Starting phenix.real_space_refine on Thu Jun 12 21:40:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ep1_19871/06_2025/9ep1_19871.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ep1_19871/06_2025/9ep1_19871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ep1_19871/06_2025/9ep1_19871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ep1_19871/06_2025/9ep1_19871.map" model { file = "/net/cci-nas-00/data/ceres_data/9ep1_19871/06_2025/9ep1_19871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ep1_19871/06_2025/9ep1_19871.cif" } resolution = 4.0 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= 0.016 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 91 5.16 5 C 9140 2.51 5 N 2444 2.21 5 O 2658 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14333 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3778 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 26, 'TRANS': 490} Chain breaks: 5 Unresolved non-hydrogen bonds: 354 Unresolved non-hydrogen angles: 440 Unresolved non-hydrogen dihedrals: 290 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 11, 'TYR:plan': 4, 'ASN:plan1': 5, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 10, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 202 Chain: "B" Number of atoms: 3601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3601 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 451} Chain breaks: 2 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 8, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 134 Chain: "C" Number of atoms: 2733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2733 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 18, 'TRANS': 341} Chain breaks: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 65 Chain: "D" Number of atoms: 4221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 4221 Classifications: {'peptide': 561} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 543} Chain breaks: 9 Unresolved non-hydrogen bonds: 415 Unresolved non-hydrogen angles: 524 Unresolved non-hydrogen dihedrals: 350 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 6, 'GLU:plan': 8, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 255 Time building chain proxies: 12.78, per 1000 atoms: 0.89 Number of scatterers: 14333 At special positions: 0 Unit cell: (174.66, 124.64, 218.94, 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 91 16.00 O 2658 8.00 N 2444 7.00 C 9140 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: 3.43 Conformation dependent library (CDL) restraints added in 2.1 seconds 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3700 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 9 sheets defined 61.3% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 17 through 22 removed outlier: 4.400A pdb=" N GLU A 22 " --> pdb=" O TYR A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 70 Processing helix chain 'A' and resid 92 through 96 Processing helix chain 'A' and resid 97 through 109 Processing helix chain 'A' and resid 116 through 120 removed outlier: 4.384A pdb=" N CYS A 120 " --> pdb=" O PRO A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 134 Processing helix chain 'A' and resid 137 through 147 Processing helix chain 'A' and resid 168 through 193 removed outlier: 3.771A pdb=" N ASN A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 255 removed outlier: 3.797A pdb=" N PHE A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 291 Processing helix chain 'A' and resid 344 through 356 Processing helix chain 'A' and resid 414 through 424 Processing helix chain 'A' and resid 443 through 456 Processing helix chain 'A' and resid 462 through 466 Processing helix chain 'A' and resid 471 through 473 No H-bonds generated for 'chain 'A' and resid 471 through 473' Processing helix chain 'A' and resid 474 through 482 removed outlier: 4.472A pdb=" N VAL A 482 " --> pdb=" O ALA A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 508 Processing helix chain 'A' and resid 524 through 543 removed outlier: 3.510A pdb=" N HIS A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 546 No H-bonds generated for 'chain 'A' and resid 544 through 546' Processing helix chain 'A' and resid 547 through 561 Processing helix chain 'B' and resid 10 through 14 Processing helix chain 'B' and resid 27 through 45 Processing helix chain 'B' and resid 69 through 77 removed outlier: 3.666A pdb=" N LEU B 73 " --> pdb=" O ASP B 69 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU B 75 " --> pdb=" O ASN B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 103 removed outlier: 3.949A pdb=" N ALA B 91 " --> pdb=" O CYS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 137 removed outlier: 3.846A pdb=" N ASN B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLN B 135 " --> pdb=" O ALA B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 166 removed outlier: 3.808A pdb=" N GLN B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 178 Processing helix chain 'B' and resid 193 through 209 Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 298 through 302 Processing helix chain 'B' and resid 309 through 321 Processing helix chain 'B' and resid 360 through 364 removed outlier: 3.727A pdb=" N GLY B 364 " --> pdb=" O PRO B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 367 No H-bonds generated for 'chain 'B' and resid 365 through 367' Processing helix chain 'B' and resid 373 through 375 No H-bonds generated for 'chain 'B' and resid 373 through 375' Processing helix chain 'B' and resid 408 through 425 removed outlier: 3.922A pdb=" N LEU B 412 " --> pdb=" O LYS B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 448 Processing helix chain 'B' and resid 449 through 466 Processing helix chain 'B' and resid 472 through 490 Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 12 through 35 Processing helix chain 'C' and resid 41 through 52 removed outlier: 3.969A pdb=" N VAL C 45 " --> pdb=" O ASP C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 85 Processing helix chain 'C' and resid 87 through 100 Processing helix chain 'C' and resid 106 through 125 Processing helix chain 'C' and resid 126 through 139 removed outlier: 3.609A pdb=" N GLN C 138 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG C 139 " --> pdb=" O SER C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 158 removed outlier: 3.787A pdb=" N CYS C 145 " --> pdb=" O PRO C 141 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG C 147 " --> pdb=" O VAL C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 169 removed outlier: 3.838A pdb=" N LEU C 167 " --> pdb=" O SER C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 174 Processing helix chain 'C' and resid 174 through 189 Processing helix chain 'C' and resid 193 through 197 Processing helix chain 'C' and resid 199 through 213 Processing helix chain 'C' and resid 214 through 217 removed outlier: 3.792A pdb=" N ILE C 217 " --> pdb=" O PRO C 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 214 through 217' Processing helix chain 'C' and resid 218 through 224 removed outlier: 4.131A pdb=" N THR C 224 " --> pdb=" O THR C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 258 Proline residue: C 251 - end of helix Processing helix chain 'C' and resid 277 through 308 removed outlier: 3.627A pdb=" N LEU C 303 " --> pdb=" O MET C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 320 No H-bonds generated for 'chain 'C' and resid 318 through 320' Processing helix chain 'C' and resid 321 through 336 removed outlier: 4.253A pdb=" N LEU C 325 " --> pdb=" O HIS C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 362 Processing helix chain 'C' and resid 368 through 376 Processing helix chain 'C' and resid 382 through 391 Processing helix chain 'D' and resid 2 through 18 removed outlier: 3.856A pdb=" N ASP D 6 " --> pdb=" O SER D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 36 Processing helix chain 'D' and resid 39 through 54 removed outlier: 3.686A pdb=" N GLN D 43 " --> pdb=" O ASP D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 70 removed outlier: 3.589A pdb=" N TYR D 64 " --> pdb=" O GLY D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 88 removed outlier: 3.523A pdb=" N TRP D 77 " --> pdb=" O GLN D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 106 removed outlier: 3.548A pdb=" N THR D 105 " --> pdb=" O SER D 101 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU D 106 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 122 Processing helix chain 'D' and resid 124 through 139 removed outlier: 3.599A pdb=" N LEU D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU D 135 " --> pdb=" O MET D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 162 removed outlier: 5.261A pdb=" N VAL D 148 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLY D 149 " --> pdb=" O GLN D 145 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 177 Processing helix chain 'D' and resid 177 through 185 removed outlier: 3.674A pdb=" N LEU D 181 " --> pdb=" O ASP D 177 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE D 182 " --> pdb=" O VAL D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 212 Processing helix chain 'D' and resid 254 through 271 Processing helix chain 'D' and resid 282 through 296 Processing helix chain 'D' and resid 303 through 329 removed outlier: 4.043A pdb=" N THR D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 426 removed outlier: 3.908A pdb=" N LEU D 426 " --> pdb=" O LEU D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 440 Processing helix chain 'D' and resid 446 through 460 Processing helix chain 'D' and resid 461 through 476 Processing helix chain 'D' and resid 493 through 506 removed outlier: 4.064A pdb=" N ILE D 497 " --> pdb=" O GLN D 493 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 506 " --> pdb=" O CYS D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 521 Processing helix chain 'D' and resid 556 through 577 Proline residue: D 562 - end of helix Processing helix chain 'D' and resid 583 through 592 Processing helix chain 'D' and resid 600 through 615 Processing helix chain 'D' and resid 621 through 625 Processing helix chain 'D' and resid 628 through 638 Processing helix chain 'D' and resid 673 through 683 removed outlier: 3.967A pdb=" N MET D 679 " --> pdb=" O PHE D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 686 No H-bonds generated for 'chain 'D' and resid 684 through 686' Processing helix chain 'D' and resid 689 through 701 Processing helix chain 'D' and resid 703 through 708 Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 87 removed outlier: 3.589A pdb=" N HIS A 86 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N THR A 10 " --> pdb=" O ASN A 77 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE A 79 " --> pdb=" O THR A 10 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE A 12 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N SER A 81 " --> pdb=" O PHE A 12 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL A 14 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LYS A 9 " --> pdb=" O ARG A 159 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE A 161 " --> pdb=" O LYS A 9 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N VAL A 11 " --> pdb=" O ILE A 161 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ILE A 163 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL A 13 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A 203 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR A 231 " --> pdb=" O CYS A 202 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 257 through 260 removed outlier: 4.394A pdb=" N HIS A 286 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ARG A 336 " --> pdb=" O HIS A 286 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL A 388 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ALA A 334 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LEU A 386 " --> pdb=" O ALA A 334 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ARG A 336 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ILE A 384 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LEU A 389 " --> pdb=" O SER A 374 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N SER A 374 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE A 373 " --> pdb=" O GLN A 364 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N GLN A 364 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N HIS A 375 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 427 through 429 Processing sheet with id=AA4, first strand: chain 'B' and resid 7 through 8 removed outlier: 3.722A pdb=" N PHE B 56 " --> pdb=" O MET B 7 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N THR B 51 " --> pdb=" O PRO B 65 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU B 53 " --> pdb=" O MET B 63 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N MET B 63 " --> pdb=" O LEU B 53 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 7 through 8 removed outlier: 3.722A pdb=" N PHE B 56 " --> pdb=" O MET B 7 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N THR B 3 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N VAL B 54 " --> pdb=" O THR B 3 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS B 151 " --> pdb=" O CYS B 109 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N GLN B 184 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU B 152 " --> pdb=" O GLN B 184 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N PHE B 186 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE B 154 " --> pdb=" O PHE B 186 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 16 through 17 removed outlier: 4.272A pdb=" N TYR B 25 " --> pdb=" O VAL B 17 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 326 through 327 removed outlier: 3.784A pdb=" N GLU B 252 " --> pdb=" O GLN B 327 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N LEU B 251 " --> pdb=" O HIS B 213 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B 215 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ILE B 253 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N LYS B 217 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 221 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B 274 " --> pdb=" O GLN B 226 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU B 348 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET B 335 " --> pdb=" O SER B 351 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 257 through 258 Processing sheet with id=AA9, first strand: chain 'D' and resid 345 through 347 removed outlier: 3.713A pdb=" N LEU D 553 " --> pdb=" O VAL D 346 " (cutoff:3.500A) 839 hydrogen bonds defined for protein. 2448 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: 5.21 Time building geometry restraints manager: 4.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4748 1.34 - 1.46: 3117 1.46 - 1.58: 6605 1.58 - 1.70: 0 1.70 - 1.82: 136 Bond restraints: 14606 Sorted by residual: bond pdb=" CG GLU D 418 " pdb=" CD GLU D 418 " ideal model delta sigma weight residual 1.516 1.467 0.049 2.50e-02 1.60e+03 3.87e+00 bond pdb=" CB ARG A 530 " pdb=" CG ARG A 530 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.69e+00 bond pdb=" CB LYS D 431 " pdb=" CG LYS D 431 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.11e+00 bond pdb=" CB MET B 350 " pdb=" CG MET B 350 " ideal model delta sigma weight residual 1.520 1.489 0.031 3.00e-02 1.11e+03 1.09e+00 bond pdb=" CA GLU D 418 " pdb=" CB GLU D 418 " ideal model delta sigma weight residual 1.528 1.545 -0.017 1.66e-02 3.63e+03 1.06e+00 ... (remaining 14601 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 19592 2.03 - 4.05: 234 4.05 - 6.08: 50 6.08 - 8.10: 13 8.10 - 10.13: 4 Bond angle restraints: 19893 Sorted by residual: angle pdb=" CA GLU D 418 " pdb=" CB GLU D 418 " pdb=" CG GLU D 418 " ideal model delta sigma weight residual 114.10 122.82 -8.72 2.00e+00 2.50e-01 1.90e+01 angle pdb=" N GLU D 418 " pdb=" CA GLU D 418 " pdb=" CB GLU D 418 " ideal model delta sigma weight residual 110.28 116.86 -6.58 1.55e+00 4.16e-01 1.80e+01 angle pdb=" C TRP D 445 " pdb=" CA TRP D 445 " pdb=" CB TRP D 445 " ideal model delta sigma weight residual 116.34 110.72 5.62 1.40e+00 5.10e-01 1.61e+01 angle pdb=" C MET B 63 " pdb=" N VAL B 64 " pdb=" CA VAL B 64 " ideal model delta sigma weight residual 122.85 119.66 3.19 8.70e-01 1.32e+00 1.34e+01 angle pdb=" CA ARG A 530 " pdb=" CB ARG A 530 " pdb=" CG ARG A 530 " ideal model delta sigma weight residual 114.10 121.41 -7.31 2.00e+00 2.50e-01 1.33e+01 ... (remaining 19888 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 7639 17.19 - 34.38: 932 34.38 - 51.57: 213 51.57 - 68.76: 51 68.76 - 85.95: 16 Dihedral angle restraints: 8851 sinusoidal: 3205 harmonic: 5646 Sorted by residual: dihedral pdb=" CA PRO A 460 " pdb=" C PRO A 460 " pdb=" N MET A 461 " pdb=" CA MET A 461 " ideal model delta harmonic sigma weight residual 180.00 -158.28 -21.72 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA SER B 168 " pdb=" C SER B 168 " pdb=" N LEU B 169 " pdb=" CA LEU B 169 " ideal model delta harmonic sigma weight residual 180.00 160.41 19.59 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ASP A 341 " pdb=" C ASP A 341 " pdb=" N VAL A 342 " pdb=" CA VAL A 342 " ideal model delta harmonic sigma weight residual -180.00 -162.38 -17.62 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 8848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1885 0.046 - 0.091: 399 0.091 - 0.136: 87 0.136 - 0.182: 4 0.182 - 0.227: 2 Chirality restraints: 2377 Sorted by residual: chirality pdb=" CG LEU B 445 " pdb=" CB LEU B 445 " pdb=" CD1 LEU B 445 " pdb=" CD2 LEU B 445 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA GLU D 418 " pdb=" N GLU D 418 " pdb=" C GLU D 418 " pdb=" CB GLU D 418 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.31e-01 chirality pdb=" CG LEU B 178 " pdb=" CB LEU B 178 " pdb=" CD1 LEU B 178 " pdb=" CD2 LEU B 178 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.90e-01 ... (remaining 2374 not shown) Planarity restraints: 2554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 232 " -0.033 5.00e-02 4.00e+02 5.06e-02 4.09e+00 pdb=" N PRO B 233 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 233 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 233 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 433 " -0.009 2.00e-02 2.50e+03 1.35e-02 3.17e+00 pdb=" CG PHE D 433 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE D 433 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE D 433 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE D 433 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 433 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE D 433 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 265 " 0.027 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO B 266 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 266 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 266 " 0.022 5.00e-02 4.00e+02 ... (remaining 2551 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2239 2.75 - 3.29: 14784 3.29 - 3.83: 24129 3.83 - 4.36: 26087 4.36 - 4.90: 44812 Nonbonded interactions: 112051 Sorted by model distance: nonbonded pdb=" OD2 ASP A 68 " pdb=" OG SER B 398 " model vdw 2.217 3.040 nonbonded pdb=" O ARG B 462 " pdb=" OG1 THR B 465 " model vdw 2.223 3.040 nonbonded pdb=" O ARG C 373 " pdb=" OG SER C 377 " model vdw 2.229 3.040 nonbonded pdb=" O LEU D 705 " pdb=" OG1 THR D 708 " model vdw 2.260 3.040 nonbonded pdb=" OG SER A 374 " pdb=" ND1 HIS A 375 " model vdw 2.263 3.120 ... (remaining 112046 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 137.280 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: 0.670 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 38.760 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 180.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 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 0.049 14606 Z= 0.152 Angle : 0.600 10.128 19893 Z= 0.305 Chirality : 0.039 0.227 2377 Planarity : 0.004 0.051 2554 Dihedral : 16.420 85.951 5151 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.90 % Favored : 95.00 % Rotamer: Outliers : 3.02 % Allowed : 25.88 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: 0.58 (0.21), residues: 1879 helix: 1.84 (0.16), residues: 1039 sheet: -3.40 (0.39), residues: 154 loop : -0.95 (0.26), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 318 HIS 0.004 0.001 HIS A 235 PHE 0.030 0.001 PHE D 433 TYR 0.010 0.001 TYR B 337 ARG 0.002 0.000 ARG B 270 Details of bonding type rmsd hydrogen bonds : bond 0.16705 ( 838) hydrogen bonds : angle 5.67365 ( 2448) covalent geometry : bond 0.00343 (14606) covalent geometry : angle 0.60044 (19893) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 155 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7697 (tp) REVERT: A 102 MET cc_start: 0.8556 (tpp) cc_final: 0.8302 (tpp) REVERT: A 459 TRP cc_start: 0.9100 (OUTLIER) cc_final: 0.8019 (t60) REVERT: B 123 ARG cc_start: 0.8436 (tpp80) cc_final: 0.8092 (tpt90) REVERT: B 156 CYS cc_start: 0.8238 (p) cc_final: 0.7782 (p) REVERT: B 185 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8500 (mt) REVERT: B 322 MET cc_start: 0.8315 (mtm) cc_final: 0.7767 (mtp) REVERT: B 449 PHE cc_start: 0.9052 (OUTLIER) cc_final: 0.8809 (t80) REVERT: C 360 MET cc_start: 0.0010 (tpt) cc_final: -0.0531 (mtt) REVERT: C 382 ASN cc_start: 0.0333 (t0) cc_final: -0.0174 (t0) REVERT: D 323 PHE cc_start: 0.8821 (t80) cc_final: 0.8611 (t80) REVERT: D 603 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8439 (tm) outliers start: 44 outliers final: 32 residues processed: 188 average time/residue: 0.2010 time to fit residues: 61.3006 Evaluate side-chains 189 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 459 TRP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 449 PHE Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain C residue 179 CYS Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 590 ILE Chi-restraints excluded: chain D residue 603 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 1.9990 chunk 144 optimal weight: 20.0000 chunk 80 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 149 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 111 optimal weight: 40.0000 chunk 173 optimal weight: 6.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS A 198 GLN ** A 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 GLN ** B 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 HIS D 588 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.173284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.149233 restraints weight = 32277.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.145401 restraints weight = 56484.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.143262 restraints weight = 53316.655| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 14606 Z= 0.312 Angle : 0.684 10.855 19893 Z= 0.351 Chirality : 0.043 0.208 2377 Planarity : 0.004 0.052 2554 Dihedral : 6.407 69.982 2068 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.81 % Favored : 93.08 % Rotamer: Outliers : 6.52 % Allowed : 22.10 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: 0.36 (0.20), residues: 1879 helix: 1.70 (0.16), residues: 1076 sheet: -3.65 (0.37), residues: 148 loop : -1.25 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 318 HIS 0.011 0.001 HIS B 314 PHE 0.022 0.002 PHE D 433 TYR 0.018 0.002 TYR B 337 ARG 0.005 0.000 ARG D 417 Details of bonding type rmsd hydrogen bonds : bond 0.04126 ( 838) hydrogen bonds : angle 4.62886 ( 2448) covalent geometry : bond 0.00727 (14606) covalent geometry : angle 0.68390 (19893) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 155 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7611 (ttm) REVERT: A 206 LEU cc_start: 0.8225 (tp) cc_final: 0.7758 (tt) REVERT: A 451 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.7962 (tt0) REVERT: A 459 TRP cc_start: 0.9031 (OUTLIER) cc_final: 0.8601 (t-100) REVERT: B 156 CYS cc_start: 0.7971 (p) cc_final: 0.7573 (p) REVERT: B 185 ILE cc_start: 0.8929 (mm) cc_final: 0.8562 (mt) REVERT: B 245 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.8036 (mtpt) REVERT: B 449 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.8668 (t80) REVERT: C 157 CYS cc_start: 0.3313 (OUTLIER) cc_final: 0.2650 (p) REVERT: C 306 THR cc_start: 0.3889 (p) cc_final: 0.3602 (p) REVERT: C 382 ASN cc_start: -0.1257 (t0) cc_final: -0.1795 (t0) REVERT: D 603 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8325 (tm) outliers start: 95 outliers final: 62 residues processed: 237 average time/residue: 0.1923 time to fit residues: 73.3428 Evaluate side-chains 217 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 148 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 459 TRP Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 449 PHE Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 445 TRP Chi-restraints excluded: chain D residue 513 CYS Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 590 ILE Chi-restraints excluded: chain D residue 603 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 697 PHE Chi-restraints excluded: chain D residue 698 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 61 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 128 optimal weight: 30.0000 chunk 13 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 63 optimal weight: 0.0980 chunk 182 optimal weight: 0.3980 chunk 74 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 83 optimal weight: 0.2980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.176968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.149204 restraints weight = 32636.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.143757 restraints weight = 54268.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.142278 restraints weight = 54049.642| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14606 Z= 0.131 Angle : 0.563 8.804 19893 Z= 0.281 Chirality : 0.039 0.228 2377 Planarity : 0.004 0.048 2554 Dihedral : 5.495 57.584 2046 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.04 % Favored : 95.85 % Rotamer: Outliers : 3.91 % Allowed : 24.30 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: 0.61 (0.21), residues: 1879 helix: 1.85 (0.16), residues: 1080 sheet: -3.42 (0.37), residues: 156 loop : -1.09 (0.26), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 440 HIS 0.004 0.001 HIS A 235 PHE 0.021 0.001 PHE D 433 TYR 0.015 0.001 TYR D 325 ARG 0.002 0.000 ARG D 417 Details of bonding type rmsd hydrogen bonds : bond 0.03498 ( 838) hydrogen bonds : angle 4.30014 ( 2448) covalent geometry : bond 0.00296 (14606) covalent geometry : angle 0.56330 (19893) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 158 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7153 (tp30) REVERT: A 451 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7609 (tt0) REVERT: A 459 TRP cc_start: 0.9022 (OUTLIER) cc_final: 0.8013 (t-100) REVERT: B 156 CYS cc_start: 0.7974 (p) cc_final: 0.7609 (p) REVERT: B 185 ILE cc_start: 0.8749 (mm) cc_final: 0.8441 (mt) REVERT: B 449 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.8623 (t80) REVERT: C 157 CYS cc_start: 0.3144 (t) cc_final: 0.2393 (p) REVERT: C 382 ASN cc_start: -0.1052 (t0) cc_final: -0.1423 (t0) REVERT: D 455 MET cc_start: 0.7417 (tpp) cc_final: 0.7213 (tpp) REVERT: D 603 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8377 (tm) outliers start: 57 outliers final: 30 residues processed: 206 average time/residue: 0.1999 time to fit residues: 66.2589 Evaluate side-chains 183 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 459 TRP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 449 PHE Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 603 LEU Chi-restraints excluded: chain D residue 697 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 105 optimal weight: 30.0000 chunk 144 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 131 optimal weight: 40.0000 chunk 40 optimal weight: 0.6980 chunk 181 optimal weight: 1.9990 chunk 119 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 HIS D 588 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.173176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.149341 restraints weight = 32357.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.145771 restraints weight = 56814.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.144083 restraints weight = 52954.326| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 14606 Z= 0.318 Angle : 0.683 10.422 19893 Z= 0.346 Chirality : 0.043 0.162 2377 Planarity : 0.004 0.049 2554 Dihedral : 5.444 51.509 2035 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.03 % Favored : 92.92 % Rotamer: Outliers : 5.77 % Allowed : 23.27 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: 0.45 (0.20), residues: 1879 helix: 1.79 (0.16), residues: 1078 sheet: -3.48 (0.37), residues: 153 loop : -1.29 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 318 HIS 0.011 0.001 HIS B 314 PHE 0.024 0.002 PHE D 433 TYR 0.015 0.001 TYR B 337 ARG 0.004 0.000 ARG D 417 Details of bonding type rmsd hydrogen bonds : bond 0.03798 ( 838) hydrogen bonds : angle 4.51098 ( 2448) covalent geometry : bond 0.00740 (14606) covalent geometry : angle 0.68269 (19893) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 153 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7599 (ttm) REVERT: A 393 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8025 (ttp80) REVERT: A 424 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7250 (tp30) REVERT: A 451 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.7930 (tt0) REVERT: A 459 TRP cc_start: 0.9049 (OUTLIER) cc_final: 0.8604 (t-100) REVERT: B 156 CYS cc_start: 0.7999 (p) cc_final: 0.7585 (p) REVERT: B 185 ILE cc_start: 0.8884 (mm) cc_final: 0.8536 (mt) REVERT: B 336 LEU cc_start: 0.9613 (OUTLIER) cc_final: 0.9413 (tp) REVERT: C 157 CYS cc_start: 0.4034 (t) cc_final: 0.3193 (p) REVERT: C 306 THR cc_start: 0.3874 (p) cc_final: 0.3594 (p) REVERT: C 382 ASN cc_start: -0.1231 (t0) cc_final: -0.1461 (t0) REVERT: D 603 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8375 (tm) outliers start: 84 outliers final: 54 residues processed: 224 average time/residue: 0.2038 time to fit residues: 72.8794 Evaluate side-chains 206 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 145 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 459 TRP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 513 CYS Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 590 ILE Chi-restraints excluded: chain D residue 603 LEU Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 697 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 158 optimal weight: 0.8980 chunk 122 optimal weight: 7.9990 chunk 41 optimal weight: 0.5980 chunk 156 optimal weight: 7.9990 chunk 164 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 109 optimal weight: 8.9990 chunk 7 optimal weight: 0.5980 chunk 126 optimal weight: 30.0000 chunk 49 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 588 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.175406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.149079 restraints weight = 32510.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.143764 restraints weight = 54927.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.141765 restraints weight = 54626.666| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14606 Z= 0.169 Angle : 0.598 13.223 19893 Z= 0.295 Chirality : 0.040 0.242 2377 Planarity : 0.004 0.048 2554 Dihedral : 5.164 51.322 2033 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.16 % Favored : 94.78 % Rotamer: Outliers : 5.22 % Allowed : 23.75 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.21), residues: 1879 helix: 1.90 (0.16), residues: 1079 sheet: -3.31 (0.37), residues: 153 loop : -1.20 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 318 HIS 0.006 0.001 HIS B 314 PHE 0.030 0.001 PHE D 433 TYR 0.016 0.001 TYR D 325 ARG 0.003 0.000 ARG A 530 Details of bonding type rmsd hydrogen bonds : bond 0.03362 ( 838) hydrogen bonds : angle 4.27259 ( 2448) covalent geometry : bond 0.00389 (14606) covalent geometry : angle 0.59813 (19893) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 154 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7730 (ttm) REVERT: A 424 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7241 (tp30) REVERT: A 451 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.7699 (tt0) REVERT: A 459 TRP cc_start: 0.9022 (OUTLIER) cc_final: 0.7999 (t-100) REVERT: B 156 CYS cc_start: 0.7882 (p) cc_final: 0.7546 (p) REVERT: B 185 ILE cc_start: 0.8823 (mm) cc_final: 0.8457 (mt) REVERT: C 157 CYS cc_start: 0.3924 (t) cc_final: 0.3086 (p) REVERT: C 382 ASN cc_start: -0.1168 (t0) cc_final: -0.1452 (t0) REVERT: D 129 SER cc_start: 0.8445 (m) cc_final: 0.8077 (p) REVERT: D 603 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8421 (tm) outliers start: 76 outliers final: 47 residues processed: 219 average time/residue: 0.1998 time to fit residues: 71.3193 Evaluate side-chains 202 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 150 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 459 TRP Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 603 LEU Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 697 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 130 optimal weight: 40.0000 chunk 34 optimal weight: 0.0980 chunk 35 optimal weight: 0.9980 chunk 136 optimal weight: 6.9990 chunk 5 optimal weight: 0.1980 chunk 23 optimal weight: 1.9990 chunk 108 optimal weight: 50.0000 chunk 70 optimal weight: 0.8980 chunk 36 optimal weight: 0.0050 chunk 139 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.176580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.150395 restraints weight = 32292.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.143669 restraints weight = 53827.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.142283 restraints weight = 54425.192| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14606 Z= 0.131 Angle : 0.579 10.508 19893 Z= 0.281 Chirality : 0.039 0.190 2377 Planarity : 0.004 0.047 2554 Dihedral : 4.910 51.266 2030 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.84 % Favored : 95.05 % Rotamer: Outliers : 4.26 % Allowed : 24.85 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.21), residues: 1879 helix: 2.03 (0.16), residues: 1079 sheet: -3.21 (0.38), residues: 155 loop : -1.12 (0.26), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 318 HIS 0.005 0.001 HIS A 235 PHE 0.025 0.001 PHE D 433 TYR 0.018 0.001 TYR D 325 ARG 0.002 0.000 ARG B 123 Details of bonding type rmsd hydrogen bonds : bond 0.03103 ( 838) hydrogen bonds : angle 4.11752 ( 2448) covalent geometry : bond 0.00303 (14606) covalent geometry : angle 0.57900 (19893) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 159 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7700 (ttm) REVERT: A 424 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7205 (tp30) REVERT: A 451 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.7646 (tt0) REVERT: A 459 TRP cc_start: 0.9031 (OUTLIER) cc_final: 0.8042 (t-100) REVERT: B 156 CYS cc_start: 0.7893 (p) cc_final: 0.7674 (p) REVERT: B 164 GLN cc_start: 0.7129 (OUTLIER) cc_final: 0.6194 (mt0) REVERT: B 185 ILE cc_start: 0.8793 (mm) cc_final: 0.8423 (mt) REVERT: B 449 PHE cc_start: 0.8951 (OUTLIER) cc_final: 0.8676 (t80) REVERT: C 157 CYS cc_start: 0.3828 (t) cc_final: 0.3015 (p) REVERT: C 382 ASN cc_start: -0.1170 (t0) cc_final: -0.1468 (t0) REVERT: D 129 SER cc_start: 0.8660 (m) cc_final: 0.8357 (p) REVERT: D 603 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8341 (tm) outliers start: 62 outliers final: 35 residues processed: 212 average time/residue: 0.2054 time to fit residues: 70.2396 Evaluate side-chains 193 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 151 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 459 TRP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 449 PHE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 603 LEU Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 697 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 167 optimal weight: 5.9990 chunk 181 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 127 optimal weight: 8.9990 chunk 87 optimal weight: 0.0670 chunk 161 optimal weight: 0.3980 chunk 92 optimal weight: 2.9990 chunk 178 optimal weight: 0.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.176365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.151244 restraints weight = 32558.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.145379 restraints weight = 50428.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.143078 restraints weight = 54019.642| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14606 Z= 0.147 Angle : 0.599 11.367 19893 Z= 0.292 Chirality : 0.040 0.240 2377 Planarity : 0.004 0.044 2554 Dihedral : 4.765 51.488 2027 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.95 % Favored : 94.94 % Rotamer: Outliers : 3.91 % Allowed : 25.12 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: 0.78 (0.21), residues: 1879 helix: 2.03 (0.16), residues: 1082 sheet: -3.15 (0.37), residues: 158 loop : -1.14 (0.26), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 533 HIS 0.005 0.001 HIS A 235 PHE 0.026 0.001 PHE D 433 TYR 0.017 0.001 TYR D 325 ARG 0.002 0.000 ARG B 27 Details of bonding type rmsd hydrogen bonds : bond 0.03133 ( 838) hydrogen bonds : angle 4.11381 ( 2448) covalent geometry : bond 0.00343 (14606) covalent geometry : angle 0.59880 (19893) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 157 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7274 (tp30) REVERT: A 451 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.7667 (tt0) REVERT: A 459 TRP cc_start: 0.9031 (OUTLIER) cc_final: 0.7972 (t60) REVERT: B 156 CYS cc_start: 0.7922 (p) cc_final: 0.7492 (p) REVERT: B 185 ILE cc_start: 0.8802 (mm) cc_final: 0.8444 (mt) REVERT: B 449 PHE cc_start: 0.8914 (OUTLIER) cc_final: 0.8686 (t80) REVERT: B 478 GLN cc_start: 0.6755 (mm-40) cc_final: 0.6512 (mm-40) REVERT: C 157 CYS cc_start: 0.4205 (t) cc_final: 0.3317 (p) REVERT: C 382 ASN cc_start: -0.1221 (t0) cc_final: -0.1474 (t0) REVERT: D 129 SER cc_start: 0.8657 (m) cc_final: 0.8386 (p) REVERT: D 603 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8361 (tm) outliers start: 57 outliers final: 41 residues processed: 206 average time/residue: 0.2535 time to fit residues: 85.3584 Evaluate side-chains 198 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 152 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 459 TRP Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 449 PHE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 603 LEU Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 697 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 73 optimal weight: 0.9980 chunk 144 optimal weight: 9.9990 chunk 5 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 181 optimal weight: 0.3980 chunk 115 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 141 optimal weight: 9.9990 chunk 189 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.175837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.149565 restraints weight = 32394.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.143886 restraints weight = 53355.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.141672 restraints weight = 56307.941| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14606 Z= 0.177 Angle : 0.626 12.055 19893 Z= 0.303 Chirality : 0.041 0.268 2377 Planarity : 0.004 0.044 2554 Dihedral : 4.797 51.837 2027 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.27 % Favored : 94.62 % Rotamer: Outliers : 4.60 % Allowed : 24.64 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: 0.76 (0.21), residues: 1879 helix: 1.99 (0.16), residues: 1083 sheet: -3.13 (0.38), residues: 155 loop : -1.15 (0.26), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 440 HIS 0.006 0.001 HIS B 314 PHE 0.026 0.002 PHE D 433 TYR 0.017 0.001 TYR D 424 ARG 0.003 0.000 ARG D 417 Details of bonding type rmsd hydrogen bonds : bond 0.03193 ( 838) hydrogen bonds : angle 4.17226 ( 2448) covalent geometry : bond 0.00414 (14606) covalent geometry : angle 0.62565 (19893) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 154 time to evaluate : 4.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7649 (ttm) REVERT: A 424 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7336 (tp30) REVERT: A 451 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.7725 (tt0) REVERT: A 459 TRP cc_start: 0.9023 (OUTLIER) cc_final: 0.8544 (t-100) REVERT: B 156 CYS cc_start: 0.7904 (p) cc_final: 0.7415 (p) REVERT: B 185 ILE cc_start: 0.8802 (mm) cc_final: 0.8443 (mt) REVERT: B 449 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.8689 (t80) REVERT: C 157 CYS cc_start: 0.4264 (t) cc_final: 0.3347 (p) REVERT: C 382 ASN cc_start: -0.1171 (t0) cc_final: -0.1470 (t0) REVERT: D 603 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8366 (tm) outliers start: 67 outliers final: 51 residues processed: 210 average time/residue: 0.2851 time to fit residues: 100.4745 Evaluate side-chains 207 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 150 time to evaluate : 2.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 459 TRP Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 449 PHE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 590 ILE Chi-restraints excluded: chain D residue 603 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 697 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 27 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 137 optimal weight: 9.9990 chunk 41 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 181 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 588 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.174406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.148216 restraints weight = 32374.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.142203 restraints weight = 54604.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.139890 restraints weight = 56767.914| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 14606 Z= 0.251 Angle : 0.697 12.356 19893 Z= 0.342 Chirality : 0.042 0.264 2377 Planarity : 0.004 0.043 2554 Dihedral : 5.028 52.444 2027 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.76 % Favored : 93.13 % Rotamer: Outliers : 4.67 % Allowed : 24.57 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: 0.61 (0.20), residues: 1879 helix: 1.92 (0.16), residues: 1085 sheet: -3.19 (0.37), residues: 152 loop : -1.32 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 440 HIS 0.009 0.001 HIS B 314 PHE 0.018 0.002 PHE D 433 TYR 0.015 0.001 TYR B 337 ARG 0.006 0.000 ARG A 552 Details of bonding type rmsd hydrogen bonds : bond 0.03477 ( 838) hydrogen bonds : angle 4.33354 ( 2448) covalent geometry : bond 0.00589 (14606) covalent geometry : angle 0.69733 (19893) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 155 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7666 (ttm) REVERT: A 424 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7410 (tp30) REVERT: A 451 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.7874 (tt0) REVERT: A 459 TRP cc_start: 0.9081 (OUTLIER) cc_final: 0.8596 (t-100) REVERT: B 156 CYS cc_start: 0.7984 (p) cc_final: 0.7491 (p) REVERT: B 185 ILE cc_start: 0.8857 (mm) cc_final: 0.8507 (mt) REVERT: B 478 GLN cc_start: 0.6835 (mm-40) cc_final: 0.6599 (mm-40) REVERT: C 157 CYS cc_start: 0.4468 (t) cc_final: 0.3573 (p) REVERT: C 178 CYS cc_start: -0.2921 (m) cc_final: -0.3250 (m) REVERT: C 292 LEU cc_start: -0.1058 (OUTLIER) cc_final: -0.1522 (pp) REVERT: C 306 THR cc_start: 0.4292 (p) cc_final: 0.4025 (p) REVERT: C 360 MET cc_start: -0.1035 (mmm) cc_final: -0.1357 (mtt) REVERT: C 382 ASN cc_start: -0.1253 (t0) cc_final: -0.1584 (t0) REVERT: D 315 MET cc_start: 0.7851 (ppp) cc_final: 0.7625 (ppp) REVERT: D 603 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8422 (tm) outliers start: 68 outliers final: 52 residues processed: 213 average time/residue: 0.2189 time to fit residues: 76.7359 Evaluate side-chains 211 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 153 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 406 CYS Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 459 TRP Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 590 ILE Chi-restraints excluded: chain D residue 603 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 697 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 51 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 chunk 126 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 100 optimal weight: 30.0000 chunk 121 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 588 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.174978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.148696 restraints weight = 32307.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.143377 restraints weight = 54470.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.141095 restraints weight = 52781.484| |-----------------------------------------------------------------------------| r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14606 Z= 0.213 Angle : 0.679 14.545 19893 Z= 0.329 Chirality : 0.042 0.361 2377 Planarity : 0.004 0.044 2554 Dihedral : 5.006 52.882 2027 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.59 % Favored : 94.31 % Rotamer: Outliers : 4.12 % Allowed : 25.26 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: 0.61 (0.20), residues: 1879 helix: 1.90 (0.16), residues: 1081 sheet: -3.51 (0.37), residues: 138 loop : -1.25 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 440 HIS 0.007 0.001 HIS B 314 PHE 0.021 0.002 PHE B 449 TYR 0.014 0.001 TYR B 337 ARG 0.003 0.000 ARG D 287 Details of bonding type rmsd hydrogen bonds : bond 0.03409 ( 838) hydrogen bonds : angle 4.29386 ( 2448) covalent geometry : bond 0.00497 (14606) covalent geometry : angle 0.67879 (19893) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 156 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7645 (ttm) REVERT: A 424 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7260 (tp30) REVERT: A 451 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.7805 (tt0) REVERT: A 459 TRP cc_start: 0.9061 (OUTLIER) cc_final: 0.8604 (t-100) REVERT: B 156 CYS cc_start: 0.7902 (p) cc_final: 0.7605 (p) REVERT: B 185 ILE cc_start: 0.8846 (mm) cc_final: 0.8506 (mt) REVERT: B 478 GLN cc_start: 0.6809 (mm-40) cc_final: 0.6550 (mm-40) REVERT: C 157 CYS cc_start: 0.4474 (t) cc_final: 0.3537 (p) REVERT: C 178 CYS cc_start: -0.2863 (m) cc_final: -0.3185 (m) REVERT: C 292 LEU cc_start: -0.0950 (OUTLIER) cc_final: -0.1430 (pp) REVERT: C 306 THR cc_start: 0.4443 (p) cc_final: 0.4173 (p) REVERT: C 360 MET cc_start: -0.1138 (mmm) cc_final: -0.1404 (mtm) REVERT: C 382 ASN cc_start: -0.1289 (t0) cc_final: -0.1545 (t0) REVERT: D 603 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8440 (tm) outliers start: 60 outliers final: 52 residues processed: 208 average time/residue: 0.2042 time to fit residues: 69.4414 Evaluate side-chains 212 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 154 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 406 CYS Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 459 TRP Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 590 ILE Chi-restraints excluded: chain D residue 603 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 697 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 56 optimal weight: 0.7980 chunk 183 optimal weight: 0.2980 chunk 49 optimal weight: 1.9990 chunk 188 optimal weight: 0.5980 chunk 126 optimal weight: 2.9990 chunk 110 optimal weight: 0.0270 chunk 154 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 66 optimal weight: 0.2980 chunk 143 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.176999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.151005 restraints weight = 32562.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.145045 restraints weight = 53433.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.142666 restraints weight = 55038.526| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14606 Z= 0.132 Angle : 0.642 12.221 19893 Z= 0.306 Chirality : 0.041 0.341 2377 Planarity : 0.004 0.045 2554 Dihedral : 4.809 53.468 2027 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.74 % Favored : 95.16 % Rotamer: Outliers : 3.43 % Allowed : 26.01 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: 0.76 (0.21), residues: 1879 helix: 2.01 (0.16), residues: 1081 sheet: -3.35 (0.38), residues: 139 loop : -1.19 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 440 HIS 0.004 0.001 HIS A 235 PHE 0.020 0.001 PHE D 413 TYR 0.017 0.001 TYR D 325 ARG 0.003 0.000 ARG B 441 Details of bonding type rmsd hydrogen bonds : bond 0.03118 ( 838) hydrogen bonds : angle 4.13524 ( 2448) covalent geometry : bond 0.00310 (14606) covalent geometry : angle 0.64162 (19893) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5525.46 seconds wall clock time: 98 minutes 53.40 seconds (5933.40 seconds total)