Starting phenix.real_space_refine on Tue Jun 17 23:00:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8thc_41253/06_2025/8thc_41253.cif Found real_map, /net/cci-nas-00/data/ceres_data/8thc_41253/06_2025/8thc_41253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8thc_41253/06_2025/8thc_41253.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8thc_41253/06_2025/8thc_41253.map" model { file = "/net/cci-nas-00/data/ceres_data/8thc_41253/06_2025/8thc_41253.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8thc_41253/06_2025/8thc_41253.cif" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 14 5.49 5 Mg 3 5.21 5 S 98 5.16 5 C 12925 2.51 5 N 3442 2.21 5 O 3948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20430 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3897 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 21, 'TRANS': 457} Chain breaks: 4 Chain: "B" Number of atoms: 2495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2495 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 9, 'TRANS': 308} Chain: "C" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2571 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain: "D" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2629 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 12, 'TRANS': 319} Chain: "E" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2675 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 14, 'TRANS': 324} Chain breaks: 1 Chain: "F" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1995 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 8, 'TRANS': 245} Chain: "G" Number of atoms: 2011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2011 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 8, 'TRANS': 247} Chain: "H" Number of atoms: 2003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2003 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 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: 13.08, per 1000 atoms: 0.64 Number of scatterers: 20430 At special positions: 0 Unit cell: (117.576, 122.544, 150.696, 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 98 16.00 P 14 15.00 Mg 3 11.99 O 3948 8.00 N 3442 7.00 C 12925 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.39 Conformation dependent library (CDL) restraints added in 2.7 seconds 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4906 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 17 sheets defined 50.4% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.83 Creating SS restraints... Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 240 through 245 Processing helix chain 'A' and resid 256 through 276 removed outlier: 3.906A pdb=" N LYS A 276 " --> pdb=" O HIS A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.561A pdb=" N GLN A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 387 removed outlier: 6.090A pdb=" N ASP A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ILE A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 429 Processing helix chain 'A' and resid 440 through 444 removed outlier: 3.808A pdb=" N LEU A 443 " --> pdb=" O ASP A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 455 Processing helix chain 'A' and resid 465 through 481 removed outlier: 3.503A pdb=" N VAL A 469 " --> pdb=" O SER A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 496 removed outlier: 3.556A pdb=" N LEU A 489 " --> pdb=" O CYS A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 510 Processing helix chain 'A' and resid 535 through 557 removed outlier: 3.801A pdb=" N ILE A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 581 removed outlier: 3.585A pdb=" N ASP A 581 " --> pdb=" O ASN A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 592 Processing helix chain 'A' and resid 616 through 627 removed outlier: 3.537A pdb=" N HIS A 620 " --> pdb=" O ASN A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 639 removed outlier: 3.965A pdb=" N ARG A 633 " --> pdb=" O TYR A 629 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS A 637 " --> pdb=" O ARG A 633 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU A 639 " --> pdb=" O ALA A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 661 Processing helix chain 'A' and resid 700 through 708 removed outlier: 4.044A pdb=" N LEU A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 716 Processing helix chain 'A' and resid 716 through 733 Processing helix chain 'A' and resid 773 through 781 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 55 through 68 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 85 through 99 removed outlier: 4.130A pdb=" N ILE B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LYS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 134 removed outlier: 4.432A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 removed outlier: 3.685A pdb=" N LYS B 149 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE B 150 " --> pdb=" O SER B 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 146 through 150' Processing helix chain 'B' and resid 151 through 157 Processing helix chain 'B' and resid 167 through 183 removed outlier: 3.949A pdb=" N VAL B 171 " --> pdb=" O SER B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 199 removed outlier: 3.711A pdb=" N GLU B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 217 removed outlier: 3.572A pdb=" N GLY B 217 " --> pdb=" O VAL B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 226 Processing helix chain 'B' and resid 232 through 242 Processing helix chain 'B' and resid 244 through 255 Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 281 through 302 removed outlier: 3.514A pdb=" N GLY B 302 " --> pdb=" O ARG B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 322 removed outlier: 3.628A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 27 removed outlier: 3.574A pdb=" N VAL C 27 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 44 Processing helix chain 'C' and resid 58 through 72 Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 89 through 102 Processing helix chain 'C' and resid 118 through 122 removed outlier: 4.000A pdb=" N ALA C 121 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 137 Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.683A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU C 153 " --> pdb=" O ALA C 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 149 through 153' Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 170 through 186 removed outlier: 3.613A pdb=" N VAL C 183 " --> pdb=" O ALA C 179 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS C 184 " --> pdb=" O ASN C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 202 removed outlier: 4.136A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 Processing helix chain 'C' and resid 228 through 237 removed outlier: 3.515A pdb=" N ILE C 232 " --> pdb=" O SER C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 254 Processing helix chain 'C' and resid 255 through 271 Processing helix chain 'C' and resid 273 through 288 removed outlier: 3.683A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR C 288 " --> pdb=" O ILE C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 313 removed outlier: 4.113A pdb=" N ARG C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 334 removed outlier: 3.861A pdb=" N GLN C 319 " --> pdb=" O ASN C 315 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU C 334 " --> pdb=" O SER C 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 42 through 55 removed outlier: 4.021A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 83 Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'D' and resid 105 through 116 Processing helix chain 'D' and resid 153 through 159 Processing helix chain 'D' and resid 193 through 208 Processing helix chain 'D' and resid 215 through 225 removed outlier: 3.531A pdb=" N ARG D 219 " --> pdb=" O GLY D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 246 Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.751A pdb=" N VAL D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 278 Processing helix chain 'D' and resid 279 through 291 Processing helix chain 'D' and resid 296 through 311 removed outlier: 3.538A pdb=" N VAL D 300 " --> pdb=" O SER D 296 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR D 310 " --> pdb=" O GLU D 306 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN D 311 " --> pdb=" O TYR D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 335 removed outlier: 3.671A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 353 Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 19 through 32 removed outlier: 3.909A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 62 through 67 removed outlier: 3.643A pdb=" N TYR E 66 " --> pdb=" O PRO E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 105 removed outlier: 3.778A pdb=" N ASP E 100 " --> pdb=" O THR E 97 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY E 102 " --> pdb=" O SER E 99 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ASN E 103 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASN E 104 " --> pdb=" O MET E 101 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP E 105 " --> pdb=" O GLY E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 119 removed outlier: 3.729A pdb=" N MET E 119 " --> pdb=" O GLU E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 146 Processing helix chain 'E' and resid 147 through 161 Processing helix chain 'E' and resid 178 through 184 Processing helix chain 'E' and resid 194 through 210 Processing helix chain 'E' and resid 216 through 226 Processing helix chain 'E' and resid 229 through 245 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 292 Processing helix chain 'E' and resid 295 through 308 Processing helix chain 'E' and resid 314 through 334 Processing helix chain 'E' and resid 337 through 353 removed outlier: 3.983A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 19 removed outlier: 3.797A pdb=" N PHE F 12 " --> pdb=" O GLU F 8 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 80 Processing helix chain 'F' and resid 141 through 155 removed outlier: 3.805A pdb=" N GLN F 153 " --> pdb=" O ARG F 149 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU F 154 " --> pdb=" O ASP F 150 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER F 155 " --> pdb=" O LEU F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 166 Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 217 through 221 removed outlier: 4.354A pdb=" N SER F 220 " --> pdb=" O LYS F 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 23 removed outlier: 3.902A pdb=" N LYS G 13 " --> pdb=" O ALA G 9 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N GLY G 18 " --> pdb=" O ARG G 14 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE G 19 " --> pdb=" O ILE G 15 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ASP G 21 " --> pdb=" O ASP G 17 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N CYS G 22 " --> pdb=" O GLY G 18 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL G 23 " --> pdb=" O PHE G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 57 removed outlier: 3.683A pdb=" N ALA G 56 " --> pdb=" O GLY G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 80 Processing helix chain 'G' and resid 141 through 153 removed outlier: 3.979A pdb=" N GLN G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 194 Processing helix chain 'G' and resid 209 through 218 removed outlier: 4.223A pdb=" N GLY G 218 " --> pdb=" O ASP G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 221 No H-bonds generated for 'chain 'G' and resid 219 through 221' Processing helix chain 'H' and resid 9 through 18 removed outlier: 3.745A pdb=" N LYS H 13 " --> pdb=" O ALA H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 80 Processing helix chain 'H' and resid 141 through 153 removed outlier: 4.230A pdb=" N GLN H 153 " --> pdb=" O ARG H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 194 Processing helix chain 'H' and resid 209 through 217 Processing sheet with id=AA1, first strand: chain 'A' and resid 227 through 228 removed outlier: 4.439A pdb=" N VAL A 227 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU A 483 " --> pdb=" O VAL A 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 337 through 338 removed outlier: 6.718A pdb=" N HIS A 337 " --> pdb=" O THR A 461 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 361 through 366 Processing sheet with id=AA4, first strand: chain 'A' and resid 600 through 601 removed outlier: 6.471A pdb=" N LEU E 94 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ASN E 141 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ILE E 96 " --> pdb=" O ASN E 141 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU E 39 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N CYS E 171 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU E 41 " --> pdb=" O CYS E 171 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU E 40 " --> pdb=" O LEU E 186 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 75 through 77 removed outlier: 6.094A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET B 45 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 46 " --> pdb=" O ALA B 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 49 through 52 removed outlier: 6.064A pdb=" N LEU C 50 " --> pdb=" O PHE C 164 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 79 through 83 removed outlier: 4.161A pdb=" N LEU C 80 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 63 through 64 removed outlier: 3.983A pdb=" N TYR D 64 " --> pdb=" O PHE D 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 135 through 140 removed outlier: 5.716A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 57 through 60 removed outlier: 6.715A pdb=" N LYS F 5 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TYR F 60 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N GLU F 3 " --> pdb=" O TYR F 60 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LEU F 88 " --> pdb=" O PHE F 6 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 66 through 71 removed outlier: 3.984A pdb=" N VAL F 26 " --> pdb=" O MET F 70 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU F 25 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N VAL F 40 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASN F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN F 38 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ASP F 240 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ARG F 224 " --> pdb=" O ASP F 240 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 179 through 182 Processing sheet with id=AB4, first strand: chain 'G' and resid 60 through 61 removed outlier: 3.714A pdb=" N ARG G 61 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU G 3 " --> pdb=" O ARG G 61 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 66 through 71 removed outlier: 3.613A pdb=" N VAL G 26 " --> pdb=" O MET G 70 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU G 25 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL G 40 " --> pdb=" O LEU G 25 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ASN G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLN G 38 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP G 240 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ARG G 224 " --> pdb=" O ASP G 240 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU G 137 " --> pdb=" O ILE G 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU G 229 " --> pdb=" O SER G 135 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS G 196 " --> pdb=" O SER G 138 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 206 through 208 removed outlier: 5.904A pdb=" N SER G 157 " --> pdb=" O ASP G 172 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP G 172 " --> pdb=" O SER G 157 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE H 111 " --> pdb=" O ILE G 181 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU H 88 " --> pdb=" O PHE H 6 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA H 92 " --> pdb=" O LEU H 2 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLU H 3 " --> pdb=" O TYR H 60 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR H 60 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LYS H 5 " --> pdb=" O GLN H 58 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 68 through 71 removed outlier: 5.505A pdb=" N LEU H 25 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL H 40 " --> pdb=" O LEU H 25 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASP H 240 " --> pdb=" O ARG H 224 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG H 224 " --> pdb=" O ASP H 240 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 177 through 182 removed outlier: 3.522A pdb=" N VAL H 180 " --> pdb=" O PHE H 169 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ASP H 172 " --> pdb=" O SER H 157 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N SER H 157 " --> pdb=" O ASP H 172 " (cutoff:3.500A) 1035 hydrogen bonds defined for protein. 2988 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: 6.97 Time building geometry restraints manager: 6.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 6761 1.36 - 1.51: 5018 1.51 - 1.65: 8826 1.65 - 1.80: 77 1.80 - 1.95: 75 Bond restraints: 20757 Sorted by residual: bond pdb=" N VAL H 225 " pdb=" CA VAL H 225 " ideal model delta sigma weight residual 1.458 1.495 -0.036 1.17e-02 7.31e+03 9.57e+00 bond pdb=" N ILE A 255 " pdb=" CA ILE A 255 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.14e-02 7.69e+03 9.08e+00 bond pdb=" N LEU G 88 " pdb=" CA LEU G 88 " ideal model delta sigma weight residual 1.454 1.489 -0.034 1.15e-02 7.56e+03 8.92e+00 bond pdb=" N ILE F 128 " pdb=" CA ILE F 128 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.82e+00 bond pdb=" N THR G 87 " pdb=" CA THR G 87 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.15e-02 7.56e+03 8.27e+00 ... (remaining 20752 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 27429 1.87 - 3.75: 539 3.75 - 5.62: 89 5.62 - 7.50: 18 7.50 - 9.37: 8 Bond angle restraints: 28083 Sorted by residual: angle pdb=" N GLU F 129 " pdb=" CA GLU F 129 " pdb=" C GLU F 129 " ideal model delta sigma weight residual 113.18 107.24 5.94 1.21e+00 6.83e-01 2.41e+01 angle pdb=" CA LEU F 131 " pdb=" C LEU F 131 " pdb=" O LEU F 131 " ideal model delta sigma weight residual 121.58 117.13 4.45 1.16e+00 7.43e-01 1.47e+01 angle pdb=" CB ARG G 80 " pdb=" CG ARG G 80 " pdb=" CD ARG G 80 " ideal model delta sigma weight residual 111.30 119.81 -8.51 2.30e+00 1.89e-01 1.37e+01 angle pdb=" CA MET C 78 " pdb=" CB MET C 78 " pdb=" CG MET C 78 " ideal model delta sigma weight residual 114.10 121.50 -7.40 2.00e+00 2.50e-01 1.37e+01 angle pdb=" CA LEU G 88 " pdb=" C LEU G 88 " pdb=" O LEU G 88 " ideal model delta sigma weight residual 121.66 117.63 4.03 1.22e+00 6.72e-01 1.09e+01 ... (remaining 28078 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.01: 12010 24.01 - 48.01: 689 48.01 - 72.02: 102 72.02 - 96.03: 13 96.03 - 120.03: 1 Dihedral angle restraints: 12815 sinusoidal: 5300 harmonic: 7515 Sorted by residual: dihedral pdb=" O1B ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PB ADP E 401 " pdb=" PA ADP E 401 " ideal model delta sinusoidal sigma weight residual 300.00 179.97 120.03 1 2.00e+01 2.50e-03 3.60e+01 dihedral pdb=" CA MET C 78 " pdb=" C MET C 78 " pdb=" N VAL C 79 " pdb=" CA VAL C 79 " ideal model delta harmonic sigma weight residual 180.00 160.13 19.87 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA MET A 334 " pdb=" C MET A 334 " pdb=" N ILE A 335 " pdb=" CA ILE A 335 " ideal model delta harmonic sigma weight residual 180.00 160.27 19.73 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 12812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2836 0.059 - 0.119: 405 0.119 - 0.178: 46 0.178 - 0.237: 6 0.237 - 0.297: 3 Chirality restraints: 3296 Sorted by residual: chirality pdb=" CB ILE C 106 " pdb=" CA ILE C 106 " pdb=" CG1 ILE C 106 " pdb=" CG2 ILE C 106 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CB ILE G 128 " pdb=" CA ILE G 128 " pdb=" CG1 ILE G 128 " pdb=" CG2 ILE G 128 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB ILE A 219 " pdb=" CA ILE A 219 " pdb=" CG1 ILE A 219 " pdb=" CG2 ILE A 219 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 3293 not shown) Planarity restraints: 3557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 224 " 0.253 9.50e-02 1.11e+02 1.13e-01 7.92e+00 pdb=" NE ARG H 224 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG H 224 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG H 224 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG H 224 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS F 190 " 0.046 5.00e-02 4.00e+02 6.98e-02 7.79e+00 pdb=" N PRO F 191 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO F 191 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO F 191 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 97 " 0.045 5.00e-02 4.00e+02 6.84e-02 7.49e+00 pdb=" N PRO E 98 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO E 98 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 98 " 0.038 5.00e-02 4.00e+02 ... (remaining 3554 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 406 2.69 - 3.25: 20090 3.25 - 3.80: 32085 3.80 - 4.35: 41577 4.35 - 4.90: 68369 Nonbonded interactions: 162527 Sorted by model distance: nonbonded pdb=" OG1 THR C 60 " pdb="MG MG C 402 " model vdw 2.142 2.170 nonbonded pdb=" O2B AGS D 401 " pdb="MG MG D 402 " model vdw 2.163 2.170 nonbonded pdb=" OG1 THR B 56 " pdb="MG MG B 402 " model vdw 2.179 2.170 nonbonded pdb=" OH TYR C 71 " pdb=" O PHE C 111 " model vdw 2.244 3.040 nonbonded pdb=" OG SER E 99 " pdb=" OE2 GLU E 142 " model vdw 2.262 3.040 ... (remaining 162522 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' selection = (chain 'G' and resid 1 through 254) selection = (chain 'H' and resid 1 through 254) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.770 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 49.240 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.080 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20757 Z= 0.169 Angle : 0.641 9.372 28083 Z= 0.343 Chirality : 0.044 0.297 3296 Planarity : 0.005 0.113 3557 Dihedral : 14.452 120.031 7909 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.09 % Allowed : 0.52 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.17), residues: 2532 helix: 1.13 (0.15), residues: 1152 sheet: 0.38 (0.25), residues: 486 loop : -1.00 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 780 HIS 0.011 0.001 HIS D 340 PHE 0.028 0.001 PHE E 305 TYR 0.015 0.001 TYR H 133 ARG 0.010 0.000 ARG B 69 Details of bonding type rmsd hydrogen bonds : bond 0.18600 ( 1035) hydrogen bonds : angle 6.69558 ( 2988) covalent geometry : bond 0.00281 (20757) covalent geometry : angle 0.64128 (28083) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 367 time to evaluate : 2.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 LEU cc_start: 0.8648 (mm) cc_final: 0.8403 (mm) REVERT: B 73 ASP cc_start: 0.8028 (p0) cc_final: 0.7772 (p0) REVERT: C 212 LEU cc_start: 0.9416 (mm) cc_final: 0.9157 (mm) REVERT: C 276 ASP cc_start: 0.7101 (m-30) cc_final: 0.6855 (m-30) REVERT: D 145 MET cc_start: 0.2913 (mmm) cc_final: 0.2652 (tpt) REVERT: E 174 MET cc_start: 0.8072 (ppp) cc_final: 0.7819 (tmm) REVERT: F 125 PHE cc_start: 0.5475 (m-80) cc_final: 0.5265 (p90) REVERT: F 126 LEU cc_start: 0.1063 (OUTLIER) cc_final: 0.0501 (tp) REVERT: F 239 PHE cc_start: 0.2416 (m-10) cc_final: 0.2197 (m-10) REVERT: G 1 MET cc_start: 0.2991 (tmm) cc_final: 0.2624 (tpt) REVERT: G 14 ARG cc_start: 0.7128 (ptm-80) cc_final: 0.6715 (ptm-80) REVERT: G 70 MET cc_start: 0.5866 (pmm) cc_final: 0.5516 (pmm) REVERT: G 120 ASP cc_start: 0.5891 (t0) cc_final: 0.4875 (p0) REVERT: G 249 PHE cc_start: 0.8334 (m-10) cc_final: 0.7997 (m-80) outliers start: 2 outliers final: 0 residues processed: 368 average time/residue: 0.2819 time to fit residues: 167.8995 Evaluate side-chains 268 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 267 time to evaluate : 2.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 126 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 211 optimal weight: 3.9990 chunk 190 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 196 optimal weight: 0.0770 chunk 76 optimal weight: 1.9990 chunk 119 optimal weight: 20.0000 chunk 146 optimal weight: 0.2980 chunk 227 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 GLN ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS ** D 340 HIS ** 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 = 0.4421 r_free = 0.4421 target = 0.149428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.115562 restraints weight = 54497.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.118118 restraints weight = 29133.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.119568 restraints weight = 18787.046| |-----------------------------------------------------------------------------| r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20757 Z= 0.120 Angle : 0.597 11.377 28083 Z= 0.298 Chirality : 0.042 0.193 3296 Planarity : 0.004 0.064 3557 Dihedral : 6.963 103.623 2821 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.87 % Allowed : 8.58 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.17), residues: 2532 helix: 1.43 (0.15), residues: 1175 sheet: 0.44 (0.25), residues: 477 loop : -0.75 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 266 HIS 0.007 0.001 HIS C 184 PHE 0.042 0.002 PHE D 187 TYR 0.025 0.001 TYR B 306 ARG 0.005 0.000 ARG C 136 Details of bonding type rmsd hydrogen bonds : bond 0.04225 ( 1035) hydrogen bonds : angle 4.96108 ( 2988) covalent geometry : bond 0.00259 (20757) covalent geometry : angle 0.59685 (28083) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 286 time to evaluate : 2.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 ASP cc_start: 0.8334 (p0) cc_final: 0.8115 (p0) REVERT: B 115 GLU cc_start: 0.8374 (pm20) cc_final: 0.7947 (pm20) REVERT: B 297 MET cc_start: 0.8673 (ttt) cc_final: 0.8350 (ttt) REVERT: D 145 MET cc_start: 0.2879 (mmm) cc_final: 0.2587 (tpt) REVERT: E 249 LYS cc_start: 0.8741 (mptt) cc_final: 0.8282 (mmtt) REVERT: F 126 LEU cc_start: 0.1702 (OUTLIER) cc_final: 0.1054 (tp) REVERT: G 1 MET cc_start: 0.3218 (tmm) cc_final: 0.2913 (tpt) REVERT: G 14 ARG cc_start: 0.7426 (ptm-80) cc_final: 0.7106 (ptm-80) REVERT: G 120 ASP cc_start: 0.5987 (t0) cc_final: 0.5256 (p0) REVERT: G 199 MET cc_start: 0.6494 (tmm) cc_final: 0.6085 (tpp) REVERT: H 42 ASP cc_start: 0.7571 (p0) cc_final: 0.7343 (p0) REVERT: H 64 HIS cc_start: 0.7255 (t70) cc_final: 0.7004 (t70) outliers start: 20 outliers final: 8 residues processed: 297 average time/residue: 0.2879 time to fit residues: 142.1541 Evaluate side-chains 270 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 261 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 245 PHE Chi-restraints excluded: chain G residue 6 PHE Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain H residue 225 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 6 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 223 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 196 optimal weight: 0.0770 chunk 170 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 chunk 228 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 HIS A 712 GLN C 184 HIS C 213 GLN C 260 HIS ** D 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 ASN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 ASN H 38 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.145551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.111345 restraints weight = 54680.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.112331 restraints weight = 32639.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.113646 restraints weight = 21232.033| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 20757 Z= 0.201 Angle : 0.635 9.421 28083 Z= 0.317 Chirality : 0.043 0.190 3296 Planarity : 0.005 0.062 3557 Dihedral : 6.980 108.939 2821 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.69 % Allowed : 12.09 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.17), residues: 2532 helix: 1.51 (0.15), residues: 1171 sheet: 0.33 (0.25), residues: 487 loop : -0.65 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 780 HIS 0.006 0.001 HIS C 184 PHE 0.022 0.002 PHE C 100 TYR 0.027 0.002 TYR B 306 ARG 0.005 0.001 ARG E 189 Details of bonding type rmsd hydrogen bonds : bond 0.04023 ( 1035) hydrogen bonds : angle 4.75943 ( 2988) covalent geometry : bond 0.00458 (20757) covalent geometry : angle 0.63492 (28083) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 261 time to evaluate : 2.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 569 THR cc_start: 0.8838 (p) cc_final: 0.8620 (p) REVERT: A 709 THR cc_start: 0.8170 (m) cc_final: 0.7676 (p) REVERT: B 73 ASP cc_start: 0.8412 (p0) cc_final: 0.8191 (p0) REVERT: B 297 MET cc_start: 0.8721 (ttt) cc_final: 0.8259 (ttt) REVERT: D 145 MET cc_start: 0.2930 (mmm) cc_final: 0.2727 (tpt) REVERT: D 168 LEU cc_start: 0.9076 (mm) cc_final: 0.8852 (mm) REVERT: E 103 ASN cc_start: 0.7600 (t0) cc_final: 0.7372 (t0) REVERT: E 135 TYR cc_start: 0.8658 (p90) cc_final: 0.8082 (p90) REVERT: E 174 MET cc_start: 0.8488 (ppp) cc_final: 0.8245 (tmm) REVERT: E 236 MET cc_start: 0.8207 (mtt) cc_final: 0.7847 (mmm) REVERT: E 249 LYS cc_start: 0.8712 (mptt) cc_final: 0.8306 (mmtt) REVERT: G 1 MET cc_start: 0.3040 (tmm) cc_final: 0.2764 (tpt) REVERT: G 14 ARG cc_start: 0.7443 (ptm-80) cc_final: 0.6939 (ptm-80) REVERT: G 99 ILE cc_start: 0.9234 (tt) cc_final: 0.8791 (mt) outliers start: 39 outliers final: 24 residues processed: 287 average time/residue: 0.2862 time to fit residues: 131.7731 Evaluate side-chains 258 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 234 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 245 PHE Chi-restraints excluded: chain G residue 6 PHE Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 225 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 249 optimal weight: 8.9990 chunk 158 optimal weight: 4.9990 chunk 187 optimal weight: 0.7980 chunk 77 optimal weight: 0.4980 chunk 179 optimal weight: 20.0000 chunk 233 optimal weight: 5.9990 chunk 146 optimal weight: 0.0050 chunk 46 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 239 optimal weight: 5.9990 chunk 82 optimal weight: 0.0070 overall best weight: 1.2614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 HIS D 60 HIS ** D 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** 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 = 0.4357 r_free = 0.4357 target = 0.144353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.110016 restraints weight = 54745.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.111425 restraints weight = 30399.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.113734 restraints weight = 21208.438| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20757 Z= 0.139 Angle : 0.597 13.919 28083 Z= 0.290 Chirality : 0.042 0.226 3296 Planarity : 0.004 0.075 3557 Dihedral : 6.595 104.703 2819 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.95 % Allowed : 13.52 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.17), residues: 2532 helix: 1.61 (0.16), residues: 1176 sheet: 0.41 (0.25), residues: 486 loop : -0.61 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 780 HIS 0.005 0.001 HIS C 184 PHE 0.018 0.001 PHE A 722 TYR 0.023 0.002 TYR A 361 ARG 0.008 0.000 ARG H 228 Details of bonding type rmsd hydrogen bonds : bond 0.03514 ( 1035) hydrogen bonds : angle 4.59634 ( 2988) covalent geometry : bond 0.00316 (20757) covalent geometry : angle 0.59720 (28083) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 256 time to evaluate : 2.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 709 THR cc_start: 0.8094 (m) cc_final: 0.7609 (p) REVERT: B 11 TRP cc_start: 0.7250 (m-10) cc_final: 0.7006 (m-10) REVERT: B 73 ASP cc_start: 0.8307 (p0) cc_final: 0.8065 (p0) REVERT: B 247 ASP cc_start: 0.8011 (t70) cc_final: 0.7750 (t70) REVERT: B 297 MET cc_start: 0.8736 (ttt) cc_final: 0.8302 (ttt) REVERT: D 145 MET cc_start: 0.2737 (mmm) cc_final: 0.2457 (tpt) REVERT: E 135 TYR cc_start: 0.8584 (p90) cc_final: 0.8000 (p90) REVERT: E 174 MET cc_start: 0.8473 (ppp) cc_final: 0.8089 (ppp) REVERT: E 249 LYS cc_start: 0.8719 (mptt) cc_final: 0.8307 (mmtt) REVERT: G 14 ARG cc_start: 0.7577 (ptm-80) cc_final: 0.7146 (ptm-80) REVERT: G 199 MET cc_start: 0.6741 (tmm) cc_final: 0.6395 (tpp) REVERT: G 249 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.7988 (m-80) REVERT: H 42 ASP cc_start: 0.7567 (p0) cc_final: 0.6992 (p0) REVERT: H 104 GLU cc_start: 0.5911 (mt-10) cc_final: 0.5562 (mt-10) REVERT: H 158 ILE cc_start: 0.8053 (mm) cc_final: 0.7806 (mm) outliers start: 45 outliers final: 26 residues processed: 286 average time/residue: 0.2800 time to fit residues: 130.1537 Evaluate side-chains 264 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 237 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 245 PHE Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 249 PHE Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 228 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 56 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 247 optimal weight: 9.9990 chunk 76 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 167 optimal weight: 0.9990 chunk 249 optimal weight: 2.9990 chunk 191 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 HIS ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 ASN D 25 GLN D 42 GLN ** D 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 GLN G 201 GLN ** H 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.139323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.101676 restraints weight = 54883.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.105969 restraints weight = 30537.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.106343 restraints weight = 17771.758| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 20757 Z= 0.249 Angle : 0.693 12.836 28083 Z= 0.343 Chirality : 0.045 0.234 3296 Planarity : 0.005 0.061 3557 Dihedral : 6.822 110.359 2819 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.51 % Allowed : 14.43 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.17), residues: 2532 helix: 1.32 (0.15), residues: 1170 sheet: 0.18 (0.25), residues: 485 loop : -0.60 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 780 HIS 0.007 0.001 HIS E 38 PHE 0.018 0.002 PHE G 19 TYR 0.029 0.002 TYR D 286 ARG 0.011 0.001 ARG H 44 Details of bonding type rmsd hydrogen bonds : bond 0.04112 ( 1035) hydrogen bonds : angle 4.79411 ( 2988) covalent geometry : bond 0.00575 (20757) covalent geometry : angle 0.69314 (28083) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 246 time to evaluate : 2.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 LEU cc_start: 0.8717 (tt) cc_final: 0.8475 (tt) REVERT: A 709 THR cc_start: 0.8210 (m) cc_final: 0.7679 (p) REVERT: B 186 TYR cc_start: 0.8157 (p90) cc_final: 0.7855 (p90) REVERT: B 247 ASP cc_start: 0.8414 (t70) cc_final: 0.8106 (t70) REVERT: B 297 MET cc_start: 0.8667 (ttt) cc_final: 0.8183 (ttt) REVERT: C 99 ASP cc_start: 0.9021 (m-30) cc_final: 0.7969 (t0) REVERT: C 279 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7535 (mp0) REVERT: D 61 MET cc_start: 0.6323 (tpp) cc_final: 0.5734 (tpp) REVERT: D 145 MET cc_start: 0.2975 (mmm) cc_final: 0.2732 (tpt) REVERT: E 135 TYR cc_start: 0.8659 (p90) cc_final: 0.8150 (p90) REVERT: E 174 MET cc_start: 0.8597 (ppp) cc_final: 0.8133 (ppp) REVERT: E 243 ASN cc_start: 0.9007 (m-40) cc_final: 0.8699 (t0) REVERT: E 249 LYS cc_start: 0.8752 (mptt) cc_final: 0.8378 (mmtt) REVERT: G 201 GLN cc_start: 0.7437 (mp10) cc_final: 0.7146 (mp10) REVERT: G 249 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.7996 (m-10) REVERT: H 104 GLU cc_start: 0.6202 (mt-10) cc_final: 0.5780 (mt-10) outliers start: 58 outliers final: 43 residues processed: 288 average time/residue: 0.3198 time to fit residues: 149.3632 Evaluate side-chains 279 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 234 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 167 CYS Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 245 PHE Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 249 PHE Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 44 ARG Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 228 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 123 optimal weight: 9.9990 chunk 146 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 chunk 235 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 182 optimal weight: 20.0000 chunk 175 optimal weight: 0.7980 chunk 184 optimal weight: 0.0670 chunk 63 optimal weight: 2.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 GLN ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 HIS D 342 GLN E 18 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.142949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.108458 restraints weight = 54552.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.110176 restraints weight = 29201.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.111293 restraints weight = 21724.926| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20757 Z= 0.119 Angle : 0.610 14.170 28083 Z= 0.296 Chirality : 0.043 0.312 3296 Planarity : 0.004 0.061 3557 Dihedral : 6.573 102.099 2819 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.82 % Allowed : 15.99 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.17), residues: 2532 helix: 1.51 (0.15), residues: 1174 sheet: 0.23 (0.25), residues: 484 loop : -0.54 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 780 HIS 0.006 0.001 HIS E 38 PHE 0.016 0.001 PHE G 6 TYR 0.023 0.001 TYR B 306 ARG 0.009 0.000 ARG G 14 Details of bonding type rmsd hydrogen bonds : bond 0.03416 ( 1035) hydrogen bonds : angle 4.54135 ( 2988) covalent geometry : bond 0.00271 (20757) covalent geometry : angle 0.60956 (28083) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 268 time to evaluate : 2.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 LEU cc_start: 0.9403 (tp) cc_final: 0.9047 (tt) REVERT: B 186 TYR cc_start: 0.7859 (p90) cc_final: 0.7619 (p90) REVERT: B 297 MET cc_start: 0.8684 (ttt) cc_final: 0.8235 (ttt) REVERT: C 99 ASP cc_start: 0.8752 (m-30) cc_final: 0.7771 (t0) REVERT: D 61 MET cc_start: 0.6264 (tpp) cc_final: 0.5785 (tpp) REVERT: D 139 LEU cc_start: 0.8172 (mm) cc_final: 0.7873 (mm) REVERT: D 145 MET cc_start: 0.2821 (mmm) cc_final: 0.2540 (tpt) REVERT: E 135 TYR cc_start: 0.8422 (p90) cc_final: 0.8002 (p90) REVERT: E 174 MET cc_start: 0.8347 (ppp) cc_final: 0.7959 (ppp) REVERT: E 249 LYS cc_start: 0.8719 (mptt) cc_final: 0.8513 (tptp) REVERT: G 14 ARG cc_start: 0.6200 (ptm-80) cc_final: 0.5810 (ptm-80) REVERT: G 95 THR cc_start: 0.5990 (p) cc_final: 0.5754 (t) REVERT: G 201 GLN cc_start: 0.7336 (mp10) cc_final: 0.7114 (mp10) REVERT: G 249 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7831 (m-10) REVERT: H 42 ASP cc_start: 0.7368 (p0) cc_final: 0.6813 (p0) REVERT: H 104 GLU cc_start: 0.6163 (mt-10) cc_final: 0.5834 (mt-10) outliers start: 42 outliers final: 32 residues processed: 296 average time/residue: 0.3047 time to fit residues: 144.1956 Evaluate side-chains 278 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 245 time to evaluate : 2.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 245 PHE Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 249 PHE Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 228 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 59 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 228 optimal weight: 3.9990 chunk 176 optimal weight: 30.0000 chunk 46 optimal weight: 9.9990 chunk 125 optimal weight: 7.9990 chunk 100 optimal weight: 8.9990 chunk 132 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 ASN ** 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 = 0.4255 r_free = 0.4255 target = 0.137985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.101569 restraints weight = 54816.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.103909 restraints weight = 29493.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.105674 restraints weight = 20034.335| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 20757 Z= 0.271 Angle : 0.726 15.402 28083 Z= 0.358 Chirality : 0.045 0.220 3296 Planarity : 0.005 0.060 3557 Dihedral : 6.940 111.311 2819 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.60 % Allowed : 16.47 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.17), residues: 2532 helix: 1.23 (0.15), residues: 1170 sheet: 0.07 (0.25), residues: 481 loop : -0.71 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 780 HIS 0.007 0.001 HIS D 265 PHE 0.024 0.002 PHE H 248 TYR 0.030 0.002 TYR D 286 ARG 0.009 0.001 ARG H 228 Details of bonding type rmsd hydrogen bonds : bond 0.04153 ( 1035) hydrogen bonds : angle 4.84446 ( 2988) covalent geometry : bond 0.00625 (20757) covalent geometry : angle 0.72561 (28083) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 249 time to evaluate : 2.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 722 PHE cc_start: 0.8486 (t80) cc_final: 0.8283 (t80) REVERT: A 776 VAL cc_start: 0.7848 (t) cc_final: 0.7602 (m) REVERT: B 115 GLU cc_start: 0.8592 (mp0) cc_final: 0.8369 (mp0) REVERT: B 128 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.8005 (ptt180) REVERT: B 186 TYR cc_start: 0.8214 (p90) cc_final: 0.7868 (p90) REVERT: B 297 MET cc_start: 0.8778 (ttt) cc_final: 0.8311 (ttt) REVERT: C 78 MET cc_start: 0.7071 (ttp) cc_final: 0.6869 (ttp) REVERT: C 99 ASP cc_start: 0.9019 (m-30) cc_final: 0.7981 (t0) REVERT: C 112 LYS cc_start: 0.8977 (mmmm) cc_final: 0.8776 (mmtm) REVERT: C 279 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7450 (mp0) REVERT: D 61 MET cc_start: 0.6485 (tpp) cc_final: 0.5889 (tpp) REVERT: D 62 LEU cc_start: 0.9001 (mm) cc_final: 0.8736 (mm) REVERT: D 139 LEU cc_start: 0.8308 (mm) cc_final: 0.7852 (mm) REVERT: D 145 MET cc_start: 0.2989 (mmm) cc_final: 0.2667 (tpt) REVERT: D 342 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8244 (mp-120) REVERT: E 135 TYR cc_start: 0.8578 (p90) cc_final: 0.8159 (p90) REVERT: E 243 ASN cc_start: 0.8969 (m-40) cc_final: 0.8613 (t0) REVERT: E 249 LYS cc_start: 0.8764 (mptt) cc_final: 0.8356 (mmtt) REVERT: G 1 MET cc_start: 0.3579 (tmm) cc_final: 0.2230 (ptm) REVERT: G 201 GLN cc_start: 0.7444 (mp10) cc_final: 0.7229 (mp10) REVERT: G 249 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7953 (m-10) REVERT: H 104 GLU cc_start: 0.6388 (mt-10) cc_final: 0.6017 (mt-10) outliers start: 60 outliers final: 45 residues processed: 292 average time/residue: 0.3027 time to fit residues: 141.1922 Evaluate side-chains 278 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 229 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 342 GLN Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 245 PHE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 249 PHE Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 44 ARG Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 228 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 122 optimal weight: 0.0570 chunk 130 optimal weight: 0.9980 chunk 169 optimal weight: 0.8980 chunk 214 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 184 optimal weight: 20.0000 chunk 22 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.141796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.106840 restraints weight = 55087.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.108673 restraints weight = 30807.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.109888 restraints weight = 20563.692| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20757 Z= 0.120 Angle : 0.631 16.251 28083 Z= 0.302 Chirality : 0.042 0.181 3296 Planarity : 0.004 0.061 3557 Dihedral : 6.660 101.518 2819 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.91 % Allowed : 17.82 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.17), residues: 2532 helix: 1.47 (0.15), residues: 1168 sheet: 0.14 (0.25), residues: 483 loop : -0.62 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 420 HIS 0.006 0.001 HIS E 38 PHE 0.027 0.001 PHE H 248 TYR 0.024 0.001 TYR B 306 ARG 0.010 0.001 ARG G 14 Details of bonding type rmsd hydrogen bonds : bond 0.03376 ( 1035) hydrogen bonds : angle 4.52217 ( 2988) covalent geometry : bond 0.00273 (20757) covalent geometry : angle 0.63118 (28083) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 267 time to evaluate : 2.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8453 (tt) REVERT: B 115 GLU cc_start: 0.8499 (mp0) cc_final: 0.8225 (mp0) REVERT: B 297 MET cc_start: 0.8828 (ttt) cc_final: 0.8405 (ttt) REVERT: C 99 ASP cc_start: 0.9025 (m-30) cc_final: 0.7992 (t0) REVERT: C 279 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7439 (mp0) REVERT: D 61 MET cc_start: 0.6598 (tpp) cc_final: 0.6066 (tpp) REVERT: D 139 LEU cc_start: 0.8427 (mm) cc_final: 0.8208 (mm) REVERT: D 145 MET cc_start: 0.2898 (mmm) cc_final: 0.2634 (tpt) REVERT: D 342 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8305 (mp-120) REVERT: E 135 TYR cc_start: 0.8458 (p90) cc_final: 0.8045 (p90) REVERT: E 174 MET cc_start: 0.8234 (ppp) cc_final: 0.7890 (ppp) REVERT: E 243 ASN cc_start: 0.9052 (m-40) cc_final: 0.8725 (t0) REVERT: E 249 LYS cc_start: 0.8722 (mptt) cc_final: 0.8437 (tptp) REVERT: G 1 MET cc_start: 0.3622 (tmm) cc_final: 0.2446 (ptm) REVERT: G 181 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8235 (tp) REVERT: G 188 MET cc_start: 0.7442 (pmm) cc_final: 0.5968 (tmm) REVERT: G 199 MET cc_start: 0.6550 (tmm) cc_final: 0.6214 (tmm) REVERT: G 249 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.7998 (m-10) REVERT: H 104 GLU cc_start: 0.6334 (mt-10) cc_final: 0.5989 (mt-10) outliers start: 44 outliers final: 28 residues processed: 299 average time/residue: 0.2933 time to fit residues: 140.8284 Evaluate side-chains 280 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 247 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 342 GLN Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 245 PHE Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 249 PHE Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 47 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 156 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 131 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 180 optimal weight: 30.0000 chunk 58 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 29 optimal weight: 20.0000 chunk 112 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 ASN ** E 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 ASN ** 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 = 0.4251 r_free = 0.4251 target = 0.138819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.102545 restraints weight = 55384.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.104965 restraints weight = 28527.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.105595 restraints weight = 20478.261| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 20757 Z= 0.252 Angle : 0.730 17.797 28083 Z= 0.357 Chirality : 0.045 0.181 3296 Planarity : 0.005 0.059 3557 Dihedral : 6.989 110.316 2819 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.08 % Allowed : 17.95 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.17), residues: 2532 helix: 1.25 (0.15), residues: 1168 sheet: -0.03 (0.25), residues: 479 loop : -0.73 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 780 HIS 0.007 0.001 HIS B 317 PHE 0.024 0.002 PHE H 248 TYR 0.028 0.002 TYR D 286 ARG 0.006 0.001 ARG D 219 Details of bonding type rmsd hydrogen bonds : bond 0.04064 ( 1035) hydrogen bonds : angle 4.79892 ( 2988) covalent geometry : bond 0.00582 (20757) covalent geometry : angle 0.72955 (28083) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 246 time to evaluate : 2.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 776 VAL cc_start: 0.7939 (t) cc_final: 0.7684 (m) REVERT: B 115 GLU cc_start: 0.8474 (mp0) cc_final: 0.8253 (mp0) REVERT: B 128 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7962 (ptt180) REVERT: B 297 MET cc_start: 0.8680 (ttt) cc_final: 0.8254 (ttt) REVERT: D 61 MET cc_start: 0.6465 (tpp) cc_final: 0.5734 (tpp) REVERT: D 139 LEU cc_start: 0.8243 (mm) cc_final: 0.7796 (mm) REVERT: D 342 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8167 (mp-120) REVERT: E 135 TYR cc_start: 0.8475 (p90) cc_final: 0.8095 (p90) REVERT: E 174 MET cc_start: 0.8233 (ppp) cc_final: 0.7890 (ppp) REVERT: E 243 ASN cc_start: 0.8921 (m-40) cc_final: 0.8662 (t0) REVERT: G 1 MET cc_start: 0.3651 (tmm) cc_final: 0.2446 (ptm) REVERT: G 188 MET cc_start: 0.7388 (pmm) cc_final: 0.5919 (tmm) REVERT: G 199 MET cc_start: 0.6964 (tmm) cc_final: 0.6675 (tmm) REVERT: G 249 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7913 (m-10) REVERT: H 104 GLU cc_start: 0.6350 (mt-10) cc_final: 0.6013 (mt-10) outliers start: 48 outliers final: 39 residues processed: 280 average time/residue: 0.2898 time to fit residues: 131.8235 Evaluate side-chains 270 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 228 time to evaluate : 2.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 342 GLN Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 224 GLN Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 245 PHE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 249 PHE Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 225 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 129 optimal weight: 0.9980 chunk 190 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 180 optimal weight: 30.0000 chunk 207 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 203 optimal weight: 6.9990 chunk 155 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 195 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.140681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.106191 restraints weight = 55780.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.105931 restraints weight = 33538.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.107595 restraints weight = 24565.533| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 20757 Z= 0.216 Angle : 0.700 16.643 28083 Z= 0.341 Chirality : 0.045 0.200 3296 Planarity : 0.004 0.058 3557 Dihedral : 6.951 105.287 2819 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.21 % Allowed : 18.38 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.17), residues: 2532 helix: 1.23 (0.15), residues: 1170 sheet: -0.08 (0.25), residues: 481 loop : -0.72 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 780 HIS 0.009 0.001 HIS A 200 PHE 0.021 0.002 PHE H 248 TYR 0.023 0.002 TYR B 306 ARG 0.005 0.001 ARG G 14 Details of bonding type rmsd hydrogen bonds : bond 0.03814 ( 1035) hydrogen bonds : angle 4.75595 ( 2988) covalent geometry : bond 0.00500 (20757) covalent geometry : angle 0.69956 (28083) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 239 time to evaluate : 2.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8403 (tt) REVERT: A 776 VAL cc_start: 0.7954 (t) cc_final: 0.7686 (m) REVERT: B 115 GLU cc_start: 0.8414 (mp0) cc_final: 0.8200 (mp0) REVERT: B 128 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7962 (ptm160) REVERT: B 297 MET cc_start: 0.8629 (ttt) cc_final: 0.8196 (ttt) REVERT: C 30 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.7965 (mm-40) REVERT: D 61 MET cc_start: 0.6387 (tpp) cc_final: 0.5757 (tpp) REVERT: D 342 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8140 (mp-120) REVERT: E 135 TYR cc_start: 0.8394 (p90) cc_final: 0.8130 (p90) REVERT: E 174 MET cc_start: 0.8129 (ppp) cc_final: 0.7792 (ppp) REVERT: E 243 ASN cc_start: 0.8861 (m-40) cc_final: 0.8639 (t0) REVERT: G 1 MET cc_start: 0.3547 (tmm) cc_final: 0.2309 (ptm) REVERT: G 42 ASP cc_start: 0.8213 (p0) cc_final: 0.7324 (t0) REVERT: G 181 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8400 (tp) REVERT: G 188 MET cc_start: 0.7390 (pmm) cc_final: 0.6022 (tmm) REVERT: G 199 MET cc_start: 0.7091 (tmm) cc_final: 0.6079 (tmm) REVERT: H 104 GLU cc_start: 0.6411 (mt-10) cc_final: 0.6073 (mt-10) REVERT: H 134 ASP cc_start: 0.4940 (p0) cc_final: 0.4292 (m-30) REVERT: H 140 PRO cc_start: 0.7340 (Cg_endo) cc_final: 0.7104 (Cg_exo) outliers start: 51 outliers final: 41 residues processed: 277 average time/residue: 0.3027 time to fit residues: 135.9758 Evaluate side-chains 284 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 238 time to evaluate : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain C residue 30 GLN Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 342 GLN Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 224 GLN Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 245 PHE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 225 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 3 optimal weight: 0.0070 chunk 33 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 184 optimal weight: 20.0000 chunk 205 optimal weight: 20.0000 chunk 238 optimal weight: 8.9990 chunk 197 optimal weight: 5.9990 chunk 2 optimal weight: 0.2980 chunk 231 optimal weight: 4.9990 chunk 245 optimal weight: 0.7980 chunk 249 optimal weight: 1.9990 overall best weight: 0.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 ASN ** E 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 229 ASN ** 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 = 0.4304 r_free = 0.4304 target = 0.141169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.106552 restraints weight = 55018.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.107603 restraints weight = 32530.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.108520 restraints weight = 22608.878| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 20757 Z= 0.126 Angle : 0.645 15.216 28083 Z= 0.311 Chirality : 0.043 0.203 3296 Planarity : 0.004 0.060 3557 Dihedral : 6.785 100.291 2819 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.99 % Allowed : 18.64 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.17), residues: 2532 helix: 1.43 (0.15), residues: 1172 sheet: 0.02 (0.25), residues: 479 loop : -0.64 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 420 HIS 0.006 0.001 HIS E 38 PHE 0.025 0.001 PHE H 248 TYR 0.023 0.001 TYR B 306 ARG 0.007 0.000 ARG G 14 Details of bonding type rmsd hydrogen bonds : bond 0.03370 ( 1035) hydrogen bonds : angle 4.53738 ( 2988) covalent geometry : bond 0.00292 (20757) covalent geometry : angle 0.64505 (28083) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6775.57 seconds wall clock time: 120 minutes 0.68 seconds (7200.68 seconds total)