp) REVERT: A 848 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7862 (tt0) REVERT: A 856 PHE cc_start: 0.7943 (m-10) cc_final: 0.7565 (m-80) REVERT: A 889 LEU cc_start: 0.9223 (mt) cc_final: 0.8912 (tt) REVERT: B 43 LYS cc_start: 0.8157 (mmtp) cc_final: 0.7766 (mmmt) REVERT: B 113 MET cc_start: 0.7633 (ptt) cc_final: 0.7266 (ppp) REVERT: B 179 GLU cc_start: 0.7094 (mm-30) cc_final: 0.6776 (tp30) REVERT: B 403 ARG cc_start: 0.8208 (mtp-110) cc_final: 0.7710 (ttp-170) REVERT: B 447 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7440 (mm) REVERT: B 821 PHE cc_start: 0.8007 (t80) cc_final: 0.7747 (t80) REVERT: B 852 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8085 (ppp) REVERT: C 59 MET cc_start: 0.7817 (mmm) cc_final: 0.7091 (mmm) REVERT: C 69 MET cc_start: 0.6674 (mpp) cc_final: 0.5617 (tpt) REVERT: D 56 GLU cc_start: 0.7270 (mm-30) cc_final: 0.6543 (tp30) REVERT: E 26 ILE cc_start: 0.7959 (mt) cc_final: 0.7469 (tt) REVERT: E 65 GLU cc_start: 0.6464 (tt0) cc_final: 0.6023 (mp0) REVERT: E 118 TYR cc_start: 0.7573 (t80) cc_final: 0.7166 (t80) REVERT: E 122 MET cc_start: 0.7962 (mtm) cc_final: 0.6849 (tpt) REVERT: F 20 MET cc_start: 0.4487 (ppp) cc_final: 0.0262 (tpt) REVERT: F 40 ARG cc_start: 0.6483 (mmp-170) cc_final: 0.6259 (ptt-90) REVERT: F 69 MET cc_start: 0.0970 (tpp) cc_final: -0.0147 (mmt) REVERT: F 90 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7594 (tp) REVERT: F 117 ASP cc_start: 0.8781 (p0) cc_final: 0.7797 (m-30) outliers start: 32 outliers final: 24 residues processed: 231 average time/residue: 0.2948 time to fit residues: 106.1506 Evaluate side-chains 231 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 204 time to evaluate : 2.097 ------------------------------------------------------------------------------- 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 31 PHE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 333 ASP 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 557 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 795 VAL Chi-restraints excluded: chain B residue 833 TYR Chi-restraints excluded: chain B residue 852 MET Chi-restraints excluded: chain C residue 42 ILE 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 117 MET Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain F residue 90 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 212 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 222 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 204 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 129 optimal weight: 0.7980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 444 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.076215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.061016 restraints weight = 129822.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.062614 restraints weight = 67686.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.063675 restraints weight = 43378.123| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3764 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3764 r_free = 0.3764 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3764 r_free = 0.3764 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.4905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19205 Z= 0.143 Angle : 0.748 15.044 25854 Z= 0.371 Chirality : 0.044 0.312 2795 Planarity : 0.004 0.120 3346 Dihedral : 7.149 151.597 2534 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.58 % Allowed : 18.11 % Favored : 80.31 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.18), residues: 2283 helix: 0.63 (0.14), residues: 1323 sheet: -1.05 (0.44), residues: 134 loop : -1.05 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 816 HIS 0.006 0.001 HIS B 581 PHE 0.027 0.001 PHE C 61 TYR 0.028 0.001 TYR E 118 ARG 0.016 0.001 ARG A 807 Details of bonding type rmsd hydrogen bonds : bond 0.03957 ( 1031) hydrogen bonds : angle 4.93497 ( 3010) covalent geometry : bond 0.00321 (19205) covalent geometry : angle 0.74780 (25854) ********************** 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 245 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 213 time to evaluate : 2.014 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: A 77 MET cc_start: 0.8154 (mmp) cc_final: 0.7661 (mmt) REVERT: A 113 MET cc_start: 0.6485 (mmt) cc_final: 0.6202 (mmt) REVERT: A 350 TYR cc_start: 0.7786 (m-80) cc_final: 0.7435 (m-80) REVERT: A 405 LYS cc_start: 0.9043 (ttmt) cc_final: 0.8796 (tttp) REVERT: A 410 TYR cc_start: 0.7582 (m-80) cc_final: 0.7364 (m-80) REVERT: A 776 MET cc_start: 0.9061 (mtm) cc_final: 0.8717 (ptp) REVERT: A 856 PHE cc_start: 0.8005 (m-10) cc_final: 0.7676 (m-80) REVERT: A 889 LEU cc_start: 0.9214 (mt) cc_final: 0.8904 (tt) REVERT: B 43 LYS cc_start: 0.8134 (mmtp) cc_final: 0.7748 (mmmt) REVERT: B 179 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6793 (tp30) REVERT: B 403 ARG cc_start: 0.8209 (mtp-110) cc_final: 0.7725 (ttp-170) REVERT: B 447 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7414 (mm) REVERT: B 852 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8213 (ppp) REVERT: C 59 MET cc_start: 0.7824 (mmm) cc_final: 0.7077 (mmm) REVERT: C 69 MET cc_start: 0.6678 (mpp) cc_final: 0.5636 (tpt) REVERT: D 56 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6515 (tp30) REVERT: E 26 ILE cc_start: 0.7906 (mt) cc_final: 0.7440 (tt) REVERT: E 65 GLU cc_start: 0.6441 (tt0) cc_final: 0.5985 (mp0) REVERT: E 118 TYR cc_start: 0.7473 (t80) cc_final: 0.7079 (t80) REVERT: E 122 MET cc_start: 0.7936 (mtm) cc_final: 0.6854 (tpt) REVERT: F 20 MET cc_start: 0.4498 (ppp) cc_final: 0.0224 (tpt) REVERT: F 40 ARG cc_start: 0.6536 (mmp-170) cc_final: 0.6298 (ptt-90) REVERT: F 90 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7567 (tp) REVERT: F 117 ASP cc_start: 0.8794 (p0) cc_final: 0.7818 (m-30) outliers start: 32 outliers final: 26 residues processed: 233 average time/residue: 0.2999 time to fit residues: 108.2594 Evaluate side-chains 235 residues out of total 2024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 206 time to evaluate : 2.250 ------------------------------------------------------------------------------- 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 760 HIS Chi-restraints excluded: chain B residue 31 PHE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 333 ASP 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 515 MET Chi-restraints excluded: chain B residue 557 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 C residue 42 ILE 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 117 MET Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 149 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 27 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 215 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 149 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.075812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.059843 restraints weight = 182860.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.061725 restraints weight = 85031.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.062958 restraints weight = 51499.268| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3745 r_free = 0.3745 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3745 r_free = 0.3745 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19205 Z= 0.153 Angle : 0.755 17.626 25854 Z= 0.376 Chirality : 0.044 0.333 2795 Planarity : 0.004 0.090 3346 Dihedral : 7.044 145.112 2534 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.48 % Allowed : 18.41 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.18), residues: 2283 helix: 0.62 (0.14), residues: 1322 sheet: -0.95 (0.46), residues: 125 loop : -1.05 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 816 HIS 0.006 0.001 HIS B 581 PHE 0.027 0.002 PHE C 61 TYR 0.027 0.002 TYR E 118 ARG 0.010 0.000 ARG A 858 Details of bonding type rmsd hydrogen bonds : bond 0.04028 ( 1031) hydrogen bonds : angle 4.97394 ( 3010) covalent geometry : bond 0.00345 (19205) covalent geometry : angle 0.75466 (25854) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9420.68 seconds wall clock time: 164 minutes 57.67 seconds (9897.67 seconds total)