Starting phenix.real_space_refine on Sat Jun 21 21:00:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bnu_16135/06_2025/8bnu_16135.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bnu_16135/06_2025/8bnu_16135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bnu_16135/06_2025/8bnu_16135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bnu_16135/06_2025/8bnu_16135.map" model { file = "/net/cci-nas-00/data/ceres_data/8bnu_16135/06_2025/8bnu_16135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bnu_16135/06_2025/8bnu_16135.cif" } resolution = 3.55 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= 0.003 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10308 atoms to isotropic. 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 80 5.16 5 C 10677 2.51 5 N 3015 2.21 5 O 3141 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16913 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3213 Classifications: {'peptide': 436} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 19, 'TRANS': 416} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 3218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3218 Classifications: {'peptide': 436} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 19, 'TRANS': 416} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 5204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 5204 Classifications: {'peptide': 710} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 671} Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 99 Chain: "D" Number of atoms: 5278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 5278 Classifications: {'peptide': 710} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 671} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 53 Time building chain proxies: 10.38, per 1000 atoms: 0.61 Number of scatterers: 16913 At special positions: 0 Unit cell: (183.816, 129.168, 94.392, 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 80 16.00 O 3141 8.00 N 3015 7.00 C 10677 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.59 Conformation dependent library (CDL) restraints added in 2.3 seconds 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4152 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 15 sheets defined 51.0% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.15 Creating SS restraints... Processing helix chain 'A' and resid 36 through 50 removed outlier: 3.987A pdb=" N LEU A 40 " --> pdb=" O PRO A 36 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 84 removed outlier: 3.799A pdb=" N GLU A 79 " --> pdb=" O ASN A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 100 through 115 Processing helix chain 'A' and resid 138 through 150 removed outlier: 4.000A pdb=" N ARG A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LEU A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 161 removed outlier: 3.501A pdb=" N ARG A 156 " --> pdb=" O THR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 196 removed outlier: 3.672A pdb=" N GLN A 190 " --> pdb=" O ASP A 186 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET A 191 " --> pdb=" O THR A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 211 Processing helix chain 'A' and resid 213 through 220 Processing helix chain 'A' and resid 287 through 293 Processing helix chain 'A' and resid 317 through 331 Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 349 through 358 Processing helix chain 'A' and resid 359 through 366 removed outlier: 3.863A pdb=" N ALA A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 391 removed outlier: 3.697A pdb=" N TYR A 390 " --> pdb=" O GLY A 386 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 386 through 391' Processing helix chain 'A' and resid 396 through 413 removed outlier: 3.615A pdb=" N ARG A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET A 401 " --> pdb=" O THR A 397 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 402 " --> pdb=" O GLY A 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 53 Processing helix chain 'B' and resid 75 through 84 removed outlier: 3.785A pdb=" N GLU B 79 " --> pdb=" O ASN B 75 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 99 No H-bonds generated for 'chain 'B' and resid 97 through 99' Processing helix chain 'B' and resid 100 through 116 Processing helix chain 'B' and resid 137 through 150 removed outlier: 3.532A pdb=" N ARG B 142 " --> pdb=" O LYS B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 161 removed outlier: 4.123A pdb=" N LEU B 157 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 196 removed outlier: 3.642A pdb=" N THR B 187 " --> pdb=" O ARG B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 220 Processing helix chain 'B' and resid 249 through 254 Processing helix chain 'B' and resid 287 through 293 Processing helix chain 'B' and resid 317 through 331 Proline residue: B 324 - end of helix Processing helix chain 'B' and resid 333 through 337 removed outlier: 3.562A pdb=" N LEU B 337 " --> pdb=" O MET B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 358 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 396 through 412 Processing helix chain 'C' and resid 32 through 48 removed outlier: 3.861A pdb=" N ARG C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA C 41 " --> pdb=" O SER C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 79 through 99 removed outlier: 3.877A pdb=" N ALA C 83 " --> pdb=" O THR C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 123 Processing helix chain 'C' and resid 140 through 144 Processing helix chain 'C' and resid 150 through 159 Proline residue: C 156 - end of helix Processing helix chain 'C' and resid 160 through 170 removed outlier: 4.687A pdb=" N GLU C 166 " --> pdb=" O SER C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 183 Processing helix chain 'C' and resid 190 through 192 No H-bonds generated for 'chain 'C' and resid 190 through 192' Processing helix chain 'C' and resid 193 through 204 Processing helix chain 'C' and resid 216 through 220 removed outlier: 3.930A pdb=" N LEU C 219 " --> pdb=" O GLU C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 241 Processing helix chain 'C' and resid 247 through 261 Processing helix chain 'C' and resid 261 through 277 Processing helix chain 'C' and resid 279 through 298 removed outlier: 3.794A pdb=" N GLN C 283 " --> pdb=" O THR C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 330 Processing helix chain 'C' and resid 341 through 362 removed outlier: 3.602A pdb=" N ILE C 345 " --> pdb=" O ASN C 341 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG C 362 " --> pdb=" O GLY C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 375 removed outlier: 3.644A pdb=" N ASP C 371 " --> pdb=" O ALA C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 413 Processing helix chain 'C' and resid 428 through 434 Processing helix chain 'C' and resid 438 through 440 No H-bonds generated for 'chain 'C' and resid 438 through 440' Processing helix chain 'C' and resid 466 through 480 Processing helix chain 'C' and resid 494 through 512 Proline residue: C 501 - end of helix removed outlier: 3.726A pdb=" N GLN C 512 " --> pdb=" O ARG C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 526 removed outlier: 3.602A pdb=" N PHE C 526 " --> pdb=" O ALA C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 540 Processing helix chain 'C' and resid 540 through 545 Processing helix chain 'C' and resid 547 through 556 removed outlier: 3.792A pdb=" N LEU C 551 " --> pdb=" O ILE C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 560 Processing helix chain 'C' and resid 566 through 571 Processing helix chain 'C' and resid 600 through 605 Processing helix chain 'C' and resid 614 through 636 removed outlier: 3.689A pdb=" N GLU C 636 " --> pdb=" O ARG C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 652 Processing helix chain 'C' and resid 656 through 660 Processing helix chain 'C' and resid 661 through 670 Processing helix chain 'C' and resid 671 through 686 removed outlier: 4.001A pdb=" N VAL C 675 " --> pdb=" O ALA C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 690 Processing helix chain 'C' and resid 692 through 702 Processing helix chain 'D' and resid 32 through 49 removed outlier: 3.985A pdb=" N ALA D 36 " --> pdb=" O LYS D 32 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG D 40 " --> pdb=" O ALA D 36 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA D 41 " --> pdb=" O SER D 37 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN D 49 " --> pdb=" O GLN D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 76 removed outlier: 3.750A pdb=" N ILE D 74 " --> pdb=" O ASP D 70 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN D 76 " --> pdb=" O ASN D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 99 removed outlier: 3.726A pdb=" N ALA D 83 " --> pdb=" O THR D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 122 Processing helix chain 'D' and resid 153 through 160 Processing helix chain 'D' and resid 160 through 171 Processing helix chain 'D' and resid 175 through 183 Processing helix chain 'D' and resid 193 through 204 removed outlier: 3.820A pdb=" N GLU D 200 " --> pdb=" O GLU D 196 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU D 201 " --> pdb=" O ALA D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 220 removed outlier: 4.144A pdb=" N LEU D 219 " --> pdb=" O GLU D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 241 Processing helix chain 'D' and resid 247 through 261 removed outlier: 3.535A pdb=" N LEU D 251 " --> pdb=" O THR D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 277 removed outlier: 3.518A pdb=" N ALA D 277 " --> pdb=" O PHE D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 298 removed outlier: 3.635A pdb=" N GLN D 283 " --> pdb=" O THR D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 330 Processing helix chain 'D' and resid 341 through 356 removed outlier: 3.562A pdb=" N ILE D 345 " --> pdb=" O ASN D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 362 Processing helix chain 'D' and resid 366 through 375 removed outlier: 3.747A pdb=" N LYS D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 413 Processing helix chain 'D' and resid 428 through 434 Processing helix chain 'D' and resid 438 through 440 No H-bonds generated for 'chain 'D' and resid 438 through 440' Processing helix chain 'D' and resid 466 through 480 Processing helix chain 'D' and resid 494 through 512 Proline residue: D 501 - end of helix removed outlier: 3.730A pdb=" N GLN D 512 " --> pdb=" O ARG D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 527 removed outlier: 3.719A pdb=" N ILE D 519 " --> pdb=" O ARG D 515 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY D 527 " --> pdb=" O LEU D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 540 removed outlier: 3.799A pdb=" N GLY D 540 " --> pdb=" O LEU D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 546 Processing helix chain 'D' and resid 546 through 555 removed outlier: 4.432A pdb=" N VAL D 550 " --> pdb=" O LYS D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 571 Processing helix chain 'D' and resid 575 through 580 removed outlier: 3.756A pdb=" N ASN D 579 " --> pdb=" O LYS D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 605 removed outlier: 3.796A pdb=" N LEU D 604 " --> pdb=" O ALA D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.960A pdb=" N ALA D 619 " --> pdb=" O ALA D 615 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU D 636 " --> pdb=" O ARG D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 652 Processing helix chain 'D' and resid 656 through 660 Processing helix chain 'D' and resid 661 through 669 Processing helix chain 'D' and resid 671 through 686 removed outlier: 4.018A pdb=" N VAL D 675 " --> pdb=" O ALA D 671 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA D 676 " --> pdb=" O GLY D 672 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE D 677 " --> pdb=" O GLU D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 690 Processing helix chain 'D' and resid 692 through 702 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 22 removed outlier: 4.004A pdb=" N ILE A 283 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLY A 20 " --> pdb=" O ALA A 281 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA A 281 " --> pdb=" O GLY A 20 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ARG A 22 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA A 279 " --> pdb=" O ARG A 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 22 removed outlier: 4.004A pdb=" N ILE A 283 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLY A 20 " --> pdb=" O ALA A 281 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA A 281 " --> pdb=" O GLY A 20 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ARG A 22 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA A 279 " --> pdb=" O ARG A 22 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL A 63 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ALA A 126 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLY A 65 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N SER A 128 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU A 62 " --> pdb=" O TYR A 93 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL A 95 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE A 64 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER A 94 " --> pdb=" O SER B 96 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 303 through 308 removed outlier: 3.563A pdb=" N SER A 303 " --> pdb=" O VAL A 432 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 15 through 22 removed outlier: 4.537A pdb=" N ILE B 17 " --> pdb=" O MET B 285 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N MET B 285 " --> pdb=" O ILE B 17 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER B 19 " --> pdb=" O ILE B 283 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 15 through 22 removed outlier: 4.537A pdb=" N ILE B 17 " --> pdb=" O MET B 285 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N MET B 285 " --> pdb=" O ILE B 17 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER B 19 " --> pdb=" O ILE B 283 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY B 65 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA B 126 " --> pdb=" O GLY B 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 303 through 308 removed outlier: 3.530A pdb=" N SER B 303 " --> pdb=" O VAL B 432 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 9 through 11 removed outlier: 6.516A pdb=" N VAL C 55 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ALA C 107 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N PHE C 57 " --> pdb=" O ALA C 107 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ARG C 126 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N VAL C 189 " --> pdb=" O ARG C 126 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N CYS C 128 " --> pdb=" O VAL C 189 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AA9, first strand: chain 'C' and resid 64 through 66 removed outlier: 7.711A pdb=" N LEU C 113 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY C 137 " --> pdb=" O CYS C 112 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 377 through 379 removed outlier: 5.819A pdb=" N ILE C 392 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N PHE C 420 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU C 445 " --> pdb=" O PHE C 420 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N SER C 422 " --> pdb=" O LEU C 445 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 584 through 585 removed outlier: 3.651A pdb=" N LEU C 585 " --> pdb=" O GLN C 596 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLN C 596 " --> pdb=" O LEU C 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 7 through 11 removed outlier: 6.659A pdb=" N ALA D 17 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL D 58 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE D 19 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL D 55 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ALA D 107 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N PHE D 57 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ARG D 126 " --> pdb=" O ASP D 187 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N VAL D 189 " --> pdb=" O ARG D 126 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N CYS D 128 " --> pdb=" O VAL D 189 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=AB5, first strand: chain 'D' and resid 112 through 113 removed outlier: 6.860A pdb=" N CYS D 112 " --> pdb=" O GLY D 137 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 377 through 380 removed outlier: 6.224A pdb=" N ILE D 392 " --> pdb=" O ALA D 421 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ASN D 423 " --> pdb=" O ILE D 392 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N GLU D 394 " --> pdb=" O ASN D 423 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE D 420 " --> pdb=" O ILE D 443 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU D 445 " --> pdb=" O PHE D 420 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N SER D 422 " --> pdb=" O LEU D 445 " (cutoff:3.500A) 806 hydrogen bonds defined for protein. 2346 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: 6.32 Time building geometry restraints manager: 5.41 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: 3714 1.33 - 1.45: 3365 1.45 - 1.57: 9983 1.57 - 1.69: 0 1.69 - 1.81: 138 Bond restraints: 17200 Sorted by residual: bond pdb=" CG GLN B 404 " pdb=" CD GLN B 404 " ideal model delta sigma weight residual 1.516 1.470 0.046 2.50e-02 1.60e+03 3.45e+00 bond pdb=" CB TYR A 93 " pdb=" CG TYR A 93 " ideal model delta sigma weight residual 1.512 1.471 0.041 2.20e-02 2.07e+03 3.40e+00 bond pdb=" CG1 ILE B 354 " pdb=" CD1 ILE B 354 " ideal model delta sigma weight residual 1.513 1.443 0.070 3.90e-02 6.57e+02 3.22e+00 bond pdb=" CG TYR A 93 " pdb=" CD1 TYR A 93 " ideal model delta sigma weight residual 1.389 1.353 0.036 2.10e-02 2.27e+03 2.97e+00 bond pdb=" CB GLN B 104 " pdb=" CG GLN B 104 " ideal model delta sigma weight residual 1.520 1.469 0.051 3.00e-02 1.11e+03 2.89e+00 ... (remaining 17195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 22809 2.09 - 4.17: 454 4.17 - 6.26: 72 6.26 - 8.34: 7 8.34 - 10.43: 5 Bond angle restraints: 23347 Sorted by residual: angle pdb=" N ARG D 664 " pdb=" CA ARG D 664 " pdb=" C ARG D 664 " ideal model delta sigma weight residual 111.36 103.66 7.70 1.09e+00 8.42e-01 4.99e+01 angle pdb=" C LEU A 165 " pdb=" CA LEU A 165 " pdb=" CB LEU A 165 " ideal model delta sigma weight residual 115.89 110.27 5.62 1.32e+00 5.74e-01 1.81e+01 angle pdb=" N GLU C 200 " pdb=" CA GLU C 200 " pdb=" CB GLU C 200 " ideal model delta sigma weight residual 110.39 116.92 -6.53 1.66e+00 3.63e-01 1.55e+01 angle pdb=" N GLN C 679 " pdb=" CA GLN C 679 " pdb=" CB GLN C 679 " ideal model delta sigma weight residual 110.12 115.52 -5.40 1.47e+00 4.63e-01 1.35e+01 angle pdb=" C VAL C 199 " pdb=" N GLU C 200 " pdb=" CA GLU C 200 " ideal model delta sigma weight residual 120.72 114.59 6.13 1.67e+00 3.59e-01 1.35e+01 ... (remaining 23342 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 9491 17.82 - 35.63: 757 35.63 - 53.45: 132 53.45 - 71.26: 17 71.26 - 89.08: 19 Dihedral angle restraints: 10416 sinusoidal: 3934 harmonic: 6482 Sorted by residual: dihedral pdb=" CA GLY C 670 " pdb=" C GLY C 670 " pdb=" N ALA C 671 " pdb=" CA ALA C 671 " ideal model delta harmonic sigma weight residual -180.00 -156.58 -23.42 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA GLU C 205 " pdb=" C GLU C 205 " pdb=" N ARG C 206 " pdb=" CA ARG C 206 " ideal model delta harmonic sigma weight residual 180.00 157.06 22.94 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA ASP A 203 " pdb=" C ASP A 203 " pdb=" N ALA A 204 " pdb=" CA ALA A 204 " ideal model delta harmonic sigma weight residual 180.00 159.14 20.86 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 10413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2331 0.068 - 0.136: 390 0.136 - 0.204: 11 0.204 - 0.273: 2 0.273 - 0.341: 1 Chirality restraints: 2735 Sorted by residual: chirality pdb=" CB ILE B 17 " pdb=" CA ILE B 17 " pdb=" CG1 ILE B 17 " pdb=" CG2 ILE B 17 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CB VAL D 396 " pdb=" CA VAL D 396 " pdb=" CG1 VAL D 396 " pdb=" CG2 VAL D 396 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CB ILE D 66 " pdb=" CA ILE D 66 " pdb=" CG1 ILE D 66 " pdb=" CG2 ILE D 66 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 2732 not shown) Planarity restraints: 3063 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 64 " -0.032 2.00e-02 2.50e+03 2.84e-02 1.41e+01 pdb=" CG PHE A 64 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE A 64 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 64 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 64 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 64 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 64 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 64 " 0.025 2.00e-02 2.50e+03 2.50e-02 1.10e+01 pdb=" CG PHE B 64 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE B 64 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE B 64 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 64 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 64 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 64 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 663 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.04e+00 pdb=" C PHE D 663 " 0.052 2.00e-02 2.50e+03 pdb=" O PHE D 663 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG D 664 " -0.018 2.00e-02 2.50e+03 ... (remaining 3060 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 366 2.67 - 3.23: 17702 3.23 - 3.78: 26568 3.78 - 4.34: 34379 4.34 - 4.90: 56047 Nonbonded interactions: 135062 Sorted by model distance: nonbonded pdb=" OG SER B 102 " pdb=" O ALA B 395 " model vdw 2.110 3.040 nonbonded pdb=" OG1 THR D 8 " pdb=" OG1 THR D 20 " model vdw 2.125 3.040 nonbonded pdb=" O ALA A 348 " pdb=" N THR A 350 " model vdw 2.154 3.120 nonbonded pdb=" OG1 THR D 152 " pdb=" OE1 GLN D 153 " model vdw 2.159 3.040 nonbonded pdb=" OG SER A 102 " pdb=" O ALA A 395 " model vdw 2.167 3.040 ... (remaining 135057 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 126 or (resid 127 and (name N or name CA or name \ C or name O or name CB )) or resid 128 through 201 or (resid 202 and (name N or \ name CA or name C or name O or name CB )) or resid 203 through 291 or (resid 29 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 293 through \ 324 or (resid 325 through 326 and (name N or name CA or name C or name O or name \ CB )) or resid 327 through 436)) selection = (chain 'B' and (resid 1 through 52 or (resid 53 and (name N or name CA or name C \ or name O or name CB )) or resid 54 through 164 or (resid 165 through 167 and ( \ name N or name CA or name C or name O or name CB )) or resid 168 through 260 or \ (resid 261 and (name N or name CA or name C or name O or name CB )) or resid 262 \ through 436)) } ncs_group { reference = (chain 'C' and (resid 1 through 87 or (resid 88 and (name N or name CA or name C \ or name O or name CB )) or resid 89 through 266 or (resid 267 through 272 and ( \ name N or name CA or name C or name O or name CB )) or resid 273 through 710)) selection = (chain 'D' and ((resid 1 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 34 or (resid 35 through 36 and (name N or name CA \ or name C or name O or name CB )) or resid 37 through 49 or (resid 50 through 5 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 52 or (resid \ 53 and (name N or name CA or name C or name O or name CB )) or resid 54 through \ 91 or (resid 92 and (name N or name CA or name C or name O or name CB )) or res \ id 93 through 214 or (resid 215 through 217 and (name N or name CA or name C or \ name O or name CB )) or resid 218 through 224 or (resid 225 through 226 and (nam \ e N or name CA or name C or name O or name CB )) or resid 227 through 268 or (re \ sid 269 through 272 and (name N or name CA or name C or name O or name CB )) or \ resid 273 through 295 or (resid 296 through 297 and (name N or name CA or name C \ or name O or name CB )) or resid 298 through 365 or (resid 366 through 369 and \ (name N or name CA or name C or name O or name CB )) or resid 370 through 400 or \ (resid 401 and (name N or name CA or name C or name O or name CB )) or resid 40 \ 2 through 663 or (resid 664 and (name N or name CA or name C or name O or name C \ B )) or resid 665 through 666 or (resid 667 and (name N or name CA or name C or \ name O or name CB )) or resid 668 through 697 or (resid 698 and (name N or name \ CA or name C or name O or name CB )) or resid 699 through 707 or (resid 708 thro \ ugh 710 and (name N or name CA or name C or name O or name CB )))) } 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: 5.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.020 Extract box with map and model: 0.770 Check model and map are aligned: 0.110 Set scattering table: 0.170 Process input model: 42.300 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 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 : 0.006 0.070 17200 Z= 0.262 Angle : 0.735 10.426 23347 Z= 0.388 Chirality : 0.048 0.341 2735 Planarity : 0.005 0.062 3063 Dihedral : 13.696 89.076 6264 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.19 % Favored : 91.37 % Rotamer: Outliers : 0.18 % Allowed : 0.53 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.84 (0.18), residues: 2284 helix: 0.44 (0.17), residues: 1020 sheet: -0.51 (0.32), residues: 284 loop : -1.62 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP D 706 HIS 0.009 0.001 HIS D 417 PHE 0.065 0.002 PHE A 64 TYR 0.044 0.002 TYR A 93 ARG 0.010 0.001 ARG A 10 Details of bonding type rmsd hydrogen bonds : bond 0.16076 ( 800) hydrogen bonds : angle 6.94801 ( 2346) covalent geometry : bond 0.00597 (17200) covalent geometry : angle 0.73507 (23347) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 228 time to evaluate : 1.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ASP cc_start: 0.8499 (m-30) cc_final: 0.7810 (t0) REVERT: A 127 ASP cc_start: 0.8041 (t0) cc_final: 0.7799 (t0) REVERT: A 169 MET cc_start: 0.8687 (mmp) cc_final: 0.8464 (mmp) REVERT: B 169 MET cc_start: 0.8765 (mmp) cc_final: 0.8502 (mmp) REVERT: B 225 GLU cc_start: 0.7688 (pm20) cc_final: 0.7480 (pm20) REVERT: C 538 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8720 (mm-30) REVERT: D 28 MET cc_start: 0.8642 (mmp) cc_final: 0.7976 (mmm) REVERT: D 81 GLN cc_start: 0.8545 (mp10) cc_final: 0.8322 (mp10) REVERT: D 624 MET cc_start: 0.8597 (tpt) cc_final: 0.8364 (tpt) outliers start: 3 outliers final: 1 residues processed: 231 average time/residue: 0.2989 time to fit residues: 104.3326 Evaluate side-chains 146 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 496 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 2.9990 chunk 172 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 133 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 190 GLN ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 446 HIS D 496 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.101345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.067974 restraints weight = 34781.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.070728 restraints weight = 17877.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.072557 restraints weight = 11714.065| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17200 Z= 0.185 Angle : 0.669 10.661 23347 Z= 0.342 Chirality : 0.046 0.222 2735 Planarity : 0.005 0.071 3063 Dihedral : 5.184 87.900 2463 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.96 % Favored : 92.69 % Rotamer: Outliers : 1.58 % Allowed : 11.53 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.67 (0.18), residues: 2284 helix: 0.63 (0.17), residues: 1030 sheet: -0.55 (0.32), residues: 285 loop : -1.59 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 706 HIS 0.004 0.001 HIS A 210 PHE 0.035 0.002 PHE A 64 TYR 0.020 0.002 TYR A 93 ARG 0.005 0.001 ARG A 10 Details of bonding type rmsd hydrogen bonds : bond 0.04201 ( 800) hydrogen bonds : angle 5.10522 ( 2346) covalent geometry : bond 0.00433 (17200) covalent geometry : angle 0.66918 (23347) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ASN cc_start: 0.8828 (t0) cc_final: 0.8497 (t0) REVERT: B 162 ARG cc_start: 0.8251 (mtm110) cc_final: 0.7290 (ttp80) REVERT: B 169 MET cc_start: 0.8759 (mmp) cc_final: 0.8503 (mmp) REVERT: B 177 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7255 (mm-30) REVERT: C 28 MET cc_start: 0.8594 (mmm) cc_final: 0.8328 (mpp) REVERT: D 28 MET cc_start: 0.8766 (mmp) cc_final: 0.8495 (mmt) REVERT: D 231 MET cc_start: 0.8110 (tmm) cc_final: 0.7641 (tmm) outliers start: 27 outliers final: 16 residues processed: 176 average time/residue: 0.2688 time to fit residues: 73.3124 Evaluate side-chains 153 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 653 ILE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 273 PHE Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 620 GLU Chi-restraints excluded: chain D residue 653 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 221 optimal weight: 0.9990 chunk 101 optimal weight: 0.3980 chunk 127 optimal weight: 6.9990 chunk 137 optimal weight: 4.9990 chunk 208 optimal weight: 7.9990 chunk 142 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 98 optimal weight: 0.0270 chunk 131 optimal weight: 0.0770 chunk 213 optimal weight: 0.0770 overall best weight: 0.2754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN D 72 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.103821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.079417 restraints weight = 34677.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.081739 restraints weight = 26860.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.081400 restraints weight = 24035.949| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.091 17200 Z= 0.109 Angle : 0.581 8.746 23347 Z= 0.293 Chirality : 0.043 0.217 2735 Planarity : 0.005 0.057 3063 Dihedral : 4.830 87.391 2461 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.56 % Favored : 94.13 % Rotamer: Outliers : 2.34 % Allowed : 13.76 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.47 (0.18), residues: 2284 helix: 0.80 (0.17), residues: 1042 sheet: -0.17 (0.33), residues: 267 loop : -1.58 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 353 HIS 0.005 0.001 HIS D 462 PHE 0.010 0.001 PHE C 583 TYR 0.018 0.001 TYR C 502 ARG 0.006 0.000 ARG A 10 Details of bonding type rmsd hydrogen bonds : bond 0.03314 ( 800) hydrogen bonds : angle 4.70253 ( 2346) covalent geometry : bond 0.00242 (17200) covalent geometry : angle 0.58148 (23347) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 1.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ASN cc_start: 0.8783 (t0) cc_final: 0.8463 (t0) REVERT: B 162 ARG cc_start: 0.8320 (mtm110) cc_final: 0.7486 (ttp80) REVERT: B 169 MET cc_start: 0.8676 (mmp) cc_final: 0.8473 (mmp) REVERT: B 177 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7255 (mm-30) REVERT: C 28 MET cc_start: 0.8437 (mmm) cc_final: 0.7951 (mpp) REVERT: C 146 LEU cc_start: 0.8092 (pp) cc_final: 0.7862 (pp) REVERT: C 228 LEU cc_start: 0.8822 (tp) cc_final: 0.8579 (tt) REVERT: C 404 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8502 (mp10) REVERT: D 38 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7606 (pp30) REVERT: D 231 MET cc_start: 0.7957 (tmm) cc_final: 0.7729 (tmm) outliers start: 40 outliers final: 16 residues processed: 188 average time/residue: 0.2671 time to fit residues: 78.9084 Evaluate side-chains 158 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 404 GLN Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 651 PHE Chi-restraints excluded: chain C residue 653 ILE Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 273 PHE Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 620 GLU Chi-restraints excluded: chain D residue 651 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 11 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 153 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 167 optimal weight: 0.9990 chunk 171 optimal weight: 5.9990 chunk 169 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN D 343 GLN D 579 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.100143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.066678 restraints weight = 35122.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.069432 restraints weight = 18074.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.071242 restraints weight = 11848.984| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 17200 Z= 0.208 Angle : 0.643 9.058 23347 Z= 0.325 Chirality : 0.045 0.199 2735 Planarity : 0.005 0.060 3063 Dihedral : 4.882 80.611 2461 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.83 % Favored : 92.86 % Rotamer: Outliers : 3.10 % Allowed : 15.52 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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 (0.18), residues: 2284 helix: 0.80 (0.17), residues: 1042 sheet: -0.42 (0.31), residues: 279 loop : -1.63 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 353 HIS 0.006 0.001 HIS B 407 PHE 0.031 0.002 PHE B 64 TYR 0.021 0.002 TYR A 93 ARG 0.011 0.000 ARG D 680 Details of bonding type rmsd hydrogen bonds : bond 0.03861 ( 800) hydrogen bonds : angle 4.74986 ( 2346) covalent geometry : bond 0.00494 (17200) covalent geometry : angle 0.64266 (23347) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 137 time to evaluate : 1.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ASN cc_start: 0.8853 (t0) cc_final: 0.8483 (t0) REVERT: B 162 ARG cc_start: 0.8399 (mtm110) cc_final: 0.7498 (ttp80) REVERT: B 169 MET cc_start: 0.8738 (mmp) cc_final: 0.8483 (mmp) REVERT: C 146 LEU cc_start: 0.8216 (pp) cc_final: 0.7982 (pp) REVERT: C 404 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8524 (mp10) REVERT: C 678 MET cc_start: 0.7977 (ppp) cc_final: 0.7423 (ppp) REVERT: D 38 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7481 (pp30) REVERT: D 231 MET cc_start: 0.8213 (tmm) cc_final: 0.7907 (tmm) REVERT: D 503 ILE cc_start: 0.9508 (OUTLIER) cc_final: 0.9291 (mp) outliers start: 53 outliers final: 32 residues processed: 176 average time/residue: 0.2692 time to fit residues: 75.7533 Evaluate side-chains 163 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 2.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 404 GLN Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 651 PHE Chi-restraints excluded: chain C residue 653 ILE Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 273 PHE Chi-restraints excluded: chain D residue 503 ILE Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 620 GLU Chi-restraints excluded: chain D residue 651 PHE Chi-restraints excluded: chain D residue 653 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 63 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 198 optimal weight: 8.9990 chunk 78 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 211 optimal weight: 0.0170 chunk 213 optimal weight: 6.9990 overall best weight: 1.9624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 GLN ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.100093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.068751 restraints weight = 35172.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.070395 restraints weight = 19555.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.072839 restraints weight = 12537.373| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17200 Z= 0.188 Angle : 0.625 9.412 23347 Z= 0.317 Chirality : 0.044 0.270 2735 Planarity : 0.005 0.060 3063 Dihedral : 4.841 74.368 2461 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.57 % Favored : 93.13 % Rotamer: Outliers : 3.51 % Allowed : 17.15 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.51 (0.18), residues: 2284 helix: 0.83 (0.17), residues: 1042 sheet: -0.29 (0.32), residues: 263 loop : -1.66 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 353 HIS 0.005 0.001 HIS B 407 PHE 0.021 0.002 PHE B 64 TYR 0.020 0.001 TYR A 93 ARG 0.004 0.000 ARG C 701 Details of bonding type rmsd hydrogen bonds : bond 0.03708 ( 800) hydrogen bonds : angle 4.66975 ( 2346) covalent geometry : bond 0.00444 (17200) covalent geometry : angle 0.62537 (23347) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 139 time to evaluate : 2.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ASN cc_start: 0.8891 (t0) cc_final: 0.8535 (t0) REVERT: B 162 ARG cc_start: 0.8446 (mtm110) cc_final: 0.7590 (ttp80) REVERT: B 169 MET cc_start: 0.8756 (mmp) cc_final: 0.8491 (mmp) REVERT: C 146 LEU cc_start: 0.8282 (pp) cc_final: 0.8057 (pp) REVERT: C 166 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7886 (tm-30) REVERT: C 404 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8544 (mp10) REVERT: C 678 MET cc_start: 0.8173 (ppp) cc_final: 0.7693 (ppp) REVERT: D 38 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7706 (pp30) REVERT: D 231 MET cc_start: 0.8258 (tmm) cc_final: 0.7952 (tmm) REVERT: D 443 ILE cc_start: 0.9275 (tt) cc_final: 0.9030 (tt) REVERT: D 503 ILE cc_start: 0.9461 (OUTLIER) cc_final: 0.9242 (mp) outliers start: 60 outliers final: 38 residues processed: 183 average time/residue: 0.2745 time to fit residues: 80.9534 Evaluate side-chains 171 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 129 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 404 GLN Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 651 PHE Chi-restraints excluded: chain C residue 653 ILE Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 273 PHE Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 503 ILE Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 651 PHE Chi-restraints excluded: chain D residue 653 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 151 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 65 optimal weight: 0.4980 chunk 198 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 GLN ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.101164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.070067 restraints weight = 34978.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.072034 restraints weight = 18970.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.073375 restraints weight = 11986.791| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17200 Z= 0.129 Angle : 0.586 9.578 23347 Z= 0.294 Chirality : 0.042 0.205 2735 Planarity : 0.005 0.059 3063 Dihedral : 4.704 69.636 2461 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.17 % Favored : 93.52 % Rotamer: Outliers : 3.16 % Allowed : 18.50 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.40 (0.18), residues: 2284 helix: 0.96 (0.17), residues: 1045 sheet: -0.21 (0.32), residues: 263 loop : -1.66 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 353 HIS 0.004 0.001 HIS B 407 PHE 0.011 0.001 PHE C 583 TYR 0.017 0.001 TYR C 502 ARG 0.004 0.000 ARG C 701 Details of bonding type rmsd hydrogen bonds : bond 0.03318 ( 800) hydrogen bonds : angle 4.54114 ( 2346) covalent geometry : bond 0.00303 (17200) covalent geometry : angle 0.58587 (23347) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 141 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ASN cc_start: 0.8850 (t0) cc_final: 0.8492 (t0) REVERT: B 162 ARG cc_start: 0.8454 (mtm110) cc_final: 0.7624 (ttp80) REVERT: B 169 MET cc_start: 0.8733 (mmp) cc_final: 0.8484 (mmp) REVERT: C 146 LEU cc_start: 0.8270 (pp) cc_final: 0.8050 (pp) REVERT: C 166 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7923 (tm-30) REVERT: C 232 VAL cc_start: 0.9115 (p) cc_final: 0.8760 (m) REVERT: C 404 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8553 (mp10) REVERT: C 678 MET cc_start: 0.8240 (ppp) cc_final: 0.7772 (ppp) REVERT: D 38 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7822 (pp30) REVERT: D 231 MET cc_start: 0.8268 (tmm) cc_final: 0.7947 (tmm) REVERT: D 443 ILE cc_start: 0.9263 (tt) cc_final: 0.9030 (tt) REVERT: D 452 GLU cc_start: 0.7657 (pm20) cc_final: 0.7395 (mp0) outliers start: 54 outliers final: 31 residues processed: 181 average time/residue: 0.3595 time to fit residues: 103.8332 Evaluate side-chains 170 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 404 GLN Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain C residue 651 PHE Chi-restraints excluded: chain C residue 653 ILE Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 651 PHE Chi-restraints excluded: chain D residue 653 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 98 optimal weight: 5.9990 chunk 152 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 169 optimal weight: 5.9990 chunk 16 optimal weight: 0.2980 chunk 154 optimal weight: 5.9990 chunk 197 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.100806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.067393 restraints weight = 34756.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.070218 restraints weight = 17861.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.072053 restraints weight = 11598.241| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17200 Z= 0.151 Angle : 0.601 10.804 23347 Z= 0.300 Chirality : 0.043 0.186 2735 Planarity : 0.005 0.059 3063 Dihedral : 4.662 63.370 2461 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.30 % Favored : 93.39 % Rotamer: Outliers : 3.10 % Allowed : 19.50 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.37 (0.18), residues: 2284 helix: 0.96 (0.17), residues: 1050 sheet: -0.25 (0.32), residues: 263 loop : -1.62 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 706 HIS 0.004 0.001 HIS B 407 PHE 0.016 0.001 PHE B 64 TYR 0.018 0.001 TYR A 93 ARG 0.005 0.000 ARG C 701 Details of bonding type rmsd hydrogen bonds : bond 0.03385 ( 800) hydrogen bonds : angle 4.49473 ( 2346) covalent geometry : bond 0.00356 (17200) covalent geometry : angle 0.60112 (23347) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 136 time to evaluate : 1.808 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: B 169 MET cc_start: 0.8694 (mmp) cc_final: 0.8471 (mmp) REVERT: C 166 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7914 (tm-30) REVERT: C 404 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8555 (mp10) REVERT: C 678 MET cc_start: 0.8282 (ppp) cc_final: 0.7821 (ppp) REVERT: D 38 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7773 (pp30) REVERT: D 231 MET cc_start: 0.8306 (tmm) cc_final: 0.7970 (tmm) REVERT: D 443 ILE cc_start: 0.9249 (tt) cc_final: 0.9009 (tt) REVERT: D 571 ASN cc_start: 0.8621 (p0) cc_final: 0.8409 (m-40) outliers start: 53 outliers final: 38 residues processed: 173 average time/residue: 0.3246 time to fit residues: 89.5684 Evaluate side-chains 174 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 133 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 404 GLN Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain C residue 651 PHE Chi-restraints excluded: chain C residue 653 ILE Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 620 GLU Chi-restraints excluded: chain D residue 651 PHE Chi-restraints excluded: chain D residue 653 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 59 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 30 optimal weight: 0.4980 chunk 208 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 164 optimal weight: 8.9990 chunk 104 optimal weight: 0.2980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.100888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.067425 restraints weight = 34847.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.070204 restraints weight = 17838.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.072061 restraints weight = 11672.173| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17200 Z= 0.146 Angle : 0.597 10.339 23347 Z= 0.297 Chirality : 0.043 0.167 2735 Planarity : 0.005 0.058 3063 Dihedral : 4.608 64.413 2461 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.17 % Favored : 93.52 % Rotamer: Outliers : 2.99 % Allowed : 20.14 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.34 (0.18), residues: 2284 helix: 0.98 (0.17), residues: 1050 sheet: -0.23 (0.32), residues: 263 loop : -1.58 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 706 HIS 0.004 0.001 HIS B 407 PHE 0.013 0.001 PHE B 64 TYR 0.017 0.001 TYR A 93 ARG 0.008 0.000 ARG B 162 Details of bonding type rmsd hydrogen bonds : bond 0.03334 ( 800) hydrogen bonds : angle 4.46145 ( 2346) covalent geometry : bond 0.00344 (17200) covalent geometry : angle 0.59707 (23347) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 136 time to evaluate : 2.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 169 MET cc_start: 0.8682 (mmp) cc_final: 0.8471 (mmp) REVERT: C 166 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7958 (tm-30) REVERT: C 404 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8559 (mp10) REVERT: C 678 MET cc_start: 0.8311 (ppp) cc_final: 0.7846 (ppp) REVERT: D 231 MET cc_start: 0.8315 (tmm) cc_final: 0.7978 (tmm) REVERT: D 443 ILE cc_start: 0.9252 (tt) cc_final: 0.9020 (tt) REVERT: D 698 MET cc_start: 0.7962 (mmm) cc_final: 0.7752 (mmm) outliers start: 51 outliers final: 36 residues processed: 174 average time/residue: 0.2659 time to fit residues: 74.9858 Evaluate side-chains 169 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 404 GLN Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain C residue 651 PHE Chi-restraints excluded: chain C residue 653 ILE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 651 PHE Chi-restraints excluded: chain D residue 653 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 141 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 129 optimal weight: 0.0060 chunk 21 optimal weight: 0.5980 chunk 107 optimal weight: 20.0000 chunk 144 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 186 optimal weight: 4.9990 overall best weight: 0.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 GLN ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.101497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.068144 restraints weight = 35056.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.070958 restraints weight = 17851.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.072825 restraints weight = 11665.722| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17200 Z= 0.125 Angle : 0.615 10.955 23347 Z= 0.304 Chirality : 0.042 0.155 2735 Planarity : 0.005 0.058 3063 Dihedral : 4.580 73.013 2461 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.26 % Favored : 93.43 % Rotamer: Outliers : 2.17 % Allowed : 21.02 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.28 (0.18), residues: 2284 helix: 1.01 (0.17), residues: 1049 sheet: -0.16 (0.32), residues: 263 loop : -1.55 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 706 HIS 0.004 0.001 HIS D 462 PHE 0.015 0.001 PHE D 35 TYR 0.016 0.001 TYR C 502 ARG 0.006 0.000 ARG C 701 Details of bonding type rmsd hydrogen bonds : bond 0.03146 ( 800) hydrogen bonds : angle 4.41710 ( 2346) covalent geometry : bond 0.00293 (17200) covalent geometry : angle 0.61530 (23347) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 2.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ASN cc_start: 0.8842 (t0) cc_final: 0.8456 (t0) REVERT: A 408 GLU cc_start: 0.8286 (tp30) cc_final: 0.7882 (tp30) REVERT: B 169 MET cc_start: 0.8690 (mmp) cc_final: 0.8472 (mmp) REVERT: B 436 GLU cc_start: 0.7652 (pm20) cc_final: 0.7112 (pm20) REVERT: C 166 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7949 (tm-30) REVERT: C 404 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8546 (mp10) REVERT: C 584 TYR cc_start: 0.7273 (m-10) cc_final: 0.6991 (m-10) REVERT: C 678 MET cc_start: 0.8303 (ppp) cc_final: 0.7834 (ppp) REVERT: D 231 MET cc_start: 0.8338 (tmm) cc_final: 0.7990 (tmm) REVERT: D 443 ILE cc_start: 0.9237 (tt) cc_final: 0.9000 (tt) outliers start: 37 outliers final: 30 residues processed: 163 average time/residue: 0.2913 time to fit residues: 77.2045 Evaluate side-chains 163 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 404 GLN Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 651 PHE Chi-restraints excluded: chain C residue 653 ILE Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 651 PHE Chi-restraints excluded: chain D residue 653 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 158 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 163 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 172 optimal weight: 0.6980 chunk 54 optimal weight: 0.3980 chunk 2 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 23 optimal weight: 0.0570 chunk 99 optimal weight: 8.9990 chunk 132 optimal weight: 0.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.102224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.068960 restraints weight = 34711.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.071804 restraints weight = 17554.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.073642 restraints weight = 11382.878| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17200 Z= 0.110 Angle : 0.607 10.938 23347 Z= 0.298 Chirality : 0.042 0.177 2735 Planarity : 0.005 0.057 3063 Dihedral : 4.466 72.595 2461 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.95 % Favored : 93.74 % Rotamer: Outliers : 1.87 % Allowed : 21.14 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.21 (0.18), residues: 2284 helix: 1.06 (0.17), residues: 1049 sheet: -0.04 (0.33), residues: 261 loop : -1.53 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 706 HIS 0.004 0.000 HIS D 462 PHE 0.015 0.001 PHE D 35 TYR 0.014 0.001 TYR A 93 ARG 0.005 0.000 ARG C 701 Details of bonding type rmsd hydrogen bonds : bond 0.02966 ( 800) hydrogen bonds : angle 4.36982 ( 2346) covalent geometry : bond 0.00256 (17200) covalent geometry : angle 0.60668 (23347) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 1.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ASN cc_start: 0.8809 (t0) cc_final: 0.8421 (t0) REVERT: A 408 GLU cc_start: 0.8277 (tp30) cc_final: 0.7886 (tp30) REVERT: B 162 ARG cc_start: 0.8409 (mtm110) cc_final: 0.7377 (ttp80) REVERT: B 169 MET cc_start: 0.8685 (mmp) cc_final: 0.8476 (mmp) REVERT: C 166 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7958 (tm-30) REVERT: C 404 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8543 (mp10) REVERT: C 584 TYR cc_start: 0.7208 (m-10) cc_final: 0.6926 (m-10) REVERT: C 678 MET cc_start: 0.8263 (ppp) cc_final: 0.7787 (ppp) REVERT: D 231 MET cc_start: 0.8334 (tmm) cc_final: 0.7986 (tmm) REVERT: D 443 ILE cc_start: 0.9228 (tt) cc_final: 0.8989 (tt) outliers start: 32 outliers final: 25 residues processed: 164 average time/residue: 0.2817 time to fit residues: 75.7121 Evaluate side-chains 162 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 404 GLN Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 651 PHE Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 651 PHE Chi-restraints excluded: chain D residue 653 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 29 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 227 optimal weight: 0.7980 chunk 221 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 210 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 213 optimal weight: 2.9990 chunk 163 optimal weight: 7.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 446 HIS ** C 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.100375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.067027 restraints weight = 34822.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.069772 restraints weight = 17936.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.071586 restraints weight = 11795.547| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17200 Z= 0.168 Angle : 0.637 10.568 23347 Z= 0.315 Chirality : 0.043 0.194 2735 Planarity : 0.005 0.059 3063 Dihedral : 4.622 78.253 2461 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.52 % Favored : 93.17 % Rotamer: Outliers : 2.05 % Allowed : 21.02 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.30 (0.18), residues: 2284 helix: 0.98 (0.17), residues: 1049 sheet: -0.20 (0.32), residues: 263 loop : -1.53 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 706 HIS 0.006 0.001 HIS B 407 PHE 0.017 0.001 PHE B 64 TYR 0.022 0.001 TYR A 93 ARG 0.005 0.000 ARG B 162 Details of bonding type rmsd hydrogen bonds : bond 0.03436 ( 800) hydrogen bonds : angle 4.42548 ( 2346) covalent geometry : bond 0.00396 (17200) covalent geometry : angle 0.63707 (23347) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7010.35 seconds wall clock time: 128 minutes 13.61 seconds (7693.61 seconds total)