Starting phenix.real_space_refine on Wed Feb 12 16:05:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wxw_32882/02_2025/7wxw_32882_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wxw_32882/02_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_32882/02_2025/7wxw_32882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wxw_32882/02_2025/7wxw_32882.map" model { file = "/net/cci-nas-00/data/ceres_data/7wxw_32882/02_2025/7wxw_32882_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wxw_32882/02_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-5592/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: 4.90, per 1000 atoms: 0.60 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: 1.87 Conformation dependent library (CDL) restraints added in 1.2 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: 0.90 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: 2.22 Time building geometry restraints manager: 2.19 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 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: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.860 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.720 ------------------------------------------------------------------------------- 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 8292 Z= 0.329 Angle : 0.779 8.363 11238 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 *********************** 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 : 0.767 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: 1.2087 time to fit residues: 245.9091 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 : 0.814 ------------------------------------------------------------------------------- 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 = 0.126950 restraints weight = 10888.354| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.33 r_work: 0.3521 rms_B_bonded: 2.84 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: 0.7518 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 8292 Z= 0.248 Angle : 0.599 7.738 11238 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 *********************** 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 : 0.921 Fit side-chains revert: symmetry clash REVERT: R 677 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7649 (mpt) REVERT: R 724 SER cc_start: 0.6251 (t) cc_final: 0.6033 (t) REVERT: A 211 LYS cc_start: 0.8696 (mttp) cc_final: 0.8447 (mttt) REVERT: A 309 GLU cc_start: 0.7527 (pm20) cc_final: 0.7132 (pm20) REVERT: A 314 GLU cc_start: 0.7663 (mp0) cc_final: 0.7302 (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: 1.3064 time to fit residues: 244.4958 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 : 0.892 ------------------------------------------------------------------------------- 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: 0.9980 chunk 55 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 93 optimal weight: 0.0980 chunk 78 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 B 176 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.152577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.127303 restraints weight = 11029.224| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.33 r_work: 0.3523 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8292 Z= 0.242 Angle : 0.570 8.455 11238 Z= 0.305 Chirality : 0.043 0.140 1280 Planarity : 0.004 0.058 1421 Dihedral : 4.902 40.183 1115 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.82 % Allowed : 11.75 % Favored : 85.42 % 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: -0.65 (0.25), residues: 1018 helix: 0.76 (0.28), residues: 356 sheet: 0.56 (0.36), residues: 203 loop : -1.91 (0.24), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.022 0.002 PHE R 667 TYR 0.017 0.001 TYR D 60 ARG 0.002 0.000 ARG B 256 *********************** 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 196 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: R 677 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7788 (mpt) REVERT: R 724 SER cc_start: 0.6135 (t) cc_final: 0.5908 (t) REVERT: A 211 LYS cc_start: 0.8629 (mttp) cc_final: 0.8315 (mttt) REVERT: A 252 ASP cc_start: 0.7675 (t0) cc_final: 0.7133 (p0) REVERT: A 309 GLU cc_start: 0.7489 (pm20) cc_final: 0.7078 (pm20) REVERT: A 314 GLU cc_start: 0.7673 (mp0) cc_final: 0.7298 (mp0) REVERT: A 347 ARG cc_start: 0.7337 (OUTLIER) cc_final: 0.6469 (mtm-85) REVERT: A 385 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.7297 (mpt180) outliers start: 25 outliers final: 15 residues processed: 178 average time/residue: 1.3273 time to fit residues: 249.4546 Evaluate side-chains 182 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 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 296 LEU Chi-restraints excluded: chain A residue 347 ARG 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 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 217 MET 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: 3.9990 chunk 35 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 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 = 0.3965 r_free = 0.3965 target = 0.152273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.127002 restraints weight = 10914.068| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.32 r_work: 0.3522 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8292 Z= 0.254 Angle : 0.582 9.090 11238 Z= 0.309 Chirality : 0.043 0.140 1280 Planarity : 0.004 0.059 1421 Dihedral : 4.803 38.436 1115 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.73 % Allowed : 13.11 % Favored : 83.16 % 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: -0.47 (0.25), residues: 1018 helix: 0.98 (0.28), residues: 350 sheet: 0.65 (0.36), residues: 209 loop : -1.87 (0.25), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.022 0.002 PHE R 667 TYR 0.019 0.002 TYR D 60 ARG 0.002 0.000 ARG D 118 *********************** 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 199 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 166 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: R 677 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7773 (mpt) REVERT: R 724 SER cc_start: 0.6011 (t) cc_final: 0.5761 (t) REVERT: R 766 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7527 (mp) REVERT: A 211 LYS cc_start: 0.8607 (mttp) cc_final: 0.8288 (mttt) REVERT: A 309 GLU cc_start: 0.7505 (pm20) cc_final: 0.7065 (pm20) REVERT: A 314 GLU cc_start: 0.7669 (mp0) cc_final: 0.7286 (mp0) REVERT: A 347 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.6491 (mtm-85) REVERT: A 385 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.7278 (mpt180) REVERT: B 46 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7828 (ptt-90) REVERT: B 150 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8013 (mmt90) outliers start: 33 outliers final: 17 residues processed: 178 average time/residue: 1.3064 time to fit residues: 245.6129 Evaluate side-chains 184 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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 R residue 766 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 347 ARG 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 150 ARG 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: 0.4980 chunk 62 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 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 = 0.3967 r_free = 0.3967 target = 0.152613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.127494 restraints weight = 10816.756| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.30 r_work: 0.3526 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8292 Z= 0.247 Angle : 0.576 9.638 11238 Z= 0.303 Chirality : 0.043 0.140 1280 Planarity : 0.004 0.059 1421 Dihedral : 4.704 36.136 1115 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.50 % Allowed : 15.59 % Favored : 80.90 % 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: -0.32 (0.25), residues: 1018 helix: 1.06 (0.28), residues: 356 sheet: 0.68 (0.35), residues: 215 loop : -1.78 (0.25), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.020 0.002 PHE R 667 TYR 0.020 0.001 TYR D 60 ARG 0.002 0.000 ARG B 150 *********************** 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 192 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: R 677 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7761 (mpt) REVERT: R 724 SER cc_start: 0.5933 (t) cc_final: 0.5673 (t) REVERT: R 766 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7520 (mp) REVERT: A 211 LYS cc_start: 0.8603 (mttp) cc_final: 0.8284 (mttt) REVERT: A 252 ASP cc_start: 0.7740 (t0) cc_final: 0.7259 (p0) REVERT: A 309 GLU cc_start: 0.7499 (pm20) cc_final: 0.7049 (pm20) REVERT: A 314 GLU cc_start: 0.7672 (mp0) cc_final: 0.7284 (mp0) REVERT: A 347 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.6483 (mtm-85) REVERT: A 385 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7244 (mpt180) REVERT: B 46 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7837 (ptt180) outliers start: 31 outliers final: 19 residues processed: 170 average time/residue: 1.3187 time to fit residues: 236.7109 Evaluate side-chains 181 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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 R residue 766 LEU Chi-restraints excluded: chain R residue 841 LEU 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 296 LEU Chi-restraints excluded: chain A residue 347 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 27 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 123 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 = 0.3960 r_free = 0.3960 target = 0.151763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.126556 restraints weight = 10854.946| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.31 r_work: 0.3516 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8292 Z= 0.280 Angle : 0.594 10.367 11238 Z= 0.313 Chirality : 0.044 0.145 1280 Planarity : 0.004 0.059 1421 Dihedral : 4.741 33.342 1115 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.18 % Allowed : 15.14 % Favored : 80.68 % 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: -0.30 (0.25), residues: 1018 helix: 1.08 (0.28), residues: 356 sheet: 0.73 (0.35), residues: 215 loop : -1.79 (0.25), residues: 447 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 0.019 0.002 TYR D 60 ARG 0.005 0.000 ARG A 38 *********************** 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 196 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 159 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: R 597 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7724 (tt) REVERT: R 606 ILE cc_start: 0.7763 (mm) cc_final: 0.7338 (tt) REVERT: R 677 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7766 (mpt) REVERT: R 724 SER cc_start: 0.5932 (t) cc_final: 0.5670 (t) REVERT: R 766 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7523 (mp) REVERT: A 211 LYS cc_start: 0.8630 (mttp) cc_final: 0.8299 (mttt) REVERT: A 252 ASP cc_start: 0.7747 (t0) cc_final: 0.7260 (p0) REVERT: A 309 GLU cc_start: 0.7528 (pm20) cc_final: 0.7052 (pm20) REVERT: A 314 GLU cc_start: 0.7657 (mp0) cc_final: 0.7273 (mp0) REVERT: A 347 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.6482 (mtm-85) REVERT: A 356 ARG cc_start: 0.7448 (ttm170) cc_final: 0.7071 (ttm170) REVERT: A 385 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7224 (mpt180) REVERT: B 46 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7857 (ptt180) REVERT: B 150 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8070 (mmt90) outliers start: 37 outliers final: 20 residues processed: 176 average time/residue: 1.3883 time to fit residues: 259.2429 Evaluate side-chains 183 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 597 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 207 ILE Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 347 ARG 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 71 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 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 150 ARG 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: 0.5980 chunk 43 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 47 optimal weight: 0.0670 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 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 = 0.3979 r_free = 0.3979 target = 0.153528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.128243 restraints weight = 10947.002| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.31 r_work: 0.3536 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8292 Z= 0.208 Angle : 0.552 9.853 11238 Z= 0.292 Chirality : 0.043 0.181 1280 Planarity : 0.004 0.057 1421 Dihedral : 4.490 26.884 1115 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.29 % Allowed : 15.37 % Favored : 80.34 % 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: -0.15 (0.26), residues: 1018 helix: 1.33 (0.28), residues: 350 sheet: 0.77 (0.35), residues: 214 loop : -1.75 (0.25), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.019 0.002 PHE R 667 TYR 0.021 0.001 TYR D 60 ARG 0.002 0.000 ARG A 232 *********************** 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 198 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 0.852 Fit side-chains revert: symmetry clash REVERT: R 597 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7714 (tt) REVERT: R 606 ILE cc_start: 0.7775 (mm) cc_final: 0.7369 (tt) REVERT: R 677 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7768 (mpt) REVERT: R 724 SER cc_start: 0.5633 (t) cc_final: 0.5397 (t) REVERT: R 766 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7511 (mp) REVERT: A 211 LYS cc_start: 0.8616 (mttp) cc_final: 0.8409 (mttt) REVERT: A 252 ASP cc_start: 0.7682 (t0) cc_final: 0.7193 (p0) REVERT: A 309 GLU cc_start: 0.7498 (pm20) cc_final: 0.7029 (pm20) REVERT: A 314 GLU cc_start: 0.7651 (mp0) cc_final: 0.7273 (mp0) REVERT: A 347 ARG cc_start: 0.7337 (OUTLIER) cc_final: 0.6468 (mtm-85) REVERT: A 385 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7224 (mpt180) REVERT: B 46 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7821 (ptt180) REVERT: B 150 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8063 (mmt90) outliers start: 38 outliers final: 23 residues processed: 177 average time/residue: 1.3029 time to fit residues: 243.7987 Evaluate side-chains 195 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 597 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 799 LEU Chi-restraints excluded: chain R residue 841 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 347 ARG 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 71 SER Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 104 THR 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 150 ARG Chi-restraints excluded: chain B residue 198 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 71 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 18 optimal weight: 0.0070 chunk 98 optimal weight: 0.0060 chunk 14 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 30 optimal weight: 0.1980 overall best weight: 0.3414 ------------------------------------------------------------------------------- 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 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 220 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 = 0.3999 r_free = 0.3999 target = 0.155115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.129842 restraints weight = 10998.206| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.33 r_work: 0.3562 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8292 Z= 0.160 Angle : 0.526 9.417 11238 Z= 0.278 Chirality : 0.042 0.158 1280 Planarity : 0.004 0.055 1421 Dihedral : 4.235 23.344 1115 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.28 % Allowed : 16.61 % Favored : 80.11 % 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: 0.10 (0.26), residues: 1018 helix: 1.62 (0.29), residues: 349 sheet: 0.82 (0.35), residues: 214 loop : -1.63 (0.26), residues: 455 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 0.022 0.001 TYR D 60 ARG 0.005 0.000 ARG B 96 *********************** 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 192 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: R 573 MET cc_start: 0.8474 (mmt) cc_final: 0.8271 (mtt) REVERT: R 606 ILE cc_start: 0.7760 (mm) cc_final: 0.7369 (tt) REVERT: R 639 VAL cc_start: 0.7354 (OUTLIER) cc_final: 0.7121 (t) REVERT: R 766 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7441 (mp) REVERT: R 799 LEU cc_start: 0.7933 (mp) cc_final: 0.7732 (mt) REVERT: A 211 LYS cc_start: 0.8644 (mttp) cc_final: 0.8345 (mttt) REVERT: A 252 ASP cc_start: 0.7636 (t0) cc_final: 0.7106 (p0) REVERT: A 309 GLU cc_start: 0.7488 (pm20) cc_final: 0.7030 (pm20) REVERT: A 314 GLU cc_start: 0.7648 (mp0) cc_final: 0.7259 (mp0) REVERT: A 347 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.6447 (mtm-85) REVERT: A 385 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7211 (mpt180) REVERT: B 46 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7834 (ptt180) REVERT: B 150 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8076 (mmt90) REVERT: B 234 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.8306 (m-80) outliers start: 29 outliers final: 12 residues processed: 177 average time/residue: 1.4271 time to fit residues: 266.0038 Evaluate side-chains 182 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 639 VAL Chi-restraints excluded: chain R residue 687 ILE 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 347 ARG 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 46 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 198 LEU 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: 0.9980 chunk 41 optimal weight: 1.9990 chunk 46 optimal weight: 0.0070 chunk 38 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 60 optimal weight: 0.0010 chunk 26 optimal weight: 0.4980 chunk 78 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.4004 ------------------------------------------------------------------------------- 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 ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 123 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 = 0.3997 r_free = 0.3997 target = 0.155010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.129484 restraints weight = 11117.253| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.36 r_work: 0.3557 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8292 Z= 0.170 Angle : 0.520 6.817 11238 Z= 0.277 Chirality : 0.042 0.157 1280 Planarity : 0.004 0.055 1421 Dihedral : 4.152 19.938 1115 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.60 % Allowed : 18.31 % Favored : 79.10 % 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: 0.15 (0.26), residues: 1018 helix: 1.65 (0.28), residues: 351 sheet: 0.76 (0.35), residues: 220 loop : -1.57 (0.26), residues: 447 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 0.017 0.001 PHE R 667 TYR 0.022 0.001 TYR D 60 ARG 0.005 0.000 ARG B 96 *********************** 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 185 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: R 606 ILE cc_start: 0.7741 (mm) cc_final: 0.7340 (tt) REVERT: R 639 VAL cc_start: 0.7298 (OUTLIER) cc_final: 0.7085 (t) REVERT: R 766 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7491 (mp) REVERT: A 211 LYS cc_start: 0.8632 (mttp) cc_final: 0.8349 (mttt) REVERT: A 252 ASP cc_start: 0.7711 (t0) cc_final: 0.7178 (p0) REVERT: A 309 GLU cc_start: 0.7475 (pm20) cc_final: 0.7026 (pm20) REVERT: A 347 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.6449 (mtm-85) REVERT: A 356 ARG cc_start: 0.7392 (ttm170) cc_final: 0.7010 (ttm170) REVERT: A 385 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7203 (mpt180) REVERT: D 123 GLN cc_start: 0.8359 (tp-100) cc_final: 0.7833 (tp40) REVERT: B 46 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7826 (ptt180) REVERT: B 150 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8308 (mmt90) REVERT: B 234 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.8354 (m-80) outliers start: 23 outliers final: 13 residues processed: 173 average time/residue: 1.3470 time to fit residues: 245.6372 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 : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 639 VAL Chi-restraints excluded: chain R residue 682 LEU Chi-restraints excluded: chain R residue 693 MET Chi-restraints excluded: chain R residue 766 LEU Chi-restraints excluded: chain A residue 347 ARG 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 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 198 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: 2.9990 chunk 50 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 23 optimal weight: 0.0670 chunk 0 optimal weight: 1.9990 chunk 60 optimal weight: 0.0040 chunk 79 optimal weight: 0.0770 chunk 62 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 chunk 72 optimal weight: 0.0030 chunk 86 optimal weight: 0.0980 overall best weight: 0.0498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN B 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.159454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.134223 restraints weight = 10962.156| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.35 r_work: 0.3635 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8292 Z= 0.119 Angle : 0.481 6.679 11238 Z= 0.254 Chirality : 0.041 0.155 1280 Planarity : 0.004 0.054 1421 Dihedral : 3.715 15.986 1115 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.69 % Allowed : 18.76 % Favored : 79.55 % 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: 0.41 (0.26), residues: 1018 helix: 1.84 (0.29), residues: 354 sheet: 0.95 (0.35), residues: 231 loop : -1.52 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 36 HIS 0.002 0.000 HIS R 696 PHE 0.014 0.001 PHE A 212 TYR 0.023 0.001 TYR D 60 ARG 0.004 0.000 ARG B 96 ********************** 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 187 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: A 252 ASP cc_start: 0.7626 (t0) cc_final: 0.6991 (p0) REVERT: A 309 GLU cc_start: 0.7521 (pm20) cc_final: 0.7072 (pm20) REVERT: A 314 GLU cc_start: 0.7647 (mp0) cc_final: 0.7250 (mp0) REVERT: A 356 ARG cc_start: 0.7329 (ttm170) cc_final: 0.6909 (ttm170) REVERT: A 392 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7813 (mm-30) REVERT: D 77 ASN cc_start: 0.6579 (m-40) cc_final: 0.6308 (m110) REVERT: B 46 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7857 (ptt180) REVERT: B 234 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.8250 (m-80) REVERT: B 333 ASP cc_start: 0.7187 (p0) cc_final: 0.6847 (p0) outliers start: 15 outliers final: 7 residues processed: 176 average time/residue: 1.3252 time to fit residues: 246.1782 Evaluate side-chains 172 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 163 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 687 ILE 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 98 SER Chi-restraints excluded: chain B residue 234 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: 0.6980 chunk 86 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 85 optimal weight: 0.0670 chunk 58 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 294 GLN D 31 ASN D 123 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 = 0.154348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.128730 restraints weight = 11002.800| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.33 r_work: 0.3541 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8292 Z= 0.239 Angle : 0.569 7.035 11238 Z= 0.301 Chirality : 0.043 0.158 1280 Planarity : 0.004 0.057 1421 Dihedral : 4.172 19.552 1115 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.58 % Allowed : 20.23 % Favored : 78.19 % 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: 0.25 (0.26), residues: 1018 helix: 1.67 (0.28), residues: 353 sheet: 0.87 (0.35), residues: 220 loop : -1.51 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.006 0.001 HIS B 225 PHE 0.019 0.002 PHE R 667 TYR 0.017 0.001 TYR D 95 ARG 0.004 0.000 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7242.68 seconds wall clock time: 128 minutes 0.17 seconds (7680.17 seconds total)