Starting phenix.real_space_refine on Fri Jun 13 03:25:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fa7_50268/06_2025/9fa7_50268.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fa7_50268/06_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_50268/06_2025/9fa7_50268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fa7_50268/06_2025/9fa7_50268.map" model { file = "/net/cci-nas-00/data/ceres_data/9fa7_50268/06_2025/9fa7_50268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fa7_50268/06_2025/9fa7_50268.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 5, 'GLU:plan': 3, '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: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 12} 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: {'GLN:plan1': 4, 'ARG:plan': 11, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 13, 'HIS:plan': 3} 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: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 9, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 166 Time building chain proxies: 11.82, per 1000 atoms: 0.80 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: 3.45 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.43 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: 4.62 Time building geometry restraints manager: 4.12 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: 11.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 36.790 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.060 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.610 ------------------------------------------------------------------------------- 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 : 9.57 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (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 TRP 0.017 0.001 TRP C 209 HIS 0.006 0.001 HIS D 186 PHE 0.021 0.001 PHE B 212 TYR 0.018 0.001 TYR B 499 ARG 0.002 0.000 ARG D 100 Details of bonding type rmsd hydrogen bonds : bond 0.16600 ( 844) hydrogen bonds : angle 6.09049 ( 2487) covalent geometry : bond 0.00298 (14999) covalent geometry : angle 0.61904 (20422) *********************** 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 : 1.676 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: 0.2484 time to fit residues: 66.2927 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 : 1.572 ------------------------------------------------------------------------------- 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 163 optimal weight: 0.7980 chunk 147 optimal weight: 0.9990 chunk 81 optimal weight: 0.4980 chunk 50 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 152 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 176 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4439 r_free = 0.4439 target = 0.200695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.184233 restraints weight = 30179.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.180808 restraints weight = 51253.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.178754 restraints weight = 53252.246| |-----------------------------------------------------------------------------| r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 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 0.037 14999 Z= 0.189 Angle : 0.608 12.868 20422 Z= 0.308 Chirality : 0.040 0.184 2438 Planarity : 0.004 0.054 2611 Dihedral : 6.366 59.458 2108 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.09 % Favored : 93.81 % Rotamer: Outliers : 4.75 % Allowed : 19.26 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.21), residues: 1921 helix: 1.81 (0.16), residues: 1089 sheet: -3.23 (0.37), residues: 170 loop : -1.11 (0.26), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 318 HIS 0.007 0.001 HIS B 41 PHE 0.020 0.002 PHE A 385 TYR 0.014 0.001 TYR A 62 ARG 0.013 0.000 ARG C 147 Details of bonding type rmsd hydrogen bonds : bond 0.04111 ( 844) hydrogen bonds : angle 4.66424 ( 2487) covalent geometry : bond 0.00436 (14999) covalent geometry : angle 0.60794 (20422) *********************** 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: 72 poor density : 152 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 GLU cc_start: 0.1956 (pp20) cc_final: 0.1173 (pp20) REVERT: C 94 ILE cc_start: -0.2485 (OUTLIER) cc_final: -0.2842 (mt) REVERT: C 98 LEU cc_start: -0.3639 (OUTLIER) cc_final: -0.4301 (tp) REVERT: C 328 GLU cc_start: -0.0532 (pt0) cc_final: -0.2036 (pp20) REVERT: D 1 MET cc_start: -0.1564 (ttt) cc_final: -0.2267 (ttt) REVERT: D 551 LYS cc_start: 0.8240 (mtmt) cc_final: 0.7344 (mttt) REVERT: A 402 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.7942 (tp) REVERT: A 425 ASN cc_start: 0.9021 (OUTLIER) cc_final: 0.8663 (t0) REVERT: A 451 GLN cc_start: 0.9119 (OUTLIER) cc_final: 0.8127 (tt0) REVERT: A 455 HIS cc_start: 0.8202 (OUTLIER) cc_final: 0.7702 (t-90) REVERT: B 155 MET cc_start: 0.7103 (OUTLIER) cc_final: 0.6879 (mtp) REVERT: B 200 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.7227 (tpp) outliers start: 72 outliers final: 35 residues processed: 207 average time/residue: 0.2532 time to fit residues: 79.9871 Evaluate side-chains 183 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 140 time to evaluate : 1.840 ------------------------------------------------------------------------------- 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 101 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 250 LEU 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 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 68 ARG Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 155 MET 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 17 optimal weight: 7.9990 chunk 168 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 176 optimal weight: 0.0970 chunk 31 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 71 optimal weight: 0.0970 chunk 137 optimal weight: 0.8980 chunk 150 optimal weight: 0.2980 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 492 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 = 0.4455 r_free = 0.4455 target = 0.201690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.185283 restraints weight = 30658.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.182270 restraints weight = 52470.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.180429 restraints weight = 49753.642| |-----------------------------------------------------------------------------| r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14999 Z= 0.127 Angle : 0.579 11.449 20422 Z= 0.288 Chirality : 0.039 0.307 2438 Planarity : 0.004 0.040 2611 Dihedral : 5.826 57.221 2086 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.62 % Favored : 94.33 % Rotamer: Outliers : 3.36 % Allowed : 20.58 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.21), residues: 1921 helix: 1.88 (0.16), residues: 1089 sheet: -2.97 (0.38), residues: 168 loop : -1.09 (0.26), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 318 HIS 0.005 0.001 HIS D 492 PHE 0.014 0.001 PHE D 139 TYR 0.013 0.001 TYR A 62 ARG 0.006 0.000 ARG C 147 Details of bonding type rmsd hydrogen bonds : bond 0.03566 ( 844) hydrogen bonds : angle 4.41283 ( 2487) covalent geometry : bond 0.00284 (14999) covalent geometry : angle 0.57894 (20422) *********************** 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 197 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 146 time to evaluate : 1.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 GLU cc_start: 0.1900 (pp20) cc_final: 0.1073 (pp20) REVERT: C 94 ILE cc_start: -0.2522 (OUTLIER) cc_final: -0.2927 (mt) REVERT: C 98 LEU cc_start: -0.3654 (OUTLIER) cc_final: -0.4350 (tp) REVERT: C 307 GLU cc_start: 0.3455 (OUTLIER) cc_final: 0.0842 (pt0) REVERT: C 328 GLU cc_start: -0.0767 (pt0) cc_final: -0.1884 (pp20) REVERT: D 1 MET cc_start: -0.1590 (ttt) cc_final: -0.2282 (ttt) REVERT: D 603 LEU cc_start: 0.8327 (tp) cc_final: 0.8048 (tp) REVERT: D 695 HIS cc_start: 0.7293 (OUTLIER) cc_final: 0.6446 (t-170) REVERT: A 60 MET cc_start: 0.8215 (mmm) cc_final: 0.7834 (mmm) REVERT: A 66 MET cc_start: 0.9247 (tpt) cc_final: 0.8716 (tpp) REVERT: A 402 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.7921 (tp) REVERT: A 425 ASN cc_start: 0.8964 (OUTLIER) cc_final: 0.8596 (t0) REVERT: A 451 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.7865 (tt0) REVERT: A 455 HIS cc_start: 0.8180 (OUTLIER) cc_final: 0.7659 (t-90) REVERT: B 200 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7247 (tpp) outliers start: 51 outliers final: 22 residues processed: 181 average time/residue: 0.2598 time to fit residues: 74.9746 Evaluate side-chains 171 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 2.042 ------------------------------------------------------------------------------- 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 294 TYR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 496 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 331 CYS Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 396 LEU 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 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 245 LYS Chi-restraints excluded: chain B residue 264 SER 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 56 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 154 optimal weight: 0.5980 chunk 1 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 176 optimal weight: 0.2980 chunk 118 optimal weight: 2.9990 chunk 138 optimal weight: 0.0870 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.201876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.185968 restraints weight = 30127.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.181984 restraints weight = 43728.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.179942 restraints weight = 46120.171| |-----------------------------------------------------------------------------| r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6427 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14999 Z= 0.139 Angle : 0.573 13.836 20422 Z= 0.284 Chirality : 0.039 0.178 2438 Planarity : 0.004 0.041 2611 Dihedral : 5.607 55.738 2081 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.93 % Favored : 94.01 % Rotamer: Outliers : 3.50 % Allowed : 20.32 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.21), residues: 1921 helix: 1.91 (0.16), residues: 1091 sheet: -2.96 (0.38), residues: 170 loop : -1.08 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 318 HIS 0.009 0.001 HIS A 171 PHE 0.017 0.001 PHE B 449 TYR 0.013 0.001 TYR A 62 ARG 0.004 0.000 ARG B 230 Details of bonding type rmsd hydrogen bonds : bond 0.03343 ( 844) hydrogen bonds : angle 4.24409 ( 2487) covalent geometry : bond 0.00319 (14999) covalent geometry : angle 0.57340 (20422) *********************** 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 201 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 148 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 94 ILE cc_start: -0.2548 (OUTLIER) cc_final: -0.2928 (mt) REVERT: C 98 LEU cc_start: -0.3703 (OUTLIER) cc_final: -0.4309 (tp) REVERT: C 307 GLU cc_start: 0.3480 (OUTLIER) cc_final: 0.0881 (pt0) REVERT: C 328 GLU cc_start: -0.0875 (pt0) cc_final: -0.1945 (pp20) REVERT: D 1 MET cc_start: -0.1631 (ttt) cc_final: -0.2315 (ttt) REVERT: D 520 MET cc_start: 0.7968 (mmt) cc_final: 0.7753 (mmp) REVERT: D 551 LYS cc_start: 0.8027 (mtmt) cc_final: 0.7605 (mttp) REVERT: D 695 HIS cc_start: 0.7313 (OUTLIER) cc_final: 0.6504 (t-170) REVERT: A 66 MET cc_start: 0.9189 (tpt) cc_final: 0.8839 (tpp) REVERT: A 402 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.7900 (tp) REVERT: A 451 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.7925 (tt0) REVERT: A 455 HIS cc_start: 0.8174 (OUTLIER) cc_final: 0.7705 (t-90) REVERT: B 200 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7263 (tpp) outliers start: 53 outliers final: 32 residues processed: 186 average time/residue: 0.2276 time to fit residues: 67.4686 Evaluate side-chains 180 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 1.611 ------------------------------------------------------------------------------- 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 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 496 LEU Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 693 VAL 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 250 LEU 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 422 MET 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 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 249 THR 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 174 optimal weight: 0.0040 chunk 99 optimal weight: 2.9990 chunk 180 optimal weight: 0.0970 chunk 70 optimal weight: 2.9990 chunk 121 optimal weight: 0.4980 chunk 129 optimal weight: 0.0980 chunk 181 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 128 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 overall best weight: 0.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN A 543 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.202043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.186693 restraints weight = 30978.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.183136 restraints weight = 49339.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.181320 restraints weight = 50520.767| |-----------------------------------------------------------------------------| r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6370 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14999 Z= 0.115 Angle : 0.571 16.384 20422 Z= 0.279 Chirality : 0.038 0.233 2438 Planarity : 0.003 0.039 2611 Dihedral : 5.387 59.012 2075 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.84 % Favored : 95.11 % Rotamer: Outliers : 3.69 % Allowed : 20.45 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.21), residues: 1921 helix: 2.00 (0.16), residues: 1084 sheet: -2.81 (0.38), residues: 168 loop : -1.10 (0.26), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 318 HIS 0.008 0.001 HIS A 171 PHE 0.018 0.001 PHE B 449 TYR 0.025 0.001 TYR D 325 ARG 0.004 0.000 ARG B 441 Details of bonding type rmsd hydrogen bonds : bond 0.03184 ( 844) hydrogen bonds : angle 4.11887 ( 2487) covalent geometry : bond 0.00258 (14999) covalent geometry : angle 0.57060 (20422) *********************** 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 208 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 152 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 94 ILE cc_start: -0.2606 (OUTLIER) cc_final: -0.2978 (mt) REVERT: C 98 LEU cc_start: -0.3641 (OUTLIER) cc_final: -0.4238 (tp) REVERT: C 307 GLU cc_start: 0.3311 (OUTLIER) cc_final: 0.0603 (pt0) REVERT: C 328 GLU cc_start: -0.0899 (pt0) cc_final: -0.1958 (pp20) REVERT: D 1 MET cc_start: -0.1643 (ttt) cc_final: -0.2338 (ttt) REVERT: D 520 MET cc_start: 0.7873 (mmt) cc_final: 0.7639 (mmp) REVERT: D 551 LYS cc_start: 0.8008 (mtmt) cc_final: 0.7531 (mttt) REVERT: D 695 HIS cc_start: 0.7297 (OUTLIER) cc_final: 0.6515 (t-170) REVERT: A 60 MET cc_start: 0.8186 (mmm) cc_final: 0.7551 (mmm) REVERT: A 66 MET cc_start: 0.9132 (tpt) cc_final: 0.8910 (tpp) REVERT: A 131 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6504 (tm-30) REVERT: A 267 MET cc_start: 0.7224 (tpp) cc_final: 0.6604 (tpp) REVERT: A 402 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.7961 (tp) REVERT: A 455 HIS cc_start: 0.8374 (OUTLIER) cc_final: 0.7716 (t-90) REVERT: B 83 TYR cc_start: 0.8451 (m-10) cc_final: 0.8099 (m-10) REVERT: B 200 MET cc_start: 0.7566 (OUTLIER) cc_final: 0.7361 (tpp) outliers start: 56 outliers final: 34 residues processed: 193 average time/residue: 0.2264 time to fit residues: 70.0416 Evaluate side-chains 185 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 143 time to evaluate : 1.619 ------------------------------------------------------------------------------- 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 496 LEU 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 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 396 LEU 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 455 HIS Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 95 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 264 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 403 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 150 optimal weight: 0.1980 chunk 89 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 64 optimal weight: 0.5980 chunk 162 optimal weight: 0.5980 chunk 25 optimal weight: 9.9990 chunk 153 optimal weight: 0.1980 chunk 30 optimal weight: 2.9990 chunk 165 optimal weight: 0.0060 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.202064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.185953 restraints weight = 30983.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.182077 restraints weight = 53878.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.180994 restraints weight = 59983.025| |-----------------------------------------------------------------------------| r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6380 moved from start: 0.1738 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= 0.118 Angle : 0.569 10.587 20422 Z= 0.280 Chirality : 0.038 0.218 2438 Planarity : 0.003 0.039 2611 Dihedral : 4.842 53.184 2069 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.15 % Favored : 94.79 % Rotamer: Outliers : 3.69 % Allowed : 20.45 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.21), residues: 1921 helix: 2.05 (0.16), residues: 1086 sheet: -2.75 (0.38), residues: 168 loop : -1.11 (0.26), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 318 HIS 0.008 0.001 HIS A 171 PHE 0.018 0.001 PHE B 449 TYR 0.037 0.001 TYR D 325 ARG 0.005 0.000 ARG B 441 Details of bonding type rmsd hydrogen bonds : bond 0.03145 ( 844) hydrogen bonds : angle 4.05546 ( 2487) covalent geometry : bond 0.00268 (14999) covalent geometry : angle 0.56875 (20422) *********************** 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 201 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 145 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 94 ILE cc_start: -0.2646 (OUTLIER) cc_final: -0.3023 (mt) REVERT: C 98 LEU cc_start: -0.3722 (OUTLIER) cc_final: -0.4286 (tp) REVERT: C 307 GLU cc_start: 0.3410 (OUTLIER) cc_final: 0.0714 (pt0) REVERT: C 328 GLU cc_start: -0.1049 (pt0) cc_final: -0.2034 (pp20) REVERT: D 1 MET cc_start: -0.1712 (ttt) cc_final: -0.2384 (ttt) REVERT: D 494 ARG cc_start: 0.6738 (OUTLIER) cc_final: 0.6376 (ttp80) REVERT: D 520 MET cc_start: 0.7936 (mmt) cc_final: 0.7681 (mmt) REVERT: D 662 THR cc_start: -0.1684 (OUTLIER) cc_final: -0.2024 (m) REVERT: D 679 MET cc_start: 0.7563 (tpp) cc_final: 0.7321 (tpp) REVERT: D 695 HIS cc_start: 0.7286 (OUTLIER) cc_final: 0.6539 (t-170) REVERT: A 60 MET cc_start: 0.8184 (mmm) cc_final: 0.7820 (mmm) REVERT: A 66 MET cc_start: 0.9078 (tpt) cc_final: 0.8844 (tpp) REVERT: A 267 MET cc_start: 0.7165 (tpp) cc_final: 0.6539 (tpp) REVERT: A 402 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.7857 (tp) REVERT: A 455 HIS cc_start: 0.8407 (OUTLIER) cc_final: 0.7699 (t-90) REVERT: B 83 TYR cc_start: 0.8361 (m-10) cc_final: 0.8046 (m-10) outliers start: 56 outliers final: 37 residues processed: 187 average time/residue: 0.2272 time to fit residues: 68.4254 Evaluate side-chains 185 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 140 time to evaluate : 1.742 ------------------------------------------------------------------------------- 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 496 LEU Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 648 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 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 386 LEU 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 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 243 ILE Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 403 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 20 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 175 optimal weight: 0.4980 chunk 160 optimal weight: 0.9990 chunk 152 optimal weight: 0.4980 chunk 27 optimal weight: 6.9990 chunk 173 optimal weight: 0.9980 chunk 146 optimal weight: 0.4980 chunk 117 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 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 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.200449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.184394 restraints weight = 30148.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.180966 restraints weight = 50425.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.179077 restraints weight = 52133.751| |-----------------------------------------------------------------------------| r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6434 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14999 Z= 0.176 Angle : 0.628 18.699 20422 Z= 0.306 Chirality : 0.040 0.249 2438 Planarity : 0.004 0.041 2611 Dihedral : 4.790 54.059 2066 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.83 % Favored : 94.12 % Rotamer: Outliers : 4.29 % Allowed : 20.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.21), residues: 1921 helix: 1.98 (0.16), residues: 1092 sheet: -2.90 (0.38), residues: 170 loop : -1.07 (0.26), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 318 HIS 0.005 0.001 HIS B 41 PHE 0.025 0.001 PHE B 449 TYR 0.025 0.001 TYR D 325 ARG 0.005 0.000 ARG B 441 Details of bonding type rmsd hydrogen bonds : bond 0.03284 ( 844) hydrogen bonds : angle 4.19579 ( 2487) covalent geometry : bond 0.00412 (14999) covalent geometry : angle 0.62795 (20422) *********************** 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 210 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 145 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 94 ILE cc_start: -0.2650 (OUTLIER) cc_final: -0.3026 (mt) REVERT: C 98 LEU cc_start: -0.3732 (OUTLIER) cc_final: -0.4296 (tp) REVERT: C 131 GLU cc_start: 0.3510 (pp20) cc_final: 0.2515 (pp20) REVERT: C 168 LYS cc_start: -0.1226 (OUTLIER) cc_final: -0.1436 (mmpt) REVERT: C 307 GLU cc_start: 0.3646 (OUTLIER) cc_final: 0.0982 (pt0) REVERT: C 328 GLU cc_start: -0.1126 (pt0) cc_final: -0.2088 (pp20) REVERT: D 1 MET cc_start: -0.1699 (ttt) cc_final: -0.2310 (ttt) REVERT: D 455 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7066 (mpp) REVERT: D 494 ARG cc_start: 0.6828 (OUTLIER) cc_final: 0.6498 (ttp80) REVERT: D 551 LYS cc_start: 0.8178 (mtmt) cc_final: 0.7903 (mttt) REVERT: D 662 THR cc_start: -0.1711 (OUTLIER) cc_final: -0.2037 (m) REVERT: D 695 HIS cc_start: 0.7330 (OUTLIER) cc_final: 0.6611 (t-170) REVERT: A 66 MET cc_start: 0.9190 (tpt) cc_final: 0.8870 (tpp) REVERT: A 267 MET cc_start: 0.7231 (tpp) cc_final: 0.6542 (tpp) REVERT: A 402 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.7898 (tp) REVERT: A 420 GLU cc_start: 0.7449 (tm-30) cc_final: 0.7060 (tm-30) REVERT: A 455 HIS cc_start: 0.8446 (OUTLIER) cc_final: 0.7718 (t-90) REVERT: B 83 TYR cc_start: 0.8460 (m-10) cc_final: 0.8179 (m-10) REVERT: B 200 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7484 (ttm) outliers start: 65 outliers final: 47 residues processed: 194 average time/residue: 0.2228 time to fit residues: 69.5615 Evaluate side-chains 201 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 143 time to evaluate : 1.612 ------------------------------------------------------------------------------- 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 168 LYS 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 455 MET 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 648 LEU Chi-restraints excluded: chain D residue 662 THR Chi-restraints excluded: chain D residue 693 VAL 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 122 ILE 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 455 HIS Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 67 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 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 Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 403 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 17 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 190 optimal weight: 0.3980 chunk 47 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 151 optimal weight: 0.6980 chunk 123 optimal weight: 0.0270 chunk 192 optimal weight: 0.9980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 654 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.200748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.183673 restraints weight = 30170.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.179073 restraints weight = 51969.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.178071 restraints weight = 60131.469| |-----------------------------------------------------------------------------| r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6472 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14999 Z= 0.156 Angle : 0.628 16.695 20422 Z= 0.303 Chirality : 0.040 0.249 2438 Planarity : 0.004 0.039 2611 Dihedral : 4.801 54.353 2066 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.47 % Favored : 94.48 % Rotamer: Outliers : 3.89 % Allowed : 21.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.21), residues: 1921 helix: 1.92 (0.16), residues: 1093 sheet: -2.91 (0.37), residues: 170 loop : -1.03 (0.26), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 318 HIS 0.011 0.001 HIS A 171 PHE 0.027 0.001 PHE B 449 TYR 0.037 0.001 TYR D 325 ARG 0.004 0.000 ARG B 441 Details of bonding type rmsd hydrogen bonds : bond 0.03204 ( 844) hydrogen bonds : angle 4.16311 ( 2487) covalent geometry : bond 0.00363 (14999) covalent geometry : angle 0.62786 (20422) *********************** 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 206 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 147 time to evaluate : 1.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 94 ILE cc_start: -0.2687 (OUTLIER) cc_final: -0.3065 (mt) REVERT: C 98 LEU cc_start: -0.3818 (OUTLIER) cc_final: -0.4343 (tp) REVERT: C 131 GLU cc_start: 0.3588 (pp20) cc_final: 0.2585 (pp20) REVERT: C 307 GLU cc_start: 0.3698 (OUTLIER) cc_final: 0.1042 (pt0) REVERT: C 328 GLU cc_start: -0.1098 (pt0) cc_final: -0.2029 (pp20) REVERT: D 1 MET cc_start: -0.1769 (ttt) cc_final: -0.2367 (ttt) REVERT: D 455 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7160 (mpp) REVERT: D 494 ARG cc_start: 0.6871 (OUTLIER) cc_final: 0.6511 (ttp80) REVERT: D 551 LYS cc_start: 0.8210 (mtmt) cc_final: 0.7849 (mttt) REVERT: D 662 THR cc_start: -0.1858 (OUTLIER) cc_final: -0.2161 (m) REVERT: D 695 HIS cc_start: 0.7283 (OUTLIER) cc_final: 0.6534 (t-170) REVERT: A 66 MET cc_start: 0.9006 (tpt) cc_final: 0.8685 (tpp) REVERT: A 267 MET cc_start: 0.7242 (tpp) cc_final: 0.6566 (tpp) REVERT: A 402 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.7784 (tp) REVERT: A 420 GLU cc_start: 0.7548 (tm-30) cc_final: 0.7098 (tm-30) REVERT: A 455 HIS cc_start: 0.8386 (OUTLIER) cc_final: 0.7728 (t-90) REVERT: B 200 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7784 (tpp) outliers start: 59 outliers final: 43 residues processed: 191 average time/residue: 0.2417 time to fit residues: 74.1692 Evaluate side-chains 191 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 138 time to evaluate : 1.678 ------------------------------------------------------------------------------- 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 455 MET 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 648 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 134 CYS Chi-restraints excluded: chain A residue 250 LEU 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 386 LEU 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 455 HIS Chi-restraints excluded: chain A residue 462 ILE 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 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 249 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 403 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 100 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 30 optimal weight: 30.0000 chunk 173 optimal weight: 0.4980 chunk 178 optimal weight: 0.1980 chunk 29 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.199298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.183133 restraints weight = 29746.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.179492 restraints weight = 52363.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.177191 restraints weight = 54323.449| |-----------------------------------------------------------------------------| r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14999 Z= 0.207 Angle : 0.661 13.511 20422 Z= 0.327 Chirality : 0.042 0.373 2438 Planarity : 0.004 0.041 2611 Dihedral : 4.954 55.001 2066 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.45 % Favored : 93.49 % Rotamer: Outliers : 4.22 % Allowed : 21.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.20), residues: 1921 helix: 1.84 (0.16), residues: 1095 sheet: -3.09 (0.37), residues: 170 loop : -1.11 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 209 HIS 0.010 0.001 HIS A 171 PHE 0.029 0.002 PHE B 449 TYR 0.032 0.001 TYR D 325 ARG 0.005 0.000 ARG B 230 Details of bonding type rmsd hydrogen bonds : bond 0.03375 ( 844) hydrogen bonds : angle 4.30258 ( 2487) covalent geometry : bond 0.00487 (14999) covalent geometry : angle 0.66119 (20422) *********************** 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 206 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 142 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 94 ILE cc_start: -0.2654 (OUTLIER) cc_final: -0.3032 (mt) REVERT: C 98 LEU cc_start: -0.3860 (OUTLIER) cc_final: -0.4386 (tp) REVERT: C 131 GLU cc_start: 0.3538 (pp20) cc_final: 0.2541 (pp20) REVERT: C 307 GLU cc_start: 0.3665 (OUTLIER) cc_final: 0.1009 (pt0) REVERT: C 328 GLU cc_start: -0.1126 (pt0) cc_final: -0.2095 (pp20) REVERT: D 1 MET cc_start: -0.1697 (ttt) cc_final: -0.2316 (ttt) REVERT: D 455 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7338 (mpp) REVERT: D 494 ARG cc_start: 0.6985 (OUTLIER) cc_final: 0.6652 (ttp80) REVERT: D 551 LYS cc_start: 0.8257 (mtmt) cc_final: 0.7843 (mttp) REVERT: D 662 THR cc_start: -0.1769 (OUTLIER) cc_final: -0.2070 (m) REVERT: D 695 HIS cc_start: 0.7306 (OUTLIER) cc_final: 0.6674 (t-170) REVERT: A 66 MET cc_start: 0.9138 (tpt) cc_final: 0.8801 (tpp) REVERT: A 402 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.7899 (tp) REVERT: A 420 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7158 (tm-30) REVERT: A 451 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8010 (tt0) REVERT: A 455 HIS cc_start: 0.8413 (OUTLIER) cc_final: 0.7673 (t-90) REVERT: B 83 TYR cc_start: 0.8521 (m-10) cc_final: 0.8198 (m-10) REVERT: B 200 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7711 (tpp) outliers start: 64 outliers final: 48 residues processed: 190 average time/residue: 0.2235 time to fit residues: 67.6341 Evaluate side-chains 200 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 141 time to evaluate : 1.788 ------------------------------------------------------------------------------- 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 455 MET 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 589 VAL Chi-restraints excluded: chain D residue 648 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 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 386 LEU 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 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 A residue 462 ILE Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 67 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 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 249 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 403 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 32 optimal weight: 30.0000 chunk 117 optimal weight: 0.3980 chunk 123 optimal weight: 0.9980 chunk 115 optimal weight: 0.0980 chunk 146 optimal weight: 0.1980 chunk 138 optimal weight: 0.2980 chunk 78 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 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 146 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.201271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.184519 restraints weight = 30032.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.181475 restraints weight = 51455.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.179178 restraints weight = 53492.069| |-----------------------------------------------------------------------------| r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14999 Z= 0.128 Angle : 0.627 13.536 20422 Z= 0.304 Chirality : 0.040 0.411 2438 Planarity : 0.004 0.039 2611 Dihedral : 4.834 56.651 2066 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.31 % Favored : 94.64 % Rotamer: Outliers : 3.69 % Allowed : 22.03 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.21), residues: 1921 helix: 1.98 (0.16), residues: 1080 sheet: -2.94 (0.37), residues: 170 loop : -1.05 (0.25), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 318 HIS 0.011 0.001 HIS A 171 PHE 0.035 0.001 PHE B 449 TYR 0.033 0.001 TYR D 325 ARG 0.004 0.000 ARG B 230 Details of bonding type rmsd hydrogen bonds : bond 0.03104 ( 844) hydrogen bonds : angle 4.15282 ( 2487) covalent geometry : bond 0.00293 (14999) covalent geometry : angle 0.62722 (20422) ********************** 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 200 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 144 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 94 ILE cc_start: -0.2659 (OUTLIER) cc_final: -0.3037 (mt) REVERT: C 98 LEU cc_start: -0.3871 (OUTLIER) cc_final: -0.4389 (tp) REVERT: C 131 GLU cc_start: 0.3518 (pp20) cc_final: 0.2513 (pp20) REVERT: C 307 GLU cc_start: 0.3729 (OUTLIER) cc_final: 0.1051 (pt0) REVERT: C 328 GLU cc_start: -0.1081 (pt0) cc_final: -0.2059 (pp20) REVERT: D 1 MET cc_start: -0.1730 (ttt) cc_final: -0.2361 (ttt) REVERT: D 455 MET cc_start: 0.7671 (OUTLIER) cc_final: 0.7215 (mpp) REVERT: D 494 ARG cc_start: 0.6909 (OUTLIER) cc_final: 0.6524 (ttp80) REVERT: D 662 THR cc_start: -0.1730 (OUTLIER) cc_final: -0.2020 (m) REVERT: D 695 HIS cc_start: 0.7268 (OUTLIER) cc_final: 0.6583 (t-170) REVERT: A 66 MET cc_start: 0.9090 (tpt) cc_final: 0.8824 (tpp) REVERT: A 267 MET cc_start: 0.7141 (tpp) cc_final: 0.6549 (tpp) REVERT: A 402 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.7811 (tp) REVERT: A 420 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7370 (tm-30) REVERT: A 455 HIS cc_start: 0.8414 (OUTLIER) cc_final: 0.7703 (t-90) REVERT: B 83 TYR cc_start: 0.8406 (m-10) cc_final: 0.8137 (m-10) REVERT: B 200 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7791 (tpp) outliers start: 56 outliers final: 41 residues processed: 186 average time/residue: 0.2298 time to fit residues: 68.3606 Evaluate side-chains 191 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 140 time to evaluate : 1.718 ------------------------------------------------------------------------------- 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 455 MET 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 648 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 134 CYS Chi-restraints excluded: chain A residue 250 LEU 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 386 LEU 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 455 HIS Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain B residue 4 VAL 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 245 LYS Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 403 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 174 optimal weight: 0.0170 chunk 77 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 46 optimal weight: 20.0000 chunk 167 optimal weight: 0.6980 chunk 31 optimal weight: 7.9990 chunk 159 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 175 optimal weight: 0.5980 chunk 136 optimal weight: 0.4980 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.199708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.182756 restraints weight = 29735.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.178547 restraints weight = 53223.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.177134 restraints weight = 60823.089| |-----------------------------------------------------------------------------| r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14999 Z= 0.189 Angle : 0.659 12.819 20422 Z= 0.323 Chirality : 0.041 0.397 2438 Planarity : 0.004 0.039 2611 Dihedral : 4.744 55.148 2064 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.56 % Favored : 93.39 % Rotamer: Outliers : 3.89 % Allowed : 21.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.21), residues: 1921 helix: 1.90 (0.16), residues: 1089 sheet: -3.04 (0.37), residues: 170 loop : -1.06 (0.26), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 318 HIS 0.010 0.001 HIS A 171 PHE 0.032 0.002 PHE B 449 TYR 0.030 0.001 TYR D 325 ARG 0.004 0.000 ARG B 441 Details of bonding type rmsd hydrogen bonds : bond 0.03325 ( 844) hydrogen bonds : angle 4.26104 ( 2487) covalent geometry : bond 0.00445 (14999) covalent geometry : angle 0.65936 (20422) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5007.81 seconds wall clock time: 88 minutes 38.78 seconds (5318.78 seconds total)