Starting phenix.real_space_refine on Tue Nov 18 13:12:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ep1_19871/11_2025/9ep1_19871.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ep1_19871/11_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ep1_19871/11_2025/9ep1_19871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ep1_19871/11_2025/9ep1_19871.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ep1_19871/11_2025/9ep1_19871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ep1_19871/11_2025/9ep1_19871.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: {'TYR:plan': 4, 'HIS:plan': 3, 'PHE:plan': 2, 'ASP:plan': 7, 'GLU:plan': 10, 'GLN:plan1': 4, 'ARG:plan': 11, 'ASN:plan1': 5} 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: {'ASP:plan': 7, 'GLN:plan1': 2, 'ARG:plan': 6, 'GLU:plan': 8, 'ASN:plan1': 8, 'PHE:plan': 2, 'TYR:plan': 1} 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, 'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 2, 'PHE:plan': 1, 'ASP:plan': 1} 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: {'ARG:plan': 14, 'PHE:plan': 6, 'ASN:plan1': 8, 'ASP:plan': 3, 'TYR:plan': 7, 'GLU:plan': 8, 'TRP:plan': 1, 'HIS:plan': 2, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 255 Time building chain proxies: 3.44, per 1000 atoms: 0.24 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: 1.26 Conformation dependent library (CDL) restraints added in 693.0 milliseconds 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: 0.51 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: 2.49 Time building geometry restraints manager: 1.68 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: 20.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.370 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.280 ------------------------------------------------------------------------------- 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 : 9.48 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (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 ARG 0.002 0.000 ARG B 270 TYR 0.010 0.001 TYR B 337 PHE 0.030 0.001 PHE D 433 TRP 0.017 0.001 TRP A 318 HIS 0.004 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00343 (14606) covalent geometry : angle 0.60044 (19893) hydrogen bonds : bond 0.16705 ( 838) hydrogen bonds : angle 5.67365 ( 2448) *********************** 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 : 0.575 Fit side-chains 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: 0.7768 (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: 0.8438 (tm) outliers start: 44 outliers final: 32 residues processed: 188 average time/residue: 0.0901 time to fit residues: 27.7067 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 : 0.566 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 107 optimal weight: 50.0000 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 40.0000 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.171498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.148193 restraints weight = 32607.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.144023 restraints weight = 57931.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.142192 restraints weight = 58579.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.141688 restraints weight = 58194.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.139635 restraints weight = 51342.750| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.080 14606 Z= 0.431 Angle : 0.791 12.260 19893 Z= 0.408 Chirality : 0.046 0.194 2377 Planarity : 0.005 0.053 2554 Dihedral : 6.849 78.949 2068 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.82 % Favored : 92.02 % Rotamer: Outliers : 7.62 % Allowed : 22.03 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.20), residues: 1879 helix: 1.56 (0.16), residues: 1068 sheet: -3.76 (0.37), residues: 149 loop : -1.35 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 270 TYR 0.021 0.002 TYR B 337 PHE 0.028 0.002 PHE A 421 TRP 0.030 0.002 TRP A 318 HIS 0.015 0.002 HIS B 314 Details of bonding type rmsd covalent geometry : bond 0.01000 (14606) covalent geometry : angle 0.79108 (19893) hydrogen bonds : bond 0.04715 ( 838) hydrogen bonds : angle 4.90997 ( 2448) *********************** 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 265 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 154 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7617 (ttm) REVERT: A 206 LEU cc_start: 0.8247 (tp) cc_final: 0.7809 (tt) REVERT: A 393 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.8032 (ttp80) REVERT: A 424 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7255 (tp30) REVERT: A 451 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8044 (tt0) REVERT: A 459 TRP cc_start: 0.9045 (OUTLIER) cc_final: 0.8612 (t-100) REVERT: B 156 CYS cc_start: 0.7981 (p) cc_final: 0.7681 (p) REVERT: B 185 ILE cc_start: 0.8977 (mm) cc_final: 0.8619 (mt) REVERT: B 449 PHE cc_start: 0.8956 (OUTLIER) cc_final: 0.8692 (t80) REVERT: C 157 CYS cc_start: 0.3276 (OUTLIER) cc_final: 0.2552 (p) REVERT: C 306 THR cc_start: 0.4037 (p) cc_final: 0.3751 (p) REVERT: C 360 MET cc_start: -0.0438 (tpt) cc_final: -0.0699 (mtt) REVERT: C 382 ASN cc_start: -0.1268 (t0) cc_final: -0.1838 (t0) REVERT: D 603 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8385 (tm) outliers start: 111 outliers final: 73 residues processed: 251 average time/residue: 0.0947 time to fit residues: 38.5833 Evaluate side-chains 230 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 149 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 47 ILE 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 122 ILE Chi-restraints excluded: chain A residue 132 THR 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 392 SER 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 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 549 LYS 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 45 ASN 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 67 THR 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 152 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 253 ILE 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 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 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 147 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 56 optimal weight: 0.0980 chunk 60 optimal weight: 0.5980 chunk 173 optimal weight: 1.9990 chunk 110 optimal weight: 30.0000 chunk 81 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 156 optimal weight: 6.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4350 r_free = 0.4350 target = 0.176037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.149183 restraints weight = 32616.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.143219 restraints weight = 55135.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.141236 restraints weight = 53275.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.140572 restraints weight = 53705.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.139933 restraints weight = 42961.650| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.1149 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= 0.146 Angle : 0.581 7.890 19893 Z= 0.293 Chirality : 0.040 0.235 2377 Planarity : 0.004 0.051 2554 Dihedral : 5.905 57.786 2049 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.42 % Favored : 95.48 % Rotamer: Outliers : 4.46 % Allowed : 24.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.21), residues: 1879 helix: 1.81 (0.16), residues: 1078 sheet: -3.43 (0.37), residues: 153 loop : -1.19 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 417 TYR 0.017 0.001 TYR D 325 PHE 0.022 0.001 PHE D 433 TRP 0.019 0.002 TRP D 440 HIS 0.005 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00331 (14606) covalent geometry : angle 0.58077 (19893) hydrogen bonds : bond 0.03607 ( 838) hydrogen bonds : angle 4.39543 ( 2448) *********************** 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 225 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 160 time to evaluate : 0.596 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: 0.7711 (ttm) REVERT: A 451 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7713 (tt0) REVERT: A 459 TRP cc_start: 0.9046 (OUTLIER) cc_final: 0.7972 (t-100) REVERT: B 156 CYS cc_start: 0.7893 (p) cc_final: 0.7532 (p) REVERT: B 185 ILE cc_start: 0.8799 (mm) cc_final: 0.8399 (mt) REVERT: B 449 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8605 (t80) REVERT: C 157 CYS cc_start: 0.3117 (t) cc_final: 0.2310 (p) REVERT: C 360 MET cc_start: -0.0565 (tpt) cc_final: -0.0868 (mtt) REVERT: C 382 ASN cc_start: -0.1076 (t0) cc_final: -0.1469 (t0) REVERT: D 176 CYS cc_start: 0.6989 (m) cc_final: 0.6690 (t) REVERT: D 603 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8333 (tm) outliers start: 65 outliers final: 37 residues processed: 213 average time/residue: 0.0982 time to fit residues: 33.6007 Evaluate side-chains 191 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 149 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 108 VAL 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 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 474 VAL Chi-restraints excluded: chain A residue 505 GLU 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 59 LEU Chi-restraints excluded: chain B residue 98 ILE 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 263 SER 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 179 LEU Chi-restraints excluded: chain D residue 351 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 629 ILE 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 179 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 123 optimal weight: 20.0000 chunk 71 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 107 optimal weight: 30.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.4338 r_free = 0.4338 target = 0.175099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.147611 restraints weight = 32582.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.141559 restraints weight = 54983.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.139539 restraints weight = 56473.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.139104 restraints weight = 49235.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.138360 restraints weight = 40680.539| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14606 Z= 0.199 Angle : 0.599 9.877 19893 Z= 0.299 Chirality : 0.040 0.196 2377 Planarity : 0.004 0.049 2554 Dihedral : 5.684 57.187 2044 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.12 % Favored : 93.77 % Rotamer: Outliers : 5.15 % Allowed : 24.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.20), residues: 1879 helix: 1.87 (0.16), residues: 1080 sheet: -3.28 (0.39), residues: 144 loop : -1.28 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 270 TYR 0.014 0.001 TYR D 325 PHE 0.024 0.002 PHE D 433 TRP 0.017 0.001 TRP A 318 HIS 0.007 0.001 HIS B 314 Details of bonding type rmsd covalent geometry : bond 0.00462 (14606) covalent geometry : angle 0.59884 (19893) hydrogen bonds : bond 0.03498 ( 838) hydrogen bonds : angle 4.31630 ( 2448) *********************** 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 229 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 154 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7673 (ttm) REVERT: A 451 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.7800 (tt0) REVERT: A 459 TRP cc_start: 0.9086 (OUTLIER) cc_final: 0.8628 (t-100) REVERT: B 156 CYS cc_start: 0.7927 (p) cc_final: 0.7520 (p) REVERT: B 185 ILE cc_start: 0.8799 (mm) cc_final: 0.8431 (mt) REVERT: C 157 CYS cc_start: 0.3649 (t) cc_final: 0.2854 (p) REVERT: C 203 LEU cc_start: 0.5205 (mt) cc_final: 0.4934 (pt) REVERT: C 360 MET cc_start: -0.0593 (tpt) cc_final: -0.0856 (mtt) REVERT: C 382 ASN cc_start: -0.1084 (t0) cc_final: -0.1443 (t0) REVERT: D 603 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8446 (tm) outliers start: 75 outliers final: 52 residues processed: 215 average time/residue: 0.0930 time to fit residues: 32.6491 Evaluate side-chains 206 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 150 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 291 VAL Chi-restraints excluded: chain A residue 319 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 474 VAL Chi-restraints excluded: chain A residue 505 GLU 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 59 LEU 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 126 LEU 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 258 ASP Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 311 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 456 VAL 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 179 LEU Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 418 GLU 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 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 128 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 180 optimal weight: 0.0970 chunk 85 optimal weight: 0.1980 chunk 50 optimal weight: 3.9990 chunk 57 optimal weight: 0.2980 chunk 148 optimal weight: 8.9990 chunk 160 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 157 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 588 HIS D 647 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.175778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.149651 restraints weight = 32490.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.144902 restraints weight = 56064.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.142711 restraints weight = 56174.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.141843 restraints weight = 52907.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.140350 restraints weight = 44473.426| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14606 Z= 0.161 Angle : 0.574 9.691 19893 Z= 0.284 Chirality : 0.040 0.225 2377 Planarity : 0.004 0.047 2554 Dihedral : 5.412 51.659 2041 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.95 % Favored : 94.94 % Rotamer: Outliers : 4.94 % Allowed : 24.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.21), residues: 1879 helix: 1.95 (0.16), residues: 1080 sheet: -3.19 (0.39), residues: 145 loop : -1.20 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 287 TYR 0.015 0.001 TYR D 325 PHE 0.026 0.001 PHE D 433 TRP 0.015 0.001 TRP A 318 HIS 0.005 0.001 HIS B 314 Details of bonding type rmsd covalent geometry : bond 0.00375 (14606) covalent geometry : angle 0.57446 (19893) hydrogen bonds : bond 0.03274 ( 838) hydrogen bonds : angle 4.18225 ( 2448) *********************** 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 229 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 157 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7685 (ttm) REVERT: A 424 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7234 (tp30) REVERT: A 451 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.7715 (tt0) REVERT: A 459 TRP cc_start: 0.9042 (OUTLIER) cc_final: 0.8003 (t-100) REVERT: B 156 CYS cc_start: 0.7871 (p) cc_final: 0.7450 (p) REVERT: B 185 ILE cc_start: 0.8766 (mm) cc_final: 0.8381 (mt) REVERT: C 157 CYS cc_start: 0.3788 (t) cc_final: 0.2981 (p) REVERT: C 203 LEU cc_start: 0.5150 (mt) cc_final: 0.4940 (pt) REVERT: C 382 ASN cc_start: -0.1143 (t0) cc_final: -0.1475 (t0) REVERT: D 603 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8361 (tm) outliers start: 72 outliers final: 46 residues processed: 216 average time/residue: 0.0971 time to fit residues: 34.0518 Evaluate side-chains 203 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 152 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 319 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 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 505 GLU 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 59 LEU 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 246 VAL Chi-restraints excluded: chain B residue 258 ASP 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 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 179 LEU Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 513 CYS 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 158 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 185 optimal weight: 0.4980 chunk 52 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4345 r_free = 0.4345 target = 0.175663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.148261 restraints weight = 32241.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.142688 restraints weight = 53568.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.140937 restraints weight = 55689.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.140607 restraints weight = 53249.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.139901 restraints weight = 43993.700| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14606 Z= 0.172 Angle : 0.597 10.493 19893 Z= 0.292 Chirality : 0.040 0.239 2377 Planarity : 0.004 0.046 2554 Dihedral : 5.240 51.336 2035 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.48 % Favored : 94.41 % Rotamer: Outliers : 5.08 % Allowed : 24.50 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.21), residues: 1879 helix: 1.98 (0.16), residues: 1081 sheet: -3.21 (0.38), residues: 155 loop : -1.17 (0.26), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 27 TYR 0.014 0.001 TYR D 325 PHE 0.025 0.001 PHE D 433 TRP 0.016 0.001 TRP A 318 HIS 0.006 0.001 HIS B 314 Details of bonding type rmsd covalent geometry : bond 0.00402 (14606) covalent geometry : angle 0.59708 (19893) hydrogen bonds : bond 0.03230 ( 838) hydrogen bonds : angle 4.17581 ( 2448) *********************** 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 234 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 160 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7632 (ttm) REVERT: A 424 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7229 (tp30) REVERT: A 451 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.7702 (tt0) REVERT: A 459 TRP cc_start: 0.9053 (OUTLIER) cc_final: 0.8046 (t-100) REVERT: B 13 MET cc_start: 0.8037 (tpp) cc_final: 0.7836 (ttm) REVERT: B 156 CYS cc_start: 0.7872 (p) cc_final: 0.7409 (p) REVERT: B 185 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8389 (mt) REVERT: B 449 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.8668 (t80) REVERT: C 157 CYS cc_start: 0.3867 (t) cc_final: 0.3009 (p) REVERT: C 382 ASN cc_start: -0.1099 (t0) cc_final: -0.1451 (t0) REVERT: D 129 SER cc_start: 0.8794 (m) cc_final: 0.8485 (p) REVERT: D 603 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8351 (tm) outliers start: 74 outliers final: 48 residues processed: 222 average time/residue: 0.0975 time to fit residues: 35.1695 Evaluate side-chains 212 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 157 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 291 VAL Chi-restraints excluded: chain A residue 319 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 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 505 GLU 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 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 258 ASP 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 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 179 LEU Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 418 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 142 optimal weight: 20.0000 chunk 43 optimal weight: 0.0770 chunk 107 optimal weight: 50.0000 chunk 166 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 111 optimal weight: 20.0000 chunk 38 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 110 optimal weight: 0.0170 chunk 48 optimal weight: 0.7980 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.176701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.150537 restraints weight = 32149.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.144690 restraints weight = 53101.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.142265 restraints weight = 57013.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.142004 restraints weight = 53434.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.140508 restraints weight = 45297.385| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14606 Z= 0.134 Angle : 0.603 13.272 19893 Z= 0.292 Chirality : 0.040 0.235 2377 Planarity : 0.004 0.045 2554 Dihedral : 5.048 51.419 2034 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.58 % Favored : 95.32 % Rotamer: Outliers : 4.39 % Allowed : 24.91 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.21), residues: 1879 helix: 1.98 (0.16), residues: 1080 sheet: -3.11 (0.38), residues: 158 loop : -1.16 (0.26), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 423 TYR 0.014 0.001 TYR D 325 PHE 0.024 0.001 PHE D 433 TRP 0.012 0.001 TRP A 318 HIS 0.005 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00311 (14606) covalent geometry : angle 0.60321 (19893) hydrogen bonds : bond 0.03105 ( 838) hydrogen bonds : angle 4.12766 ( 2448) *********************** 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 226 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 162 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7225 (tp30) REVERT: A 451 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7636 (tt0) REVERT: A 459 TRP cc_start: 0.9048 (OUTLIER) cc_final: 0.7947 (t60) REVERT: B 156 CYS cc_start: 0.7809 (p) cc_final: 0.7315 (p) REVERT: B 185 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8358 (mt) REVERT: B 449 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.8635 (t80) REVERT: B 478 GLN cc_start: 0.6878 (mm-40) cc_final: 0.6606 (mm-40) REVERT: C 157 CYS cc_start: 0.4095 (t) cc_final: 0.3194 (p) REVERT: C 382 ASN cc_start: -0.1176 (t0) cc_final: -0.1478 (t0) REVERT: D 129 SER cc_start: 0.8738 (m) cc_final: 0.8520 (p) REVERT: D 424 TYR cc_start: 0.4290 (OUTLIER) cc_final: 0.4061 (m-10) REVERT: D 603 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8323 (tm) outliers start: 64 outliers final: 41 residues processed: 214 average time/residue: 0.0961 time to fit residues: 33.3737 Evaluate side-chains 204 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 156 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 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 319 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 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 505 GLU 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 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 258 ASP Chi-restraints excluded: chain B residue 267 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 449 PHE 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 351 VAL Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 424 TYR 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 137 optimal weight: 8.9990 chunk 123 optimal weight: 0.0000 chunk 87 optimal weight: 0.4980 chunk 159 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 125 optimal weight: 9.9990 chunk 85 optimal weight: 0.5980 chunk 102 optimal weight: 6.9990 chunk 126 optimal weight: 20.0000 chunk 63 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- 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 = 0.4357 r_free = 0.4357 target = 0.176662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.152108 restraints weight = 32248.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.145300 restraints weight = 50255.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.142833 restraints weight = 61139.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.142702 restraints weight = 54758.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.141532 restraints weight = 44171.573| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14606 Z= 0.142 Angle : 0.601 10.709 19893 Z= 0.292 Chirality : 0.040 0.267 2377 Planarity : 0.004 0.043 2554 Dihedral : 4.804 51.704 2029 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.68 % Favored : 95.21 % Rotamer: Outliers : 3.98 % Allowed : 25.53 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.21), residues: 1879 helix: 2.04 (0.16), residues: 1081 sheet: -3.07 (0.37), residues: 158 loop : -1.15 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 27 TYR 0.014 0.001 TYR D 325 PHE 0.027 0.001 PHE D 433 TRP 0.036 0.001 TRP D 440 HIS 0.005 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00330 (14606) covalent geometry : angle 0.60103 (19893) hydrogen bonds : bond 0.03083 ( 838) hydrogen bonds : angle 4.08103 ( 2448) *********************** 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 214 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 156 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7266 (tp30) REVERT: A 451 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.7700 (tt0) REVERT: A 459 TRP cc_start: 0.9082 (OUTLIER) cc_final: 0.7953 (t60) REVERT: B 156 CYS cc_start: 0.7809 (p) cc_final: 0.7336 (p) REVERT: B 185 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8355 (mt) REVERT: B 449 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8608 (t80) REVERT: C 157 CYS cc_start: 0.4068 (t) cc_final: 0.3172 (p) REVERT: C 178 CYS cc_start: -0.3097 (m) cc_final: -0.3393 (m) REVERT: C 382 ASN cc_start: -0.1194 (t0) cc_final: -0.1481 (t0) REVERT: D 129 SER cc_start: 0.8581 (m) cc_final: 0.8330 (p) REVERT: D 424 TYR cc_start: 0.4225 (OUTLIER) cc_final: 0.4019 (m-10) REVERT: D 603 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8312 (tm) outliers start: 58 outliers final: 45 residues processed: 204 average time/residue: 0.0987 time to fit residues: 32.7310 Evaluate side-chains 207 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 155 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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 99 GLN Chi-restraints excluded: chain A residue 101 LEU 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 319 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 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 505 GLU 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 51 THR Chi-restraints excluded: chain B residue 72 THR 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 258 ASP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 360 LEU 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 47 TYR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 135 LEU 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 418 GLU Chi-restraints excluded: chain D residue 424 TYR 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 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 174 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 chunk 95 optimal weight: 0.5980 chunk 64 optimal weight: 5.9990 chunk 107 optimal weight: 30.0000 chunk 94 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 chunk 104 optimal weight: 30.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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** ** 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 = 0.175031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.148844 restraints weight = 32326.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.143991 restraints weight = 54550.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.141077 restraints weight = 54295.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.140081 restraints weight = 51240.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.137905 restraints weight = 45214.750| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.1773 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= 0.218 Angle : 0.643 9.972 19893 Z= 0.317 Chirality : 0.042 0.238 2377 Planarity : 0.004 0.042 2554 Dihedral : 4.937 52.435 2027 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.17 % Favored : 93.72 % Rotamer: Outliers : 4.74 % Allowed : 25.12 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.21), residues: 1879 helix: 1.97 (0.16), residues: 1081 sheet: -3.10 (0.38), residues: 154 loop : -1.23 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 417 TYR 0.013 0.001 TYR B 337 PHE 0.027 0.002 PHE D 433 TRP 0.024 0.002 TRP D 440 HIS 0.005 0.001 HIS D 146 Details of bonding type rmsd covalent geometry : bond 0.00507 (14606) covalent geometry : angle 0.64291 (19893) hydrogen bonds : bond 0.03321 ( 838) hydrogen bonds : angle 4.23264 ( 2448) *********************** 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 228 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 159 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7636 (ttm) REVERT: A 424 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7331 (tp30) REVERT: A 451 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.7799 (tt0) REVERT: A 459 TRP cc_start: 0.9045 (OUTLIER) cc_final: 0.8580 (t-100) REVERT: B 156 CYS cc_start: 0.7873 (p) cc_final: 0.7403 (p) REVERT: B 185 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8457 (mt) REVERT: B 478 GLN cc_start: 0.6914 (mm-40) cc_final: 0.6672 (mm-40) REVERT: C 157 CYS cc_start: 0.4197 (t) cc_final: 0.3299 (p) REVERT: C 178 CYS cc_start: -0.3026 (m) cc_final: -0.3322 (m) REVERT: C 203 LEU cc_start: 0.5002 (mt) cc_final: 0.4772 (pt) REVERT: C 306 THR cc_start: 0.4342 (p) cc_final: 0.4079 (p) REVERT: C 382 ASN cc_start: -0.1151 (t0) cc_final: -0.1467 (t0) REVERT: D 129 SER cc_start: 0.8631 (m) cc_final: 0.8369 (p) REVERT: D 315 MET cc_start: 0.7887 (ppp) cc_final: 0.7607 (ppp) REVERT: D 603 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8369 (tm) outliers start: 69 outliers final: 51 residues processed: 214 average time/residue: 0.0956 time to fit residues: 32.9987 Evaluate side-chains 218 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 161 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 319 CYS 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 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 505 GLU 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 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 185 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 258 ASP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 360 LEU 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 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 418 GLU 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 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 190 optimal weight: 0.3980 chunk 109 optimal weight: 50.0000 chunk 130 optimal weight: 0.5980 chunk 154 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 159 optimal weight: 9.9990 chunk 85 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.176508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.149878 restraints weight = 32270.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.143938 restraints weight = 53817.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.141992 restraints weight = 53723.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.141708 restraints weight = 48574.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.140811 restraints weight = 39495.590| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14606 Z= 0.150 Angle : 0.622 10.526 19893 Z= 0.302 Chirality : 0.041 0.265 2377 Planarity : 0.004 0.044 2554 Dihedral : 4.850 55.526 2027 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.63 % Favored : 95.26 % Rotamer: Outliers : 3.84 % Allowed : 25.94 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.21), residues: 1879 helix: 2.01 (0.16), residues: 1078 sheet: -3.30 (0.39), residues: 138 loop : -1.17 (0.25), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 417 TYR 0.020 0.001 TYR D 424 PHE 0.033 0.002 PHE D 433 TRP 0.025 0.002 TRP D 440 HIS 0.004 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00350 (14606) covalent geometry : angle 0.62239 (19893) hydrogen bonds : bond 0.03194 ( 838) hydrogen bonds : angle 4.11759 ( 2448) ********************** 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: 56 poor density : 160 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7611 (ttm) REVERT: A 424 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7239 (tp30) REVERT: A 451 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.7706 (tt0) REVERT: A 459 TRP cc_start: 0.9091 (OUTLIER) cc_final: 0.8025 (t60) REVERT: B 156 CYS cc_start: 0.7799 (p) cc_final: 0.7375 (p) REVERT: B 185 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8401 (mt) REVERT: C 157 CYS cc_start: 0.3957 (t) cc_final: 0.3160 (p) REVERT: C 178 CYS cc_start: -0.3136 (m) cc_final: -0.3400 (m) REVERT: C 203 LEU cc_start: 0.5128 (mt) cc_final: 0.4925 (pp) REVERT: C 382 ASN cc_start: -0.1091 (t0) cc_final: -0.1447 (t0) REVERT: D 129 SER cc_start: 0.8669 (m) cc_final: 0.8388 (p) REVERT: D 454 ASP cc_start: 0.7026 (t70) cc_final: 0.6822 (t70) REVERT: D 603 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8353 (tm) outliers start: 56 outliers final: 46 residues processed: 204 average time/residue: 0.0931 time to fit residues: 31.0508 Evaluate side-chains 208 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 156 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL 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 319 CYS 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 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 505 GLU 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 51 THR Chi-restraints excluded: chain B residue 72 THR 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 192 LEU 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 268 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 C residue 80 ASN 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 179 LEU Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 418 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 39 optimal weight: 0.0470 chunk 47 optimal weight: 6.9990 chunk 88 optimal weight: 0.3980 chunk 105 optimal weight: 30.0000 chunk 180 optimal weight: 0.6980 chunk 99 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 123 optimal weight: 20.0000 chunk 7 optimal weight: 0.0970 chunk 31 optimal weight: 0.0970 chunk 43 optimal weight: 0.5980 overall best weight: 0.2474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN D 588 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.177877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.152097 restraints weight = 32554.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.145965 restraints weight = 51883.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.144044 restraints weight = 56672.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.143629 restraints weight = 51714.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.142224 restraints weight = 41658.428| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14606 Z= 0.116 Angle : 0.616 11.393 19893 Z= 0.297 Chirality : 0.040 0.272 2377 Planarity : 0.004 0.045 2554 Dihedral : 4.729 59.255 2027 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.10 % Favored : 95.80 % Rotamer: Outliers : 3.09 % Allowed : 26.77 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.20), residues: 1879 helix: 2.04 (0.16), residues: 1079 sheet: -3.09 (0.40), residues: 137 loop : -1.16 (0.25), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 423 TYR 0.015 0.001 TYR D 325 PHE 0.024 0.001 PHE D 323 TRP 0.025 0.002 TRP D 440 HIS 0.005 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00261 (14606) covalent geometry : angle 0.61646 (19893) hydrogen bonds : bond 0.03051 ( 838) hydrogen bonds : angle 4.02327 ( 2448) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2706.39 seconds wall clock time: 47 minutes 41.25 seconds (2861.25 seconds total)