Starting phenix.real_space_refine on Tue Nov 18 13:55:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fa7_50268/11_2025/9fa7_50268.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fa7_50268/11_2025/9fa7_50268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fa7_50268/11_2025/9fa7_50268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fa7_50268/11_2025/9fa7_50268.map" model { file = "/net/cci-nas-00/data/ceres_data/9fa7_50268/11_2025/9fa7_50268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fa7_50268/11_2025/9fa7_50268.cif" } 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= 0.017 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 97 5.16 5 C 9395 2.51 5 N 2513 2.21 5 O 2707 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s 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: 14712 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2770 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 18, 'TRANS': 341} Chain breaks: 2 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "D" Number of atoms: 4647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4647 Classifications: {'peptide': 599} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 579} Chain breaks: 7 Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 361 Unresolved non-hydrogen dihedrals: 248 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 12, 'ASN:plan1': 5, 'PHE:plan': 3, 'ASP:plan': 4, 'TYR:plan': 6, 'GLU:plan': 5, 'TRP:plan': 1, 'GLN:plan1': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 198 Chain: "A" Number of atoms: 3737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3737 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 26, 'TRANS': 490} Chain breaks: 5 Unresolved non-hydrogen bonds: 397 Unresolved non-hydrogen angles: 497 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'TYR:plan': 4, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 13, 'ASP:plan': 10, 'GLN:plan1': 4, 'ARG:plan': 11, 'ASN:plan1': 5, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 232 Chain: "B" Number of atoms: 3558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3558 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 451} Chain breaks: 2 Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 293 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 10, 'ASN:plan1': 9, 'ARG:plan': 7, 'GLN:plan1': 3, 'GLU:plan': 9, 'PHE:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 166 Time building chain proxies: 3.63, per 1000 atoms: 0.25 Number of scatterers: 14712 At special positions: 0 Unit cell: (185.32, 127.92, 213.2, 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 97 16.00 O 2707 8.00 N 2513 7.00 C 9395 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: 1.30 Conformation dependent library (CDL) restraints added in 788.3 milliseconds 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3768 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 8 sheets defined 60.2% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'C' and resid 1 through 9 Processing helix chain 'C' and resid 12 through 35 Processing helix chain 'C' and resid 41 through 52 removed outlier: 3.832A 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 Processing helix chain 'C' and resid 141 through 158 removed outlier: 3.610A pdb=" N ARG C 147 " --> pdb=" O VAL C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 169 removed outlier: 3.682A pdb=" N LEU C 167 " --> pdb=" O SER C 163 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN C 169 " --> pdb=" O GLN C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 173 Processing helix chain 'C' and resid 174 through 189 Processing helix chain 'C' and resid 199 through 213 removed outlier: 3.518A pdb=" N ASP C 213 " --> pdb=" O TRP C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 217 removed outlier: 3.922A 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 Processing helix chain 'C' and resid 239 through 257 Proline residue: C 251 - end of helix Processing helix chain 'C' and resid 277 through 308 removed outlier: 3.786A pdb=" N LEU C 303 " --> pdb=" O MET C 299 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS C 308 " --> pdb=" O HIS C 304 " (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: 3.730A 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 17 removed outlier: 3.761A 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 52 removed outlier: 3.786A pdb=" N GLN D 43 " --> pdb=" O ASP D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 70 Processing helix chain 'D' and resid 73 through 88 Processing helix chain 'D' and resid 95 through 106 removed outlier: 3.743A 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 Processing helix chain 'D' and resid 142 through 161 removed outlier: 4.730A pdb=" N VAL D 148 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLY D 149 " --> pdb=" O GLN D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 177 Processing helix chain 'D' and resid 177 through 184 removed outlier: 3.596A pdb=" N LEU D 181 " --> pdb=" O ASP D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 212 removed outlier: 3.517A pdb=" N LYS D 197 " --> pdb=" O ASN D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 272 Processing helix chain 'D' and resid 282 through 296 removed outlier: 3.929A pdb=" N HIS D 286 " --> pdb=" O GLY D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 329 removed outlier: 4.104A pdb=" N THR D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 426 removed outlier: 3.727A pdb=" N LEU D 426 " --> pdb=" O LEU D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 441 removed outlier: 3.603A pdb=" N GLU D 432 " --> pdb=" O PHE D 428 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TRP D 440 " --> pdb=" O ILE D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 460 Processing helix chain 'D' and resid 462 through 476 Processing helix chain 'D' and resid 490 through 505 removed outlier: 4.234A pdb=" N ARG D 494 " --> pdb=" O LEU D 490 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 523 removed outlier: 3.616A pdb=" N TYR D 522 " --> pdb=" O ASP D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 577 Proline residue: D 562 - end of helix Processing helix chain 'D' and resid 583 through 593 Processing helix chain 'D' and resid 600 through 615 Processing helix chain 'D' and resid 621 through 626 removed outlier: 3.533A pdb=" N TYR D 625 " --> pdb=" O ASN D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 641 removed outlier: 3.769A pdb=" N GLU D 634 " --> pdb=" O ASP D 630 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR D 637 " --> pdb=" O GLU D 633 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU D 638 " --> pdb=" O GLU D 634 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG D 639 " --> pdb=" O PHE D 635 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR D 640 " --> pdb=" O ALA D 636 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN D 641 " --> pdb=" O TYR D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 660 Processing helix chain 'D' and resid 667 through 686 removed outlier: 4.147A pdb=" N PHE D 675 " --> pdb=" O VAL D 671 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG D 676 " --> pdb=" O LYS D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 701 Processing helix chain 'D' and resid 704 through 709 removed outlier: 4.053A pdb=" N THR D 708 " --> pdb=" O LEU D 704 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU D 709 " --> pdb=" O LEU D 705 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 704 through 709' Processing helix chain 'A' and resid 17 through 22 removed outlier: 4.161A 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 97 through 109 Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.528A pdb=" N CYS A 119 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N CYS A 120 " --> pdb=" O PRO A 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 120' Processing helix chain 'A' and resid 122 through 134 removed outlier: 3.617A pdb=" N CYS A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 147 Processing helix chain 'A' and resid 168 through 193 removed outlier: 3.931A pdb=" N ASN A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 255 removed outlier: 3.893A pdb=" N PHE A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 291 removed outlier: 3.569A pdb=" N VAL A 291 " --> pdb=" O ASP A 288 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 288 through 291' Processing helix chain 'A' and resid 344 through 356 Processing helix chain 'A' and resid 414 through 425 Processing helix chain 'A' and resid 443 through 456 Processing helix chain 'A' and resid 462 through 466 Processing helix chain 'A' and resid 474 through 482 removed outlier: 4.011A 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: 3.665A 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: 3.988A pdb=" N LEU B 73 " --> pdb=" O ASP B 69 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU B 75 " --> pdb=" O ASN B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 103 removed outlier: 3.603A pdb=" N ALA B 91 " --> pdb=" O CYS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 137 removed outlier: 4.123A pdb=" N ASN B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N GLN B 135 " --> pdb=" O ALA B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 168 removed outlier: 3.767A pdb=" N GLN B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASP B 167 " --> pdb=" O LEU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 178 removed outlier: 3.527A pdb=" N ASP B 177 " --> pdb=" O GLU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 208 Processing helix chain 'B' and resid 258 through 263 removed outlier: 3.744A pdb=" N SER B 263 " --> pdb=" O ILE B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 309 through 321 Processing helix chain 'B' and resid 360 through 364 removed outlier: 3.675A 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 408 through 425 removed outlier: 3.840A 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 removed outlier: 3.892A pdb=" N LEU B 453 " --> pdb=" O PHE B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 490 Processing sheet with id=AA1, first strand: chain 'D' and resid 345 through 347 Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 87 removed outlier: 3.759A pdb=" N HIS A 86 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 80 " --> pdb=" O HIS A 86 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N THR A 10 " --> pdb=" O ASN A 77 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ILE A 79 " --> pdb=" O THR A 10 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N PHE A 12 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N SER A 81 " --> pdb=" O PHE A 12 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A 14 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 163 " --> pdb=" O VAL A 13 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU A 203 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR A 231 " --> pdb=" O CYS A 202 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU A 226 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 257 through 260 removed outlier: 4.356A pdb=" N HIS A 286 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ARG A 336 " --> pdb=" O HIS A 286 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR A 335 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ILE A 384 " --> pdb=" O ILE A 337 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE A 373 " --> pdb=" O GLN A 364 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLN A 364 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N HIS A 375 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 360 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU A 361 " --> pdb=" O CYS A 319 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 427 through 429 Processing sheet with id=AA5, first strand: chain 'B' and resid 7 through 8 removed outlier: 3.567A pdb=" N PHE B 56 " --> pdb=" O MET B 7 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N THR B 51 " --> pdb=" O PRO B 65 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LEU B 53 " --> pdb=" O MET B 63 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET B 63 " --> pdb=" O LEU B 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 7 through 8 removed outlier: 3.567A pdb=" N PHE B 56 " --> pdb=" O MET B 7 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N THR B 3 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N VAL B 54 " --> pdb=" O THR B 3 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 16 through 17 removed outlier: 4.137A pdb=" N TYR B 25 " --> pdb=" O VAL B 17 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 212 through 218 removed outlier: 4.500A pdb=" N PHE B 212 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET B 335 " --> pdb=" O SER B 351 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N TRP B 332 " --> pdb=" O LEU B 328 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 326 " --> pdb=" O GLY B 334 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE B 325 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU B 252 " --> pdb=" O GLN B 327 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLY B 329 " --> pdb=" O ASP B 250 " (cutoff:3.500A) removed outlier: 10.640A pdb=" N ASP B 250 " --> pdb=" O GLY B 329 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N LEU B 251 " --> pdb=" O HIS B 213 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL B 215 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ILE B 253 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LYS B 217 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N GLY B 255 " --> pdb=" O LYS B 217 " (cutoff:3.500A) 845 hydrogen bonds defined for protein. 2487 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: 2.62 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3884 1.33 - 1.45: 2448 1.45 - 1.57: 8521 1.57 - 1.69: 0 1.69 - 1.81: 146 Bond restraints: 14999 Sorted by residual: bond pdb=" N HIS D 186 " pdb=" CA HIS D 186 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.22e+00 bond pdb=" N ASP D 187 " pdb=" CA ASP D 187 " ideal model delta sigma weight residual 1.457 1.486 -0.028 1.29e-02 6.01e+03 4.75e+00 bond pdb=" CG HIS D 186 " pdb=" CD2 HIS D 186 " ideal model delta sigma weight residual 1.354 1.338 0.016 1.10e-02 8.26e+03 2.21e+00 bond pdb=" CG GLU C 307 " pdb=" CD GLU C 307 " ideal model delta sigma weight residual 1.516 1.479 0.037 2.50e-02 1.60e+03 2.13e+00 bond pdb=" SD MET C 205 " pdb=" CE MET C 205 " ideal model delta sigma weight residual 1.791 1.756 0.035 2.50e-02 1.60e+03 1.99e+00 ... (remaining 14994 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 20042 1.93 - 3.86: 313 3.86 - 5.79: 46 5.79 - 7.72: 13 7.72 - 9.65: 8 Bond angle restraints: 20422 Sorted by residual: angle pdb=" CA LYS C 150 " pdb=" CB LYS C 150 " pdb=" CG LYS C 150 " ideal model delta sigma weight residual 114.10 122.70 -8.60 2.00e+00 2.50e-01 1.85e+01 angle pdb=" C GLU D 130 " pdb=" N MET D 131 " pdb=" CA MET D 131 " ideal model delta sigma weight residual 121.58 113.25 8.33 1.95e+00 2.63e-01 1.82e+01 angle pdb=" N ASN D 580 " pdb=" CA ASN D 580 " pdb=" C ASN D 580 " ideal model delta sigma weight residual 108.45 113.63 -5.18 1.26e+00 6.30e-01 1.69e+01 angle pdb=" N VAL A 229 " pdb=" CA VAL A 229 " pdb=" C VAL A 229 " ideal model delta sigma weight residual 112.43 108.93 3.50 9.20e-01 1.18e+00 1.45e+01 angle pdb=" C HIS D 186 " pdb=" CA HIS D 186 " pdb=" CB HIS D 186 " ideal model delta sigma weight residual 110.42 117.83 -7.41 1.99e+00 2.53e-01 1.39e+01 ... (remaining 20417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 7940 17.80 - 35.60: 878 35.60 - 53.40: 202 53.40 - 71.20: 54 71.20 - 89.00: 10 Dihedral angle restraints: 9084 sinusoidal: 3330 harmonic: 5754 Sorted by residual: dihedral pdb=" CA LEU D 525 " pdb=" C LEU D 525 " pdb=" N PRO D 526 " pdb=" CA PRO D 526 " ideal model delta harmonic sigma weight residual -180.00 -156.07 -23.93 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA VAL D 524 " pdb=" C VAL D 524 " pdb=" N LEU D 525 " pdb=" CA LEU D 525 " ideal model delta harmonic sigma weight residual 180.00 158.31 21.69 0 5.00e+00 4.00e-02 1.88e+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 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 9081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1737 0.036 - 0.071: 520 0.071 - 0.106: 144 0.106 - 0.142: 35 0.142 - 0.177: 2 Chirality restraints: 2438 Sorted by residual: chirality pdb=" CA MET D 131 " pdb=" N MET D 131 " pdb=" C MET D 131 " pdb=" CB MET D 131 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.87e-01 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 -2.44 -0.14 2.00e-01 2.50e+01 5.25e-01 chirality pdb=" CG LEU A 88 " pdb=" CB LEU A 88 " pdb=" CD1 LEU A 88 " pdb=" CD2 LEU A 88 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 2435 not shown) Planarity restraints: 2611 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 351 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.95e+00 pdb=" C VAL D 351 " -0.042 2.00e-02 2.50e+03 pdb=" O VAL D 351 " 0.016 2.00e-02 2.50e+03 pdb=" N SER D 352 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 144 " -0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO B 145 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 145 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 145 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 264 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO B 265 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 265 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 265 " 0.022 5.00e-02 4.00e+02 ... (remaining 2608 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1398 2.74 - 3.28: 15254 3.28 - 3.82: 24770 3.82 - 4.36: 26960 4.36 - 4.90: 45985 Nonbonded interactions: 114367 Sorted by model distance: nonbonded pdb=" OE1 GLN A 93 " pdb=" OH TYR A 139 " model vdw 2.203 3.040 nonbonded pdb=" O ARG B 462 " pdb=" OG1 THR B 465 " model vdw 2.211 3.040 nonbonded pdb=" O CYS D 292 " pdb=" ND2 ASN D 296 " model vdw 2.234 3.120 nonbonded pdb=" OH TYR D 355 " pdb=" OE2 GLU D 596 " model vdw 2.246 3.040 nonbonded pdb=" OD2 ASP A 15 " pdb=" OG1 THR A 164 " model vdw 2.265 3.040 ... (remaining 114362 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: 14.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.440 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.570 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 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 0.037 14999 Z= 0.140 Angle : 0.619 9.653 20422 Z= 0.325 Chirality : 0.038 0.177 2438 Planarity : 0.003 0.041 2611 Dihedral : 16.132 88.996 5316 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.52 % Favored : 94.43 % Rotamer: Outliers : 1.91 % Allowed : 23.48 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % 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: 0.35 (0.21), residues: 1921 helix: 1.71 (0.16), residues: 1070 sheet: -3.26 (0.38), residues: 162 loop : -1.22 (0.25), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 100 TYR 0.018 0.001 TYR B 499 PHE 0.021 0.001 PHE B 212 TRP 0.017 0.001 TRP C 209 HIS 0.006 0.001 HIS D 186 Details of bonding type rmsd covalent geometry : bond 0.00298 (14999) covalent geometry : angle 0.61904 (20422) hydrogen bonds : bond 0.16600 ( 844) hydrogen bonds : angle 6.09049 ( 2487) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.640 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: C 46 GLU cc_start: 0.2205 (pp20) cc_final: 0.1476 (pp20) REVERT: C 328 GLU cc_start: -0.1190 (pt0) cc_final: -0.2225 (pp20) REVERT: C 372 LEU cc_start: -0.5480 (OUTLIER) cc_final: -0.5907 (mt) REVERT: D 1 MET cc_start: -0.1641 (ttt) cc_final: -0.2311 (ttt) REVERT: D 455 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.6827 (mpp) REVERT: D 520 MET cc_start: 0.8151 (mmm) cc_final: 0.7879 (mmp) REVERT: D 551 LYS cc_start: 0.8251 (mtmt) cc_final: 0.7484 (mttt) REVERT: A 60 MET cc_start: 0.7925 (mmm) cc_final: 0.7577 (mmm) REVERT: A 66 MET cc_start: 0.9223 (tpt) cc_final: 0.8644 (tpt) REVERT: A 425 ASN cc_start: 0.8860 (OUTLIER) cc_final: 0.8536 (t0) REVERT: A 451 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8064 (tt0) REVERT: A 455 HIS cc_start: 0.8208 (OUTLIER) cc_final: 0.7580 (t-90) REVERT: B 200 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.7000 (tpp) outliers start: 29 outliers final: 23 residues processed: 173 average time/residue: 0.1153 time to fit residues: 31.0715 Evaluate side-chains 174 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 209 TRP Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 412 SER Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 403 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 50.0000 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.2980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 296 ASN D 330 GLN D 492 HIS D 621 ASN A 8 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.200886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.184136 restraints weight = 30139.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.180823 restraints weight = 51855.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.178455 restraints weight = 54597.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.178125 restraints weight = 52764.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.177429 restraints weight = 39134.538| |-----------------------------------------------------------------------------| r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14999 Z= 0.182 Angle : 0.604 13.935 20422 Z= 0.306 Chirality : 0.039 0.183 2438 Planarity : 0.004 0.046 2611 Dihedral : 6.351 59.621 2108 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.99 % Favored : 93.91 % Rotamer: Outliers : 4.68 % Allowed : 19.39 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % 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: 0.54 (0.21), residues: 1921 helix: 1.82 (0.16), residues: 1089 sheet: -3.21 (0.37), residues: 170 loop : -1.10 (0.26), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 147 TYR 0.014 0.001 TYR A 62 PHE 0.020 0.001 PHE A 385 TRP 0.008 0.001 TRP A 318 HIS 0.007 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00419 (14999) covalent geometry : angle 0.60450 (20422) hydrogen bonds : bond 0.04139 ( 844) hydrogen bonds : angle 4.65288 ( 2487) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 153 time to evaluate : 0.628 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: C 46 GLU cc_start: 0.2020 (pp20) cc_final: 0.1231 (pp20) REVERT: C 94 ILE cc_start: -0.2514 (OUTLIER) cc_final: -0.2876 (mt) REVERT: C 98 LEU cc_start: -0.3734 (OUTLIER) cc_final: -0.4369 (tp) REVERT: C 328 GLU cc_start: -0.0621 (pt0) cc_final: -0.2052 (pp20) REVERT: D 1 MET cc_start: -0.1635 (ttt) cc_final: -0.2320 (ttt) REVERT: D 551 LYS cc_start: 0.8229 (mtmt) cc_final: 0.7330 (mttt) REVERT: D 603 LEU cc_start: 0.8368 (tp) cc_final: 0.8127 (tp) REVERT: A 402 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.7931 (tp) REVERT: A 425 ASN cc_start: 0.9006 (OUTLIER) cc_final: 0.8631 (t0) REVERT: A 451 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8121 (tt0) REVERT: A 455 HIS cc_start: 0.8183 (OUTLIER) cc_final: 0.7676 (t-90) REVERT: B 188 ILE cc_start: 0.7971 (tt) cc_final: 0.7683 (tt) REVERT: B 200 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.7204 (tpp) outliers start: 71 outliers final: 33 residues processed: 206 average time/residue: 0.1165 time to fit residues: 36.8783 Evaluate side-chains 182 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 209 TRP Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 492 HIS Chi-restraints excluded: chain D residue 596 GLU Chi-restraints excluded: chain D residue 697 PHE Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 403 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 125 optimal weight: 0.9980 chunk 56 optimal weight: 0.0670 chunk 33 optimal weight: 0.3980 chunk 165 optimal weight: 0.9990 chunk 166 optimal weight: 0.1980 chunk 20 optimal weight: 5.9990 chunk 18 optimal weight: 0.3980 chunk 189 optimal weight: 0.2980 chunk 17 optimal weight: 40.0000 chunk 91 optimal weight: 0.0370 chunk 186 optimal weight: 0.0070 overall best weight: 0.1214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 395 HIS A 93 GLN A 171 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.202996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.186959 restraints weight = 31139.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.183073 restraints weight = 52086.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.180449 restraints weight = 58731.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.179756 restraints weight = 57487.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.178730 restraints weight = 49839.801| |-----------------------------------------------------------------------------| r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14999 Z= 0.110 Angle : 0.569 11.413 20422 Z= 0.283 Chirality : 0.038 0.266 2438 Planarity : 0.004 0.039 2611 Dihedral : 5.757 57.125 2086 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.79 % Favored : 95.16 % Rotamer: Outliers : 3.03 % Allowed : 20.58 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % 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: 1921 helix: 1.92 (0.16), residues: 1083 sheet: -2.85 (0.38), residues: 168 loop : -1.00 (0.26), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 147 TYR 0.023 0.001 TYR D 325 PHE 0.013 0.001 PHE D 139 TRP 0.007 0.001 TRP D 23 HIS 0.016 0.001 HIS D 492 Details of bonding type rmsd covalent geometry : bond 0.00228 (14999) covalent geometry : angle 0.56895 (20422) hydrogen bonds : bond 0.03482 ( 844) hydrogen bonds : angle 4.34134 ( 2487) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 156 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 GLU cc_start: 0.1959 (pp20) cc_final: 0.1154 (pp20) REVERT: C 94 ILE cc_start: -0.2605 (OUTLIER) cc_final: -0.3008 (mt) REVERT: C 98 LEU cc_start: -0.3804 (OUTLIER) cc_final: -0.4411 (tp) REVERT: C 307 GLU cc_start: 0.3625 (OUTLIER) cc_final: 0.1060 (pt0) REVERT: C 328 GLU cc_start: -0.0935 (pt0) cc_final: -0.1945 (pp20) REVERT: D 1 MET cc_start: -0.1717 (ttt) cc_final: -0.2382 (ttt) REVERT: D 679 MET cc_start: 0.7827 (tpp) cc_final: 0.7285 (tpp) REVERT: D 695 HIS cc_start: 0.7230 (OUTLIER) cc_final: 0.6431 (t-170) REVERT: A 60 MET cc_start: 0.8187 (mmm) cc_final: 0.7626 (mmm) REVERT: A 66 MET cc_start: 0.9241 (tpt) cc_final: 0.8908 (tpt) REVERT: A 267 MET cc_start: 0.7246 (tpp) cc_final: 0.6628 (tpp) REVERT: A 425 ASN cc_start: 0.8900 (OUTLIER) cc_final: 0.8556 (t0) REVERT: A 451 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.7698 (tt0) REVERT: A 455 HIS cc_start: 0.8152 (OUTLIER) cc_final: 0.7617 (t-90) REVERT: B 188 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7689 (tt) REVERT: B 200 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7228 (tpp) outliers start: 46 outliers final: 18 residues processed: 189 average time/residue: 0.0999 time to fit residues: 30.3937 Evaluate side-chains 169 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 209 TRP Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 695 HIS Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 154 optimal weight: 0.6980 chunk 180 optimal weight: 0.4980 chunk 98 optimal weight: 0.0000 chunk 59 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 39 optimal weight: 20.0000 chunk 31 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 124 optimal weight: 0.0040 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 HIS B 164 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.201667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.185552 restraints weight = 30777.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.182631 restraints weight = 51687.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.180271 restraints weight = 47981.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.178712 restraints weight = 51208.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.176994 restraints weight = 52755.626| |-----------------------------------------------------------------------------| r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6487 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14999 Z= 0.136 Angle : 0.566 10.501 20422 Z= 0.282 Chirality : 0.039 0.176 2438 Planarity : 0.004 0.039 2611 Dihedral : 5.484 54.809 2079 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.93 % Favored : 94.01 % Rotamer: Outliers : 2.97 % Allowed : 21.37 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % 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: 1921 helix: 1.92 (0.16), residues: 1093 sheet: -2.81 (0.38), residues: 168 loop : -1.11 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 230 TYR 0.022 0.001 TYR D 325 PHE 0.017 0.001 PHE B 449 TRP 0.008 0.001 TRP A 318 HIS 0.009 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00309 (14999) covalent geometry : angle 0.56596 (20422) hydrogen bonds : bond 0.03328 ( 844) hydrogen bonds : angle 4.21382 ( 2487) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 144 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 94 ILE cc_start: -0.2601 (OUTLIER) cc_final: -0.2983 (mt) REVERT: C 98 LEU cc_start: -0.3784 (OUTLIER) cc_final: -0.4368 (tp) REVERT: C 307 GLU cc_start: 0.3661 (OUTLIER) cc_final: 0.1115 (pt0) REVERT: C 328 GLU cc_start: -0.0961 (pt0) cc_final: -0.1964 (pp20) REVERT: D 1 MET cc_start: -0.1747 (ttt) cc_final: -0.2421 (ttt) REVERT: D 520 MET cc_start: 0.7853 (mmt) cc_final: 0.7632 (mmt) REVERT: D 551 LYS cc_start: 0.8062 (mtmt) cc_final: 0.7640 (mttt) REVERT: D 695 HIS cc_start: 0.7320 (OUTLIER) cc_final: 0.6485 (t-170) REVERT: A 60 MET cc_start: 0.8181 (mmm) cc_final: 0.7770 (mmm) REVERT: A 66 MET cc_start: 0.9177 (tpt) cc_final: 0.8751 (tpp) REVERT: A 267 MET cc_start: 0.7278 (tpp) cc_final: 0.6589 (tpp) REVERT: A 402 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.7875 (tp) REVERT: A 425 ASN cc_start: 0.8952 (OUTLIER) cc_final: 0.8707 (t0) REVERT: A 455 HIS cc_start: 0.8154 (OUTLIER) cc_final: 0.7471 (t-90) REVERT: B 188 ILE cc_start: 0.7952 (tt) cc_final: 0.7721 (tt) REVERT: B 200 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.7286 (tpp) outliers start: 45 outliers final: 25 residues processed: 176 average time/residue: 0.1066 time to fit residues: 29.8994 Evaluate side-chains 173 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 209 TRP Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 695 HIS Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 51 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 168 optimal weight: 0.4980 chunk 156 optimal weight: 1.9990 chunk 182 optimal weight: 0.0060 chunk 162 optimal weight: 0.8980 chunk 154 optimal weight: 0.6980 chunk 151 optimal weight: 0.3980 chunk 149 optimal weight: 0.1980 chunk 5 optimal weight: 4.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.202127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.185068 restraints weight = 30967.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.182714 restraints weight = 55946.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.180767 restraints weight = 46977.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.179194 restraints weight = 48345.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.177397 restraints weight = 51860.939| |-----------------------------------------------------------------------------| r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14999 Z= 0.122 Angle : 0.564 15.645 20422 Z= 0.279 Chirality : 0.038 0.223 2438 Planarity : 0.003 0.038 2611 Dihedral : 5.184 59.380 2074 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.05 % Favored : 94.90 % Rotamer: Outliers : 3.63 % Allowed : 20.25 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % 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: 1921 helix: 1.99 (0.16), residues: 1087 sheet: -2.77 (0.38), residues: 168 loop : -1.14 (0.26), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 441 TYR 0.024 0.001 TYR D 325 PHE 0.019 0.001 PHE B 449 TRP 0.007 0.001 TRP A 318 HIS 0.008 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00278 (14999) covalent geometry : angle 0.56354 (20422) hydrogen bonds : bond 0.03190 ( 844) hydrogen bonds : angle 4.10211 ( 2487) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 149 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 94 ILE cc_start: -0.2669 (OUTLIER) cc_final: -0.3044 (mt) REVERT: C 98 LEU cc_start: -0.3805 (OUTLIER) cc_final: -0.4373 (tp) REVERT: C 307 GLU cc_start: 0.3535 (OUTLIER) cc_final: 0.0941 (pt0) REVERT: C 328 GLU cc_start: -0.0989 (pt0) cc_final: -0.1978 (pp20) REVERT: D 1 MET cc_start: -0.1781 (ttt) cc_final: -0.2467 (ttt) REVERT: D 695 HIS cc_start: 0.7280 (OUTLIER) cc_final: 0.6508 (t-170) REVERT: A 60 MET cc_start: 0.8146 (mmm) cc_final: 0.7927 (mmm) REVERT: A 66 MET cc_start: 0.9136 (tpt) cc_final: 0.8881 (tpp) REVERT: A 131 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6479 (tm-30) REVERT: A 267 MET cc_start: 0.7239 (tpp) cc_final: 0.6584 (tpp) REVERT: A 402 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.7870 (tp) REVERT: A 455 HIS cc_start: 0.8136 (OUTLIER) cc_final: 0.7579 (t-90) REVERT: B 188 ILE cc_start: 0.7891 (OUTLIER) cc_final: 0.7655 (tt) outliers start: 55 outliers final: 28 residues processed: 188 average time/residue: 0.1099 time to fit residues: 32.9230 Evaluate side-chains 177 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 209 TRP Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 695 HIS Chi-restraints excluded: chain D residue 697 PHE Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 189 optimal weight: 0.9990 chunk 137 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 chunk 111 optimal weight: 0.0870 chunk 12 optimal weight: 0.0270 chunk 127 optimal weight: 3.9990 chunk 165 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 179 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.201809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.184647 restraints weight = 30069.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.181428 restraints weight = 50737.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.179253 restraints weight = 51191.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.179012 restraints weight = 49371.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.178276 restraints weight = 38172.569| |-----------------------------------------------------------------------------| r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14999 Z= 0.136 Angle : 0.577 10.521 20422 Z= 0.285 Chirality : 0.039 0.223 2438 Planarity : 0.004 0.038 2611 Dihedral : 4.923 57.700 2069 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.31 % Favored : 94.64 % Rotamer: Outliers : 3.89 % Allowed : 19.99 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % 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: 0.76 (0.21), residues: 1921 helix: 2.00 (0.16), residues: 1087 sheet: -2.80 (0.38), residues: 170 loop : -1.12 (0.26), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 441 TYR 0.033 0.001 TYR D 325 PHE 0.018 0.001 PHE B 449 TRP 0.008 0.001 TRP A 318 HIS 0.008 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00314 (14999) covalent geometry : angle 0.57735 (20422) hydrogen bonds : bond 0.03184 ( 844) hydrogen bonds : angle 4.10166 ( 2487) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 146 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 94 ILE cc_start: -0.2666 (OUTLIER) cc_final: -0.3046 (mt) REVERT: C 98 LEU cc_start: -0.3818 (OUTLIER) cc_final: -0.4364 (tp) REVERT: C 307 GLU cc_start: 0.3578 (OUTLIER) cc_final: 0.0854 (pt0) REVERT: C 328 GLU cc_start: -0.0984 (pt0) cc_final: -0.1976 (pp20) REVERT: D 1 MET cc_start: -0.1743 (ttt) cc_final: -0.2408 (ttt) REVERT: D 494 ARG cc_start: 0.6863 (OUTLIER) cc_final: 0.6412 (ttp80) REVERT: D 662 THR cc_start: -0.1711 (OUTLIER) cc_final: -0.2041 (m) REVERT: D 679 MET cc_start: 0.7625 (tpp) cc_final: 0.7317 (tpp) REVERT: D 695 HIS cc_start: 0.7268 (OUTLIER) cc_final: 0.6519 (t-170) REVERT: A 66 MET cc_start: 0.9223 (tpt) cc_final: 0.8964 (tpp) REVERT: A 131 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6489 (tm-30) REVERT: A 267 MET cc_start: 0.7209 (tpp) cc_final: 0.6562 (tpp) REVERT: A 402 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.7860 (tp) REVERT: A 424 GLU cc_start: 0.8296 (tm-30) cc_final: 0.8004 (tm-30) REVERT: A 425 ASN cc_start: 0.9022 (OUTLIER) cc_final: 0.8735 (t0) REVERT: A 451 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: A 455 HIS cc_start: 0.8369 (OUTLIER) cc_final: 0.7647 (t-90) REVERT: B 83 TYR cc_start: 0.8480 (m-10) cc_final: 0.8120 (m-10) REVERT: B 200 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7432 (ttm) outliers start: 59 outliers final: 34 residues processed: 190 average time/residue: 0.1047 time to fit residues: 31.5656 Evaluate side-chains 187 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 141 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 209 TRP Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 494 ARG Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 662 THR Chi-restraints excluded: chain D residue 695 HIS Chi-restraints excluded: chain D residue 697 PHE Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 53 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 91 optimal weight: 0.3980 chunk 121 optimal weight: 0.0980 chunk 142 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 83 optimal weight: 0.4980 chunk 65 optimal weight: 0.0980 chunk 85 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 200 ASN ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 HIS A 425 ASN ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.202212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.184802 restraints weight = 30100.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.180380 restraints weight = 51609.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.178282 restraints weight = 60570.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.178144 restraints weight = 57281.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.177327 restraints weight = 41937.500| |-----------------------------------------------------------------------------| r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14999 Z= 0.124 Angle : 0.595 14.314 20422 Z= 0.289 Chirality : 0.039 0.223 2438 Planarity : 0.003 0.038 2611 Dihedral : 4.702 53.095 2066 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.00 % Favored : 94.95 % Rotamer: Outliers : 3.50 % Allowed : 21.64 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % 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: 0.78 (0.21), residues: 1921 helix: 2.03 (0.16), residues: 1088 sheet: -2.74 (0.38), residues: 168 loop : -1.14 (0.26), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 426 TYR 0.031 0.001 TYR D 325 PHE 0.023 0.001 PHE B 449 TRP 0.008 0.001 TRP A 318 HIS 0.004 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00283 (14999) covalent geometry : angle 0.59466 (20422) hydrogen bonds : bond 0.03135 ( 844) hydrogen bonds : angle 4.08520 ( 2487) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 141 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 94 ILE cc_start: -0.2709 (OUTLIER) cc_final: -0.3097 (mt) REVERT: C 98 LEU cc_start: -0.3969 (OUTLIER) cc_final: -0.4483 (tp) REVERT: C 307 GLU cc_start: 0.3838 (OUTLIER) cc_final: 0.1243 (pt0) REVERT: C 328 GLU cc_start: -0.1286 (pt0) cc_final: -0.2118 (pp20) REVERT: D 1 MET cc_start: -0.1876 (ttt) cc_final: -0.2524 (ttt) REVERT: D 494 ARG cc_start: 0.6877 (OUTLIER) cc_final: 0.6462 (ttp80) REVERT: D 551 LYS cc_start: 0.8079 (mttt) cc_final: 0.7718 (mttp) REVERT: D 662 THR cc_start: -0.1748 (OUTLIER) cc_final: -0.2067 (m) REVERT: D 679 MET cc_start: 0.7666 (tpp) cc_final: 0.7385 (tpp) REVERT: D 695 HIS cc_start: 0.7198 (OUTLIER) cc_final: 0.6503 (t-170) REVERT: A 60 MET cc_start: 0.7954 (mmm) cc_final: 0.7424 (mmm) REVERT: A 66 MET cc_start: 0.9187 (tpt) cc_final: 0.8807 (tpp) REVERT: A 131 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.6451 (tm-30) REVERT: A 267 MET cc_start: 0.7184 (tpp) cc_final: 0.6554 (tpp) REVERT: A 402 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.7877 (tp) REVERT: A 424 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7867 (tm-30) REVERT: A 425 ASN cc_start: 0.8941 (OUTLIER) cc_final: 0.8679 (t0) REVERT: A 451 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.7755 (tt0) REVERT: A 455 HIS cc_start: 0.8409 (OUTLIER) cc_final: 0.7533 (t-90) REVERT: B 83 TYR cc_start: 0.8406 (m-10) cc_final: 0.8158 (m-10) REVERT: B 200 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7435 (ttm) outliers start: 53 outliers final: 33 residues processed: 179 average time/residue: 0.1097 time to fit residues: 31.3280 Evaluate side-chains 184 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 139 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 209 TRP Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 494 ARG Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 662 THR Chi-restraints excluded: chain D residue 695 HIS Chi-restraints excluded: chain D residue 697 PHE Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 67 optimal weight: 0.7980 chunk 180 optimal weight: 0.0970 chunk 176 optimal weight: 0.5980 chunk 48 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 157 optimal weight: 0.2980 chunk 18 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 6 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 184 optimal weight: 4.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.201505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.185314 restraints weight = 30210.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.181503 restraints weight = 51907.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.179954 restraints weight = 55550.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.178861 restraints weight = 57125.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.177630 restraints weight = 48574.030| |-----------------------------------------------------------------------------| r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14999 Z= 0.146 Angle : 0.603 13.218 20422 Z= 0.294 Chirality : 0.039 0.222 2438 Planarity : 0.004 0.039 2611 Dihedral : 4.722 53.421 2066 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.47 % Favored : 94.48 % Rotamer: Outliers : 3.89 % Allowed : 20.84 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % 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: 1921 helix: 2.02 (0.16), residues: 1088 sheet: -2.80 (0.38), residues: 170 loop : -1.07 (0.26), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 426 TYR 0.030 0.001 TYR D 325 PHE 0.026 0.001 PHE B 449 TRP 0.009 0.001 TRP C 209 HIS 0.009 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00340 (14999) covalent geometry : angle 0.60313 (20422) hydrogen bonds : bond 0.03168 ( 844) hydrogen bonds : angle 4.09828 ( 2487) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 143 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 94 ILE cc_start: -0.2704 (OUTLIER) cc_final: -0.3084 (mt) REVERT: C 98 LEU cc_start: -0.3903 (OUTLIER) cc_final: -0.4431 (tp) REVERT: C 307 GLU cc_start: 0.3775 (OUTLIER) cc_final: 0.1156 (pt0) REVERT: C 328 GLU cc_start: -0.1229 (pt0) cc_final: -0.2095 (pp20) REVERT: D 1 MET cc_start: -0.1834 (ttt) cc_final: -0.2407 (ttt) REVERT: D 494 ARG cc_start: 0.6860 (OUTLIER) cc_final: 0.6483 (ttp80) REVERT: D 551 LYS cc_start: 0.8107 (mttt) cc_final: 0.7875 (mttt) REVERT: D 608 VAL cc_start: 0.8660 (m) cc_final: 0.8343 (t) REVERT: D 662 THR cc_start: -0.1734 (OUTLIER) cc_final: -0.2052 (m) REVERT: D 679 MET cc_start: 0.7564 (tpp) cc_final: 0.7206 (tpp) REVERT: D 695 HIS cc_start: 0.7227 (OUTLIER) cc_final: 0.6517 (t-170) REVERT: A 60 MET cc_start: 0.8052 (mmm) cc_final: 0.7575 (mmm) REVERT: A 66 MET cc_start: 0.9164 (tpt) cc_final: 0.8834 (tpp) REVERT: A 267 MET cc_start: 0.7214 (tpp) cc_final: 0.6520 (tpp) REVERT: A 402 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.7852 (tp) REVERT: A 424 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7897 (tm-30) REVERT: A 451 GLN cc_start: 0.9086 (OUTLIER) cc_final: 0.7806 (tt0) REVERT: A 455 HIS cc_start: 0.8405 (OUTLIER) cc_final: 0.7514 (t-90) REVERT: B 83 TYR cc_start: 0.8400 (m-10) cc_final: 0.8136 (m-10) REVERT: B 200 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7237 (ttm) outliers start: 59 outliers final: 39 residues processed: 189 average time/residue: 0.1092 time to fit residues: 32.9076 Evaluate side-chains 190 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 141 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 209 TRP Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 494 ARG Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 662 THR Chi-restraints excluded: chain D residue 695 HIS Chi-restraints excluded: chain D residue 697 PHE Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 137 optimal weight: 1.9990 chunk 185 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 chunk 102 optimal weight: 0.0170 chunk 170 optimal weight: 0.7980 chunk 12 optimal weight: 20.0000 chunk 168 optimal weight: 0.8980 chunk 8 optimal weight: 30.0000 chunk 92 optimal weight: 0.9980 chunk 121 optimal weight: 0.0770 chunk 101 optimal weight: 0.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 146 HIS ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN A 493 ASN ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.201181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.186249 restraints weight = 29947.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.182353 restraints weight = 44335.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.180965 restraints weight = 49720.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.178208 restraints weight = 51441.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.176319 restraints weight = 57382.006| |-----------------------------------------------------------------------------| r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14999 Z= 0.140 Angle : 0.610 14.331 20422 Z= 0.297 Chirality : 0.039 0.237 2438 Planarity : 0.004 0.039 2611 Dihedral : 4.758 54.040 2066 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.31 % Favored : 94.64 % Rotamer: Outliers : 3.69 % Allowed : 21.17 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % 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: 0.81 (0.21), residues: 1921 helix: 2.03 (0.16), residues: 1084 sheet: -2.81 (0.38), residues: 170 loop : -1.03 (0.26), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 441 TYR 0.029 0.001 TYR D 325 PHE 0.031 0.001 PHE B 449 TRP 0.009 0.001 TRP C 209 HIS 0.010 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00324 (14999) covalent geometry : angle 0.60950 (20422) hydrogen bonds : bond 0.03124 ( 844) hydrogen bonds : angle 4.07869 ( 2487) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 154 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 94 ILE cc_start: -0.2738 (OUTLIER) cc_final: -0.3119 (mt) REVERT: C 98 LEU cc_start: -0.3932 (OUTLIER) cc_final: -0.4421 (tp) REVERT: C 307 GLU cc_start: 0.3815 (OUTLIER) cc_final: 0.1160 (pt0) REVERT: C 328 GLU cc_start: -0.1273 (pt0) cc_final: -0.2108 (pp20) REVERT: D 1 MET cc_start: -0.1831 (ttt) cc_final: -0.2410 (ttt) REVERT: D 494 ARG cc_start: 0.6814 (OUTLIER) cc_final: 0.6457 (ttp80) REVERT: D 551 LYS cc_start: 0.8137 (mttt) cc_final: 0.7921 (mttt) REVERT: D 662 THR cc_start: -0.1728 (OUTLIER) cc_final: -0.2002 (m) REVERT: D 679 MET cc_start: 0.7597 (tpp) cc_final: 0.7273 (tpp) REVERT: D 695 HIS cc_start: 0.7199 (OUTLIER) cc_final: 0.6530 (t-170) REVERT: A 66 MET cc_start: 0.9048 (tpt) cc_final: 0.8802 (tpp) REVERT: A 131 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6486 (tm-30) REVERT: A 267 MET cc_start: 0.7212 (tpp) cc_final: 0.6551 (tpp) REVERT: A 402 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.7833 (tp) REVERT: A 420 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7341 (tm-30) REVERT: A 451 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.7858 (tt0) REVERT: A 455 HIS cc_start: 0.8400 (OUTLIER) cc_final: 0.7564 (t-90) REVERT: B 200 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7762 (tpp) outliers start: 56 outliers final: 37 residues processed: 195 average time/residue: 0.1063 time to fit residues: 32.8660 Evaluate side-chains 192 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 144 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 209 TRP Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 494 ARG Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 662 THR Chi-restraints excluded: chain D residue 695 HIS Chi-restraints excluded: chain D residue 697 PHE Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 65 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 chunk 79 optimal weight: 0.2980 chunk 158 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 163 optimal weight: 0.0980 chunk 95 optimal weight: 0.0770 chunk 186 optimal weight: 0.1980 chunk 36 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.2738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.202561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.184993 restraints weight = 29630.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.181109 restraints weight = 53876.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.179730 restraints weight = 59367.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.178716 restraints weight = 57329.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.177812 restraints weight = 48733.152| |-----------------------------------------------------------------------------| r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6474 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14999 Z= 0.117 Angle : 0.624 14.042 20422 Z= 0.303 Chirality : 0.040 0.367 2438 Planarity : 0.004 0.038 2611 Dihedral : 4.528 53.261 2064 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.15 % Favored : 94.79 % Rotamer: Outliers : 2.97 % Allowed : 22.23 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % 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: 0.85 (0.21), residues: 1921 helix: 2.03 (0.16), residues: 1087 sheet: -2.68 (0.38), residues: 168 loop : -1.01 (0.26), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 441 TYR 0.029 0.001 TYR D 325 PHE 0.035 0.001 PHE B 449 TRP 0.012 0.001 TRP C 209 HIS 0.012 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00267 (14999) covalent geometry : angle 0.62420 (20422) hydrogen bonds : bond 0.03045 ( 844) hydrogen bonds : angle 4.06530 ( 2487) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 146 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 94 ILE cc_start: -0.2741 (OUTLIER) cc_final: -0.3117 (mt) REVERT: C 98 LEU cc_start: -0.3974 (OUTLIER) cc_final: -0.4459 (tp) REVERT: C 307 GLU cc_start: 0.3885 (OUTLIER) cc_final: 0.1254 (pt0) REVERT: C 328 GLU cc_start: -0.1332 (pt0) cc_final: -0.2129 (pp20) REVERT: D 1 MET cc_start: -0.1886 (ttt) cc_final: -0.2456 (ttt) REVERT: D 494 ARG cc_start: 0.6811 (OUTLIER) cc_final: 0.6446 (ttp80) REVERT: D 662 THR cc_start: -0.1745 (OUTLIER) cc_final: -0.2024 (m) REVERT: D 679 MET cc_start: 0.7624 (tpp) cc_final: 0.7339 (tpp) REVERT: D 695 HIS cc_start: 0.7154 (OUTLIER) cc_final: 0.6450 (t-170) REVERT: A 66 MET cc_start: 0.8985 (tpt) cc_final: 0.8758 (tpp) REVERT: A 131 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.6407 (tm-30) REVERT: A 267 MET cc_start: 0.7163 (tpp) cc_final: 0.6561 (tpp) REVERT: A 420 GLU cc_start: 0.7488 (tm-30) cc_final: 0.7245 (tm-30) REVERT: A 451 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.7803 (tt0) REVERT: A 455 HIS cc_start: 0.8372 (OUTLIER) cc_final: 0.7505 (t-90) REVERT: B 200 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7758 (tpp) outliers start: 45 outliers final: 33 residues processed: 179 average time/residue: 0.1027 time to fit residues: 29.4539 Evaluate side-chains 186 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 143 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 209 TRP Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 494 ARG Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 662 THR Chi-restraints excluded: chain D residue 695 HIS Chi-restraints excluded: chain D residue 697 PHE Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 23 optimal weight: 30.0000 chunk 77 optimal weight: 0.4980 chunk 169 optimal weight: 0.0070 chunk 31 optimal weight: 40.0000 chunk 182 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 97 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 168 optimal weight: 0.5980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 GLN ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.201477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.184038 restraints weight = 29439.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.180945 restraints weight = 51757.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.178934 restraints weight = 52930.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.176603 restraints weight = 50582.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.174219 restraints weight = 54253.256| |-----------------------------------------------------------------------------| r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14999 Z= 0.148 Angle : 0.634 13.251 20422 Z= 0.311 Chirality : 0.040 0.390 2438 Planarity : 0.004 0.054 2611 Dihedral : 4.556 53.287 2064 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.99 % Favored : 93.96 % Rotamer: Outliers : 3.10 % Allowed : 22.36 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % 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: 0.87 (0.21), residues: 1921 helix: 2.05 (0.16), residues: 1085 sheet: -2.70 (0.38), residues: 170 loop : -1.00 (0.26), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 441 TYR 0.028 0.001 TYR D 325 PHE 0.033 0.001 PHE B 449 TRP 0.008 0.001 TRP A 318 HIS 0.012 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00346 (14999) covalent geometry : angle 0.63418 (20422) hydrogen bonds : bond 0.03133 ( 844) hydrogen bonds : angle 4.11510 ( 2487) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2673.53 seconds wall clock time: 47 minutes 9.93 seconds (2829.93 seconds total)