Starting phenix.real_space_refine on Fri Jun 6 19:13:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wxw_32882/06_2025/7wxw_32882_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wxw_32882/06_2025/7wxw_32882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wxw_32882/06_2025/7wxw_32882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wxw_32882/06_2025/7wxw_32882.map" model { file = "/net/cci-nas-00/data/ceres_data/7wxw_32882/06_2025/7wxw_32882_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wxw_32882/06_2025/7wxw_32882_neut.cif" } resolution = 2.84 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= 0.001 sd= 0.020 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: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 5176 2.51 5 N 1407 2.21 5 O 1486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8121 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2179 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 10, 'TRANS': 266} Chain breaks: 1 Chain: "C" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "A" Number of atoms: 1942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1942 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Chain: "D" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 331} Time building chain proxies: 5.32, per 1000 atoms: 0.66 Number of scatterers: 8121 At special positions: 0 Unit cell: (84.7, 100.1, 133.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1486 8.00 N 1407 7.00 C 5176 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 657 " - pdb=" SG CYS R 733 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 1.1 seconds 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1934 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 40.8% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'R' and resid 568 through 573 removed outlier: 3.978A pdb=" N LEU R 572 " --> pdb=" O PHE R 569 " (cutoff:3.500A) Processing helix chain 'R' and resid 581 through 610 removed outlier: 3.700A pdb=" N LYS R 586 " --> pdb=" O PHE R 582 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TRP R 587 " --> pdb=" O PRO R 583 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE R 588 " --> pdb=" O VAL R 584 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLY R 594 " --> pdb=" O TYR R 590 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE R 610 " --> pdb=" O ILE R 606 " (cutoff:3.500A) Processing helix chain 'R' and resid 617 through 646 removed outlier: 3.712A pdb=" N THR R 646 " --> pdb=" O ILE R 642 " (cutoff:3.500A) Processing helix chain 'R' and resid 655 through 687 removed outlier: 3.892A pdb=" N ALA R 659 " --> pdb=" O GLY R 655 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL R 661 " --> pdb=" O CYS R 657 " (cutoff:3.500A) Processing helix chain 'R' and resid 694 through 707 removed outlier: 3.573A pdb=" N MET R 698 " --> pdb=" O ALA R 694 " (cutoff:3.500A) Processing helix chain 'R' and resid 708 through 722 removed outlier: 3.556A pdb=" N ILE R 712 " --> pdb=" O GLY R 708 " (cutoff:3.500A) Processing helix chain 'R' and resid 723 through 725 No H-bonds generated for 'chain 'R' and resid 723 through 725' Processing helix chain 'R' and resid 744 through 767 Proline residue: R 750 - end of helix removed outlier: 3.607A pdb=" N ALA R 753 " --> pdb=" O VAL R 749 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE R 754 " --> pdb=" O PRO R 750 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL R 755 " --> pdb=" O ALA R 751 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N VAL R 757 " --> pdb=" O ALA R 753 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL R 760 " --> pdb=" O ALA R 756 " (cutoff:3.500A) Processing helix chain 'R' and resid 785 through 794 Processing helix chain 'R' and resid 795 through 801 removed outlier: 4.153A pdb=" N LEU R 799 " --> pdb=" O ILE R 795 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU R 800 " --> pdb=" O LEU R 796 " (cutoff:3.500A) Processing helix chain 'R' and resid 802 through 805 Processing helix chain 'R' and resid 806 through 811 removed outlier: 3.969A pdb=" N THR R 810 " --> pdb=" O PHE R 806 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE R 811 " --> pdb=" O GLY R 807 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 806 through 811' Processing helix chain 'R' and resid 818 through 828 removed outlier: 3.654A pdb=" N PHE R 823 " --> pdb=" O TRP R 819 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA R 824 " --> pdb=" O HIS R 820 " (cutoff:3.500A) Processing helix chain 'R' and resid 829 through 838 Processing helix chain 'R' and resid 842 through 854 removed outlier: 3.623A pdb=" N ARG R 846 " --> pdb=" O ASP R 842 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 23 Processing helix chain 'C' and resid 31 through 44 removed outlier: 4.029A pdb=" N ALA C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU C 42 " --> pdb=" O MET C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 59 removed outlier: 3.538A pdb=" N ASN C 59 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.629A pdb=" N GLN A 29 " --> pdb=" O MET A 25 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 removed outlier: 3.780A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.676A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.547A pdb=" N SER A 275 " --> pdb=" O ASN A 271 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.993A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.677A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.710A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 390 removed outlier: 3.640A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.669A pdb=" N ASN D 31 " --> pdb=" O THR D 28 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.734A pdb=" N LYS D 65 " --> pdb=" O GLY D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.551A pdb=" N THR D 91 " --> pdb=" O PRO D 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 removed outlier: 3.684A pdb=" N ALA B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 214 removed outlier: 6.379A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 10.330A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.646A pdb=" N LEU D 18 " --> pdb=" O MET D 83 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET D 83 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER D 71 " --> pdb=" O TYR D 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.125A pdb=" N GLY D 10 " --> pdb=" O THR D 125 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL D 93 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET D 34 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE D 51 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER D 59 " --> pdb=" O ASP D 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.917A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 330 " --> pdb=" O CYS B 317 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.147A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.698A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 7.074A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.992A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.943A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.126A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 924 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: 2.31 Time building geometry restraints manager: 2.45 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: 2636 1.34 - 1.46: 2015 1.46 - 1.59: 3567 1.59 - 1.71: 0 1.71 - 1.83: 74 Bond restraints: 8292 Sorted by residual: bond pdb=" CA GLY R 655 " pdb=" C GLY R 655 " ideal model delta sigma weight residual 1.514 1.531 -0.016 1.41e-02 5.03e+03 1.34e+00 bond pdb=" CA GLY B 64 " pdb=" C GLY B 64 " ideal model delta sigma weight residual 1.522 1.510 0.012 1.06e-02 8.90e+03 1.28e+00 bond pdb=" CG LEU D 20 " pdb=" CD1 LEU D 20 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.26e+00 bond pdb=" CA HIS R 665 " pdb=" C HIS R 665 " ideal model delta sigma weight residual 1.524 1.510 0.014 1.28e-02 6.10e+03 1.23e+00 bond pdb=" N GLY R 655 " pdb=" CA GLY R 655 " ideal model delta sigma weight residual 1.449 1.465 -0.016 1.45e-02 4.76e+03 1.19e+00 ... (remaining 8287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 10758 1.67 - 3.35: 386 3.35 - 5.02: 73 5.02 - 6.69: 17 6.69 - 8.36: 4 Bond angle restraints: 11238 Sorted by residual: angle pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 121.70 128.85 -7.15 1.80e+00 3.09e-01 1.58e+01 angle pdb=" N ASP B 291 " pdb=" CA ASP B 291 " pdb=" C ASP B 291 " ideal model delta sigma weight residual 110.80 118.53 -7.73 2.13e+00 2.20e-01 1.32e+01 angle pdb=" N ALA B 104 " pdb=" CA ALA B 104 " pdb=" C ALA B 104 " ideal model delta sigma weight residual 108.46 113.90 -5.44 1.51e+00 4.39e-01 1.30e+01 angle pdb=" N TYR D 94 " pdb=" CA TYR D 94 " pdb=" C TYR D 94 " ideal model delta sigma weight residual 108.41 113.97 -5.56 1.63e+00 3.76e-01 1.16e+01 angle pdb=" N LYS A 17 " pdb=" CA LYS A 17 " pdb=" C LYS A 17 " ideal model delta sigma weight residual 111.07 107.44 3.63 1.07e+00 8.73e-01 1.15e+01 ... (remaining 11233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.16: 4559 18.16 - 36.32: 298 36.32 - 54.48: 44 54.48 - 72.64: 11 72.64 - 90.79: 7 Dihedral angle restraints: 4919 sinusoidal: 1930 harmonic: 2989 Sorted by residual: dihedral pdb=" CA GLN R 815 " pdb=" C GLN R 815 " pdb=" N ASN R 816 " pdb=" CA ASN R 816 " ideal model delta harmonic sigma weight residual -180.00 -138.00 -42.00 0 5.00e+00 4.00e-02 7.06e+01 dihedral pdb=" CB CYS R 657 " pdb=" SG CYS R 657 " pdb=" SG CYS R 733 " pdb=" CB CYS R 733 " ideal model delta sinusoidal sigma weight residual -86.00 -130.02 44.02 1 1.00e+01 1.00e-02 2.70e+01 dihedral pdb=" CA ALA B 104 " pdb=" C ALA B 104 " pdb=" N TYR B 105 " pdb=" CA TYR B 105 " ideal model delta harmonic sigma weight residual 180.00 160.17 19.83 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 4916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1095 0.069 - 0.137: 171 0.137 - 0.206: 10 0.206 - 0.275: 3 0.275 - 0.343: 1 Chirality restraints: 1280 Sorted by residual: chirality pdb=" CA CYS R 657 " pdb=" N CYS R 657 " pdb=" C CYS R 657 " pdb=" CB CYS R 657 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CA GLN B 75 " pdb=" N GLN B 75 " pdb=" C GLN B 75 " pdb=" CB GLN B 75 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA THR B 196 " pdb=" N THR B 196 " pdb=" C THR B 196 " pdb=" CB THR B 196 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 1277 not shown) Planarity restraints: 1421 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE R 666 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.08e+00 pdb=" C PHE R 666 " -0.046 2.00e-02 2.50e+03 pdb=" O PHE R 666 " 0.017 2.00e-02 2.50e+03 pdb=" N PHE R 667 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.043 5.00e-02 4.00e+02 6.55e-02 6.86e+00 pdb=" N PRO B 236 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR R 664 " -0.012 2.00e-02 2.50e+03 2.50e-02 6.27e+00 pdb=" C THR R 664 " 0.043 2.00e-02 2.50e+03 pdb=" O THR R 664 " -0.016 2.00e-02 2.50e+03 pdb=" N HIS R 665 " -0.015 2.00e-02 2.50e+03 ... (remaining 1418 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1854 2.78 - 3.31: 6917 3.31 - 3.84: 12032 3.84 - 4.37: 13717 4.37 - 4.90: 25112 Nonbonded interactions: 59632 Sorted by model distance: nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.256 3.040 nonbonded pdb=" OD1 ASP R 813 " pdb=" N SER R 814 " model vdw 2.264 3.120 nonbonded pdb=" O ARG B 314 " pdb=" OG SER B 331 " model vdw 2.315 3.040 nonbonded pdb=" OD1 ASP D 50 " pdb=" N ILE D 51 " model vdw 2.333 3.120 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.334 3.040 ... (remaining 59627 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.970 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 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 : 0.005 0.044 8294 Z= 0.227 Angle : 0.779 8.363 11242 Z= 0.454 Chirality : 0.050 0.343 1280 Planarity : 0.006 0.066 1421 Dihedral : 12.888 90.794 2979 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.04 (0.23), residues: 1018 helix: -0.95 (0.26), residues: 356 sheet: -0.03 (0.36), residues: 197 loop : -2.27 (0.23), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 82 HIS 0.009 0.002 HIS A 357 PHE 0.021 0.002 PHE R 569 TYR 0.021 0.002 TYR D 95 ARG 0.005 0.000 ARG B 150 Details of bonding type rmsd hydrogen bonds : bond 0.17501 ( 330) hydrogen bonds : angle 7.05953 ( 924) SS BOND : bond 0.00045 ( 2) SS BOND : angle 1.69519 ( 4) covalent geometry : bond 0.00509 ( 8292) covalent geometry : angle 0.77883 (11238) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: R 699 MET cc_start: 0.7298 (mmt) cc_final: 0.6984 (mpp) REVERT: R 724 SER cc_start: 0.6396 (t) cc_final: 0.6164 (t) REVERT: C 21 MET cc_start: 0.7263 (mtm) cc_final: 0.7018 (mtm) REVERT: A 309 GLU cc_start: 0.7047 (pm20) cc_final: 0.6650 (pm20) REVERT: A 378 ASP cc_start: 0.7463 (m-30) cc_final: 0.7213 (m-30) REVERT: B 45 MET cc_start: 0.8211 (mtp) cc_final: 0.8004 (mtp) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 1.1927 time to fit residues: 242.5922 Evaluate side-chains 172 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.0270 chunk 75 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 815 GLN A 29 GLN A 236 GLN B 176 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.152243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.126951 restraints weight = 10888.358| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.33 r_work: 0.3522 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8294 Z= 0.166 Angle : 0.600 7.738 11242 Z= 0.323 Chirality : 0.044 0.142 1280 Planarity : 0.005 0.060 1421 Dihedral : 5.175 44.314 1115 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.37 % Allowed : 9.83 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.25), residues: 1018 helix: 0.29 (0.27), residues: 353 sheet: 0.40 (0.36), residues: 203 loop : -2.03 (0.24), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.021 0.002 PHE R 667 TYR 0.017 0.001 TYR D 95 ARG 0.005 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.06862 ( 330) hydrogen bonds : angle 4.70219 ( 924) SS BOND : bond 0.00153 ( 2) SS BOND : angle 1.21194 ( 4) covalent geometry : bond 0.00382 ( 8292) covalent geometry : angle 0.59946 (11238) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: R 677 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7646 (mpt) REVERT: R 724 SER cc_start: 0.6251 (t) cc_final: 0.6033 (t) REVERT: A 211 LYS cc_start: 0.8695 (mttp) cc_final: 0.8446 (mttt) REVERT: A 309 GLU cc_start: 0.7527 (pm20) cc_final: 0.7131 (pm20) REVERT: A 314 GLU cc_start: 0.7665 (mp0) cc_final: 0.7305 (mp0) REVERT: A 378 ASP cc_start: 0.7764 (m-30) cc_final: 0.7446 (m-30) outliers start: 21 outliers final: 12 residues processed: 177 average time/residue: 1.2995 time to fit residues: 243.0283 Evaluate side-chains 177 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 639 VAL Chi-restraints excluded: chain R residue 677 MET Chi-restraints excluded: chain R residue 693 MET Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 93 optimal weight: 0.2980 chunk 78 optimal weight: 0.9980 chunk 96 optimal weight: 0.0270 chunk 83 optimal weight: 0.0570 chunk 73 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 695 GLN R 815 GLN A 213 GLN A 236 GLN B 176 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.154276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.128941 restraints weight = 11026.454| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.35 r_work: 0.3547 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8294 Z= 0.120 Angle : 0.528 7.910 11242 Z= 0.283 Chirality : 0.042 0.131 1280 Planarity : 0.004 0.056 1421 Dihedral : 4.672 38.105 1115 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.37 % Allowed : 12.09 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.52 (0.25), residues: 1018 helix: 0.93 (0.28), residues: 354 sheet: 0.57 (0.36), residues: 203 loop : -1.86 (0.24), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.018 0.001 PHE R 667 TYR 0.018 0.001 TYR D 60 ARG 0.002 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.05392 ( 330) hydrogen bonds : angle 4.23232 ( 924) SS BOND : bond 0.00062 ( 2) SS BOND : angle 0.68167 ( 4) covalent geometry : bond 0.00262 ( 8292) covalent geometry : angle 0.52781 (11238) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.859 Fit side-chains revert: symmetry clash REVERT: R 677 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7782 (mpt) REVERT: R 724 SER cc_start: 0.6048 (t) cc_final: 0.5831 (t) REVERT: A 211 LYS cc_start: 0.8637 (mttp) cc_final: 0.8428 (mttt) REVERT: A 309 GLU cc_start: 0.7480 (pm20) cc_final: 0.7066 (pm20) REVERT: A 314 GLU cc_start: 0.7683 (mp0) cc_final: 0.7312 (mp0) REVERT: A 378 ASP cc_start: 0.7747 (m-30) cc_final: 0.7530 (m-30) REVERT: A 385 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.7309 (mpt180) outliers start: 21 outliers final: 8 residues processed: 179 average time/residue: 1.2832 time to fit residues: 242.4807 Evaluate side-chains 177 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 167 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 639 VAL Chi-restraints excluded: chain R residue 677 MET Chi-restraints excluded: chain R residue 693 MET Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 815 GLN A 236 GLN D 31 ASN B 176 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.151850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.126470 restraints weight = 10894.431| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.32 r_work: 0.3517 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8294 Z= 0.177 Angle : 0.597 9.395 11242 Z= 0.315 Chirality : 0.044 0.144 1280 Planarity : 0.004 0.057 1421 Dihedral : 4.813 39.054 1115 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.05 % Allowed : 13.33 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.46 (0.25), residues: 1018 helix: 0.98 (0.28), residues: 350 sheet: 0.69 (0.36), residues: 204 loop : -1.86 (0.25), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.008 0.001 HIS A 357 PHE 0.021 0.002 PHE R 667 TYR 0.018 0.002 TYR D 60 ARG 0.002 0.000 ARG D 38 Details of bonding type rmsd hydrogen bonds : bond 0.06346 ( 330) hydrogen bonds : angle 4.28733 ( 924) SS BOND : bond 0.00213 ( 2) SS BOND : angle 1.03125 ( 4) covalent geometry : bond 0.00422 ( 8292) covalent geometry : angle 0.59668 (11238) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: R 677 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7782 (mpt) REVERT: R 724 SER cc_start: 0.6068 (t) cc_final: 0.5814 (t) REVERT: R 766 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7594 (mp) REVERT: A 211 LYS cc_start: 0.8634 (mttp) cc_final: 0.8303 (mttt) REVERT: A 252 ASP cc_start: 0.7732 (t0) cc_final: 0.7134 (p0) REVERT: A 309 GLU cc_start: 0.7499 (pm20) cc_final: 0.7057 (pm20) REVERT: A 314 GLU cc_start: 0.7681 (mp0) cc_final: 0.7294 (mp0) REVERT: A 356 ARG cc_start: 0.7461 (ttm170) cc_final: 0.7161 (ttm170) REVERT: A 378 ASP cc_start: 0.7798 (m-30) cc_final: 0.7571 (m-30) REVERT: A 385 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7273 (mpt180) REVERT: B 46 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7837 (ptt-90) outliers start: 27 outliers final: 18 residues processed: 176 average time/residue: 1.2174 time to fit residues: 227.1046 Evaluate side-chains 181 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 595 ILE Chi-restraints excluded: chain R residue 639 VAL Chi-restraints excluded: chain R residue 677 MET Chi-restraints excluded: chain R residue 693 MET Chi-restraints excluded: chain R residue 699 MET Chi-restraints excluded: chain R residue 766 LEU Chi-restraints excluded: chain R residue 841 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 56 optimal weight: 0.0000 chunk 62 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 0.0970 chunk 38 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 overall best weight: 0.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 815 GLN A 213 GLN A 236 GLN D 31 ASN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 220 GLN B 239 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.154367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.129047 restraints weight = 10803.794| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.31 r_work: 0.3548 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8294 Z= 0.125 Angle : 0.540 9.182 11242 Z= 0.284 Chirality : 0.042 0.164 1280 Planarity : 0.004 0.056 1421 Dihedral : 4.478 33.389 1115 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.28 % Allowed : 14.35 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.19 (0.26), residues: 1018 helix: 1.30 (0.28), residues: 350 sheet: 0.72 (0.36), residues: 209 loop : -1.73 (0.25), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.018 0.001 PHE R 667 TYR 0.020 0.001 TYR D 60 ARG 0.002 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.05123 ( 330) hydrogen bonds : angle 4.06974 ( 924) SS BOND : bond 0.00144 ( 2) SS BOND : angle 0.65927 ( 4) covalent geometry : bond 0.00283 ( 8292) covalent geometry : angle 0.54016 (11238) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: A 54 SER cc_start: 0.8161 (OUTLIER) cc_final: 0.7938 (p) REVERT: A 211 LYS cc_start: 0.8602 (mttp) cc_final: 0.8393 (mttt) REVERT: A 252 ASP cc_start: 0.7677 (t0) cc_final: 0.7088 (p0) REVERT: A 309 GLU cc_start: 0.7489 (pm20) cc_final: 0.7036 (pm20) REVERT: A 314 GLU cc_start: 0.7684 (mp0) cc_final: 0.7296 (mp0) REVERT: A 378 ASP cc_start: 0.7746 (m-30) cc_final: 0.7519 (m-30) REVERT: A 385 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7194 (mpt180) REVERT: B 46 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7935 (ptt180) outliers start: 29 outliers final: 18 residues processed: 170 average time/residue: 1.2439 time to fit residues: 223.7941 Evaluate side-chains 181 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 639 VAL Chi-restraints excluded: chain R residue 693 MET Chi-restraints excluded: chain R residue 699 MET Chi-restraints excluded: chain R residue 841 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 27 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 69 optimal weight: 0.2980 chunk 52 optimal weight: 0.0870 chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 32 optimal weight: 0.0060 chunk 61 optimal weight: 1.9990 overall best weight: 0.3774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 815 GLN A 236 GLN D 31 ASN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.155076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.129825 restraints weight = 10854.942| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.29 r_work: 0.3561 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8294 Z= 0.114 Angle : 0.521 9.202 11242 Z= 0.274 Chirality : 0.042 0.137 1280 Planarity : 0.004 0.055 1421 Dihedral : 4.275 28.044 1115 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.05 % Allowed : 15.25 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.02 (0.26), residues: 1018 helix: 1.51 (0.28), residues: 351 sheet: 0.81 (0.36), residues: 209 loop : -1.64 (0.25), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.016 0.001 PHE R 667 TYR 0.021 0.001 TYR D 60 ARG 0.004 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.04695 ( 330) hydrogen bonds : angle 3.97982 ( 924) SS BOND : bond 0.00118 ( 2) SS BOND : angle 0.51923 ( 4) covalent geometry : bond 0.00252 ( 8292) covalent geometry : angle 0.52097 (11238) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: R 639 VAL cc_start: 0.7319 (OUTLIER) cc_final: 0.7105 (t) REVERT: R 766 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7472 (mp) REVERT: A 54 SER cc_start: 0.8121 (OUTLIER) cc_final: 0.7901 (p) REVERT: A 211 LYS cc_start: 0.8621 (mttp) cc_final: 0.8296 (mttt) REVERT: A 309 GLU cc_start: 0.7474 (pm20) cc_final: 0.7022 (pm20) REVERT: A 314 GLU cc_start: 0.7655 (mp0) cc_final: 0.7275 (mp0) REVERT: A 378 ASP cc_start: 0.7698 (m-30) cc_final: 0.7474 (m-30) REVERT: A 385 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7200 (mpt180) REVERT: B 46 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7924 (ptt180) outliers start: 27 outliers final: 15 residues processed: 172 average time/residue: 1.2863 time to fit residues: 233.6341 Evaluate side-chains 181 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 639 VAL Chi-restraints excluded: chain R residue 693 MET Chi-restraints excluded: chain R residue 766 LEU Chi-restraints excluded: chain R residue 841 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 36 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 69 optimal weight: 0.1980 chunk 47 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 0.0470 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 815 GLN A 236 GLN D 31 ASN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.154275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.128918 restraints weight = 10909.079| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.33 r_work: 0.3548 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8294 Z= 0.127 Angle : 0.529 7.036 11242 Z= 0.280 Chirality : 0.042 0.135 1280 Planarity : 0.004 0.055 1421 Dihedral : 4.265 24.710 1115 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.39 % Allowed : 14.92 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.13 (0.26), residues: 1018 helix: 1.61 (0.28), residues: 350 sheet: 0.78 (0.35), residues: 219 loop : -1.58 (0.26), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.018 0.001 PHE R 667 TYR 0.020 0.001 TYR D 60 ARG 0.004 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.05016 ( 330) hydrogen bonds : angle 4.01073 ( 924) SS BOND : bond 0.00166 ( 2) SS BOND : angle 0.63888 ( 4) covalent geometry : bond 0.00291 ( 8292) covalent geometry : angle 0.52882 (11238) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: R 606 ILE cc_start: 0.7730 (mm) cc_final: 0.7309 (tt) REVERT: R 639 VAL cc_start: 0.7335 (OUTLIER) cc_final: 0.7100 (t) REVERT: R 766 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7516 (mp) REVERT: A 54 SER cc_start: 0.8199 (OUTLIER) cc_final: 0.7997 (p) REVERT: A 211 LYS cc_start: 0.8634 (mttp) cc_final: 0.8416 (mttt) REVERT: A 213 GLN cc_start: 0.8457 (mt0) cc_final: 0.8228 (tt0) REVERT: A 252 ASP cc_start: 0.7856 (t0) cc_final: 0.7314 (p0) REVERT: A 309 GLU cc_start: 0.7470 (pm20) cc_final: 0.7014 (pm20) REVERT: A 314 GLU cc_start: 0.7683 (mp0) cc_final: 0.7289 (mp0) REVERT: A 356 ARG cc_start: 0.7387 (ttm170) cc_final: 0.6990 (ttm170) REVERT: A 378 ASP cc_start: 0.7737 (m-30) cc_final: 0.7528 (m-30) REVERT: A 385 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.7210 (mpt180) REVERT: D 123 GLN cc_start: 0.8471 (tp-100) cc_final: 0.7761 (tp40) REVERT: B 46 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7846 (ptt180) REVERT: B 219 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8190 (mtm180) REVERT: B 234 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.8265 (m-80) outliers start: 30 outliers final: 17 residues processed: 181 average time/residue: 1.3162 time to fit residues: 251.2437 Evaluate side-chains 186 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 639 VAL Chi-restraints excluded: chain R residue 693 MET Chi-restraints excluded: chain R residue 766 LEU Chi-restraints excluded: chain R residue 841 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 71 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 18 optimal weight: 0.0270 chunk 98 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN D 31 ASN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.154329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.128871 restraints weight = 10932.177| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.34 r_work: 0.3543 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8294 Z= 0.132 Angle : 0.532 7.007 11242 Z= 0.282 Chirality : 0.042 0.136 1280 Planarity : 0.004 0.055 1421 Dihedral : 4.263 23.329 1115 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.16 % Allowed : 15.59 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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 (0.26), residues: 1018 helix: 1.61 (0.29), residues: 350 sheet: 0.83 (0.34), residues: 230 loop : -1.59 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.017 0.001 PHE R 667 TYR 0.020 0.001 TYR D 60 ARG 0.004 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.05087 ( 330) hydrogen bonds : angle 4.03644 ( 924) SS BOND : bond 0.00179 ( 2) SS BOND : angle 0.63752 ( 4) covalent geometry : bond 0.00306 ( 8292) covalent geometry : angle 0.53159 (11238) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 0.969 Fit side-chains revert: symmetry clash REVERT: R 606 ILE cc_start: 0.7802 (mm) cc_final: 0.7387 (tt) REVERT: R 639 VAL cc_start: 0.7344 (OUTLIER) cc_final: 0.7103 (t) REVERT: R 766 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7513 (mp) REVERT: A 211 LYS cc_start: 0.8642 (mttp) cc_final: 0.8432 (mttt) REVERT: A 252 ASP cc_start: 0.7822 (t0) cc_final: 0.7270 (p0) REVERT: A 309 GLU cc_start: 0.7454 (pm20) cc_final: 0.7001 (pm20) REVERT: A 314 GLU cc_start: 0.7675 (mp0) cc_final: 0.7279 (mp0) REVERT: A 356 ARG cc_start: 0.7419 (ttm170) cc_final: 0.7025 (ttm170) REVERT: A 378 ASP cc_start: 0.7745 (m-30) cc_final: 0.7534 (m-30) REVERT: A 385 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.7215 (mpt180) REVERT: B 46 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7858 (ptt180) REVERT: B 219 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.8177 (mtm180) REVERT: B 234 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.8268 (m-80) outliers start: 28 outliers final: 20 residues processed: 169 average time/residue: 1.3412 time to fit residues: 239.4318 Evaluate side-chains 185 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 639 VAL Chi-restraints excluded: chain R residue 693 MET Chi-restraints excluded: chain R residue 699 MET Chi-restraints excluded: chain R residue 766 LEU Chi-restraints excluded: chain R residue 799 LEU Chi-restraints excluded: chain R residue 841 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 31 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 82 optimal weight: 0.0470 chunk 35 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 26 optimal weight: 0.4980 chunk 78 optimal weight: 0.0970 chunk 55 optimal weight: 1.9990 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 236 GLN D 31 ASN B 176 GLN B 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.155665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.130204 restraints weight = 11131.916| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.37 r_work: 0.3562 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8294 Z= 0.110 Angle : 0.505 6.545 11242 Z= 0.268 Chirality : 0.041 0.131 1280 Planarity : 0.004 0.054 1421 Dihedral : 4.061 18.859 1115 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.05 % Allowed : 15.93 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.32 (0.26), residues: 1018 helix: 1.75 (0.29), residues: 351 sheet: 0.86 (0.35), residues: 218 loop : -1.44 (0.26), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.016 0.001 PHE R 667 TYR 0.022 0.001 TYR D 60 ARG 0.003 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.04354 ( 330) hydrogen bonds : angle 3.95569 ( 924) SS BOND : bond 0.00142 ( 2) SS BOND : angle 0.41911 ( 4) covalent geometry : bond 0.00245 ( 8292) covalent geometry : angle 0.50503 (11238) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: R 606 ILE cc_start: 0.7750 (mm) cc_final: 0.7335 (tt) REVERT: R 639 VAL cc_start: 0.7298 (OUTLIER) cc_final: 0.7096 (t) REVERT: R 766 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7480 (mp) REVERT: A 211 LYS cc_start: 0.8635 (mttp) cc_final: 0.8342 (mttt) REVERT: A 252 ASP cc_start: 0.7786 (t0) cc_final: 0.7273 (p0) REVERT: A 309 GLU cc_start: 0.7468 (pm20) cc_final: 0.7025 (pm20) REVERT: A 314 GLU cc_start: 0.7669 (mp0) cc_final: 0.7273 (mp0) REVERT: A 356 ARG cc_start: 0.7341 (ttm170) cc_final: 0.6964 (ttm170) REVERT: A 378 ASP cc_start: 0.7723 (m-30) cc_final: 0.7510 (m-30) REVERT: A 385 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7187 (mpt180) REVERT: B 46 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7920 (ptt180) REVERT: B 100 VAL cc_start: 0.8742 (p) cc_final: 0.8531 (t) REVERT: B 234 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.8223 (m-80) outliers start: 27 outliers final: 18 residues processed: 176 average time/residue: 1.5850 time to fit residues: 294.2160 Evaluate side-chains 185 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 639 VAL Chi-restraints excluded: chain R residue 693 MET Chi-restraints excluded: chain R residue 766 LEU Chi-restraints excluded: chain R residue 799 LEU Chi-restraints excluded: chain R residue 841 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 70 optimal weight: 0.0970 chunk 50 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 60 optimal weight: 0.0070 chunk 79 optimal weight: 0.9990 chunk 62 optimal weight: 0.0370 chunk 81 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 86 optimal weight: 0.0980 overall best weight: 0.1874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN D 31 ASN B 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.157523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.132115 restraints weight = 10838.633| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.32 r_work: 0.3593 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8294 Z= 0.094 Angle : 0.486 5.799 11242 Z= 0.257 Chirality : 0.041 0.126 1280 Planarity : 0.004 0.054 1421 Dihedral : 3.878 16.924 1115 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.26 % Allowed : 17.06 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.43 (0.26), residues: 1018 helix: 1.88 (0.29), residues: 353 sheet: 0.87 (0.35), residues: 219 loop : -1.40 (0.26), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 99 HIS 0.003 0.001 HIS A 357 PHE 0.015 0.001 PHE A 212 TYR 0.022 0.001 TYR D 60 ARG 0.005 0.000 ARG A 22 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 330) hydrogen bonds : angle 3.92937 ( 924) SS BOND : bond 0.00137 ( 2) SS BOND : angle 0.26280 ( 4) covalent geometry : bond 0.00197 ( 8292) covalent geometry : angle 0.48563 (11238) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.905 Fit side-chains revert: symmetry clash REVERT: R 606 ILE cc_start: 0.7696 (mm) cc_final: 0.7312 (tt) REVERT: R 766 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7395 (mp) REVERT: R 799 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7710 (mt) REVERT: A 211 LYS cc_start: 0.8616 (mttp) cc_final: 0.8362 (mttt) REVERT: A 252 ASP cc_start: 0.7748 (t0) cc_final: 0.7224 (p0) REVERT: A 309 GLU cc_start: 0.7451 (pm20) cc_final: 0.7014 (pm20) REVERT: A 356 ARG cc_start: 0.7282 (ttm170) cc_final: 0.6918 (ttm170) REVERT: A 378 ASP cc_start: 0.7686 (m-30) cc_final: 0.7461 (m-30) REVERT: D 123 GLN cc_start: 0.8332 (tp40) cc_final: 0.7963 (tp40) REVERT: B 46 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7907 (ptt180) REVERT: B 234 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.8269 (m-80) REVERT: B 333 ASP cc_start: 0.7475 (p0) cc_final: 0.7096 (p0) outliers start: 20 outliers final: 9 residues processed: 172 average time/residue: 1.3543 time to fit residues: 246.4044 Evaluate side-chains 176 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 766 LEU Chi-restraints excluded: chain R residue 799 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 99 optimal weight: 2.9990 chunk 86 optimal weight: 0.2980 chunk 24 optimal weight: 0.0470 chunk 85 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 47 optimal weight: 0.4980 chunk 73 optimal weight: 0.0010 chunk 29 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 overall best weight: 0.2884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 213 GLN A 236 GLN D 31 ASN B 239 ASN B 293 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.156895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.131448 restraints weight = 10988.833| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.34 r_work: 0.3581 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8294 Z= 0.101 Angle : 0.496 5.859 11242 Z= 0.261 Chirality : 0.041 0.129 1280 Planarity : 0.004 0.054 1421 Dihedral : 3.860 17.153 1115 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.47 % Allowed : 18.08 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.50 (0.26), residues: 1018 helix: 1.94 (0.29), residues: 354 sheet: 0.93 (0.35), residues: 218 loop : -1.38 (0.26), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.016 0.001 PHE R 667 TYR 0.021 0.001 TYR D 60 ARG 0.005 0.000 ARG A 22 Details of bonding type rmsd hydrogen bonds : bond 0.03965 ( 330) hydrogen bonds : angle 3.89151 ( 924) SS BOND : bond 0.00108 ( 2) SS BOND : angle 0.38622 ( 4) covalent geometry : bond 0.00221 ( 8292) covalent geometry : angle 0.49610 (11238) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7483.99 seconds wall clock time: 129 minutes 37.49 seconds (7777.49 seconds total)