Starting phenix.real_space_refine on Mon Aug 25 04:22:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bnu_16135/08_2025/8bnu_16135.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bnu_16135/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8bnu_16135/08_2025/8bnu_16135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bnu_16135/08_2025/8bnu_16135.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bnu_16135/08_2025/8bnu_16135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bnu_16135/08_2025/8bnu_16135.map" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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, 'ASP:plan': 4, 'GLU:plan': 3, 'ARG:plan': 3} 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, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2} 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: {'GLU:plan': 6, 'PHE:plan': 1, 'ARG:plan': 10, 'GLN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 2, 'ARG:plan': 6, 'ASP:plan': 2, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 53 Time building chain proxies: 3.30, per 1000 atoms: 0.20 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: 1.44 Conformation dependent library (CDL) restraints added in 537.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.42 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: 2.64 Time building geometry restraints manager: 1.88 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: 2.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.590 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.830 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.010 0.001 ARG A 10 TYR 0.044 0.002 TYR A 93 PHE 0.065 0.002 PHE A 64 TRP 0.043 0.003 TRP D 706 HIS 0.009 0.001 HIS D 417 Details of bonding type rmsd covalent geometry : bond 0.00597 (17200) covalent geometry : angle 0.73507 (23347) hydrogen bonds : bond 0.16076 ( 800) hydrogen bonds : angle 6.94801 ( 2346) *********************** 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 : 0.645 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: 0.1153 time to fit residues: 40.3091 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 : 0.579 ------------------------------------------------------------------------------- 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 216 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.0060 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 9.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 GLN ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN D 64 ASN D 446 HIS D 496 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.102505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.071238 restraints weight = 34607.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.073000 restraints weight = 18508.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.075494 restraints weight = 11894.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.075513 restraints weight = 10258.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.075219 restraints weight = 8994.420| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17200 Z= 0.149 Angle : 0.649 10.407 23347 Z= 0.330 Chirality : 0.045 0.226 2735 Planarity : 0.005 0.060 3063 Dihedral : 5.109 89.829 2463 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.61 % Favored : 93.04 % Rotamer: Outliers : 1.41 % Allowed : 10.83 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.18), residues: 2284 helix: 0.69 (0.17), residues: 1028 sheet: -0.43 (0.32), residues: 285 loop : -1.58 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 10 TYR 0.018 0.001 TYR A 93 PHE 0.029 0.001 PHE A 64 TRP 0.021 0.002 TRP D 706 HIS 0.004 0.001 HIS D 462 Details of bonding type rmsd covalent geometry : bond 0.00342 (17200) covalent geometry : angle 0.64879 (23347) hydrogen bonds : bond 0.04210 ( 800) hydrogen bonds : angle 5.16784 ( 2346) *********************** 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 185 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 MET cc_start: 0.8689 (mmp) cc_final: 0.8481 (mmp) REVERT: B 162 ARG cc_start: 0.8348 (mtm110) cc_final: 0.7363 (ttp80) REVERT: B 169 MET cc_start: 0.8797 (mmp) cc_final: 0.8540 (mmp) REVERT: B 177 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7202 (mm-30) REVERT: C 28 MET cc_start: 0.8639 (mmm) cc_final: 0.8359 (mpp) REVERT: D 28 MET cc_start: 0.8766 (mmp) cc_final: 0.8378 (mmt) REVERT: D 231 MET cc_start: 0.8074 (tmm) cc_final: 0.7594 (tmm) outliers start: 24 outliers final: 13 residues processed: 176 average time/residue: 0.1161 time to fit residues: 31.7806 Evaluate side-chains 153 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain B residue 130 SER 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 653 ILE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 96 GLU 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 653 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 11 optimal weight: 1.9990 chunk 180 optimal weight: 8.9990 chunk 188 optimal weight: 5.9990 chunk 157 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 165 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 200 optimal weight: 9.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 190 GLN ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 ASN D 343 GLN D 579 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.099726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.069253 restraints weight = 35729.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.070803 restraints weight = 18468.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.071570 restraints weight = 12423.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.072020 restraints weight = 12191.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.072121 restraints weight = 10470.867| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 17200 Z= 0.209 Angle : 0.651 8.632 23347 Z= 0.333 Chirality : 0.046 0.218 2735 Planarity : 0.005 0.061 3063 Dihedral : 5.073 82.549 2461 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.31 % Favored : 92.38 % Rotamer: Outliers : 2.75 % Allowed : 13.99 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.18), residues: 2284 helix: 0.70 (0.17), residues: 1037 sheet: -0.47 (0.31), residues: 279 loop : -1.64 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 701 TYR 0.022 0.002 TYR A 93 PHE 0.037 0.002 PHE B 64 TRP 0.014 0.001 TRP D 353 HIS 0.005 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00498 (17200) covalent geometry : angle 0.65114 (23347) hydrogen bonds : bond 0.04127 ( 800) hydrogen bonds : angle 4.83378 ( 2346) *********************** 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 193 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 146 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.8451 (m-10) REVERT: A 243 ASN cc_start: 0.8867 (t0) cc_final: 0.8514 (t0) REVERT: B 162 ARG cc_start: 0.8364 (mtm110) cc_final: 0.7432 (ttp80) REVERT: B 169 MET cc_start: 0.8766 (mmp) cc_final: 0.8485 (mmp) REVERT: B 177 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7303 (mm-30) REVERT: C 146 LEU cc_start: 0.8280 (pp) cc_final: 0.8071 (pp) REVERT: C 228 LEU cc_start: 0.8921 (tp) cc_final: 0.8609 (tt) REVERT: D 231 MET cc_start: 0.8095 (tmm) cc_final: 0.7822 (tmm) outliers start: 47 outliers final: 26 residues processed: 180 average time/residue: 0.1083 time to fit residues: 30.6460 Evaluate side-chains 158 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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 190 GLN Chi-restraints excluded: chain A residue 286 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 266 THR 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 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 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 565 VAL Chi-restraints excluded: chain D residue 651 PHE Chi-restraints excluded: chain D residue 653 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 200 optimal weight: 8.9990 chunk 164 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 219 optimal weight: 0.9990 chunk 227 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 62 optimal weight: 0.0770 chunk 27 optimal weight: 0.7980 chunk 112 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- 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 64 ASN ** 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 = 0.3622 r_free = 0.3622 target = 0.101199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.067727 restraints weight = 35118.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.070492 restraints weight = 17848.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.072396 restraints weight = 11659.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.073597 restraints weight = 8854.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.074350 restraints weight = 7421.275| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17200 Z= 0.137 Angle : 0.602 8.718 23347 Z= 0.304 Chirality : 0.043 0.174 2735 Planarity : 0.005 0.057 3063 Dihedral : 4.853 79.004 2461 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.00 % Favored : 93.70 % Rotamer: Outliers : 3.10 % Allowed : 16.28 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.18), residues: 2284 helix: 0.81 (0.17), residues: 1043 sheet: -0.44 (0.31), residues: 279 loop : -1.65 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 701 TYR 0.017 0.001 TYR C 502 PHE 0.019 0.001 PHE A 64 TRP 0.009 0.001 TRP D 353 HIS 0.003 0.001 HIS D 462 Details of bonding type rmsd covalent geometry : bond 0.00325 (17200) covalent geometry : angle 0.60232 (23347) hydrogen bonds : bond 0.03467 ( 800) hydrogen bonds : angle 4.65600 ( 2346) *********************** 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 199 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 146 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ASN cc_start: 0.8833 (t0) cc_final: 0.8486 (t0) REVERT: B 162 ARG cc_start: 0.8295 (mtm110) cc_final: 0.7452 (ttp80) REVERT: B 169 MET cc_start: 0.8702 (mmp) cc_final: 0.8477 (mmp) REVERT: C 146 LEU cc_start: 0.8159 (pp) cc_final: 0.7933 (pp) REVERT: C 228 LEU cc_start: 0.8913 (tp) cc_final: 0.8705 (tt) REVERT: C 404 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8529 (mp10) REVERT: C 678 MET cc_start: 0.8042 (ppp) cc_final: 0.7458 (ppp) REVERT: D 231 MET cc_start: 0.8167 (tmm) cc_final: 0.7867 (tmm) REVERT: D 443 ILE cc_start: 0.9246 (tt) cc_final: 0.8997 (tt) REVERT: D 503 ILE cc_start: 0.9467 (OUTLIER) cc_final: 0.9251 (mp) outliers start: 53 outliers final: 25 residues processed: 186 average time/residue: 0.0965 time to fit residues: 29.2299 Evaluate side-chains 161 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 134 THR 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 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 410 VAL Chi-restraints excluded: chain D residue 503 ILE Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 530 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 121 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 202 optimal weight: 0.9980 chunk 216 optimal weight: 10.0000 chunk 136 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 224 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 211 optimal weight: 0.0470 chunk 14 optimal weight: 0.8980 overall best weight: 1.1882 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.101217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.067804 restraints weight = 34821.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.070664 restraints weight = 17830.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.072537 restraints weight = 11504.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.073741 restraints weight = 8716.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.074520 restraints weight = 7305.163| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2529 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= 0.137 Angle : 0.598 9.361 23347 Z= 0.300 Chirality : 0.043 0.282 2735 Planarity : 0.005 0.057 3063 Dihedral : 4.738 73.713 2461 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.17 % Favored : 93.52 % Rotamer: Outliers : 2.87 % Allowed : 17.39 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.18), residues: 2284 helix: 0.93 (0.17), residues: 1045 sheet: -0.17 (0.32), residues: 263 loop : -1.67 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 701 TYR 0.020 0.001 TYR C 502 PHE 0.014 0.001 PHE B 64 TRP 0.009 0.001 TRP D 353 HIS 0.005 0.001 HIS B 407 Details of bonding type rmsd covalent geometry : bond 0.00324 (17200) covalent geometry : angle 0.59766 (23347) hydrogen bonds : bond 0.03359 ( 800) hydrogen bonds : angle 4.57215 ( 2346) *********************** 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 193 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 144 time to evaluate : 0.521 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: 0.8833 (t0) cc_final: 0.8446 (t0) REVERT: B 162 ARG cc_start: 0.8337 (mtm110) cc_final: 0.7522 (ttp80) REVERT: B 169 MET cc_start: 0.8693 (mmp) cc_final: 0.8468 (mmp) REVERT: B 266 THR cc_start: 0.9082 (OUTLIER) cc_final: 0.8875 (p) REVERT: C 146 LEU cc_start: 0.8206 (pp) cc_final: 0.7981 (pp) REVERT: C 228 LEU cc_start: 0.8852 (tp) cc_final: 0.8574 (tt) REVERT: C 678 MET cc_start: 0.8215 (ppp) cc_final: 0.7764 (ppp) REVERT: D 167 MET cc_start: 0.8347 (mmm) cc_final: 0.8084 (mmm) REVERT: D 231 MET cc_start: 0.8235 (tmm) cc_final: 0.7937 (tmm) REVERT: D 443 ILE cc_start: 0.9234 (tt) cc_final: 0.8990 (tt) REVERT: D 503 ILE cc_start: 0.9467 (OUTLIER) cc_final: 0.9253 (mp) outliers start: 49 outliers final: 33 residues processed: 180 average time/residue: 0.1046 time to fit residues: 30.1388 Evaluate side-chains 169 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 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 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 266 THR Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 404 GLN 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 410 VAL Chi-restraints excluded: chain D residue 503 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 198 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 210 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 177 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 446 HIS ** 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 = 0.3584 r_free = 0.3584 target = 0.098867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.065382 restraints weight = 34961.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.068095 restraints weight = 18021.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.069882 restraints weight = 11819.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.071023 restraints weight = 9050.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.071759 restraints weight = 7630.631| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 17200 Z= 0.240 Angle : 0.665 9.942 23347 Z= 0.337 Chirality : 0.045 0.235 2735 Planarity : 0.005 0.060 3063 Dihedral : 4.926 63.297 2461 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.66 % Favored : 92.03 % Rotamer: Outliers : 3.45 % Allowed : 19.26 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.18), residues: 2284 helix: 0.78 (0.17), residues: 1053 sheet: -0.42 (0.32), residues: 263 loop : -1.71 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 97 TYR 0.022 0.002 TYR A 93 PHE 0.026 0.002 PHE B 64 TRP 0.014 0.002 TRP D 706 HIS 0.005 0.001 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00565 (17200) covalent geometry : angle 0.66457 (23347) hydrogen bonds : bond 0.04017 ( 800) hydrogen bonds : angle 4.70076 ( 2346) *********************** 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 192 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 133 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.7593 (mmm160) cc_final: 0.7333 (mmm160) REVERT: B 169 MET cc_start: 0.8687 (mmp) cc_final: 0.8473 (mmp) REVERT: B 266 THR cc_start: 0.9138 (OUTLIER) cc_final: 0.8914 (p) REVERT: C 23 VAL cc_start: 0.8413 (OUTLIER) cc_final: 0.8207 (m) REVERT: C 678 MET cc_start: 0.8297 (ppp) cc_final: 0.7848 (ppp) REVERT: D 167 MET cc_start: 0.8409 (mmm) cc_final: 0.8072 (mmm) REVERT: D 443 ILE cc_start: 0.9282 (tt) cc_final: 0.9024 (tt) outliers start: 59 outliers final: 36 residues processed: 174 average time/residue: 0.1005 time to fit residues: 28.1813 Evaluate side-chains 166 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 275 LEU 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 B residue 266 THR Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 404 GLN 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 58 VAL 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 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 47 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 127 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 123 optimal weight: 0.9990 chunk 153 optimal weight: 0.8980 chunk 170 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** ** D 38 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 = 0.3623 r_free = 0.3623 target = 0.101231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.068047 restraints weight = 34711.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.070846 restraints weight = 17691.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.072689 restraints weight = 11539.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.073865 restraints weight = 8772.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.074664 restraints weight = 7353.805| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17200 Z= 0.122 Angle : 0.601 11.039 23347 Z= 0.299 Chirality : 0.043 0.202 2735 Planarity : 0.005 0.057 3063 Dihedral : 4.673 64.634 2461 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.91 % Favored : 93.78 % Rotamer: Outliers : 2.58 % Allowed : 20.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.18), residues: 2284 helix: 0.96 (0.17), residues: 1052 sheet: -0.22 (0.32), residues: 261 loop : -1.62 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 701 TYR 0.018 0.001 TYR C 502 PHE 0.011 0.001 PHE D 35 TRP 0.012 0.001 TRP D 706 HIS 0.004 0.001 HIS D 462 Details of bonding type rmsd covalent geometry : bond 0.00286 (17200) covalent geometry : angle 0.60083 (23347) hydrogen bonds : bond 0.03195 ( 800) hydrogen bonds : angle 4.49218 ( 2346) *********************** 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 181 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 137 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.7570 (mmm160) cc_final: 0.7350 (mmm160) REVERT: A 243 ASN cc_start: 0.8842 (t0) cc_final: 0.8456 (t0) REVERT: A 408 GLU cc_start: 0.8311 (tp30) cc_final: 0.7885 (tp30) REVERT: B 266 THR cc_start: 0.9106 (OUTLIER) cc_final: 0.8890 (p) REVERT: C 404 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8517 (mp10) REVERT: C 584 TYR cc_start: 0.7215 (m-10) cc_final: 0.6962 (m-10) REVERT: C 678 MET cc_start: 0.8306 (ppp) cc_final: 0.7866 (ppp) REVERT: D 167 MET cc_start: 0.8382 (mmm) cc_final: 0.8078 (mmm) REVERT: D 443 ILE cc_start: 0.9245 (tt) cc_final: 0.8996 (tt) REVERT: D 452 GLU cc_start: 0.7617 (pm20) cc_final: 0.7403 (mp0) outliers start: 44 outliers final: 28 residues processed: 168 average time/residue: 0.1016 time to fit residues: 27.3646 Evaluate side-chains 162 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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 93 TYR Chi-restraints excluded: chain A residue 186 ASP 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 43 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 B residue 227 MET Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 23 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 360 VAL Chi-restraints excluded: chain C residue 404 GLN 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 210 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 223 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.101565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.068246 restraints weight = 34830.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.071071 restraints weight = 17787.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.072938 restraints weight = 11560.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.074098 restraints weight = 8801.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.074873 restraints weight = 7401.590| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17200 Z= 0.122 Angle : 0.597 11.428 23347 Z= 0.296 Chirality : 0.042 0.169 2735 Planarity : 0.005 0.056 3063 Dihedral : 4.553 69.776 2461 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.04 % Favored : 93.65 % Rotamer: Outliers : 2.28 % Allowed : 20.96 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.18), residues: 2284 helix: 1.02 (0.17), residues: 1050 sheet: -0.20 (0.32), residues: 263 loop : -1.57 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 162 TYR 0.016 0.001 TYR C 502 PHE 0.012 0.001 PHE D 35 TRP 0.010 0.001 TRP D 706 HIS 0.004 0.001 HIS D 462 Details of bonding type rmsd covalent geometry : bond 0.00287 (17200) covalent geometry : angle 0.59746 (23347) hydrogen bonds : bond 0.03091 ( 800) hydrogen bonds : angle 4.41458 ( 2346) *********************** 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 178 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ASN cc_start: 0.8819 (t0) cc_final: 0.8421 (t0) REVERT: A 408 GLU cc_start: 0.8299 (tp30) cc_final: 0.7903 (tp30) REVERT: B 184 MET cc_start: 0.8438 (mmm) cc_final: 0.8205 (mtp) REVERT: B 266 THR cc_start: 0.9096 (OUTLIER) cc_final: 0.8895 (p) REVERT: C 404 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8512 (mp10) REVERT: C 584 TYR cc_start: 0.7188 (m-10) cc_final: 0.6911 (m-10) REVERT: C 678 MET cc_start: 0.8282 (ppp) cc_final: 0.7830 (ppp) REVERT: D 28 MET cc_start: 0.8623 (mmt) cc_final: 0.8192 (mmp) REVERT: D 167 MET cc_start: 0.8397 (mmm) cc_final: 0.8099 (mmm) REVERT: D 443 ILE cc_start: 0.9222 (tt) cc_final: 0.8976 (tt) outliers start: 39 outliers final: 30 residues processed: 166 average time/residue: 0.0969 time to fit residues: 26.0074 Evaluate side-chains 164 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 168 LEU 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 43 MET Chi-restraints excluded: chain B residue 49 LEU 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 B residue 266 THR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 404 GLN 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 530 VAL Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 651 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 170 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 162 optimal weight: 5.9990 chunk 151 optimal weight: 0.1980 chunk 77 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 43 optimal weight: 0.1980 chunk 97 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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** ** D 38 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 = 0.3621 r_free = 0.3621 target = 0.101041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.070595 restraints weight = 34730.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.072273 restraints weight = 18091.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.072579 restraints weight = 11812.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.073246 restraints weight = 11696.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.073284 restraints weight = 10382.528| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2996 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= 0.142 Angle : 0.609 10.690 23347 Z= 0.301 Chirality : 0.043 0.170 2735 Planarity : 0.005 0.057 3063 Dihedral : 4.544 68.997 2461 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.39 % Favored : 93.30 % Rotamer: Outliers : 2.81 % Allowed : 20.73 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.18), residues: 2284 helix: 1.03 (0.17), residues: 1052 sheet: -0.20 (0.32), residues: 263 loop : -1.57 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 701 TYR 0.016 0.001 TYR A 93 PHE 0.013 0.001 PHE D 35 TRP 0.009 0.001 TRP D 706 HIS 0.004 0.001 HIS D 462 Details of bonding type rmsd covalent geometry : bond 0.00337 (17200) covalent geometry : angle 0.60853 (23347) hydrogen bonds : bond 0.03220 ( 800) hydrogen bonds : angle 4.43205 ( 2346) *********************** 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 181 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 133 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 436 GLU cc_start: 0.7609 (pm20) cc_final: 0.7063 (pm20) REVERT: C 404 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8504 (mp10) REVERT: C 584 TYR cc_start: 0.7064 (m-10) cc_final: 0.6826 (m-10) REVERT: C 678 MET cc_start: 0.8250 (ppp) cc_final: 0.7822 (ppp) REVERT: D 167 MET cc_start: 0.8444 (mmm) cc_final: 0.8157 (mmm) REVERT: D 443 ILE cc_start: 0.9267 (tt) cc_final: 0.9033 (tt) outliers start: 48 outliers final: 34 residues processed: 171 average time/residue: 0.1089 time to fit residues: 30.4182 Evaluate side-chains 169 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 49 LEU 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 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 43 MET Chi-restraints excluded: chain B residue 49 LEU 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 23 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 404 GLN 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 161 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 161 optimal weight: 0.0870 chunk 197 optimal weight: 1.9990 chunk 182 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 165 optimal weight: 0.9980 chunk 108 optimal weight: 10.0000 chunk 44 optimal weight: 0.3980 chunk 84 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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** ** D 38 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 = 0.3639 r_free = 0.3639 target = 0.102265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.071030 restraints weight = 34664.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.072674 restraints weight = 19160.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.074022 restraints weight = 12530.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.074309 restraints weight = 10443.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.074526 restraints weight = 9866.663| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3110 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= 0.110 Angle : 0.601 11.109 23347 Z= 0.295 Chirality : 0.042 0.203 2735 Planarity : 0.005 0.056 3063 Dihedral : 4.419 68.270 2461 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.56 % Favored : 94.13 % Rotamer: Outliers : 2.17 % Allowed : 21.14 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.18), residues: 2284 helix: 1.11 (0.17), residues: 1048 sheet: -0.07 (0.33), residues: 261 loop : -1.55 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 701 TYR 0.016 0.001 TYR C 502 PHE 0.016 0.001 PHE D 35 TRP 0.009 0.001 TRP D 706 HIS 0.004 0.000 HIS D 462 Details of bonding type rmsd covalent geometry : bond 0.00256 (17200) covalent geometry : angle 0.60090 (23347) hydrogen bonds : bond 0.02924 ( 800) hydrogen bonds : angle 4.34929 ( 2346) ********************** 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 177 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 140 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ASN cc_start: 0.8747 (t0) cc_final: 0.8354 (t0) REVERT: A 408 GLU cc_start: 0.8192 (tp30) cc_final: 0.7850 (tp30) REVERT: B 184 MET cc_start: 0.8443 (mmm) cc_final: 0.8198 (mtp) REVERT: C 174 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7855 (mt) REVERT: C 404 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8529 (mp10) REVERT: C 584 TYR cc_start: 0.7185 (m-10) cc_final: 0.6963 (m-10) REVERT: C 678 MET cc_start: 0.8257 (ppp) cc_final: 0.7801 (ppp) REVERT: D 167 MET cc_start: 0.8398 (mmm) cc_final: 0.8118 (mmm) REVERT: D 443 ILE cc_start: 0.9243 (tt) cc_final: 0.9008 (tt) outliers start: 37 outliers final: 25 residues processed: 169 average time/residue: 0.1026 time to fit residues: 27.9986 Evaluate side-chains 164 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 93 TYR 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 43 MET Chi-restraints excluded: chain B residue 49 LEU 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 23 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 404 GLN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 33 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 227 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 226 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 107 optimal weight: 0.0060 chunk 54 optimal weight: 0.7980 chunk 211 optimal weight: 6.9990 chunk 192 optimal weight: 2.9990 overall best weight: 1.5400 ------------------------------------------------------------------------------- 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** ** D 38 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 = 0.3611 r_free = 0.3611 target = 0.100506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.067770 restraints weight = 34924.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.071058 restraints weight = 17620.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.073112 restraints weight = 10231.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.072951 restraints weight = 9030.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.073065 restraints weight = 8338.986| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17200 Z= 0.159 Angle : 0.628 11.067 23347 Z= 0.309 Chirality : 0.043 0.189 2735 Planarity : 0.005 0.057 3063 Dihedral : 4.586 78.289 2461 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.65 % Favored : 93.04 % Rotamer: Outliers : 2.05 % Allowed : 21.31 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.18), residues: 2284 helix: 1.04 (0.17), residues: 1052 sheet: -0.26 (0.32), residues: 267 loop : -1.51 (0.21), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 701 TYR 0.017 0.001 TYR A 93 PHE 0.016 0.001 PHE B 64 TRP 0.010 0.001 TRP D 706 HIS 0.004 0.001 HIS D 462 Details of bonding type rmsd covalent geometry : bond 0.00377 (17200) covalent geometry : angle 0.62758 (23347) hydrogen bonds : bond 0.03355 ( 800) hydrogen bonds : angle 4.40867 ( 2346) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2480.68 seconds wall clock time: 43 minutes 36.65 seconds (2616.65 seconds total)