Starting phenix.real_space_refine on Tue Nov 19 23:54:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thc_41253/11_2024/8thc_41253.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thc_41253/11_2024/8thc_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thc_41253/11_2024/8thc_41253.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thc_41253/11_2024/8thc_41253.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thc_41253/11_2024/8thc_41253.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thc_41253/11_2024/8thc_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 12.43, per 1000 atoms: 0.61 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: 4.96 Conformation dependent library (CDL) restraints added in 2.6 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: 2.19 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: 7.20 Time building geometry restraints manager: 5.74 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: 5.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.800 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 45.580 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.090 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.030 ------------------------------------------------------------------------------- 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= 0.183 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 *********************** 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 : 2.401 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: 0.2862 time to fit residues: 169.7134 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 : 2.367 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 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= 0.167 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 *********************** 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 : 2.341 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: 0.8035 (p0) cc_final: 0.7813 (p0) REVERT: B 115 GLU cc_start: 0.8276 (pm20) cc_final: 0.7771 (pm20) REVERT: B 297 MET cc_start: 0.8509 (ttt) cc_final: 0.8188 (ttt) REVERT: D 145 MET cc_start: 0.2720 (mmm) cc_final: 0.2453 (tpt) REVERT: E 249 LYS cc_start: 0.8730 (mptt) cc_final: 0.8263 (mmtt) REVERT: F 126 LEU cc_start: 0.1678 (OUTLIER) cc_final: 0.1046 (tp) REVERT: G 1 MET cc_start: 0.3158 (tmm) cc_final: 0.2859 (tpt) REVERT: G 14 ARG cc_start: 0.7536 (ptm-80) cc_final: 0.7227 (ptm-80) REVERT: G 120 ASP cc_start: 0.5918 (t0) cc_final: 0.5147 (p0) REVERT: G 199 MET cc_start: 0.6568 (tmm) cc_final: 0.6178 (tpp) REVERT: H 42 ASP cc_start: 0.7355 (p0) cc_final: 0.7097 (p0) REVERT: H 64 HIS cc_start: 0.6879 (t70) cc_final: 0.6660 (t70) outliers start: 20 outliers final: 8 residues processed: 297 average time/residue: 0.2818 time to fit residues: 136.9670 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 : 2.381 ------------------------------------------------------------------------------- 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 126 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 189 optimal weight: 30.0000 chunk 155 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 228 optimal weight: 1.9990 chunk 246 optimal weight: 0.9990 chunk 203 optimal weight: 8.9990 chunk 226 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 183 optimal weight: 30.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 F 27 ASN H 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 20757 Z= 0.308 Angle : 0.657 9.955 28083 Z= 0.327 Chirality : 0.044 0.195 3296 Planarity : 0.005 0.062 3557 Dihedral : 7.043 110.465 2821 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.91 % Allowed : 12.09 % Favored : 86.00 % 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: 1173 sheet: 0.31 (0.25), residues: 486 loop : -0.66 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 780 HIS 0.006 0.001 HIS D 265 PHE 0.023 0.002 PHE C 100 TYR 0.028 0.002 TYR D 286 ARG 0.006 0.001 ARG E 189 *********************** 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 303 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 259 time to evaluate : 2.325 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: 0.8740 (p) cc_final: 0.8436 (p) REVERT: A 588 MET cc_start: 0.8801 (mmm) cc_final: 0.8592 (mmm) REVERT: A 709 THR cc_start: 0.8221 (m) cc_final: 0.7762 (p) REVERT: B 73 ASP cc_start: 0.8143 (p0) cc_final: 0.7911 (p0) REVERT: B 297 MET cc_start: 0.8579 (ttt) cc_final: 0.8102 (ttt) REVERT: D 168 LEU cc_start: 0.8925 (mm) cc_final: 0.8693 (mm) REVERT: E 103 ASN cc_start: 0.7420 (t0) cc_final: 0.7207 (t0) REVERT: E 135 TYR cc_start: 0.8484 (p90) cc_final: 0.8061 (p90) REVERT: E 174 MET cc_start: 0.8275 (ppp) cc_final: 0.8050 (tmm) REVERT: E 249 LYS cc_start: 0.8762 (mptt) cc_final: 0.8322 (mmtt) REVERT: G 14 ARG cc_start: 0.7511 (ptm-80) cc_final: 0.6972 (ptm-80) REVERT: G 70 MET cc_start: 0.7256 (OUTLIER) cc_final: 0.7056 (pmm) REVERT: G 99 ILE cc_start: 0.9200 (tt) cc_final: 0.8712 (mt) outliers start: 44 outliers final: 26 residues processed: 288 average time/residue: 0.3007 time to fit residues: 139.5285 Evaluate side-chains 257 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 230 time to evaluate : 2.431 ------------------------------------------------------------------------------- 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 602 LEU 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 120 THR 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 C residue 279 GLU 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 70 MET 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 225 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 225 optimal weight: 5.9990 chunk 171 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 229 optimal weight: 5.9990 chunk 242 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 217 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20757 Z= 0.230 Angle : 0.605 13.942 28083 Z= 0.295 Chirality : 0.042 0.227 3296 Planarity : 0.004 0.063 3557 Dihedral : 6.620 105.329 2819 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.08 % Allowed : 14.13 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.87 (0.17), residues: 2532 helix: 1.56 (0.15), residues: 1175 sheet: 0.37 (0.25), residues: 487 loop : -0.58 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 780 HIS 0.005 0.001 HIS C 184 PHE 0.019 0.001 PHE A 722 TYR 0.023 0.002 TYR B 306 ARG 0.008 0.000 ARG H 228 *********************** 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 310 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 262 time to evaluate : 2.525 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 569 THR cc_start: 0.8741 (p) cc_final: 0.8530 (p) REVERT: A 588 MET cc_start: 0.8788 (mmm) cc_final: 0.8573 (mmm) REVERT: A 709 THR cc_start: 0.8174 (m) cc_final: 0.7696 (p) REVERT: B 73 ASP cc_start: 0.8161 (p0) cc_final: 0.7903 (p0) REVERT: B 186 TYR cc_start: 0.7661 (p90) cc_final: 0.7364 (p90) REVERT: B 297 MET cc_start: 0.8594 (ttt) cc_final: 0.8114 (ttt) REVERT: D 139 LEU cc_start: 0.8249 (mm) cc_final: 0.8026 (mm) REVERT: E 135 TYR cc_start: 0.8402 (p90) cc_final: 0.8045 (p90) REVERT: E 174 MET cc_start: 0.8289 (ppp) cc_final: 0.8002 (ppp) REVERT: E 236 MET cc_start: 0.8175 (mtt) cc_final: 0.7916 (tpt) REVERT: E 249 LYS cc_start: 0.8754 (mptt) cc_final: 0.8336 (mmtt) REVERT: G 14 ARG cc_start: 0.7615 (ptm-80) cc_final: 0.7179 (ptm-80) REVERT: G 249 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.7802 (m-80) REVERT: H 42 ASP cc_start: 0.7314 (p0) cc_final: 0.6809 (p0) REVERT: H 104 GLU cc_start: 0.5916 (mt-10) cc_final: 0.5610 (mt-10) REVERT: H 158 ILE cc_start: 0.7854 (mm) cc_final: 0.7607 (mm) outliers start: 48 outliers final: 32 residues processed: 292 average time/residue: 0.3012 time to fit residues: 141.7159 Evaluate side-chains 271 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 238 time to evaluate : 2.423 ------------------------------------------------------------------------------- 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 717 ILE Chi-restraints excluded: chain B residue 48 SER 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 279 GLU 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 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 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 202 optimal weight: 9.9990 chunk 137 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 180 optimal weight: 40.0000 chunk 100 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 167 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 123 optimal weight: 0.0050 chunk 217 optimal weight: 0.0980 chunk 61 optimal weight: 0.3980 overall best weight: 0.8596 ------------------------------------------------------------------------------- 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** D 25 GLN D 60 HIS D 342 GLN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20757 Z= 0.178 Angle : 0.589 13.173 28083 Z= 0.285 Chirality : 0.041 0.287 3296 Planarity : 0.004 0.064 3557 Dihedral : 6.504 102.019 2819 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.82 % Allowed : 15.47 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.17), residues: 2532 helix: 1.63 (0.15), residues: 1172 sheet: 0.38 (0.25), residues: 484 loop : -0.58 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 780 HIS 0.007 0.001 HIS E 38 PHE 0.018 0.001 PHE G 6 TYR 0.022 0.001 TYR A 361 ARG 0.011 0.001 ARG E 156 *********************** 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: 42 poor density : 262 time to evaluate : 2.540 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 565 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7710 (mm-30) REVERT: A 709 THR cc_start: 0.8143 (m) cc_final: 0.7666 (p) REVERT: B 73 ASP cc_start: 0.8138 (p0) cc_final: 0.7863 (p0) REVERT: B 155 GLN cc_start: 0.8599 (mt0) cc_final: 0.8373 (mt0) REVERT: B 297 MET cc_start: 0.8574 (ttt) cc_final: 0.8097 (ttt) REVERT: C 99 ASP cc_start: 0.8290 (m-30) cc_final: 0.7505 (t0) REVERT: D 109 LYS cc_start: 0.9086 (ptpt) cc_final: 0.8810 (mtmt) REVERT: D 139 LEU cc_start: 0.8232 (mm) cc_final: 0.8024 (mm) REVERT: E 135 TYR cc_start: 0.8363 (p90) cc_final: 0.8036 (p90) REVERT: E 155 ARG cc_start: 0.8468 (tmm-80) cc_final: 0.8218 (tmm-80) REVERT: E 174 MET cc_start: 0.8258 (ppp) cc_final: 0.7938 (ppp) REVERT: E 224 GLN cc_start: 0.9164 (mp10) cc_final: 0.8721 (mp10) REVERT: E 249 LYS cc_start: 0.8730 (mptt) cc_final: 0.8422 (tptp) REVERT: G 6 PHE cc_start: 0.6641 (OUTLIER) cc_final: 0.6160 (t80) REVERT: G 11 LEU cc_start: 0.7729 (tp) cc_final: 0.7307 (tp) REVERT: G 14 ARG cc_start: 0.7547 (ptm-80) cc_final: 0.7325 (ptm-80) REVERT: G 249 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7730 (m-80) REVERT: H 104 GLU cc_start: 0.5945 (mt-10) cc_final: 0.5627 (mt-10) REVERT: H 158 ILE cc_start: 0.7837 (mm) cc_final: 0.7591 (mm) outliers start: 42 outliers final: 32 residues processed: 291 average time/residue: 0.2995 time to fit residues: 141.2167 Evaluate side-chains 281 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 247 time to evaluate : 2.448 ------------------------------------------------------------------------------- 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 586 ASP 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 235 ILE Chi-restraints excluded: chain C residue 63 ILE 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 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 6 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 81 optimal weight: 1.9990 chunk 218 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 142 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 242 optimal weight: 6.9990 chunk 201 optimal weight: 10.0000 chunk 112 optimal weight: 0.6980 chunk 20 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 127 optimal weight: 0.0020 overall best weight: 1.1192 ------------------------------------------------------------------------------- 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 ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 20757 Z= 0.202 Angle : 0.588 14.220 28083 Z= 0.286 Chirality : 0.042 0.322 3296 Planarity : 0.004 0.061 3557 Dihedral : 6.475 100.648 2819 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.86 % Allowed : 16.25 % Favored : 81.88 % 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: 0.94 (0.17), residues: 2532 helix: 1.62 (0.15), residues: 1175 sheet: 0.38 (0.25), residues: 483 loop : -0.53 (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 0.024 0.001 PHE H 248 TYR 0.022 0.001 TYR B 306 ARG 0.008 0.000 ARG H 228 *********************** 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 300 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 257 time to evaluate : 2.378 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 422 MET cc_start: 0.8774 (ttm) cc_final: 0.8565 (ttm) REVERT: B 73 ASP cc_start: 0.8086 (p0) cc_final: 0.7880 (p0) REVERT: B 297 MET cc_start: 0.8622 (ttt) cc_final: 0.8143 (ttt) REVERT: C 99 ASP cc_start: 0.8354 (m-30) cc_final: 0.7603 (t0) REVERT: E 135 TYR cc_start: 0.8375 (p90) cc_final: 0.8012 (p90) REVERT: E 155 ARG cc_start: 0.8529 (tmm-80) cc_final: 0.8227 (tmm-80) REVERT: E 174 MET cc_start: 0.8294 (ppp) cc_final: 0.7938 (ppp) REVERT: E 224 GLN cc_start: 0.9192 (mp10) cc_final: 0.8744 (mp10) REVERT: E 249 LYS cc_start: 0.8726 (mptt) cc_final: 0.8479 (tptp) REVERT: G 6 PHE cc_start: 0.6570 (OUTLIER) cc_final: 0.6261 (t80) REVERT: G 14 ARG cc_start: 0.7516 (ptm-80) cc_final: 0.7190 (ptm-80) REVERT: G 95 THR cc_start: 0.5948 (p) cc_final: 0.5717 (t) REVERT: G 249 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7705 (m-10) REVERT: H 104 GLU cc_start: 0.6090 (mt-10) cc_final: 0.5814 (mt-10) outliers start: 43 outliers final: 34 residues processed: 287 average time/residue: 0.2882 time to fit residues: 132.8223 Evaluate side-chains 281 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 245 time to evaluate : 2.502 ------------------------------------------------------------------------------- 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 644 LEU 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 C residue 63 ILE Chi-restraints excluded: chain C residue 103 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 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 6 PHE Chi-restraints excluded: chain G residue 100 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 36 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 234 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 177 optimal weight: 0.6980 chunk 137 optimal weight: 0.6980 chunk 204 optimal weight: 5.9990 chunk 135 optimal weight: 0.6980 chunk 241 optimal weight: 9.9990 chunk 151 optimal weight: 2.9990 chunk 147 optimal weight: 0.2980 chunk 111 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20757 Z= 0.165 Angle : 0.582 14.634 28083 Z= 0.282 Chirality : 0.041 0.183 3296 Planarity : 0.004 0.061 3557 Dihedral : 6.403 97.728 2819 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.86 % Allowed : 16.99 % Favored : 81.14 % 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: 0.98 (0.17), residues: 2532 helix: 1.65 (0.15), residues: 1170 sheet: 0.40 (0.25), residues: 487 loop : -0.51 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 780 HIS 0.006 0.001 HIS E 38 PHE 0.022 0.001 PHE H 248 TYR 0.022 0.001 TYR B 306 ARG 0.007 0.000 ARG H 228 *********************** 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 308 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 265 time to evaluate : 2.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 297 MET cc_start: 0.8617 (ttt) cc_final: 0.8159 (ttt) REVERT: C 99 ASP cc_start: 0.8363 (m-30) cc_final: 0.7624 (t0) REVERT: D 342 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8181 (mp-120) REVERT: E 135 TYR cc_start: 0.8362 (p90) cc_final: 0.7978 (p90) REVERT: E 155 ARG cc_start: 0.8484 (tmm-80) cc_final: 0.8230 (tmm-80) REVERT: E 174 MET cc_start: 0.8176 (ppp) cc_final: 0.7829 (ppp) REVERT: E 224 GLN cc_start: 0.9179 (mp10) cc_final: 0.8727 (mp10) REVERT: E 249 LYS cc_start: 0.8706 (mptt) cc_final: 0.8478 (tptp) REVERT: G 6 PHE cc_start: 0.6662 (OUTLIER) cc_final: 0.6326 (t80) REVERT: G 95 THR cc_start: 0.5956 (p) cc_final: 0.5733 (t) REVERT: G 181 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8351 (tp) REVERT: G 188 MET cc_start: 0.7218 (pmm) cc_final: 0.5603 (tmm) REVERT: G 249 PHE cc_start: 0.8054 (OUTLIER) cc_final: 0.7700 (m-10) REVERT: H 42 ASP cc_start: 0.7130 (p0) cc_final: 0.6619 (p0) REVERT: H 140 PRO cc_start: 0.7258 (Cg_endo) cc_final: 0.7037 (Cg_exo) outliers start: 43 outliers final: 31 residues processed: 295 average time/residue: 0.3000 time to fit residues: 141.2526 Evaluate side-chains 285 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 250 time to evaluate : 2.373 ------------------------------------------------------------------------------- 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 644 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 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 103 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 222 ASP Chi-restraints excluded: chain D residue 342 GLN Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 186 LEU 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 6 PHE Chi-restraints excluded: chain G residue 139 LEU 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 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 149 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 47 optimal weight: 0.0870 chunk 46 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 chunk 164 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 190 optimal weight: 8.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20757 Z= 0.211 Angle : 0.613 15.600 28083 Z= 0.294 Chirality : 0.042 0.160 3296 Planarity : 0.004 0.077 3557 Dihedral : 6.471 97.746 2819 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.12 % Allowed : 17.25 % Favored : 80.62 % 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: 0.96 (0.17), residues: 2532 helix: 1.64 (0.15), residues: 1171 sheet: 0.38 (0.25), residues: 485 loop : -0.53 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 266 HIS 0.006 0.001 HIS E 38 PHE 0.018 0.001 PHE H 248 TYR 0.022 0.001 TYR A 361 ARG 0.008 0.000 ARG H 228 *********************** 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 301 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 252 time to evaluate : 2.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8407 (tt) REVERT: B 76 LEU cc_start: 0.9137 (tp) cc_final: 0.8936 (tt) REVERT: B 186 TYR cc_start: 0.7756 (p90) cc_final: 0.7535 (p90) REVERT: B 297 MET cc_start: 0.8649 (ttt) cc_final: 0.8186 (ttt) REVERT: C 99 ASP cc_start: 0.8398 (m-30) cc_final: 0.7709 (t0) REVERT: D 61 MET cc_start: 0.6328 (tpp) cc_final: 0.5719 (tpp) REVERT: D 342 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8135 (mp-120) REVERT: E 135 TYR cc_start: 0.8416 (p90) cc_final: 0.8064 (p90) REVERT: E 249 LYS cc_start: 0.8720 (mptt) cc_final: 0.8460 (tptp) REVERT: G 6 PHE cc_start: 0.6678 (OUTLIER) cc_final: 0.6335 (t80) REVERT: G 95 THR cc_start: 0.5953 (p) cc_final: 0.5728 (t) REVERT: G 249 PHE cc_start: 0.8054 (OUTLIER) cc_final: 0.7717 (m-10) REVERT: H 140 PRO cc_start: 0.7304 (Cg_endo) cc_final: 0.7061 (Cg_exo) outliers start: 49 outliers final: 37 residues processed: 285 average time/residue: 0.2998 time to fit residues: 136.9862 Evaluate side-chains 284 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 243 time to evaluate : 2.600 ------------------------------------------------------------------------------- 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 557 LEU 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 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 63 ILE Chi-restraints excluded: chain C residue 103 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 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 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 6 PHE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 139 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 47 LEU Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 228 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 220 optimal weight: 6.9990 chunk 231 optimal weight: 0.9990 chunk 211 optimal weight: 1.9990 chunk 225 optimal weight: 8.9990 chunk 135 optimal weight: 0.5980 chunk 98 optimal weight: 5.9990 chunk 177 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 203 optimal weight: 7.9990 chunk 213 optimal weight: 8.9990 chunk 224 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 ASN E 18 HIS ** G 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 20757 Z= 0.196 Angle : 0.616 13.894 28083 Z= 0.294 Chirality : 0.042 0.179 3296 Planarity : 0.004 0.060 3557 Dihedral : 6.451 96.991 2819 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.99 % Allowed : 17.56 % Favored : 80.45 % 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: 0.96 (0.17), residues: 2532 helix: 1.62 (0.15), residues: 1171 sheet: 0.40 (0.25), residues: 485 loop : -0.51 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 780 HIS 0.005 0.001 HIS E 38 PHE 0.020 0.001 PHE H 248 TYR 0.022 0.001 TYR B 306 ARG 0.008 0.000 ARG H 228 *********************** 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 298 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 252 time to evaluate : 2.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8409 (tt) REVERT: B 76 LEU cc_start: 0.9138 (tp) cc_final: 0.8927 (tt) REVERT: B 186 TYR cc_start: 0.7767 (p90) cc_final: 0.7540 (p90) REVERT: B 297 MET cc_start: 0.8665 (ttt) cc_final: 0.8226 (ttt) REVERT: C 99 ASP cc_start: 0.8478 (m-30) cc_final: 0.7692 (t0) REVERT: D 61 MET cc_start: 0.6293 (tpp) cc_final: 0.5812 (tpp) REVERT: D 342 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8137 (mp-120) REVERT: E 135 TYR cc_start: 0.8356 (p90) cc_final: 0.8029 (p90) REVERT: E 174 MET cc_start: 0.8041 (ppp) cc_final: 0.7776 (ppp) REVERT: G 1 MET cc_start: 0.3542 (tmm) cc_final: 0.2246 (ptm) REVERT: G 6 PHE cc_start: 0.6665 (OUTLIER) cc_final: 0.6381 (t80) REVERT: G 181 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8369 (tp) REVERT: G 188 MET cc_start: 0.7297 (pmm) cc_final: 0.5728 (tmm) REVERT: G 199 MET cc_start: 0.6745 (tmm) cc_final: 0.6231 (tmm) REVERT: G 249 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7746 (m-10) outliers start: 46 outliers final: 36 residues processed: 287 average time/residue: 0.3045 time to fit residues: 141.6766 Evaluate side-chains 282 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 241 time to evaluate : 2.385 ------------------------------------------------------------------------------- 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 644 LEU 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 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 103 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 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 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 6 PHE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 139 LEU 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 36 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 148 optimal weight: 2.9990 chunk 238 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 165 optimal weight: 7.9990 chunk 250 optimal weight: 6.9990 chunk 230 optimal weight: 0.7980 chunk 199 optimal weight: 7.9990 chunk 20 optimal weight: 0.2980 chunk 153 optimal weight: 0.0270 chunk 122 optimal weight: 4.9990 overall best weight: 1.8242 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 20757 Z= 0.267 Angle : 0.660 13.502 28083 Z= 0.318 Chirality : 0.043 0.195 3296 Planarity : 0.004 0.060 3557 Dihedral : 6.605 100.387 2819 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.91 % Allowed : 17.95 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.88 (0.17), residues: 2532 helix: 1.58 (0.15), residues: 1171 sheet: 0.35 (0.25), residues: 482 loop : -0.57 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 780 HIS 0.005 0.001 HIS E 38 PHE 0.020 0.001 PHE H 248 TYR 0.022 0.002 TYR D 129 ARG 0.008 0.001 ARG H 228 ********************** 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 296 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 252 time to evaluate : 2.147 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 128 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7883 (ptm160) REVERT: B 297 MET cc_start: 0.8641 (ttt) cc_final: 0.8193 (ttt) REVERT: C 99 ASP cc_start: 0.8595 (m-30) cc_final: 0.7824 (t0) REVERT: D 61 MET cc_start: 0.6411 (tpp) cc_final: 0.5946 (tpp) REVERT: D 342 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8135 (mp-120) REVERT: E 135 TYR cc_start: 0.8393 (p90) cc_final: 0.8038 (p90) REVERT: E 174 MET cc_start: 0.8122 (ppp) cc_final: 0.7828 (ppp) REVERT: G 1 MET cc_start: 0.3642 (tmm) cc_final: 0.2378 (ptm) REVERT: G 6 PHE cc_start: 0.6699 (OUTLIER) cc_final: 0.6343 (t80) REVERT: G 11 LEU cc_start: 0.6922 (mt) cc_final: 0.6705 (mt) REVERT: G 181 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8375 (tp) REVERT: G 188 MET cc_start: 0.7286 (pmm) cc_final: 0.5741 (tmm) REVERT: G 199 MET cc_start: 0.6894 (tmm) cc_final: 0.6621 (tmm) REVERT: G 249 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7746 (m-10) REVERT: H 104 GLU cc_start: 0.6243 (mt-10) cc_final: 0.5989 (mt-10) REVERT: H 140 PRO cc_start: 0.7271 (Cg_endo) cc_final: 0.7011 (Cg_exo) outliers start: 44 outliers final: 38 residues processed: 284 average time/residue: 0.3023 time to fit residues: 137.4639 Evaluate side-chains 281 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 238 time to evaluate : 2.398 ------------------------------------------------------------------------------- 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 557 LEU Chi-restraints excluded: chain A residue 644 LEU 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 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 C residue 63 ILE Chi-restraints excluded: chain C residue 103 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 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 224 GLN 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 6 PHE Chi-restraints excluded: chain G residue 54 VAL 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 36 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 158 optimal weight: 0.9980 chunk 212 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 29 optimal weight: 0.4980 chunk 55 optimal weight: 0.9990 chunk 199 optimal weight: 8.9990 chunk 83 optimal weight: 0.9980 chunk 204 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 201 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.141704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.107484 restraints weight = 54330.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.108477 restraints weight = 32077.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.109688 restraints weight = 21989.632| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 20757 Z= 0.233 Angle : 0.642 18.101 28083 Z= 0.308 Chirality : 0.043 0.188 3296 Planarity : 0.004 0.060 3557 Dihedral : 6.598 99.642 2819 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.95 % Allowed : 18.55 % Favored : 79.50 % 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: 0.90 (0.17), residues: 2532 helix: 1.60 (0.16), residues: 1171 sheet: 0.31 (0.25), residues: 484 loop : -0.54 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 780 HIS 0.005 0.001 HIS E 38 PHE 0.020 0.001 PHE H 248 TYR 0.022 0.002 TYR B 306 ARG 0.008 0.001 ARG H 228 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3844.16 seconds wall clock time: 72 minutes 6.54 seconds (4326.54 seconds total)