Starting phenix.real_space_refine on Tue Nov 19 03:34:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf6_29979/11_2024/8gf6_29979.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf6_29979/11_2024/8gf6_29979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf6_29979/11_2024/8gf6_29979.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf6_29979/11_2024/8gf6_29979.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf6_29979/11_2024/8gf6_29979.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf6_29979/11_2024/8gf6_29979.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.085 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 11465 2.51 5 N 3189 2.21 5 O 3550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 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: 18315 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3519 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 18, 'TRANS': 442} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MHS:plan-2': 1, 'AGM:plan-2': 1, 'SMC:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3693 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 19, 'TRANS': 464} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MHS:plan-2': 1, 'AGM:plan-2': 1, 'SMC:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 3148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3148 Classifications: {'peptide': 432} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 420} Chain: "D" Number of atoms: 3143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3143 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 419} Chain: "E" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1926 Classifications: {'peptide': 247} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 232} Chain: "F" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1926 Classifications: {'peptide': 247} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 232} Chain: "X" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 9, 'TRANS': 110} Time building chain proxies: 10.20, per 1000 atoms: 0.56 Number of scatterers: 18315 At special positions: 0 Unit cell: (99.235, 102.58, 137.145, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 3550 8.00 N 3189 7.00 C 11465 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: 4.21 Conformation dependent library (CDL) restraints added in 2.3 seconds 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4364 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 15 sheets defined 54.5% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 97 through 104 removed outlier: 3.852A pdb=" N HIS A 101 " --> pdb=" O ASP A 98 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N TYR A 102 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N VAL A 103 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 117 removed outlier: 3.789A pdb=" N GLN A 109 " --> pdb=" O ASN A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 139 through 153 removed outlier: 3.630A pdb=" N HIS A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 188 removed outlier: 3.535A pdb=" N ALA A 187 " --> pdb=" O ASP A 183 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 183 through 188' Processing helix chain 'A' and resid 197 through 202 removed outlier: 3.533A pdb=" N PHE A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 215 Processing helix chain 'A' and resid 225 through 232 removed outlier: 3.550A pdb=" N SER A 229 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR A 232 " --> pdb=" O VAL A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 253 Processing helix chain 'A' and resid 259 through 271 removed outlier: 3.717A pdb=" N LYS A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MHS A 271 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 304 Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 312 through 333 Processing helix chain 'A' and resid 354 through 371 Processing helix chain 'A' and resid 386 through 408 Processing helix chain 'A' and resid 408 through 415 Processing helix chain 'A' and resid 417 through 438 removed outlier: 3.744A pdb=" N ARG A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 459 Processing helix chain 'A' and resid 467 through 472 removed outlier: 3.930A pdb=" N SMC A 472 " --> pdb=" O LEU A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 519 removed outlier: 3.550A pdb=" N TYR A 508 " --> pdb=" O HIS A 504 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 512 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG A 519 " --> pdb=" O ALA A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 533 Processing helix chain 'A' and resid 544 through 553 removed outlier: 3.571A pdb=" N GLU A 548 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY A 550 " --> pdb=" O ARG A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 567 removed outlier: 3.650A pdb=" N ILE A 567 " --> pdb=" O SER A 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 100 removed outlier: 3.631A pdb=" N LEU B 100 " --> pdb=" O PRO B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 117 removed outlier: 3.925A pdb=" N TRP B 112 " --> pdb=" O MET B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 135 removed outlier: 3.675A pdb=" N LEU B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 154 Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 183 through 190 removed outlier: 3.999A pdb=" N GLU B 189 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 195 Processing helix chain 'B' and resid 197 through 202 removed outlier: 3.541A pdb=" N MET B 201 " --> pdb=" O ASN B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 215 Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'B' and resid 236 through 254 removed outlier: 3.556A pdb=" N ALA B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET B 247 " --> pdb=" O MET B 243 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 248 " --> pdb=" O GLN B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 269 removed outlier: 3.811A pdb=" N ALA B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASP B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 304 Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.614A pdb=" N VAL B 309 " --> pdb=" O GLN B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 328 Processing helix chain 'B' and resid 345 through 352 removed outlier: 4.037A pdb=" N THR B 348 " --> pdb=" O GLN B 345 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 350 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 371 Processing helix chain 'B' and resid 386 through 408 Processing helix chain 'B' and resid 421 through 438 removed outlier: 3.943A pdb=" N LEU B 425 " --> pdb=" O ARG B 421 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 459 removed outlier: 3.554A pdb=" N GLY B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 473 Processing helix chain 'B' and resid 474 through 476 No H-bonds generated for 'chain 'B' and resid 474 through 476' Processing helix chain 'B' and resid 487 through 491 Processing helix chain 'B' and resid 504 through 518 removed outlier: 4.180A pdb=" N HIS B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 533 removed outlier: 3.785A pdb=" N LYS B 530 " --> pdb=" O ASN B 526 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 531 " --> pdb=" O PRO B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 554 removed outlier: 3.520A pdb=" N ILE B 554 " --> pdb=" O GLY B 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 41 Processing helix chain 'C' and resid 47 through 57 Processing helix chain 'C' and resid 78 through 91 Processing helix chain 'C' and resid 114 through 121 removed outlier: 3.674A pdb=" N ILE C 118 " --> pdb=" O PRO C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 142 removed outlier: 4.328A pdb=" N THR C 128 " --> pdb=" O TYR C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 148 No H-bonds generated for 'chain 'C' and resid 146 through 148' Processing helix chain 'C' and resid 149 through 156 Processing helix chain 'C' and resid 178 through 182 Processing helix chain 'C' and resid 186 through 191 removed outlier: 4.217A pdb=" N LEU C 189 " --> pdb=" O GLY C 186 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASN C 191 " --> pdb=" O SER C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 201 Processing helix chain 'C' and resid 204 through 223 removed outlier: 3.594A pdb=" N ALA C 209 " --> pdb=" O ALA C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 241 removed outlier: 3.846A pdb=" N GLY C 237 " --> pdb=" O HIS C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 247 through 256 Processing helix chain 'C' and resid 261 through 276 removed outlier: 3.503A pdb=" N VAL C 265 " --> pdb=" O THR C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 296 through 320 removed outlier: 4.078A pdb=" N GLY C 319 " --> pdb=" O ASN C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 323 No H-bonds generated for 'chain 'C' and resid 321 through 323' Processing helix chain 'C' and resid 324 through 341 removed outlier: 4.162A pdb=" N LEU C 329 " --> pdb=" O VAL C 325 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LEU C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 347 Processing helix chain 'C' and resid 348 through 361 Processing helix chain 'C' and resid 369 through 373 Processing helix chain 'C' and resid 387 through 397 Processing helix chain 'C' and resid 405 through 418 removed outlier: 3.649A pdb=" N THR C 409 " --> pdb=" O THR C 405 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU C 412 " --> pdb=" O SER C 408 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE C 413 " --> pdb=" O THR C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 425 Processing helix chain 'C' and resid 425 through 432 Processing helix chain 'D' and resid 22 through 25 Processing helix chain 'D' and resid 29 through 41 Processing helix chain 'D' and resid 47 through 57 Processing helix chain 'D' and resid 78 through 91 Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 115 through 120 Processing helix chain 'D' and resid 125 through 144 removed outlier: 3.793A pdb=" N THR D 129 " --> pdb=" O MET D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 148 No H-bonds generated for 'chain 'D' and resid 146 through 148' Processing helix chain 'D' and resid 149 through 159 removed outlier: 3.629A pdb=" N ALA D 153 " --> pdb=" O ASP D 149 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL D 157 " --> pdb=" O ALA D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 182 removed outlier: 3.614A pdb=" N ASN D 182 " --> pdb=" O PRO D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 191 removed outlier: 4.103A pdb=" N ASN D 191 " --> pdb=" O SER D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 201 removed outlier: 3.934A pdb=" N THR D 201 " --> pdb=" O ILE D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 223 Processing helix chain 'D' and resid 228 through 241 removed outlier: 4.017A pdb=" N ARG D 232 " --> pdb=" O GLY D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 246 No H-bonds generated for 'chain 'D' and resid 244 through 246' Processing helix chain 'D' and resid 247 through 256 removed outlier: 3.915A pdb=" N VAL D 253 " --> pdb=" O VAL D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 276 Processing helix chain 'D' and resid 296 through 320 Processing helix chain 'D' and resid 324 through 341 removed outlier: 4.687A pdb=" N LEU D 330 " --> pdb=" O SER D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 347 removed outlier: 3.577A pdb=" N TYR D 347 " --> pdb=" O GLY D 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 344 through 347' Processing helix chain 'D' and resid 348 through 361 Processing helix chain 'D' and resid 387 through 398 Processing helix chain 'D' and resid 409 through 414 Processing helix chain 'D' and resid 420 through 425 Processing helix chain 'E' and resid 12 through 24 Processing helix chain 'E' and resid 33 through 42 Processing helix chain 'E' and resid 56 through 61 Processing helix chain 'E' and resid 65 through 71 Processing helix chain 'E' and resid 74 through 79 removed outlier: 3.520A pdb=" N ALA E 79 " --> pdb=" O PRO E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 110 removed outlier: 3.672A pdb=" N SER E 103 " --> pdb=" O PRO E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 141 removed outlier: 3.754A pdb=" N GLN E 133 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR E 141 " --> pdb=" O VAL E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 213 Processing helix chain 'E' and resid 226 through 246 removed outlier: 3.574A pdb=" N ILE E 230 " --> pdb=" O ASP E 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 24 Processing helix chain 'F' and resid 33 through 42 removed outlier: 3.686A pdb=" N GLY F 42 " --> pdb=" O THR F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 61 removed outlier: 4.032A pdb=" N GLY F 61 " --> pdb=" O LEU F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 71 Processing helix chain 'F' and resid 73 through 80 removed outlier: 3.995A pdb=" N ALA F 77 " --> pdb=" O ALA F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 110 Processing helix chain 'F' and resid 128 through 141 removed outlier: 4.258A pdb=" N GLN F 133 " --> pdb=" O ARG F 129 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR F 141 " --> pdb=" O VAL F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 210 removed outlier: 3.613A pdb=" N ALA F 210 " --> pdb=" O SER F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 213 No H-bonds generated for 'chain 'F' and resid 211 through 213' Processing helix chain 'F' and resid 226 through 246 Processing helix chain 'X' and resid 23 through 34 removed outlier: 5.245A pdb=" N LYS X 29 " --> pdb=" O GLU X 25 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE X 31 " --> pdb=" O ALA X 27 " (cutoff:3.500A) Processing helix chain 'X' and resid 94 through 96 No H-bonds generated for 'chain 'X' and resid 94 through 96' Processing helix chain 'X' and resid 97 through 109 removed outlier: 3.740A pdb=" N ARG X 102 " --> pdb=" O LYS X 98 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP X 106 " --> pdb=" O ARG X 102 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS X 107 " --> pdb=" O SER X 103 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET X 108 " --> pdb=" O VAL X 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 181 removed outlier: 3.529A pdb=" N TYR A 176 " --> pdb=" O HIS A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 81 removed outlier: 3.533A pdb=" N ARG B 81 " --> pdb=" O VAL X 45 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG X 42 " --> pdb=" O GLU X 91 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE X 92 " --> pdb=" O ILE X 12 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU X 15 " --> pdb=" O ARG X 116 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ARG X 116 " --> pdb=" O GLU X 15 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AA4, first strand: chain 'B' and resid 176 through 181 removed outlier: 3.671A pdb=" N TYR B 176 " --> pdb=" O HIS B 223 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 8 removed outlier: 7.191A pdb=" N VAL C 5 " --> pdb=" O SER C 17 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N SER C 17 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE C 7 " --> pdb=" O LEU C 15 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 99 through 103 removed outlier: 3.618A pdb=" N SER C 99 " --> pdb=" O GLN C 112 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER C 108 " --> pdb=" O ILE C 103 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 279 through 284 removed outlier: 5.516A pdb=" N VAL C 281 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LYS C 293 " --> pdb=" O VAL C 281 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 4 through 8 removed outlier: 7.813A pdb=" N VAL D 5 " --> pdb=" O SER D 17 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N SER D 17 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ILE D 7 " --> pdb=" O LEU D 15 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 101 through 102 removed outlier: 3.631A pdb=" N LYS D 101 " --> pdb=" O LEU D 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 279 through 284 removed outlier: 7.167A pdb=" N PHE D 291 " --> pdb=" O ASP D 282 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 83 through 88 Processing sheet with id=AB3, first strand: chain 'E' and resid 176 through 177 Processing sheet with id=AB4, first strand: chain 'F' and resid 83 through 86 Processing sheet with id=AB5, first strand: chain 'F' and resid 89 through 90 Processing sheet with id=AB6, first strand: chain 'F' and resid 177 through 179 removed outlier: 5.936A pdb=" N ILE F 183 " --> pdb=" O LEU F 200 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LYS F 187 " --> pdb=" O ARG F 196 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N ARG F 196 " --> pdb=" O LYS F 187 " (cutoff:3.500A) 867 hydrogen bonds defined for protein. 2499 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: 5.41 Time building geometry restraints manager: 4.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5378 1.33 - 1.45: 3635 1.45 - 1.58: 9449 1.58 - 1.70: 0 1.70 - 1.82: 195 Bond restraints: 18657 Sorted by residual: bond pdb=" CA LEU A 171 " pdb=" C LEU A 171 " ideal model delta sigma weight residual 1.524 1.480 0.044 1.29e-02 6.01e+03 1.14e+01 bond pdb=" CG1 ILE C 266 " pdb=" CD1 ILE C 266 " ideal model delta sigma weight residual 1.513 1.383 0.130 3.90e-02 6.57e+02 1.11e+01 bond pdb=" CA ILE B 355 " pdb=" C ILE B 355 " ideal model delta sigma weight residual 1.524 1.481 0.042 1.30e-02 5.92e+03 1.06e+01 bond pdb=" CA ASP A 173 " pdb=" C ASP A 173 " ideal model delta sigma weight residual 1.523 1.480 0.043 1.34e-02 5.57e+03 1.03e+01 bond pdb=" CA PRO B 409 " pdb=" C PRO B 409 " ideal model delta sigma weight residual 1.528 1.500 0.029 9.10e-03 1.21e+04 9.99e+00 ... (remaining 18652 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 24321 2.53 - 5.05: 796 5.05 - 7.58: 123 7.58 - 10.10: 23 10.10 - 12.63: 8 Bond angle restraints: 25271 Sorted by residual: angle pdb=" N GLN B 161 " pdb=" CA GLN B 161 " pdb=" C GLN B 161 " ideal model delta sigma weight residual 109.39 122.02 -12.63 1.59e+00 3.96e-01 6.30e+01 angle pdb=" N SER B 419 " pdb=" CA SER B 419 " pdb=" C SER B 419 " ideal model delta sigma weight residual 109.52 97.25 12.27 1.55e+00 4.16e-01 6.27e+01 angle pdb=" N GLU B 162 " pdb=" CA GLU B 162 " pdb=" C GLU B 162 " ideal model delta sigma weight residual 109.72 97.12 12.60 1.60e+00 3.91e-01 6.20e+01 angle pdb=" N LEU B 100 " pdb=" CA LEU B 100 " pdb=" C LEU B 100 " ideal model delta sigma weight residual 112.59 103.05 9.54 1.22e+00 6.72e-01 6.11e+01 angle pdb=" N GLN B 420 " pdb=" CA GLN B 420 " pdb=" C GLN B 420 " ideal model delta sigma weight residual 112.24 104.09 8.15 1.28e+00 6.10e-01 4.05e+01 ... (remaining 25266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 10045 17.97 - 35.94: 928 35.94 - 53.91: 120 53.91 - 71.89: 25 71.89 - 89.86: 13 Dihedral angle restraints: 11131 sinusoidal: 4267 harmonic: 6864 Sorted by residual: dihedral pdb=" C ASP B 353 " pdb=" N ASP B 353 " pdb=" CA ASP B 353 " pdb=" CB ASP B 353 " ideal model delta harmonic sigma weight residual -122.60 -137.73 15.13 0 2.50e+00 1.60e-01 3.66e+01 dihedral pdb=" N ASP B 353 " pdb=" C ASP B 353 " pdb=" CA ASP B 353 " pdb=" CB ASP B 353 " ideal model delta harmonic sigma weight residual 122.80 137.61 -14.81 0 2.50e+00 1.60e-01 3.51e+01 dihedral pdb=" CA PHE D 143 " pdb=" C PHE D 143 " pdb=" N GLY D 144 " pdb=" CA GLY D 144 " ideal model delta harmonic sigma weight residual -180.00 -150.69 -29.31 0 5.00e+00 4.00e-02 3.44e+01 ... (remaining 11128 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 2649 0.132 - 0.263: 130 0.263 - 0.395: 11 0.395 - 0.526: 5 0.526 - 0.658: 3 Chirality restraints: 2798 Sorted by residual: chirality pdb=" CA ASP B 353 " pdb=" N ASP B 353 " pdb=" C ASP B 353 " pdb=" CB ASP B 353 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA ASP B 354 " pdb=" N ASP B 354 " pdb=" C ASP B 354 " pdb=" CB ASP B 354 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.00e+00 chirality pdb=" CA GLN B 161 " pdb=" N GLN B 161 " pdb=" C GLN B 161 " pdb=" CB GLN B 161 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.55 2.00e-01 2.50e+01 7.43e+00 ... (remaining 2795 not shown) Planarity restraints: 3348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 498 " 0.022 2.00e-02 2.50e+03 3.22e-02 2.07e+01 pdb=" CG TYR A 498 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TYR A 498 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR A 498 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 498 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR A 498 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR A 498 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 498 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 408 " -0.056 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO B 409 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO B 409 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 409 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 104 " -0.012 2.00e-02 2.50e+03 2.29e-02 1.05e+01 pdb=" CG TYR E 104 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR E 104 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR E 104 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR E 104 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR E 104 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR E 104 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 104 " 0.001 2.00e-02 2.50e+03 ... (remaining 3345 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 274 2.59 - 3.17: 15640 3.17 - 3.75: 31165 3.75 - 4.32: 43622 4.32 - 4.90: 71599 Nonbonded interactions: 162300 Sorted by model distance: nonbonded pdb=" O SER B 419 " pdb=" CD GLN B 420 " model vdw 2.014 3.270 nonbonded pdb=" O SER B 419 " pdb=" OE1 GLN B 420 " model vdw 2.068 3.040 nonbonded pdb=" C SER B 419 " pdb=" OE1 GLN B 420 " model vdw 2.172 3.270 nonbonded pdb=" OG SER E 103 " pdb=" NE2 GLN E 122 " model vdw 2.193 3.120 nonbonded pdb=" O SER C 326 " pdb=" OG SER C 358 " model vdw 2.212 3.040 ... (remaining 162295 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 'A' selection = (chain 'B' and (resid 92 through 158 or resid 167 through 569)) } ncs_group { reference = (chain 'C' and resid 2 through 432) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 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: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 38.520 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 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 : 0.010 0.130 18657 Z= 0.618 Angle : 1.103 12.625 25271 Z= 0.621 Chirality : 0.071 0.658 2798 Planarity : 0.007 0.086 3348 Dihedral : 13.995 89.856 6767 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.32 % Allowed : 1.06 % Favored : 98.62 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.08 % 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: -2.33 (0.15), residues: 2384 helix: -1.43 (0.13), residues: 1153 sheet: -1.50 (0.42), residues: 138 loop : -1.55 (0.17), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 447 HIS 0.016 0.002 HIS B 127 PHE 0.051 0.004 PHE C 360 TYR 0.073 0.004 TYR A 498 ARG 0.012 0.001 ARG E 196 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 210 time to evaluate : 2.037 Fit side-chains revert: symmetry clash REVERT: A 500 MET cc_start: 0.8557 (pmm) cc_final: 0.8236 (pmm) REVERT: F 168 VAL cc_start: 0.8862 (t) cc_final: 0.8497 (m) outliers start: 6 outliers final: 1 residues processed: 216 average time/residue: 0.3450 time to fit residues: 110.6430 Evaluate side-chains 137 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 chunk 100 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 188 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 chunk 217 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN A 526 ASN ** B 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 ASN C 324 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 HIS ** F 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 ASN ** X 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18657 Z= 0.210 Angle : 0.630 7.583 25271 Z= 0.336 Chirality : 0.043 0.166 2798 Planarity : 0.005 0.064 3348 Dihedral : 5.691 54.538 2628 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.01 % Allowed : 7.99 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -1.10 (0.16), residues: 2384 helix: -0.06 (0.15), residues: 1158 sheet: -1.43 (0.41), residues: 134 loop : -1.30 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 447 HIS 0.008 0.001 HIS E 159 PHE 0.018 0.002 PHE C 360 TYR 0.024 0.002 TYR D 365 ARG 0.008 0.001 ARG F 111 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 2.238 Fit side-chains REVERT: A 111 MET cc_start: 0.8212 (ttp) cc_final: 0.7863 (ttp) REVERT: A 128 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7435 (tm-30) REVERT: A 284 ARG cc_start: 0.8576 (mmm160) cc_final: 0.8237 (ttt180) REVERT: A 500 MET cc_start: 0.8383 (pmm) cc_final: 0.7761 (pmm) REVERT: A 558 MET cc_start: 0.7428 (tpp) cc_final: 0.7214 (tpp) REVERT: C 59 MET cc_start: 0.7991 (ptp) cc_final: 0.7751 (ptm) REVERT: C 125 MET cc_start: 0.7525 (mmm) cc_final: 0.7173 (mmm) REVERT: D 125 MET cc_start: 0.8073 (ppp) cc_final: 0.7859 (ptm) REVERT: F 60 MET cc_start: 0.7250 (ptp) cc_final: 0.6170 (mpp) REVERT: F 220 ASN cc_start: 0.8394 (OUTLIER) cc_final: 0.8154 (t0) REVERT: X 63 LYS cc_start: 0.7908 (tppt) cc_final: 0.7400 (tppt) outliers start: 19 outliers final: 9 residues processed: 167 average time/residue: 0.3016 time to fit residues: 81.2336 Evaluate side-chains 137 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain E residue 159 HIS Chi-restraints excluded: chain F residue 220 ASN Chi-restraints excluded: chain X residue 85 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 181 optimal weight: 8.9990 chunk 148 optimal weight: 0.6980 chunk 60 optimal weight: 7.9990 chunk 218 optimal weight: 4.9990 chunk 235 optimal weight: 20.0000 chunk 194 optimal weight: 4.9990 chunk 216 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 175 optimal weight: 6.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 HIS B 220 GLN C 29 ASN ** D 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 ASN D 362 HIS ** F 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 ASN ** X 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 18657 Z= 0.325 Angle : 0.635 7.380 25271 Z= 0.338 Chirality : 0.045 0.204 2798 Planarity : 0.005 0.058 3348 Dihedral : 5.363 52.004 2628 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.43 % Allowed : 10.91 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -0.69 (0.17), residues: 2384 helix: 0.32 (0.15), residues: 1200 sheet: -1.30 (0.43), residues: 134 loop : -1.20 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 447 HIS 0.008 0.001 HIS E 159 PHE 0.021 0.002 PHE E 101 TYR 0.023 0.002 TYR C 331 ARG 0.006 0.000 ARG F 111 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 2.240 Fit side-chains REVERT: A 111 MET cc_start: 0.8253 (ttp) cc_final: 0.7908 (ttt) REVERT: A 128 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7732 (tm-30) REVERT: C 125 MET cc_start: 0.7681 (mmm) cc_final: 0.7409 (mmm) REVERT: E 92 MET cc_start: 0.7784 (mtm) cc_final: 0.7503 (mtm) REVERT: X 63 LYS cc_start: 0.7949 (tppt) cc_final: 0.7441 (tppt) outliers start: 27 outliers final: 12 residues processed: 154 average time/residue: 0.2995 time to fit residues: 73.3651 Evaluate side-chains 135 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 2.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain D residue 143 PHE Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain X residue 85 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 5.9990 chunk 164 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 219 optimal weight: 6.9990 chunk 231 optimal weight: 20.0000 chunk 114 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN C 182 ASN D 29 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 GLN ** X 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18657 Z= 0.258 Angle : 0.592 8.252 25271 Z= 0.311 Chirality : 0.043 0.166 2798 Planarity : 0.004 0.060 3348 Dihedral : 5.139 49.923 2628 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.17 % Allowed : 12.18 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -0.38 (0.17), residues: 2384 helix: 0.59 (0.15), residues: 1202 sheet: -1.21 (0.43), residues: 134 loop : -1.06 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 447 HIS 0.007 0.001 HIS E 159 PHE 0.021 0.002 PHE E 105 TYR 0.021 0.002 TYR D 365 ARG 0.007 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 2.233 Fit side-chains revert: symmetry clash REVERT: A 111 MET cc_start: 0.8226 (ttp) cc_final: 0.7971 (ttt) REVERT: A 128 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7909 (tm-30) REVERT: B 494 ASN cc_start: 0.8961 (t0) cc_final: 0.8589 (t0) REVERT: C 125 MET cc_start: 0.7691 (mmm) cc_final: 0.7474 (mmm) REVERT: D 22 MET cc_start: 0.8599 (mmp) cc_final: 0.8354 (mmm) REVERT: F 60 MET cc_start: 0.7664 (ptp) cc_final: 0.6953 (mpp) REVERT: X 28 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7780 (pm20) REVERT: X 63 LYS cc_start: 0.7952 (tppt) cc_final: 0.7316 (tppt) outliers start: 41 outliers final: 20 residues processed: 167 average time/residue: 0.2920 time to fit residues: 77.4645 Evaluate side-chains 145 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain D residue 143 PHE Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain F residue 143 MET Chi-restraints excluded: chain X residue 28 GLN Chi-restraints excluded: chain X residue 81 LEU Chi-restraints excluded: chain X residue 85 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 7.9990 chunk 131 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 160 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 118 optimal weight: 8.9990 chunk 208 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN C 315 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 73 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18657 Z= 0.260 Angle : 0.584 8.771 25271 Z= 0.307 Chirality : 0.043 0.237 2798 Planarity : 0.004 0.061 3348 Dihedral : 5.020 47.500 2628 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.69 % Allowed : 13.55 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -0.25 (0.17), residues: 2384 helix: 0.69 (0.16), residues: 1209 sheet: -1.26 (0.42), residues: 137 loop : -0.98 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 447 HIS 0.005 0.001 HIS B 223 PHE 0.018 0.002 PHE E 101 TYR 0.018 0.001 TYR D 365 ARG 0.004 0.000 ARG F 111 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 2.401 Fit side-chains revert: symmetry clash REVERT: A 111 MET cc_start: 0.8284 (ttp) cc_final: 0.8048 (ttt) REVERT: A 558 MET cc_start: 0.7481 (tpp) cc_final: 0.7253 (tpp) REVERT: B 108 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.7544 (mmm) REVERT: B 494 ASN cc_start: 0.8952 (t0) cc_final: 0.8606 (t0) REVERT: C 125 MET cc_start: 0.7787 (mmm) cc_final: 0.7562 (mmm) REVERT: X 63 LYS cc_start: 0.7905 (tppt) cc_final: 0.7439 (tppt) outliers start: 32 outliers final: 24 residues processed: 155 average time/residue: 0.3022 time to fit residues: 77.1841 Evaluate side-chains 149 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 2.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 143 PHE Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 134 CYS Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain F residue 143 MET Chi-restraints excluded: chain X residue 81 LEU Chi-restraints excluded: chain X residue 85 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 9.9990 chunk 208 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 232 optimal weight: 4.9990 chunk 192 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 121 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN A 513 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 ASN ** X 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18657 Z= 0.234 Angle : 0.569 9.133 25271 Z= 0.297 Chirality : 0.043 0.172 2798 Planarity : 0.004 0.060 3348 Dihedral : 4.916 46.139 2628 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.15 % Favored : 95.81 % Rotamer: Outliers : 1.96 % Allowed : 14.82 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -0.10 (0.18), residues: 2384 helix: 0.82 (0.16), residues: 1207 sheet: -1.09 (0.43), residues: 135 loop : -0.92 (0.19), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 447 HIS 0.004 0.001 HIS B 223 PHE 0.018 0.002 PHE E 105 TYR 0.016 0.001 TYR D 365 ARG 0.010 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 2.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 558 MET cc_start: 0.7567 (tpp) cc_final: 0.7237 (tpp) REVERT: B 108 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.7565 (mmm) REVERT: B 255 MET cc_start: 0.7991 (mpp) cc_final: 0.7384 (mtm) REVERT: B 494 ASN cc_start: 0.8926 (t0) cc_final: 0.8559 (t0) REVERT: C 168 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8265 (ptp) REVERT: X 44 MET cc_start: 0.7306 (tpt) cc_final: 0.7083 (tpt) REVERT: X 63 LYS cc_start: 0.7973 (tppt) cc_final: 0.7499 (tppt) outliers start: 37 outliers final: 23 residues processed: 157 average time/residue: 0.2840 time to fit residues: 73.3549 Evaluate side-chains 150 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain D residue 143 PHE Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 134 CYS Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain F residue 143 MET Chi-restraints excluded: chain X residue 81 LEU Chi-restraints excluded: chain X residue 85 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 169 optimal weight: 6.9990 chunk 131 optimal weight: 0.6980 chunk 195 optimal weight: 8.9990 chunk 129 optimal weight: 0.9980 chunk 231 optimal weight: 20.0000 chunk 144 optimal weight: 8.9990 chunk 141 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 ASN ** X 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18657 Z= 0.181 Angle : 0.556 11.097 25271 Z= 0.288 Chirality : 0.042 0.164 2798 Planarity : 0.004 0.061 3348 Dihedral : 4.753 45.196 2628 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.19 % Favored : 95.76 % Rotamer: Outliers : 1.96 % Allowed : 15.51 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.07 (0.18), residues: 2384 helix: 0.97 (0.16), residues: 1195 sheet: -1.01 (0.45), residues: 135 loop : -0.84 (0.19), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 447 HIS 0.005 0.001 HIS B 223 PHE 0.013 0.001 PHE E 101 TYR 0.013 0.001 TYR B 362 ARG 0.003 0.000 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 2.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 558 MET cc_start: 0.7634 (tpp) cc_final: 0.7307 (tpp) REVERT: B 108 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.7556 (mmm) REVERT: B 494 ASN cc_start: 0.8934 (t0) cc_final: 0.8590 (t0) REVERT: C 168 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8331 (ptp) REVERT: X 44 MET cc_start: 0.7179 (tpt) cc_final: 0.6960 (tpt) REVERT: X 63 LYS cc_start: 0.8002 (tppt) cc_final: 0.7600 (tppt) outliers start: 37 outliers final: 27 residues processed: 167 average time/residue: 0.2803 time to fit residues: 76.2080 Evaluate side-chains 161 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 2.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 143 PHE Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 134 CYS Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain F residue 143 MET Chi-restraints excluded: chain X residue 81 LEU Chi-restraints excluded: chain X residue 85 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 181 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18657 Z= 0.185 Angle : 0.555 9.374 25271 Z= 0.287 Chirality : 0.042 0.159 2798 Planarity : 0.004 0.060 3348 Dihedral : 4.683 46.099 2628 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.11 % Favored : 95.85 % Rotamer: Outliers : 1.91 % Allowed : 15.78 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.16 (0.18), residues: 2384 helix: 1.08 (0.16), residues: 1186 sheet: -0.95 (0.46), residues: 132 loop : -0.83 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 447 HIS 0.003 0.001 HIS B 223 PHE 0.014 0.001 PHE A 549 TYR 0.013 0.001 TYR B 362 ARG 0.012 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 2.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 558 MET cc_start: 0.7635 (tpp) cc_final: 0.7333 (tpp) REVERT: B 108 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.7631 (mmm) REVERT: B 255 MET cc_start: 0.7915 (mpp) cc_final: 0.7379 (mtm) REVERT: B 494 ASN cc_start: 0.8966 (t0) cc_final: 0.8639 (t0) REVERT: E 139 MET cc_start: 0.7742 (mmt) cc_final: 0.7501 (mmt) REVERT: X 63 LYS cc_start: 0.8018 (tppt) cc_final: 0.7606 (tppt) outliers start: 36 outliers final: 25 residues processed: 164 average time/residue: 0.3176 time to fit residues: 84.3321 Evaluate side-chains 157 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 134 CYS Chi-restraints excluded: chain F residue 143 MET Chi-restraints excluded: chain X residue 81 LEU Chi-restraints excluded: chain X residue 85 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.8980 chunk 221 optimal weight: 5.9990 chunk 202 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 169 optimal weight: 3.9990 chunk 66 optimal weight: 0.3980 chunk 194 optimal weight: 0.7980 chunk 203 optimal weight: 0.7980 chunk 214 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: