Starting phenix.real_space_refine on Tue Feb 20 07:06:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bnu_16135/02_2024/8bnu_16135.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bnu_16135/02_2024/8bnu_16135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bnu_16135/02_2024/8bnu_16135.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bnu_16135/02_2024/8bnu_16135.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bnu_16135/02_2024/8bnu_16135.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bnu_16135/02_2024/8bnu_16135.pdb" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10308 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 10677 2.51 5 N 3015 2.21 5 O 3141 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 357": "OE1" <-> "OE2" Residue "D GLU 269": "OE1" <-> "OE2" Residue "D GLU 369": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16913 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3213 Classifications: {'peptide': 436} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 19, 'TRANS': 416} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 3218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3218 Classifications: {'peptide': 436} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 19, 'TRANS': 416} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 5204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 5204 Classifications: {'peptide': 710} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 671} Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 99 Chain: "D" Number of atoms: 5278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 5278 Classifications: {'peptide': 710} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 671} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 53 Time building chain proxies: 9.25, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 6.20 Conformation dependent library (CDL) restraints added in 2.8 seconds 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4152 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 15 sheets defined 51.0% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'A' and resid 36 through 50 removed outlier: 3.987A pdb=" N LEU A 40 " --> pdb=" O PRO A 36 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 84 removed outlier: 3.799A pdb=" N GLU A 79 " --> pdb=" O ASN A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 100 through 115 Processing helix chain 'A' and resid 138 through 150 removed outlier: 4.000A pdb=" N ARG A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LEU A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 161 removed outlier: 3.501A pdb=" N ARG A 156 " --> pdb=" O THR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 196 removed outlier: 3.672A pdb=" N GLN A 190 " --> pdb=" O ASP A 186 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET A 191 " --> pdb=" O THR A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 211 Processing helix chain 'A' and resid 213 through 220 Processing helix chain 'A' and resid 287 through 293 Processing helix chain 'A' and resid 317 through 331 Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 349 through 358 Processing helix chain 'A' and resid 359 through 366 removed outlier: 3.863A pdb=" N ALA A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 391 removed outlier: 3.697A pdb=" N TYR A 390 " --> pdb=" O GLY A 386 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 386 through 391' Processing helix chain 'A' and resid 396 through 413 removed outlier: 3.615A pdb=" N ARG A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET A 401 " --> pdb=" O THR A 397 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 402 " --> pdb=" O GLY A 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 53 Processing helix chain 'B' and resid 75 through 84 removed outlier: 3.785A pdb=" N GLU B 79 " --> pdb=" O ASN B 75 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 99 No H-bonds generated for 'chain 'B' and resid 97 through 99' Processing helix chain 'B' and resid 100 through 116 Processing helix chain 'B' and resid 137 through 150 removed outlier: 3.532A pdb=" N ARG B 142 " --> pdb=" O LYS B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 161 removed outlier: 4.123A pdb=" N LEU B 157 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 196 removed outlier: 3.642A pdb=" N THR B 187 " --> pdb=" O ARG B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 220 Processing helix chain 'B' and resid 249 through 254 Processing helix chain 'B' and resid 287 through 293 Processing helix chain 'B' and resid 317 through 331 Proline residue: B 324 - end of helix Processing helix chain 'B' and resid 333 through 337 removed outlier: 3.562A pdb=" N LEU B 337 " --> pdb=" O MET B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 358 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 396 through 412 Processing helix chain 'C' and resid 32 through 48 removed outlier: 3.861A pdb=" N ARG C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA C 41 " --> pdb=" O SER C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 79 through 99 removed outlier: 3.877A pdb=" N ALA C 83 " --> pdb=" O THR C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 123 Processing helix chain 'C' and resid 140 through 144 Processing helix chain 'C' and resid 150 through 159 Proline residue: C 156 - end of helix Processing helix chain 'C' and resid 160 through 170 removed outlier: 4.687A pdb=" N GLU C 166 " --> pdb=" O SER C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 183 Processing helix chain 'C' and resid 190 through 192 No H-bonds generated for 'chain 'C' and resid 190 through 192' Processing helix chain 'C' and resid 193 through 204 Processing helix chain 'C' and resid 216 through 220 removed outlier: 3.930A pdb=" N LEU C 219 " --> pdb=" O GLU C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 241 Processing helix chain 'C' and resid 247 through 261 Processing helix chain 'C' and resid 261 through 277 Processing helix chain 'C' and resid 279 through 298 removed outlier: 3.794A pdb=" N GLN C 283 " --> pdb=" O THR C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 330 Processing helix chain 'C' and resid 341 through 362 removed outlier: 3.602A pdb=" N ILE C 345 " --> pdb=" O ASN C 341 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG C 362 " --> pdb=" O GLY C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 375 removed outlier: 3.644A pdb=" N ASP C 371 " --> pdb=" O ALA C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 413 Processing helix chain 'C' and resid 428 through 434 Processing helix chain 'C' and resid 438 through 440 No H-bonds generated for 'chain 'C' and resid 438 through 440' Processing helix chain 'C' and resid 466 through 480 Processing helix chain 'C' and resid 494 through 512 Proline residue: C 501 - end of helix removed outlier: 3.726A pdb=" N GLN C 512 " --> pdb=" O ARG C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 526 removed outlier: 3.602A pdb=" N PHE C 526 " --> pdb=" O ALA C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 540 Processing helix chain 'C' and resid 540 through 545 Processing helix chain 'C' and resid 547 through 556 removed outlier: 3.792A pdb=" N LEU C 551 " --> pdb=" O ILE C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 560 Processing helix chain 'C' and resid 566 through 571 Processing helix chain 'C' and resid 600 through 605 Processing helix chain 'C' and resid 614 through 636 removed outlier: 3.689A pdb=" N GLU C 636 " --> pdb=" O ARG C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 652 Processing helix chain 'C' and resid 656 through 660 Processing helix chain 'C' and resid 661 through 670 Processing helix chain 'C' and resid 671 through 686 removed outlier: 4.001A pdb=" N VAL C 675 " --> pdb=" O ALA C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 690 Processing helix chain 'C' and resid 692 through 702 Processing helix chain 'D' and resid 32 through 49 removed outlier: 3.985A pdb=" N ALA D 36 " --> pdb=" O LYS D 32 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG D 40 " --> pdb=" O ALA D 36 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA D 41 " --> pdb=" O SER D 37 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN D 49 " --> pdb=" O GLN D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 76 removed outlier: 3.750A pdb=" N ILE D 74 " --> pdb=" O ASP D 70 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN D 76 " --> pdb=" O ASN D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 99 removed outlier: 3.726A pdb=" N ALA D 83 " --> pdb=" O THR D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 122 Processing helix chain 'D' and resid 153 through 160 Processing helix chain 'D' and resid 160 through 171 Processing helix chain 'D' and resid 175 through 183 Processing helix chain 'D' and resid 193 through 204 removed outlier: 3.820A pdb=" N GLU D 200 " --> pdb=" O GLU D 196 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU D 201 " --> pdb=" O ALA D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 220 removed outlier: 4.144A pdb=" N LEU D 219 " --> pdb=" O GLU D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 241 Processing helix chain 'D' and resid 247 through 261 removed outlier: 3.535A pdb=" N LEU D 251 " --> pdb=" O THR D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 277 removed outlier: 3.518A pdb=" N ALA D 277 " --> pdb=" O PHE D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 298 removed outlier: 3.635A pdb=" N GLN D 283 " --> pdb=" O THR D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 330 Processing helix chain 'D' and resid 341 through 356 removed outlier: 3.562A pdb=" N ILE D 345 " --> pdb=" O ASN D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 362 Processing helix chain 'D' and resid 366 through 375 removed outlier: 3.747A pdb=" N LYS D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 413 Processing helix chain 'D' and resid 428 through 434 Processing helix chain 'D' and resid 438 through 440 No H-bonds generated for 'chain 'D' and resid 438 through 440' Processing helix chain 'D' and resid 466 through 480 Processing helix chain 'D' and resid 494 through 512 Proline residue: D 501 - end of helix removed outlier: 3.730A pdb=" N GLN D 512 " --> pdb=" O ARG D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 527 removed outlier: 3.719A pdb=" N ILE D 519 " --> pdb=" O ARG D 515 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY D 527 " --> pdb=" O LEU D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 540 removed outlier: 3.799A pdb=" N GLY D 540 " --> pdb=" O LEU D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 546 Processing helix chain 'D' and resid 546 through 555 removed outlier: 4.432A pdb=" N VAL D 550 " --> pdb=" O LYS D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 571 Processing helix chain 'D' and resid 575 through 580 removed outlier: 3.756A pdb=" N ASN D 579 " --> pdb=" O LYS D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 605 removed outlier: 3.796A pdb=" N LEU D 604 " --> pdb=" O ALA D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.960A pdb=" N ALA D 619 " --> pdb=" O ALA D 615 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU D 636 " --> pdb=" O ARG D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 652 Processing helix chain 'D' and resid 656 through 660 Processing helix chain 'D' and resid 661 through 669 Processing helix chain 'D' and resid 671 through 686 removed outlier: 4.018A pdb=" N VAL D 675 " --> pdb=" O ALA D 671 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA D 676 " --> pdb=" O GLY D 672 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE D 677 " --> pdb=" O GLU D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 690 Processing helix chain 'D' and resid 692 through 702 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 22 removed outlier: 4.004A pdb=" N ILE A 283 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLY A 20 " --> pdb=" O ALA A 281 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA A 281 " --> pdb=" O GLY A 20 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ARG A 22 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA A 279 " --> pdb=" O ARG A 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 22 removed outlier: 4.004A pdb=" N ILE A 283 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLY A 20 " --> pdb=" O ALA A 281 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA A 281 " --> pdb=" O GLY A 20 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ARG A 22 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA A 279 " --> pdb=" O ARG A 22 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL A 63 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ALA A 126 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLY A 65 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N SER A 128 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU A 62 " --> pdb=" O TYR A 93 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL A 95 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE A 64 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER A 94 " --> pdb=" O SER B 96 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 303 through 308 removed outlier: 3.563A pdb=" N SER A 303 " --> pdb=" O VAL A 432 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 15 through 22 removed outlier: 4.537A pdb=" N ILE B 17 " --> pdb=" O MET B 285 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N MET B 285 " --> pdb=" O ILE B 17 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER B 19 " --> pdb=" O ILE B 283 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 15 through 22 removed outlier: 4.537A pdb=" N ILE B 17 " --> pdb=" O MET B 285 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N MET B 285 " --> pdb=" O ILE B 17 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER B 19 " --> pdb=" O ILE B 283 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY B 65 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA B 126 " --> pdb=" O GLY B 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 303 through 308 removed outlier: 3.530A pdb=" N SER B 303 " --> pdb=" O VAL B 432 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 9 through 11 removed outlier: 6.516A pdb=" N VAL C 55 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ALA C 107 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N PHE C 57 " --> pdb=" O ALA C 107 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ARG C 126 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N VAL C 189 " --> pdb=" O ARG C 126 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N CYS C 128 " --> pdb=" O VAL C 189 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AA9, first strand: chain 'C' and resid 64 through 66 removed outlier: 7.711A pdb=" N LEU C 113 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY C 137 " --> pdb=" O CYS C 112 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 377 through 379 removed outlier: 5.819A pdb=" N ILE C 392 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N PHE C 420 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU C 445 " --> pdb=" O PHE C 420 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N SER C 422 " --> pdb=" O LEU C 445 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 584 through 585 removed outlier: 3.651A pdb=" N LEU C 585 " --> pdb=" O GLN C 596 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLN C 596 " --> pdb=" O LEU C 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 7 through 11 removed outlier: 6.659A pdb=" N ALA D 17 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL D 58 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE D 19 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL D 55 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ALA D 107 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N PHE D 57 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ARG D 126 " --> pdb=" O ASP D 187 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N VAL D 189 " --> pdb=" O ARG D 126 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N CYS D 128 " --> pdb=" O VAL D 189 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=AB5, first strand: chain 'D' and resid 112 through 113 removed outlier: 6.860A pdb=" N CYS D 112 " --> pdb=" O GLY D 137 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 377 through 380 removed outlier: 6.224A pdb=" N ILE D 392 " --> pdb=" O ALA D 421 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ASN D 423 " --> pdb=" O ILE D 392 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N GLU D 394 " --> pdb=" O ASN D 423 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE D 420 " --> pdb=" O ILE D 443 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU D 445 " --> pdb=" O PHE D 420 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N SER D 422 " --> pdb=" O LEU D 445 " (cutoff:3.500A) 806 hydrogen bonds defined for protein. 2346 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.18 Time building geometry restraints manager: 6.76 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: 98.28 - 105.41: 397 105.41 - 112.55: 9216 112.55 - 119.69: 5655 119.69 - 126.82: 7901 126.82 - 133.96: 178 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 2.440 nonbonded pdb=" OG1 THR D 8 " pdb=" OG1 THR D 20 " model vdw 2.125 2.440 nonbonded pdb=" O ALA A 348 " pdb=" N THR A 350 " model vdw 2.154 2.520 nonbonded pdb=" OG1 THR D 152 " pdb=" OE1 GLN D 153 " model vdw 2.159 2.440 nonbonded pdb=" OG SER A 102 " pdb=" O ALA A 395 " model vdw 2.167 2.440 ... (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 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: 4.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.010 Extract box with map and model: 11.140 Check model and map are aligned: 0.260 Set scattering table: 0.140 Process input model: 45.550 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.450 ------------------------------------------------------------------------------- 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= 0.404 Angle : 0.735 10.426 23347 Z= 0.388 Chirality : 0.048 0.341 2735 Planarity : 0.005 0.062 3063 Dihedral : 13.696 89.076 6264 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.19 % Favored : 91.37 % Rotamer: Outliers : 0.18 % Allowed : 0.53 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.18), residues: 2284 helix: 0.44 (0.17), residues: 1020 sheet: -0.51 (0.32), residues: 284 loop : -1.62 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP D 706 HIS 0.009 0.001 HIS D 417 PHE 0.065 0.002 PHE A 64 TYR 0.044 0.002 TYR A 93 ARG 0.010 0.001 ARG A 10 *********************** 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 fitting. rotamer outliers: 3 poor density : 228 time to evaluate : 2.062 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: 0.2933 time to fit residues: 101.7043 Evaluate side-chains 146 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 496 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 116 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 69 optimal weight: 0.2980 chunk 108 optimal weight: 10.0000 chunk 133 optimal weight: 0.8980 chunk 207 optimal weight: 0.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 ASN ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN D 446 HIS ** D 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17200 Z= 0.237 Angle : 0.629 10.349 23347 Z= 0.319 Chirality : 0.044 0.219 2735 Planarity : 0.005 0.068 3063 Dihedral : 5.135 89.923 2463 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.57 % Favored : 93.04 % Rotamer: Outliers : 1.52 % Allowed : 11.24 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.18), residues: 2284 helix: 0.73 (0.17), residues: 1026 sheet: -0.42 (0.32), residues: 285 loop : -1.61 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 706 HIS 0.003 0.001 HIS A 210 PHE 0.026 0.001 PHE A 64 TYR 0.020 0.001 TYR A 93 ARG 0.006 0.000 ARG A 10 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 158 time to evaluate : 1.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.7932 (t0) cc_final: 0.7666 (t0) REVERT: A 169 MET cc_start: 0.8694 (mmp) cc_final: 0.8455 (mmp) REVERT: A 243 ASN cc_start: 0.8964 (t0) cc_final: 0.8643 (t0) REVERT: B 162 ARG cc_start: 0.8392 (mtm110) cc_final: 0.7353 (ttp80) REVERT: B 169 MET cc_start: 0.8807 (mmp) cc_final: 0.8538 (mmp) REVERT: B 177 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7158 (mm-30) REVERT: B 225 GLU cc_start: 0.7774 (pm20) cc_final: 0.7461 (pm20) REVERT: C 538 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8687 (mm-30) REVERT: C 545 THR cc_start: 0.8600 (t) cc_final: 0.8371 (p) REVERT: D 28 MET cc_start: 0.8931 (mmp) cc_final: 0.8489 (mmt) REVERT: D 231 MET cc_start: 0.8176 (tmm) cc_final: 0.7685 (tmm) outliers start: 26 outliers final: 16 residues processed: 175 average time/residue: 0.2683 time to fit residues: 72.9234 Evaluate side-chains 154 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 138 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 129 SER 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 523 LEU Chi-restraints excluded: chain C residue 653 ILE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 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 115 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 172 optimal weight: 0.8980 chunk 140 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 chunk 207 optimal weight: 0.9980 chunk 224 optimal weight: 9.9990 chunk 184 optimal weight: 8.9990 chunk 205 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 166 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 17200 Z= 0.206 Angle : 0.577 8.375 23347 Z= 0.291 Chirality : 0.043 0.206 2735 Planarity : 0.005 0.057 3063 Dihedral : 4.821 87.620 2461 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.22 % Favored : 93.35 % Rotamer: Outliers : 2.40 % Allowed : 13.52 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.18), residues: 2284 helix: 0.91 (0.17), residues: 1040 sheet: -0.40 (0.32), residues: 285 loop : -1.56 (0.20), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 353 HIS 0.003 0.001 HIS A 210 PHE 0.019 0.001 PHE A 64 TYR 0.017 0.001 TYR C 502 ARG 0.008 0.000 ARG D 664 *********************** 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 191 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 150 time to evaluate : 1.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.7897 (t0) cc_final: 0.7629 (t0) REVERT: A 169 MET cc_start: 0.8683 (mmp) cc_final: 0.8467 (mmp) REVERT: A 243 ASN cc_start: 0.8971 (t0) cc_final: 0.8632 (t0) REVERT: B 162 ARG cc_start: 0.8423 (mtm110) cc_final: 0.7449 (ttp80) REVERT: B 169 MET cc_start: 0.8797 (mmp) cc_final: 0.8522 (mmp) REVERT: B 177 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7247 (mm-30) REVERT: C 146 LEU cc_start: 0.7668 (pp) cc_final: 0.7444 (pp) REVERT: C 228 LEU cc_start: 0.8813 (tp) cc_final: 0.8541 (tt) REVERT: C 404 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8433 (mp10) REVERT: C 454 MET cc_start: 0.9320 (mpp) cc_final: 0.9102 (mmt) REVERT: C 538 GLU cc_start: 0.8936 (tm-30) cc_final: 0.8718 (mm-30) REVERT: C 545 THR cc_start: 0.8601 (t) cc_final: 0.8376 (p) REVERT: C 678 MET cc_start: 0.7737 (ppp) cc_final: 0.7469 (ppp) REVERT: D 231 MET cc_start: 0.8237 (tmm) cc_final: 0.7931 (tmm) outliers start: 41 outliers final: 22 residues processed: 177 average time/residue: 0.2612 time to fit residues: 73.6059 Evaluate side-chains 160 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 137 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 431 MET 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 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 96 GLU Chi-restraints excluded: chain D residue 273 PHE Chi-restraints excluded: chain D residue 275 GLU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 139 optimal weight: 0.4980 chunk 208 optimal weight: 5.9990 chunk 220 optimal weight: 8.9990 chunk 108 optimal weight: 0.9980 chunk 197 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN A 190 GLN ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17200 Z= 0.224 Angle : 0.581 8.711 23347 Z= 0.291 Chirality : 0.043 0.178 2735 Planarity : 0.005 0.055 3063 Dihedral : 4.742 82.949 2461 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.35 % Favored : 93.26 % Rotamer: Outliers : 3.16 % Allowed : 15.34 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.18), residues: 2284 helix: 1.01 (0.17), residues: 1040 sheet: -0.21 (0.32), residues: 269 loop : -1.56 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 353 HIS 0.003 0.001 HIS A 210 PHE 0.021 0.001 PHE B 64 TYR 0.016 0.001 TYR A 93 ARG 0.006 0.000 ARG D 680 *********************** 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 200 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 146 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 MET cc_start: 0.8680 (mmp) cc_final: 0.8460 (mmp) REVERT: A 243 ASN cc_start: 0.9011 (t0) cc_final: 0.8602 (t0) REVERT: B 169 MET cc_start: 0.8778 (mmp) cc_final: 0.8481 (mmp) REVERT: B 177 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7341 (mm-30) REVERT: B 225 GLU cc_start: 0.7815 (pm20) cc_final: 0.7410 (pm20) REVERT: C 146 LEU cc_start: 0.7767 (pp) cc_final: 0.7512 (pp) REVERT: C 404 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8464 (mp10) REVERT: C 545 THR cc_start: 0.8586 (t) cc_final: 0.8374 (p) REVERT: C 678 MET cc_start: 0.7822 (ppp) cc_final: 0.7301 (ppp) REVERT: D 28 MET cc_start: 0.8742 (mmp) cc_final: 0.8406 (mmp) REVERT: D 231 MET cc_start: 0.8287 (tmm) cc_final: 0.7967 (tmm) REVERT: D 503 ILE cc_start: 0.9529 (OUTLIER) cc_final: 0.9328 (mp) outliers start: 54 outliers final: 28 residues processed: 184 average time/residue: 0.2492 time to fit residues: 73.4538 Evaluate side-chains 166 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 136 time to evaluate : 1.996 ------------------------------------------------------------------------------- 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 186 ASP 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 191 MET 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 166 GLU 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 626 MET 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 273 PHE Chi-restraints excluded: chain D residue 503 ILE Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 620 GLU Chi-restraints excluded: chain D residue 651 PHE Chi-restraints excluded: chain D residue 653 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 188 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 chunk 197 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 ASN ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 GLN ** D 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 17200 Z= 0.531 Angle : 0.755 10.721 23347 Z= 0.384 Chirality : 0.049 0.334 2735 Planarity : 0.006 0.058 3063 Dihedral : 5.320 70.063 2461 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.36 % Favored : 91.16 % Rotamer: Outliers : 3.51 % Allowed : 17.62 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.18), residues: 2284 helix: 0.56 (0.16), residues: 1046 sheet: -0.37 (0.33), residues: 251 loop : -1.80 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 353 HIS 0.008 0.002 HIS A 89 PHE 0.040 0.003 PHE B 64 TYR 0.024 0.002 TYR B 93 ARG 0.005 0.001 ARG A 51 *********************** 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 192 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 132 time to evaluate : 1.953 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: 0.9110 (t0) cc_final: 0.8639 (t0) REVERT: B 162 ARG cc_start: 0.8387 (mtm110) cc_final: 0.7282 (ttp80) REVERT: B 169 MET cc_start: 0.8732 (mmp) cc_final: 0.8482 (mmp) REVERT: B 177 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7370 (mm-30) REVERT: C 678 MET cc_start: 0.8182 (ppp) cc_final: 0.7716 (ppp) REVERT: D 405 GLN cc_start: 0.8715 (tm-30) cc_final: 0.8440 (tp40) REVERT: D 443 ILE cc_start: 0.9227 (tt) cc_final: 0.8966 (tt) outliers start: 60 outliers final: 40 residues processed: 174 average time/residue: 0.2540 time to fit residues: 70.9361 Evaluate side-chains 164 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 124 time to evaluate : 1.765 ------------------------------------------------------------------------------- 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 286 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain 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 96 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 404 GLN Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain C residue 651 PHE Chi-restraints excluded: chain C residue 653 ILE Chi-restraints excluded: chain C residue 690 THR 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 340 ILE Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 651 PHE Chi-restraints excluded: chain D residue 653 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 0.9990 chunk 198 optimal weight: 4.9990 chunk 43 optimal weight: 0.1980 chunk 129 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 chunk 220 optimal weight: 0.8980 chunk 183 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 115 optimal weight: 0.0770 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN D 178 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17200 Z= 0.163 Angle : 0.583 10.207 23347 Z= 0.290 Chirality : 0.042 0.227 2735 Planarity : 0.005 0.054 3063 Dihedral : 4.758 65.562 2461 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.74 % Favored : 93.91 % Rotamer: Outliers : 2.69 % Allowed : 19.38 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.18), residues: 2284 helix: 1.02 (0.17), residues: 1039 sheet: -0.25 (0.32), residues: 263 loop : -1.62 (0.20), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 353 HIS 0.002 0.001 HIS B 407 PHE 0.012 0.001 PHE D 35 TYR 0.019 0.001 TYR C 502 ARG 0.004 0.000 ARG C 701 *********************** 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 190 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 144 time to evaluate : 1.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ASN cc_start: 0.9019 (t0) cc_final: 0.8644 (t0) REVERT: A 408 GLU cc_start: 0.8450 (tp30) cc_final: 0.8024 (tp30) REVERT: B 162 ARG cc_start: 0.8382 (mtm110) cc_final: 0.7326 (ttp80) REVERT: B 169 MET cc_start: 0.8768 (mmp) cc_final: 0.8499 (mmp) REVERT: C 166 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7667 (tm-30) REVERT: C 404 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8467 (mp10) REVERT: C 584 TYR cc_start: 0.7593 (m-10) cc_final: 0.7246 (m-10) REVERT: C 678 MET cc_start: 0.8226 (ppp) cc_final: 0.7705 (ppp) REVERT: D 28 MET cc_start: 0.8718 (mmp) cc_final: 0.8459 (mmp) REVERT: D 167 MET cc_start: 0.8177 (mmm) cc_final: 0.7919 (mmm) REVERT: D 406 MET cc_start: 0.8264 (mtp) cc_final: 0.7954 (mmp) REVERT: D 443 ILE cc_start: 0.9179 (tt) cc_final: 0.8937 (tt) REVERT: D 503 ILE cc_start: 0.9510 (OUTLIER) cc_final: 0.9285 (mp) outliers start: 46 outliers final: 25 residues processed: 173 average time/residue: 0.2594 time to fit residues: 70.8870 Evaluate side-chains 163 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 135 time to evaluate : 1.935 ------------------------------------------------------------------------------- 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 91 ASP Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 90 THR 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 523 LEU Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain C residue 651 PHE Chi-restraints excluded: chain C residue 653 ILE Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 503 ILE Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 651 PHE Chi-restraints excluded: chain D residue 653 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 185 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 219 optimal weight: 8.9990 chunk 137 optimal weight: 0.0370 chunk 133 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 overall best weight: 2.5264 ------------------------------------------------------------------------------- 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** ** A 382 ASN ** 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 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 17200 Z= 0.369 Angle : 0.657 10.686 23347 Z= 0.329 Chirality : 0.045 0.216 2735 Planarity : 0.005 0.056 3063 Dihedral : 4.903 70.212 2461 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.57 % Favored : 92.03 % Rotamer: Outliers : 3.40 % Allowed : 20.08 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.18), residues: 2284 helix: 0.90 (0.17), residues: 1042 sheet: -0.42 (0.32), residues: 263 loop : -1.66 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 353 HIS 0.008 0.001 HIS B 407 PHE 0.026 0.002 PHE B 64 TYR 0.020 0.002 TYR A 93 ARG 0.004 0.000 ARG C 701 *********************** 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 193 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 135 time to evaluate : 2.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ASN cc_start: 0.9068 (t0) cc_final: 0.8595 (t0) REVERT: B 162 ARG cc_start: 0.8377 (mtm110) cc_final: 0.7300 (ttp80) REVERT: B 169 MET cc_start: 0.8736 (mmp) cc_final: 0.8481 (mmp) REVERT: C 166 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7753 (tm-30) REVERT: C 404 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8471 (mp10) REVERT: C 584 TYR cc_start: 0.7724 (m-10) cc_final: 0.7334 (m-10) REVERT: C 678 MET cc_start: 0.8333 (ppp) cc_final: 0.7833 (ppp) REVERT: D 28 MET cc_start: 0.8738 (mmp) cc_final: 0.8502 (mmp) REVERT: D 167 MET cc_start: 0.8245 (mmm) cc_final: 0.8026 (mmm) REVERT: D 443 ILE cc_start: 0.9176 (tt) cc_final: 0.8916 (tt) outliers start: 58 outliers final: 39 residues processed: 177 average time/residue: 0.2541 time to fit residues: 72.5082 Evaluate side-chains 168 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 127 time to evaluate : 1.911 ------------------------------------------------------------------------------- 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 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 285 MET 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 113 LEU Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 191 MET 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 96 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 404 GLN Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain C residue 651 PHE Chi-restraints excluded: chain C residue 653 ILE Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 651 PHE Chi-restraints excluded: chain D residue 653 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 131 optimal weight: 2.9990 chunk 66 optimal weight: 0.0670 chunk 43 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 chunk 108 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 172 optimal weight: 0.5980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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** ** A 382 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2941 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= 0.169 Angle : 0.593 10.822 23347 Z= 0.290 Chirality : 0.042 0.172 2735 Planarity : 0.005 0.055 3063 Dihedral : 4.648 75.961 2461 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.91 % Favored : 93.74 % Rotamer: Outliers : 2.93 % Allowed : 20.90 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.18), residues: 2284 helix: 1.09 (0.17), residues: 1040 sheet: -0.22 (0.32), residues: 261 loop : -1.60 (0.20), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 706 HIS 0.004 0.000 HIS B 407 PHE 0.013 0.001 PHE D 35 TYR 0.018 0.001 TYR C 502 ARG 0.005 0.000 ARG C 701 *********************** 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 193 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 143 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ASN cc_start: 0.8981 (t0) cc_final: 0.8592 (t0) REVERT: A 408 GLU cc_start: 0.8428 (tp30) cc_final: 0.7843 (tp30) REVERT: B 162 ARG cc_start: 0.8345 (mtm110) cc_final: 0.7339 (ttp80) REVERT: B 169 MET cc_start: 0.8766 (mmp) cc_final: 0.8505 (mmp) REVERT: B 266 THR cc_start: 0.9146 (OUTLIER) cc_final: 0.8943 (p) REVERT: C 166 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7740 (tm-30) REVERT: C 404 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8523 (mp10) REVERT: C 584 TYR cc_start: 0.7669 (m-10) cc_final: 0.7334 (m-10) REVERT: C 678 MET cc_start: 0.8339 (ppp) cc_final: 0.7826 (ppp) REVERT: D 28 MET cc_start: 0.8720 (mmp) cc_final: 0.8490 (mmp) REVERT: D 58 VAL cc_start: 0.9125 (t) cc_final: 0.8911 (p) REVERT: D 167 MET cc_start: 0.8245 (mmm) cc_final: 0.8032 (mmm) REVERT: D 406 MET cc_start: 0.8235 (mtp) cc_final: 0.7916 (mmp) REVERT: D 443 ILE cc_start: 0.9140 (tt) cc_final: 0.8892 (tt) outliers start: 50 outliers final: 30 residues processed: 176 average time/residue: 0.2437 time to fit residues: 69.2113 Evaluate side-chains 170 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 137 time to evaluate : 1.896 ------------------------------------------------------------------------------- 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 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 191 MET Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain C residue 404 GLN 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 4.9990 chunk 210 optimal weight: 0.8980 chunk 192 optimal weight: 1.9990 chunk 204 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 160 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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** ** A 382 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17200 Z= 0.298 Angle : 0.629 11.113 23347 Z= 0.309 Chirality : 0.044 0.177 2735 Planarity : 0.005 0.055 3063 Dihedral : 4.714 77.044 2461 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.22 % Favored : 92.38 % Rotamer: Outliers : 3.22 % Allowed : 21.25 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.18), residues: 2284 helix: 1.03 (0.17), residues: 1045 sheet: -0.34 (0.32), residues: 263 loop : -1.60 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 353 HIS 0.007 0.001 HIS B 407 PHE 0.019 0.001 PHE B 64 TYR 0.018 0.001 TYR A 93 ARG 0.005 0.000 ARG C 701 *********************** 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 189 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 134 time to evaluate : 1.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ASN cc_start: 0.9015 (t0) cc_final: 0.8547 (t0) REVERT: B 162 ARG cc_start: 0.8379 (mtm110) cc_final: 0.7319 (ttp80) REVERT: B 169 MET cc_start: 0.8739 (mmp) cc_final: 0.8491 (mmp) REVERT: B 266 THR cc_start: 0.9168 (OUTLIER) cc_final: 0.8962 (p) REVERT: B 436 GLU cc_start: 0.7879 (pm20) cc_final: 0.7626 (pm20) REVERT: C 23 VAL cc_start: 0.7915 (OUTLIER) cc_final: 0.7709 (m) REVERT: C 166 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7732 (tm-30) REVERT: C 404 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8520 (mp10) REVERT: C 584 TYR cc_start: 0.7726 (m-10) cc_final: 0.7359 (m-10) REVERT: C 678 MET cc_start: 0.8357 (ppp) cc_final: 0.7834 (ppp) REVERT: D 167 MET cc_start: 0.8243 (mmm) cc_final: 0.8040 (mmm) REVERT: D 406 MET cc_start: 0.8266 (mtp) cc_final: 0.7947 (mmp) REVERT: D 443 ILE cc_start: 0.9175 (tt) cc_final: 0.8929 (tt) outliers start: 55 outliers final: 39 residues processed: 172 average time/residue: 0.2519 time to fit residues: 70.0015 Evaluate side-chains 176 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 133 time to evaluate : 1.916 ------------------------------------------------------------------------------- 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 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 191 MET Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 190 GLN 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 117 LEU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 166 GLU 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 374 LEU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 435 HIS Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 623 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 216 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 227 optimal weight: 9.9990 chunk 209 optimal weight: 0.8980 chunk 180 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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** ** A 382 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17200 Z= 0.297 Angle : 0.635 11.604 23347 Z= 0.311 Chirality : 0.044 0.179 2735 Planarity : 0.005 0.055 3063 Dihedral : 4.743 76.670 2461 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.36 % Favored : 92.29 % Rotamer: Outliers : 2.99 % Allowed : 21.49 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.18), residues: 2284 helix: 0.98 (0.17), residues: 1046 sheet: -0.22 (0.33), residues: 251 loop : -1.65 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 353 HIS 0.006 0.001 HIS B 407 PHE 0.014 0.001 PHE D 35 TYR 0.018 0.001 TYR A 93 ARG 0.005 0.000 ARG C 701 ********************** 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 184 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 133 time to evaluate : 2.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ASN cc_start: 0.9012 (t0) cc_final: 0.8548 (t0) REVERT: B 162 ARG cc_start: 0.8385 (mtm110) cc_final: 0.7773 (ttm170) REVERT: B 169 MET cc_start: 0.8739 (mmp) cc_final: 0.8494 (mmp) REVERT: B 266 THR cc_start: 0.9193 (OUTLIER) cc_final: 0.8991 (p) REVERT: B 436 GLU cc_start: 0.7900 (pm20) cc_final: 0.7636 (pm20) REVERT: C 23 VAL cc_start: 0.7899 (OUTLIER) cc_final: 0.7695 (m) REVERT: C 166 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7711 (tm-30) REVERT: C 404 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8529 (mp10) REVERT: C 584 TYR cc_start: 0.7763 (m-10) cc_final: 0.7391 (m-10) REVERT: C 678 MET cc_start: 0.8362 (ppp) cc_final: 0.7833 (ppp) REVERT: D 167 MET cc_start: 0.8251 (mmm) cc_final: 0.8047 (mmm) REVERT: D 406 MET cc_start: 0.8239 (mtp) cc_final: 0.7923 (mmp) REVERT: D 443 ILE cc_start: 0.9178 (tt) cc_final: 0.8925 (tt) outliers start: 51 outliers final: 40 residues processed: 167 average time/residue: 0.2553 time to fit residues: 69.0454 Evaluate side-chains 177 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 133 time to evaluate : 2.067 ------------------------------------------------------------------------------- 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 186 ASP Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 190 GLN 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 117 LEU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 166 GLU 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 623 VAL 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 374 LEU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 435 HIS Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 623 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 192 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 181 optimal weight: 0.0870 chunk 75 optimal weight: 0.7980 chunk 186 optimal weight: 5.9990 chunk 22 optimal weight: 0.0870 chunk 33 optimal weight: 0.9990 chunk 159 optimal weight: 0.0970 overall best weight: 0.3934 ------------------------------------------------------------------------------- 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** ** A 382 ASN ** 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 = 0.3641 r_free = 0.3641 target = 0.102424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.069476 restraints weight = 34805.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.072346 restraints weight = 17614.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.074239 restraints weight = 11403.484| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17200 Z= 0.158 Angle : 0.590 11.343 23347 Z= 0.286 Chirality : 0.042 0.201 2735 Planarity : 0.005 0.054 3063 Dihedral : 4.510 77.312 2461 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.26 % Favored : 93.43 % Rotamer: Outliers : 2.34 % Allowed : 22.07 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.18), residues: 2284 helix: 1.16 (0.17), residues: 1041 sheet: -0.20 (0.33), residues: 263 loop : -1.54 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 706 HIS 0.003 0.000 HIS B 407 PHE 0.018 0.001 PHE D 35 TYR 0.018 0.001 TYR C 502 ARG 0.005 0.000 ARG C 701 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2930.34 seconds wall clock time: 55 minutes 2.44 seconds (3302.44 seconds total)