Starting phenix.real_space_refine on Sun Sep 13 15:42:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vvo_21405/09_2026/6vvo_21405.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vvo_21405/09_2026/6vvo_21405.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vvo_21405/09_2026/6vvo_21405.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vvo_21405/09_2026/6vvo_21405.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6vvo_21405/09_2026/6vvo_21405.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vvo_21405/09_2026/6vvo_21405.cif" model { file = "/net/cci-nas-00/data/ceres_data/6vvo_21405/09_2026/6vvo_21405.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vvo_21405/09_2026/6vvo_21405.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5510 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 14 5.49 5 Mg 4 5.21 5 S 141 5.16 5 C 12382 2.51 5 N 3350 2.21 5 O 3777 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.22s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19668 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3500 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 20, 'TRANS': 427} Chain breaks: 4 Chain: "B" Number of atoms: 2492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2492 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 12, 'TRANS': 303} Chain: "C" Number of atoms: 2486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2486 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 12, 'TRANS': 299} Chain breaks: 1 Chain: "D" Number of atoms: 2361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2361 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 11, 'TRANS': 292} Chain breaks: 3 Chain: "E" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2759 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "F" Number of atoms: 1960 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 1954 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 254, 1954 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain breaks: 1 bond proxies already assigned to first conformer: 1972 Chain: "G" Number of atoms: 1980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1980 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 7, 'TRANS': 249} Chain: "H" Number of atoms: 1975 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 256, 1972 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Conformer: "B" Number of residues, atoms: 256, 1972 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} bond proxies already assigned to first conformer: 1994 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.50, per 1000 atoms: 0.23 Number of scatterers: 19668 At special positions: 0 Unit cell: (113.42, 121.9, 139.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 141 16.00 P 14 15.00 Mg 4 11.99 O 3777 8.00 N 3350 7.00 C 12382 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS G 135 " - pdb=" SG CYS G 162 " distance=2.02 Simple disulfide: pdb=" SG CYS H 135 " - pdb=" SG CYS H 162 " 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: 1.49 Conformation dependent library (CDL) restraints added in 1.0 seconds 4922 Ramachandran restraints generated. 2461 Oldfield, 0 Emsley, 2461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4736 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 11 sheets defined 50.3% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 585 through 590 Processing helix chain 'A' and resid 606 through 617 removed outlier: 3.602A pdb=" N LEU A 611 " --> pdb=" O CYS A 607 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN A 617 " --> pdb=" O ARG A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 621 Processing helix chain 'A' and resid 656 through 668 Processing helix chain 'A' and resid 682 through 690 Processing helix chain 'A' and resid 690 through 695 removed outlier: 3.650A pdb=" N LEU A 694 " --> pdb=" O VAL A 690 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASN A 695 " --> pdb=" O ALA A 691 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 690 through 695' Processing helix chain 'A' and resid 698 through 702 Processing helix chain 'A' and resid 721 through 725 Processing helix chain 'A' and resid 732 through 743 removed outlier: 3.526A pdb=" N GLU A 736 " --> pdb=" O GLY A 732 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS A 743 " --> pdb=" O GLY A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 762 removed outlier: 3.988A pdb=" N SER A 762 " --> pdb=" O PRO A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 767 Processing helix chain 'A' and resid 776 through 792 Processing helix chain 'A' and resid 796 through 807 Processing helix chain 'A' and resid 810 through 827 Processing helix chain 'A' and resid 847 through 855 Processing helix chain 'A' and resid 866 through 876 removed outlier: 4.029A pdb=" N PHE A 874 " --> pdb=" O LYS A 870 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE A 875 " --> pdb=" O SER A 871 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS A 876 " --> pdb=" O ASP A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 889 Processing helix chain 'A' and resid 890 through 892 No H-bonds generated for 'chain 'A' and resid 890 through 892' Processing helix chain 'A' and resid 900 through 928 removed outlier: 3.726A pdb=" N MET A 906 " --> pdb=" O LYS A 902 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER A 927 " --> pdb=" O SER A 923 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS A 928 " --> pdb=" O GLN A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 942 Processing helix chain 'A' and resid 943 through 949 Processing helix chain 'A' and resid 961 through 982 removed outlier: 3.863A pdb=" N LYS A 965 " --> pdb=" O SER A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1013 Proline residue: A1009 - end of helix Processing helix chain 'A' and resid 1016 through 1028 Processing helix chain 'A' and resid 1031 through 1040 removed outlier: 3.515A pdb=" N GLU A1040 " --> pdb=" O GLU A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1066 removed outlier: 3.864A pdb=" N ALA A1061 " --> pdb=" O LYS A1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 42 Processing helix chain 'B' and resid 46 through 50 removed outlier: 3.547A pdb=" N ILE B 50 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 67 Processing helix chain 'B' and resid 81 through 95 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.186A pdb=" N ILE B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LYS B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.612A pdb=" N MET B 146 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 161 removed outlier: 4.615A pdb=" N ARG B 156 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N THR B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 194 through 210 removed outlier: 3.534A pdb=" N ILE B 198 " --> pdb=" O THR B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 226 removed outlier: 3.711A pdb=" N GLN B 226 " --> pdb=" O ILE B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 243 Processing helix chain 'B' and resid 247 through 255 removed outlier: 3.640A pdb=" N LYS B 253 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B 254 " --> pdb=" O ASN B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 274 through 288 removed outlier: 3.856A pdb=" N LYS B 280 " --> pdb=" O ASP B 276 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 305 removed outlier: 4.069A pdb=" N THR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 329 removed outlier: 3.626A pdb=" N GLU B 319 " --> pdb=" O GLU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 348 removed outlier: 3.615A pdb=" N MET B 337 " --> pdb=" O SER B 333 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 26 Processing helix chain 'C' and resid 37 through 50 Processing helix chain 'C' and resid 65 through 78 removed outlier: 3.628A pdb=" N LEU C 71 " --> pdb=" O THR C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 103 Processing helix chain 'C' and resid 103 through 110 Processing helix chain 'C' and resid 131 through 145 Processing helix chain 'C' and resid 157 through 161 Processing helix chain 'C' and resid 162 through 169 removed outlier: 3.525A pdb=" N ARG C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N CYS C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 193 Proline residue: C 184 - end of helix Processing helix chain 'C' and resid 200 through 210 removed outlier: 3.547A pdb=" N LEU C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 227 Processing helix chain 'C' and resid 233 through 239 Processing helix chain 'C' and resid 243 through 256 Processing helix chain 'C' and resid 258 through 273 Processing helix chain 'C' and resid 276 through 291 removed outlier: 3.852A pdb=" N ILE C 280 " --> pdb=" O ALA C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 313 removed outlier: 3.721A pdb=" N TYR C 310 " --> pdb=" O ALA C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 330 removed outlier: 3.599A pdb=" N GLN C 321 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER C 323 " --> pdb=" O LYS C 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 44 removed outlier: 3.584A pdb=" N TYR D 44 " --> pdb=" O TRP D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 64 Processing helix chain 'D' and resid 83 through 96 removed outlier: 3.537A pdb=" N THR D 87 " --> pdb=" O GLY D 83 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE D 88 " --> pdb=" O LYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 128 removed outlier: 3.818A pdb=" N GLN D 128 " --> pdb=" O LYS D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 170 Processing helix chain 'D' and resid 187 through 193 Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'D' and resid 223 through 234 removed outlier: 3.510A pdb=" N SER D 234 " --> pdb=" O LEU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 258 through 266 removed outlier: 3.523A pdb=" N ILE D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 283 removed outlier: 3.582A pdb=" N ILE D 274 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 299 removed outlier: 3.737A pdb=" N LEU D 289 " --> pdb=" O SER D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 316 removed outlier: 3.749A pdb=" N GLU D 316 " --> pdb=" O ASP D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 340 Processing helix chain 'D' and resid 343 through 360 Processing helix chain 'E' and resid 12 through 16 removed outlier: 3.635A pdb=" N LEU E 16 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 Processing helix chain 'E' and resid 47 through 60 Processing helix chain 'E' and resid 61 through 65 removed outlier: 3.521A pdb=" N VAL E 64 " --> pdb=" O GLY E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 120 removed outlier: 3.815A pdb=" N VAL E 107 " --> pdb=" O SER E 103 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE E 108 " --> pdb=" O ASP E 104 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN E 109 " --> pdb=" O ARG E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 155 removed outlier: 3.541A pdb=" N ALA E 147 " --> pdb=" O ASP E 143 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU E 153 " --> pdb=" O ARG E 149 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR E 155 " --> pdb=" O THR E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 171 removed outlier: 3.905A pdb=" N LYS E 170 " --> pdb=" O SER E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 177 Processing helix chain 'E' and resid 188 through 204 Processing helix chain 'E' and resid 210 through 220 removed outlier: 3.670A pdb=" N ARG E 214 " --> pdb=" O GLN E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 249 through 265 Processing helix chain 'E' and resid 267 through 284 removed outlier: 3.707A pdb=" N GLU E 273 " --> pdb=" O GLN E 269 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N HIS E 284 " --> pdb=" O GLU E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 301 removed outlier: 3.574A pdb=" N GLU E 298 " --> pdb=" O GLY E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 323 Processing helix chain 'E' and resid 327 through 349 removed outlier: 4.052A pdb=" N HIS E 331 " --> pdb=" O LYS E 327 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS E 345 " --> pdb=" O ALA E 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 20 removed outlier: 3.625A pdb=" N LYS F 13 " --> pdb=" O GLY F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 80 Processing helix chain 'F' and resid 141 through 152 Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 217 through 219 No H-bonds generated for 'chain 'F' and resid 217 through 219' Processing helix chain 'G' and resid 9 through 20 removed outlier: 3.692A pdb=" N LYS G 13 " --> pdb=" O GLY G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 80 Processing helix chain 'G' and resid 141 through 155 removed outlier: 3.960A pdb=" N HIS G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE G 154 " --> pdb=" O ASP G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 216 Processing helix chain 'G' and resid 217 through 222 Proline residue: G 220 - end of helix No H-bonds generated for 'chain 'G' and resid 217 through 222' Processing helix chain 'H' and resid 8 through 20 removed outlier: 4.395A pdb=" N LEU H 12 " --> pdb=" O GLN H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 80 Processing helix chain 'H' and resid 141 through 152 Processing helix chain 'H' and resid 209 through 216 Processing helix chain 'H' and resid 217 through 219 No H-bonds generated for 'chain 'H' and resid 217 through 219' Processing sheet with id=AA1, first strand: chain 'A' and resid 671 through 675 removed outlier: 5.696A pdb=" N SER A 671 " --> pdb=" O ALA A 716 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE A 718 " --> pdb=" O SER A 671 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N VAL A 673 " --> pdb=" O ILE A 718 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N ILE A 749 " --> pdb=" O HIS A 715 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU A 717 " --> pdb=" O ILE A 749 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N MET A 751 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N MET A 719 " --> pdb=" O MET A 751 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ALA A 647 " --> pdb=" O CYS A 750 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ALA A 646 " --> pdb=" O PHE A 768 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU A 770 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LEU A 648 " --> pdb=" O LEU A 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 102 through 105 removed outlier: 5.991A pdb=" N LYS B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ALA B 168 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE B 138 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ALA B 170 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU B 140 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 87 through 91 removed outlier: 6.162A pdb=" N LYS C 120 " --> pdb=" O ARG C 150 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N CYS C 152 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL C 122 " --> pdb=" O CYS C 152 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ILE C 154 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU C 124 " --> pdb=" O ILE C 154 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 106 through 109 removed outlier: 6.930A pdb=" N LEU D 106 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ASP D 150 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU D 108 " --> pdb=" O ASP D 150 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LYS D 145 " --> pdb=" O ARG D 175 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N CYS D 177 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL D 147 " --> pdb=" O CYS D 177 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ILE D 179 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU D 149 " --> pdb=" O ILE D 179 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 68 through 75 removed outlier: 6.083A pdb=" N LYS E 130 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ILE E 162 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL E 132 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N CYS E 164 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU E 134 " --> pdb=" O CYS E 164 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU E 38 " --> pdb=" O LEU E 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 59 through 61 removed outlier: 3.797A pdb=" N ALA F 4 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER G 172 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ALA G 157 " --> pdb=" O SER G 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 66 through 71 removed outlier: 7.494A pdb=" N GLU F 25 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N MET F 40 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N CYS F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N GLN F 38 " --> pdb=" O CYS F 27 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 203 through 208 removed outlier: 3.972A pdb=" N VAL F 203 " --> pdb=" O CYS F 162 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ALA F 157 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N SER F 172 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN F 177 " --> pdb=" O GLU H 115 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 59 through 61 removed outlier: 3.504A pdb=" N ASP G 113 " --> pdb=" O ASN H 179 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN H 179 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER H 172 " --> pdb=" O ALA H 157 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ALA H 157 " --> pdb=" O SER H 172 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 67 through 71 removed outlier: 7.122A pdb=" N GLU G 25 " --> pdb=" O MET G 40 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N MET G 40 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N CYS G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLN G 38 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 66 through 68 removed outlier: 4.628A pdb=" N LYS H 240 " --> pdb=" O THR H 224 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR H 224 " --> pdb=" O LYS H 240 " (cutoff:3.500A) 1053 hydrogen bonds defined for protein. 3008 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.11 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 6763 1.37 - 1.51: 6684 1.51 - 1.66: 6316 1.66 - 1.80: 197 1.80 - 1.95: 23 Bond restraints: 19983 Sorted by residual: bond pdb=" C TYR E 238 " pdb=" N PRO E 239 " ideal model delta sigma weight residual 1.330 1.359 -0.029 1.19e-02 7.06e+03 5.81e+00 bond pdb=" C LEU A 944 " pdb=" N PRO A 945 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.55e+00 bond pdb=" CB ASP H 58 " pdb=" CG ASP H 58 " ideal model delta sigma weight residual 1.516 1.471 0.045 2.50e-02 1.60e+03 3.26e+00 bond pdb=" CB THR A1027 " pdb=" CG2 THR A1027 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.15e+00 bond pdb=" CG1 ILE H 154 " pdb=" CD1 ILE H 154 " ideal model delta sigma weight residual 1.513 1.445 0.068 3.90e-02 6.57e+02 3.02e+00 ... (remaining 19978 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 26242 2.11 - 4.23: 678 4.23 - 6.34: 80 6.34 - 8.46: 14 8.46 - 10.57: 5 Bond angle restraints: 27019 Sorted by residual: angle pdb=" C ALA F 231 " pdb=" N ASP F 232 " pdb=" CA ASP F 232 " ideal model delta sigma weight residual 122.41 112.55 9.86 1.41e+00 5.03e-01 4.89e+01 angle pdb=" C VAL G 188 " pdb=" N ASP G 189 " pdb=" CA ASP G 189 " ideal model delta sigma weight residual 121.54 130.16 -8.62 1.91e+00 2.74e-01 2.04e+01 angle pdb=" N SER F 230 " pdb=" CA SER F 230 " pdb=" C SER F 230 " ideal model delta sigma weight residual 108.02 100.53 7.49 1.75e+00 3.27e-01 1.83e+01 angle pdb=" C ASP G 189 " pdb=" N LYS G 190 " pdb=" CA LYS G 190 " ideal model delta sigma weight residual 120.71 114.65 6.06 1.42e+00 4.96e-01 1.82e+01 angle pdb=" C THR G 185 " pdb=" N SER G 186 " pdb=" CA SER G 186 " ideal model delta sigma weight residual 121.45 130.25 -8.80 2.14e+00 2.18e-01 1.69e+01 ... (remaining 27014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.43: 12018 33.43 - 66.85: 247 66.85 - 100.28: 13 100.28 - 133.71: 3 133.71 - 167.13: 2 Dihedral angle restraints: 12283 sinusoidal: 4999 harmonic: 7284 Sorted by residual: dihedral pdb=" O2A ADP E2000 " pdb=" O3A ADP E2000 " pdb=" PA ADP E2000 " pdb=" PB ADP E2000 " ideal model delta sinusoidal sigma weight residual 300.00 132.87 167.13 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C5' ADP E2000 " pdb=" O5' ADP E2000 " pdb=" PA ADP E2000 " pdb=" O2A ADP E2000 " ideal model delta sinusoidal sigma weight residual -60.00 79.40 -139.40 1 2.00e+01 2.50e-03 4.22e+01 dihedral pdb=" CA THR C 113 " pdb=" C THR C 113 " pdb=" N ILE C 114 " pdb=" CA ILE C 114 " ideal model delta harmonic sigma weight residual -180.00 -158.21 -21.79 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 12280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2558 0.064 - 0.129: 523 0.129 - 0.193: 53 0.193 - 0.257: 6 0.257 - 0.321: 2 Chirality restraints: 3142 Sorted by residual: chirality pdb=" CB VAL H 7 " pdb=" CA VAL H 7 " pdb=" CG1 VAL H 7 " pdb=" CG2 VAL H 7 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CB ILE D 257 " pdb=" CA ILE D 257 " pdb=" CG1 ILE D 257 " pdb=" CG2 ILE D 257 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CG LEU A 944 " pdb=" CB LEU A 944 " pdb=" CD1 LEU A 944 " pdb=" CD2 LEU A 944 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 3139 not shown) Planarity restraints: 3424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU E 136 " -0.019 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" CD GLU E 136 " 0.066 2.00e-02 2.50e+03 pdb=" OE1 GLU E 136 " -0.024 2.00e-02 2.50e+03 pdb=" OE2 GLU E 136 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 299 " -0.019 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C ILE C 299 " 0.064 2.00e-02 2.50e+03 pdb=" O ILE C 299 " -0.024 2.00e-02 2.50e+03 pdb=" N HIS C 300 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR H 59 " 0.016 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C THR H 59 " -0.058 2.00e-02 2.50e+03 pdb=" O THR H 59 " 0.022 2.00e-02 2.50e+03 pdb=" N TYR H 60 " 0.020 2.00e-02 2.50e+03 ... (remaining 3421 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 129 2.51 - 3.11: 15160 3.11 - 3.71: 29281 3.71 - 4.30: 42412 4.30 - 4.90: 72701 Nonbonded interactions: 159683 Sorted by model distance: nonbonded pdb="MG MG D 401 " pdb=" O2B AGS D 402 " model vdw 1.915 2.170 nonbonded pdb="MG MG A1201 " pdb=" O1B AGS A1202 " model vdw 1.926 2.170 nonbonded pdb=" OG1 THR B 83 " pdb="MG MG B 401 " model vdw 1.930 2.170 nonbonded pdb="MG MG C 401 " pdb=" O3G AGS C 402 " model vdw 1.941 2.170 nonbonded pdb="MG MG C 401 " pdb=" O1B AGS C 402 " model vdw 1.965 2.170 ... (remaining 159678 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'F' and (resid 1 through 160 or resid 162 through 200 or resid 202 throug \ h 255)) selection = (chain 'G' and (resid 1 through 160 or resid 162 through 189 or resid 191 throug \ h 200 or resid 202 through 255)) selection = (chain 'H' and (resid 1 through 160 or resid 162 through 189 or resid 191 throug \ h 200 or resid 202 through 255)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 19.060 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 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 : 0.008 0.068 19985 Z= 0.352 Angle : 0.825 10.572 27023 Z= 0.452 Chirality : 0.052 0.321 3142 Planarity : 0.005 0.055 3424 Dihedral : 13.997 167.132 7541 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.72 % Favored : 95.16 % Rotamer: Outliers : 0.41 % Allowed : 5.91 % Favored : 93.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.15), residues: 2461 helix: -1.34 (0.13), residues: 1169 sheet: -1.84 (0.21), residues: 493 loop : -2.64 (0.19), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 214 TYR 0.026 0.002 TYR E 238 PHE 0.021 0.002 PHE D 76 TRP 0.030 0.002 TRP E 4 HIS 0.015 0.002 HIS A 715 Details of bonding type rmsd/Z covalent geometry : bond 0.00830 / 0.35 (19983) covalent geometry : angle 0.82494 / 0.45 (27019) SS BOND : bond 0.00643 / 0.34 ( 2) SS BOND : angle 1.28034 / 0.66 ( 4) hydrogen bonds : bond 0.12530 / 8.24 ( 1053) hydrogen bonds : angle 5.91780 / 4.06 ( 3008) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4922 Ramachandran restraints generated. 2461 Oldfield, 0 Emsley, 2461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4922 Ramachandran restraints generated. 2461 Oldfield, 0 Emsley, 2461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 172 time to evaluate : 0.718 Fit side-chains revert: symmetry clash REVERT: B 337 MET cc_start: 0.8526 (mmm) cc_final: 0.8277 (mmm) REVERT: F 61 ARG cc_start: 0.7906 (ttp80) cc_final: 0.7679 (ptm-80) REVERT: F 117 LYS cc_start: 0.8669 (mttt) cc_final: 0.8419 (mttp) REVERT: H 199 MET cc_start: 0.8012 (tmm) cc_final: 0.7714 (tmm) outliers start: 9 outliers final: 5 residues processed: 180 average time/residue: 0.1795 time to fit residues: 46.8937 Evaluate side-chains 126 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 121 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 188 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 601 GLN A 617 ASN ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 773 GLN A 891 HIS A 982 HIS B 71 ASN B 250 ASN B 336 GLN C 37 HIS C 55 HIS ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 HIS C 321 GLN E 22 GLN E 72 GLN E 284 HIS E 320 HIS F 177 ASN F 213 ASN G 38 GLN G 49 GLN G 108 GLN G 184 GLN G 213 ASN H 38 GLN H 44 HIS ** H 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.069632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.053617 restraints weight = 128278.979| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 3.99 r_work: 0.2611 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19985 Z= 0.124 Angle : 0.569 7.604 27023 Z= 0.294 Chirality : 0.042 0.151 3142 Planarity : 0.004 0.057 3424 Dihedral : 8.189 171.894 2714 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.05 % Allowed : 8.29 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.17), residues: 2461 helix: 0.21 (0.15), residues: 1166 sheet: -1.37 (0.21), residues: 522 loop : -1.80 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 105 TYR 0.021 0.001 TYR A 998 PHE 0.031 0.001 PHE A1062 TRP 0.015 0.001 TRP E 4 HIS 0.009 0.001 HIS A 904 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (19983) covalent geometry : angle 0.56881 / 0.29 (27019) SS BOND : bond 0.00267 / 0.13 ( 2) SS BOND : angle 0.80482 / 0.41 ( 4) hydrogen bonds : bond 0.03854 / 2.57 ( 1053) hydrogen bonds : angle 4.59380 / 3.15 ( 3008) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4922 Ramachandran restraints generated. 2461 Oldfield, 0 Emsley, 2461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4922 Ramachandran restraints generated. 2461 Oldfield, 0 Emsley, 2461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.758 Fit side-chains revert: symmetry clash REVERT: A 996 MET cc_start: 0.7747 (mpp) cc_final: 0.7004 (mpp) REVERT: B 250 ASN cc_start: 0.8770 (OUTLIER) cc_final: 0.8437 (t0) REVERT: D 229 TYR cc_start: 0.9071 (t80) cc_final: 0.8797 (t80) REVERT: E 166 ASN cc_start: 0.8088 (p0) cc_final: 0.7831 (p0) REVERT: F 49 GLN cc_start: 0.9081 (pp30) cc_final: 0.8847 (tt0) REVERT: F 61 ARG cc_start: 0.8615 (ttp80) cc_final: 0.8190 (ptm-80) REVERT: F 68 MET cc_start: 0.8733 (ttm) cc_final: 0.8293 (ttp) outliers start: 23 outliers final: 12 residues processed: 159 average time/residue: 0.1487 time to fit residues: 36.3708 Evaluate side-chains 133 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 601 GLN Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 188 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 79 optimal weight: 0.9980 chunk 63 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 121 optimal weight: 9.9990 chunk 126 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 41 optimal weight: 20.0000 chunk 4 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 937 GLN B 106 ASN ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 GLN G 38 GLN ** H 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.068251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.052129 restraints weight = 138843.675| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 3.90 r_work: 0.2591 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2591 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2591 r_free = 0.2591 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2591 r_free = 0.2591 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2591 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19985 Z= 0.182 Angle : 0.563 11.370 27023 Z= 0.286 Chirality : 0.042 0.151 3142 Planarity : 0.004 0.054 3424 Dihedral : 8.143 172.398 2713 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.19 % Allowed : 10.35 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.17), residues: 2461 helix: 0.75 (0.15), residues: 1166 sheet: -1.02 (0.22), residues: 525 loop : -1.49 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 61 TYR 0.017 0.001 TYR H 211 PHE 0.026 0.001 PHE A1062 TRP 0.012 0.001 TRP E 4 HIS 0.008 0.001 HIS A 904 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 (19983) covalent geometry : angle 0.56267 / 0.29 (27019) SS BOND : bond 0.00177 / 0.09 ( 2) SS BOND : angle 1.13418 / 0.56 ( 4) hydrogen bonds : bond 0.03732 / 2.49 ( 1053) hydrogen bonds : angle 4.40652 / 3.01 ( 3008) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4922 Ramachandran restraints generated. 2461 Oldfield, 0 Emsley, 2461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4922 Ramachandran restraints generated. 2461 Oldfield, 0 Emsley, 2461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.701 Fit side-chains REVERT: A 996 MET cc_start: 0.7705 (mpp) cc_final: 0.7176 (mmm) REVERT: C 305 MET cc_start: 0.9576 (mtp) cc_final: 0.9367 (mtp) REVERT: D 109 ASN cc_start: 0.8420 (p0) cc_final: 0.7897 (t0) REVERT: D 155 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8682 (mtp) REVERT: D 229 TYR cc_start: 0.9086 (t80) cc_final: 0.8835 (t80) REVERT: E 166 ASN cc_start: 0.8089 (p0) cc_final: 0.7781 (p0) REVERT: F 61 ARG cc_start: 0.8619 (ttp80) cc_final: 0.8216 (ptm-80) REVERT: G 16 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9054 (mm) outliers start: 26 outliers final: 13 residues processed: 145 average time/residue: 0.1398 time to fit residues: 32.1296 Evaluate side-chains 132 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 235 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 208 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 chunk 121 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 ASN ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.068996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.052943 restraints weight = 122215.084| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 4.05 r_work: 0.2592 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2594 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2594 r_free = 0.2594 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2594 r_free = 0.2594 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2594 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19985 Z= 0.117 Angle : 0.512 7.493 27023 Z= 0.260 Chirality : 0.040 0.137 3142 Planarity : 0.004 0.053 3424 Dihedral : 8.048 175.301 2712 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.28 % Allowed : 11.68 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.17), residues: 2461 helix: 1.12 (0.16), residues: 1170 sheet: -0.80 (0.23), residues: 519 loop : -1.21 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 178 TYR 0.014 0.001 TYR H 211 PHE 0.022 0.001 PHE A1062 TRP 0.008 0.001 TRP E 4 HIS 0.006 0.001 HIS A 904 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (19983) covalent geometry : angle 0.51188 / 0.26 (27019) SS BOND : bond 0.00264 / 0.13 ( 2) SS BOND : angle 0.92522 / 0.43 ( 4) hydrogen bonds : bond 0.03276 / 2.19 ( 1053) hydrogen bonds : angle 4.17472 / 2.85 ( 3008) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4922 Ramachandran restraints generated. 2461 Oldfield, 0 Emsley, 2461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4922 Ramachandran restraints generated. 2461 Oldfield, 0 Emsley, 2461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.711 Fit side-chains REVERT: A 992 ARG cc_start: 0.6254 (mtp85) cc_final: 0.5898 (ttt90) REVERT: A 996 MET cc_start: 0.7845 (mpp) cc_final: 0.7444 (mmm) REVERT: B 250 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.8504 (t0) REVERT: D 229 TYR cc_start: 0.9062 (t80) cc_final: 0.8807 (t80) REVERT: E 166 ASN cc_start: 0.7987 (p0) cc_final: 0.7699 (p0) REVERT: F 61 ARG cc_start: 0.8643 (ttp80) cc_final: 0.8277 (ptm-80) REVERT: F 108 GLN cc_start: 0.7484 (mp10) cc_final: 0.7214 (mp10) REVERT: G 16 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9018 (mm) outliers start: 28 outliers final: 17 residues processed: 148 average time/residue: 0.1470 time to fit residues: 34.0097 Evaluate side-chains 141 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 235 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 90 optimal weight: 7.9990 chunk 214 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 182 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 619 GLN ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 728 ASN ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.067808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.051921 restraints weight = 117955.745| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 3.90 r_work: 0.2566 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2565 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2565 r_free = 0.2565 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2565 r_free = 0.2565 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19985 Z= 0.183 Angle : 0.543 7.064 27023 Z= 0.275 Chirality : 0.042 0.154 3142 Planarity : 0.004 0.051 3424 Dihedral : 8.113 175.845 2712 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.42 % Allowed : 12.73 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.17), residues: 2461 helix: 1.24 (0.16), residues: 1174 sheet: -0.68 (0.23), residues: 509 loop : -1.10 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 178 TYR 0.017 0.001 TYR H 211 PHE 0.022 0.001 PHE A1062 TRP 0.013 0.001 TRP E 4 HIS 0.005 0.001 HIS A 904 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 (19983) covalent geometry : angle 0.54283 / 0.27 (27019) SS BOND : bond 0.00267 / 0.14 ( 2) SS BOND : angle 1.34323 / 0.60 ( 4) hydrogen bonds : bond 0.03516 / 2.34 ( 1053) hydrogen bonds : angle 4.21832 / 2.88 ( 3008) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4922 Ramachandran restraints generated. 2461 Oldfield, 0 Emsley, 2461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4922 Ramachandran restraints generated. 2461 Oldfield, 0 Emsley, 2461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 0.822 Fit side-chains REVERT: A 996 MET cc_start: 0.7834 (mpp) cc_final: 0.7438 (mmm) REVERT: C 254 MET cc_start: 0.9193 (mtm) cc_final: 0.8970 (mtm) REVERT: D 229 TYR cc_start: 0.9106 (t80) cc_final: 0.8871 (t80) REVERT: E 166 ASN cc_start: 0.8067 (p0) cc_final: 0.7782 (p0) REVERT: F 61 ARG cc_start: 0.8618 (ttp80) cc_final: 0.8262 (ptm-80) REVERT: F 108 GLN cc_start: 0.7509 (mp10) cc_final: 0.7232 (mp10) REVERT: G 16 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9010 (mm) REVERT: H 158 VAL cc_start: 0.9380 (OUTLIER) cc_final: 0.9142 (t) outliers start: 31 outliers final: 22 residues processed: 145 average time/residue: 0.1326 time to fit residues: 31.1690 Evaluate side-chains 144 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 131 GLN Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 235 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 0 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 230 optimal weight: 10.0000 chunk 243 optimal weight: 8.9990 chunk 94 optimal weight: 9.9990 chunk 236 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 218 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN G 204 GLN ** H 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.067088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.051459 restraints weight = 98480.247| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 3.53 r_work: 0.2570 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2569 r_free = 0.2569 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2569 r_free = 0.2569 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19985 Z= 0.210 Angle : 0.560 7.605 27023 Z= 0.284 Chirality : 0.042 0.151 3142 Planarity : 0.004 0.051 3424 Dihedral : 8.290 178.169 2712 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.60 % Allowed : 13.61 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.17), residues: 2461 helix: 1.31 (0.16), residues: 1173 sheet: -0.54 (0.23), residues: 479 loop : -1.09 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 178 TYR 0.017 0.002 TYR H 211 PHE 0.023 0.001 PHE A1062 TRP 0.017 0.001 TRP E 4 HIS 0.006 0.001 HIS A 904 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.21 (19983) covalent geometry : angle 0.55943 / 0.28 (27019) SS BOND : bond 0.00318 / 0.16 ( 2) SS BOND : angle 1.40994 / 0.62 ( 4) hydrogen bonds : bond 0.03627 / 2.41 ( 1053) hydrogen bonds : angle 4.26486 / 2.91 ( 3008) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4922 Ramachandran restraints generated. 2461 Oldfield, 0 Emsley, 2461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4922 Ramachandran restraints generated. 2461 Oldfield, 0 Emsley, 2461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 0.837 Fit side-chains REVERT: A 996 MET cc_start: 0.7661 (mpp) cc_final: 0.7373 (mmm) REVERT: D 229 TYR cc_start: 0.9092 (t80) cc_final: 0.8874 (t80) REVERT: E 166 ASN cc_start: 0.8138 (p0) cc_final: 0.7889 (p0) REVERT: E 206 ASN cc_start: 0.7935 (t0) cc_final: 0.7594 (t0) REVERT: F 61 ARG cc_start: 0.8587 (ttp80) cc_final: 0.8223 (ptm-80) REVERT: F 108 GLN cc_start: 0.7507 (mp10) cc_final: 0.7229 (mp10) REVERT: G 16 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9027 (mm) REVERT: H 158 VAL cc_start: 0.9355 (OUTLIER) cc_final: 0.9113 (t) outliers start: 35 outliers final: 28 residues processed: 145 average time/residue: 0.1299 time to fit residues: 30.4061 Evaluate side-chains 149 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 131 GLN Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 235 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 36 optimal weight: 2.9990 chunk 199 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 175 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 224 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 219 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 233 optimal weight: 3.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN G 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.068226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.052315 restraints weight = 109237.434| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 3.75 r_work: 0.2591 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2591 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2591 r_free = 0.2591 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2591 r_free = 0.2591 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2591 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19985 Z= 0.120 Angle : 0.502 7.494 27023 Z= 0.254 Chirality : 0.040 0.141 3142 Planarity : 0.003 0.051 3424 Dihedral : 8.150 175.537 2712 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.56 % Allowed : 14.15 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.17), residues: 2461 helix: 1.46 (0.16), residues: 1178 sheet: -0.46 (0.23), residues: 491 loop : -0.95 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 64 TYR 0.012 0.001 TYR H 211 PHE 0.023 0.001 PHE A1062 TRP 0.011 0.001 TRP F 28 HIS 0.005 0.001 HIS A 904 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (19983) covalent geometry : angle 0.50174 / 0.25 (27019) SS BOND : bond 0.00149 / 0.07 ( 2) SS BOND : angle 0.89649 / 0.40 ( 4) hydrogen bonds : bond 0.03206 / 2.13 ( 1053) hydrogen bonds : angle 4.07374 / 2.78 ( 3008) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4922 Ramachandran restraints generated. 2461 Oldfield, 0 Emsley, 2461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4922 Ramachandran restraints generated. 2461 Oldfield, 0 Emsley, 2461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.799 Fit side-chains REVERT: A 996 MET cc_start: 0.7629 (mpp) cc_final: 0.7283 (mmm) REVERT: D 229 TYR cc_start: 0.9086 (t80) cc_final: 0.8880 (t80) REVERT: E 79 LYS cc_start: 0.6027 (OUTLIER) cc_final: 0.5552 (tppt) REVERT: E 111 MET cc_start: 0.9278 (mmm) cc_final: 0.9035 (mmp) REVERT: E 166 ASN cc_start: 0.8040 (p0) cc_final: 0.7809 (p0) REVERT: F 61 ARG cc_start: 0.8603 (ttp80) cc_final: 0.8282 (ptm-80) REVERT: F 108 GLN cc_start: 0.7487 (mp10) cc_final: 0.7210 (mp10) REVERT: G 16 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.8976 (mm) outliers start: 34 outliers final: 24 residues processed: 153 average time/residue: 0.1339 time to fit residues: 32.8028 Evaluate side-chains 145 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1020 ASP Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 235 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 89 optimal weight: 2.9990 chunk 244 optimal weight: 10.0000 chunk 122 optimal weight: 0.0980 chunk 67 optimal weight: 2.9990 chunk 180 optimal weight: 10.0000 chunk 218 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 199 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 119 optimal weight: 9.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 GLN ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.067887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.052277 restraints weight = 89979.543| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 3.31 r_work: 0.2620 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19985 Z= 0.145 Angle : 0.513 7.500 27023 Z= 0.259 Chirality : 0.040 0.142 3142 Planarity : 0.003 0.051 3424 Dihedral : 7.799 160.414 2712 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.65 % Allowed : 14.02 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.17), residues: 2461 helix: 1.53 (0.16), residues: 1178 sheet: -0.38 (0.23), residues: 506 loop : -0.89 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 178 TYR 0.018 0.001 TYR E 238 PHE 0.024 0.001 PHE A1062 TRP 0.015 0.001 TRP F 28 HIS 0.005 0.001 HIS A 904 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (19983) covalent geometry : angle 0.51235 / 0.26 (27019) SS BOND : bond 0.00228 / 0.12 ( 2) SS BOND : angle 1.13629 / 0.50 ( 4) hydrogen bonds : bond 0.03270 / 2.18 ( 1053) hydrogen bonds : angle 4.05886 / 2.77 ( 3008) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4922 Ramachandran restraints generated. 2461 Oldfield, 0 Emsley, 2461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4922 Ramachandran restraints generated. 2461 Oldfield, 0 Emsley, 2461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 0.681 Fit side-chains REVERT: A 996 MET cc_start: 0.7584 (mpp) cc_final: 0.7237 (mmm) REVERT: E 79 LYS cc_start: 0.5962 (OUTLIER) cc_final: 0.5466 (tppt) REVERT: E 111 MET cc_start: 0.9267 (mmm) cc_final: 0.9034 (mmp) REVERT: E 166 ASN cc_start: 0.8043 (p0) cc_final: 0.7812 (p0) REVERT: E 206 ASN cc_start: 0.7922 (t0) cc_final: 0.7506 (t0) REVERT: F 61 ARG cc_start: 0.8546 (ttp80) cc_final: 0.8224 (ptm-80) REVERT: G 16 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.8963 (mm) outliers start: 36 outliers final: 30 residues processed: 150 average time/residue: 0.1344 time to fit residues: 32.4873 Evaluate side-chains 151 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1020 ASP Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 199 MET Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 235 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 98 optimal weight: 4.9990 chunk 199 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 151 optimal weight: 7.9990 chunk 241 optimal weight: 0.0270 chunk 191 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 132 optimal weight: 0.7980 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.069117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.053531 restraints weight = 119229.150| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 3.88 r_work: 0.2600 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2600 r_free = 0.2600 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2600 r_free = 0.2600 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19985 Z= 0.097 Angle : 0.487 7.843 27023 Z= 0.245 Chirality : 0.039 0.141 3142 Planarity : 0.003 0.050 3424 Dihedral : 7.280 139.783 2712 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.33 % Allowed : 14.52 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.18), residues: 2461 helix: 1.76 (0.16), residues: 1161 sheet: -0.35 (0.23), residues: 512 loop : -0.74 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 64 TYR 0.020 0.001 TYR D 229 PHE 0.024 0.001 PHE A1062 TRP 0.010 0.001 TRP E 251 HIS 0.004 0.001 HIS A 904 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (19983) covalent geometry : angle 0.48705 / 0.24 (27019) SS BOND : bond 0.00484 / 0.23 ( 2) SS BOND : angle 1.48289 / 0.66 ( 4) hydrogen bonds : bond 0.02923 / 1.96 ( 1053) hydrogen bonds : angle 3.89878 / 2.67 ( 3008) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4922 Ramachandran restraints generated. 2461 Oldfield, 0 Emsley, 2461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4922 Ramachandran restraints generated. 2461 Oldfield, 0 Emsley, 2461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.813 Fit side-chains REVERT: A 996 MET cc_start: 0.7729 (mpp) cc_final: 0.7380 (mmm) REVERT: A 1026 ASP cc_start: 0.7270 (p0) cc_final: 0.7023 (t0) REVERT: C 254 MET cc_start: 0.9178 (mtm) cc_final: 0.8942 (mtm) REVERT: E 79 LYS cc_start: 0.5911 (OUTLIER) cc_final: 0.5446 (tppt) REVERT: E 111 MET cc_start: 0.9268 (mmm) cc_final: 0.9026 (mmp) REVERT: E 166 ASN cc_start: 0.8034 (p0) cc_final: 0.7825 (p0) REVERT: F 61 ARG cc_start: 0.8642 (ttp80) cc_final: 0.8395 (ptm-80) outliers start: 29 outliers final: 26 residues processed: 148 average time/residue: 0.1390 time to fit residues: 32.6335 Evaluate side-chains 149 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1020 ASP Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 199 MET Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 152 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 164 optimal weight: 0.9990 chunk 219 optimal weight: 6.9990 chunk 231 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 161 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.068868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.053451 restraints weight = 80255.432| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 2.89 r_work: 0.2664 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19985 Z= 0.132 Angle : 0.507 7.946 27023 Z= 0.253 Chirality : 0.040 0.144 3142 Planarity : 0.003 0.050 3424 Dihedral : 7.165 134.501 2712 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.33 % Allowed : 14.57 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.18), residues: 2461 helix: 1.76 (0.16), residues: 1167 sheet: -0.28 (0.23), residues: 517 loop : -0.72 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 64 TYR 0.020 0.001 TYR E 238 PHE 0.022 0.001 PHE A1062 TRP 0.015 0.001 TRP F 28 HIS 0.006 0.001 HIS A 904 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (19983) covalent geometry : angle 0.50660 / 0.25 (27019) SS BOND : bond 0.00352 / 0.17 ( 2) SS BOND : angle 1.52250 / 0.67 ( 4) hydrogen bonds : bond 0.03092 / 2.07 ( 1053) hydrogen bonds : angle 3.93544 / 2.69 ( 3008) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4922 Ramachandran restraints generated. 2461 Oldfield, 0 Emsley, 2461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4922 Ramachandran restraints generated. 2461 Oldfield, 0 Emsley, 2461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.767 Fit side-chains REVERT: A 992 ARG cc_start: 0.6669 (mtm110) cc_final: 0.5967 (ttt90) REVERT: A 995 ASN cc_start: 0.7752 (t0) cc_final: 0.7546 (t0) REVERT: A 996 MET cc_start: 0.7618 (mpp) cc_final: 0.7153 (mmm) REVERT: B 229 MET cc_start: 0.9190 (tpp) cc_final: 0.8938 (tpt) REVERT: C 254 MET cc_start: 0.9107 (mtm) cc_final: 0.8876 (mtm) REVERT: E 79 LYS cc_start: 0.5874 (OUTLIER) cc_final: 0.5405 (tppt) REVERT: E 111 MET cc_start: 0.9238 (mmm) cc_final: 0.8994 (mmp) REVERT: E 166 ASN cc_start: 0.8008 (p0) cc_final: 0.7744 (p0) REVERT: F 61 ARG cc_start: 0.8551 (ttp80) cc_final: 0.8306 (ptm-80) outliers start: 29 outliers final: 26 residues processed: 144 average time/residue: 0.1405 time to fit residues: 32.1601 Evaluate side-chains 147 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1020 ASP Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 199 MET Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 93 optimal weight: 0.9980 chunk 196 optimal weight: 2.9990 chunk 181 optimal weight: 8.9990 chunk 226 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 197 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.069559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.053879 restraints weight = 87267.289| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 3.11 r_work: 0.2671 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19985 Z= 0.098 Angle : 0.487 8.307 27023 Z= 0.243 Chirality : 0.039 0.141 3142 Planarity : 0.003 0.050 3424 Dihedral : 6.995 134.408 2712 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.37 % Allowed : 14.57 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.18), residues: 2461 helix: 1.87 (0.16), residues: 1161 sheet: -0.19 (0.23), residues: 516 loop : -0.67 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 64 TYR 0.020 0.001 TYR B 279 PHE 0.022 0.001 PHE A1062 TRP 0.011 0.001 TRP F 28 HIS 0.004 0.001 HIS A 904 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (19983) covalent geometry : angle 0.48665 / 0.24 (27019) SS BOND : bond 0.00299 / 0.14 ( 2) SS BOND : angle 1.44028 / 0.63 ( 4) hydrogen bonds : bond 0.02908 / 1.95 ( 1053) hydrogen bonds : angle 3.84751 / 2.63 ( 3008) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3865.14 seconds wall clock time: 67 minutes 29.43 seconds (4049.43 seconds total)