Starting phenix.real_space_refine on Sat Mar 16 00:45:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tco_41156/03_2024/8tco_41156.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tco_41156/03_2024/8tco_41156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tco_41156/03_2024/8tco_41156.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tco_41156/03_2024/8tco_41156.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tco_41156/03_2024/8tco_41156.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tco_41156/03_2024/8tco_41156.pdb" } resolution = 2.8 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= 0.008 sd= 1.180 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 8420 2.51 5 N 2238 2.21 5 O 2499 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 378": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13222 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5165 Classifications: {'peptide': 643} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 612} Chain breaks: 3 Chain: "B" Number of atoms: 1817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1817 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 210} Chain: "C" Number of atoms: 2455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2455 Classifications: {'peptide': 295} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 276} Chain breaks: 3 Chain: "D" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 851 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "E" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 949 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "F" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 977 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 804 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 6.95, per 1000 atoms: 0.53 Number of scatterers: 13222 At special positions: 0 Unit cell: (89.3, 135.36, 172.96, 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 65 16.00 O 2499 8.00 N 2238 7.00 C 8420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS B 54 " distance=2.03 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS B 47 " distance=2.03 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 211 " distance=2.03 Simple disulfide: pdb=" SG CYS A 330 " - pdb=" SG CYS A 383 " distance=2.03 Simple disulfide: pdb=" SG CYS A 495 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 624 " distance=2.03 Simple disulfide: pdb=" SG CYS A 647 " - pdb=" SG CYS A 650 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS C 345 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 143 " - pdb=" SG CYS C 151 " distance=2.03 Simple disulfide: pdb=" SG CYS C 169 " - pdb=" SG CYS C 220 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 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 Links applied BETA1-4 " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG A 801 " - " ASN A 62 " " NAG C 501 " - " ASN C 350 " " NAG C 502 " - " ASN C 242 " " NAG C 503 " - " ASN C 454 " " NAG C 504 " - " ASN C 367 " " NAG C 505 " - " ASN C 130 " " NAG C 506 " - " ASN C 157 " " NAG H 1 " - " ASN C 162 " " NAG I 1 " - " ASN C 433 " " NAG J 1 " - " ASN C 219 " Time building additional restraints: 5.24 Conformation dependent library (CDL) restraints added in 2.1 seconds 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3090 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 25 sheets defined 30.2% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 93 through 98 removed outlier: 3.510A pdb=" N LEU A 96 " --> pdb=" O PRO A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 107 removed outlier: 4.068A pdb=" N PHE A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 121 Processing helix chain 'A' and resid 263 through 266 Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 308 through 326 removed outlier: 3.551A pdb=" N ARG A 314 " --> pdb=" O SER A 310 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N HIS A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ARG A 319 " --> pdb=" O ASN A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 351 Processing helix chain 'A' and resid 353 through 358 removed outlier: 4.138A pdb=" N ALA A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY A 358 " --> pdb=" O GLN A 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 353 through 358' Processing helix chain 'A' and resid 362 through 385 Processing helix chain 'A' and resid 396 through 408 Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 422 through 429 Processing helix chain 'A' and resid 431 through 435 removed outlier: 3.884A pdb=" N LEU A 434 " --> pdb=" O GLN A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 454 removed outlier: 3.946A pdb=" N LEU A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 475 removed outlier: 3.762A pdb=" N HIS A 475 " --> pdb=" O GLY A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 494 Processing helix chain 'A' and resid 496 through 506 removed outlier: 3.695A pdb=" N THR A 504 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 531 through 537 Processing helix chain 'A' and resid 538 through 539 No H-bonds generated for 'chain 'A' and resid 538 through 539' Processing helix chain 'A' and resid 540 through 544 removed outlier: 3.585A pdb=" N THR A 543 " --> pdb=" O PRO A 540 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 540 through 544' Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 671 through 680 Processing helix chain 'A' and resid 681 through 684 Processing helix chain 'B' and resid 46 through 57 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 83 through 87 removed outlier: 3.627A pdb=" N ARG B 87 " --> pdb=" O GLN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 112 Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 172 through 176 removed outlier: 4.116A pdb=" N THR B 175 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU B 176 " --> pdb=" O ILE B 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 176' Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'B' and resid 218 through 236 removed outlier: 4.107A pdb=" N PHE B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 253 removed outlier: 3.571A pdb=" N HIS B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 258 Processing helix chain 'C' and resid 148 through 162 Processing helix chain 'C' and resid 200 through 217 Processing helix chain 'C' and resid 224 through 231 Processing helix chain 'C' and resid 242 through 253 Processing helix chain 'C' and resid 323 through 337 Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 363 through 366 Processing helix chain 'C' and resid 379 through 381 No H-bonds generated for 'chain 'C' and resid 379 through 381' Processing helix chain 'C' and resid 415 through 424 Processing helix chain 'C' and resid 424 through 435 removed outlier: 3.820A pdb=" N LEU C 428 " --> pdb=" O SER C 424 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU C 430 " --> pdb=" O LEU C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 459 removed outlier: 4.091A pdb=" N LEU C 458 " --> pdb=" O ASN C 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.890A pdb=" N GLN E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.591A pdb=" N THR F 87 " --> pdb=" O SER F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 100B Processing helix chain 'F' and resid 100G through 100I No H-bonds generated for 'chain 'F' and resid 100G through 100I' Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.871A pdb=" N PHE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 52 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 92 removed outlier: 6.991A pdb=" N GLN A 86 " --> pdb=" O GLN A 82 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N SER A 77 " --> pdb=" O PHE B 181 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU B 183 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASN A 79 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N VAL B 178 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ALA B 194 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE B 189 " --> pdb=" O VAL B 210 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 126 removed outlier: 4.879A pdb=" N VAL A 281 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU A 277 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ARG A 136 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 125 through 126 removed outlier: 4.879A pdb=" N VAL A 281 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 247 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLN A 193 " --> pdb=" O CYS A 211 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 183 through 184 removed outlier: 3.521A pdb=" N THR A 183 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 361 " --> pdb=" O THR A 183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 578 through 581 Processing sheet with id=AA7, first strand: chain 'A' and resid 637 through 638 removed outlier: 7.102A pdb=" N THR A 637 " --> pdb=" O GLU A 705 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN A 665 " --> pdb=" O GLU A 656 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASP A 658 " --> pdb=" O VAL A 663 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N VAL A 663 " --> pdb=" O ASP A 658 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 99 through 100 removed outlier: 6.375A pdb=" N VAL B 99 " --> pdb=" O ARG C 236 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 151 through 155 removed outlier: 3.675A pdb=" N CYS B 159 " --> pdb=" O HIS C 449 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS C 449 " --> pdb=" O CYS B 159 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 85 through 87 Processing sheet with id=AB2, first strand: chain 'C' and resid 85 through 87 removed outlier: 3.519A pdb=" N GLY C 144 " --> pdb=" O TYR C 124 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 173 through 174 Processing sheet with id=AB4, first strand: chain 'C' and resid 186 through 191 Processing sheet with id=AB5, first strand: chain 'C' and resid 240 through 241 Processing sheet with id=AB6, first strand: chain 'C' and resid 383 through 384 removed outlier: 3.799A pdb=" N TYR C 384 " --> pdb=" O THR C 413 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB8, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.758A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AC1, first strand: chain 'E' and resid 11 through 12 removed outlier: 7.035A pdb=" N MET E 34 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N THR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 94 through 95 removed outlier: 3.771A pdb=" N VAL E 102 " --> pdb=" O ARG E 94 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AC4, first strand: chain 'F' and resid 10 through 12 removed outlier: 7.728A pdb=" N ILE F 34 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLY F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU F 56 " --> pdb=" O ASP F 52 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AC6, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AC7, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.706A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) 510 hydrogen bonds defined for protein. 1335 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.58 Time building geometry restraints manager: 5.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4229 1.34 - 1.46: 3367 1.46 - 1.59: 5841 1.59 - 1.71: 0 1.71 - 1.83: 99 Bond restraints: 13536 Sorted by residual: bond pdb=" C1 NAG C 505 " pdb=" O5 NAG C 505 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.18e+00 bond pdb=" CB ARG A 329 " pdb=" CG ARG A 329 " ideal model delta sigma weight residual 1.520 1.467 0.053 3.00e-02 1.11e+03 3.14e+00 bond pdb=" CB PRO C 141 " pdb=" CG PRO C 141 " ideal model delta sigma weight residual 1.506 1.570 -0.064 3.90e-02 6.57e+02 2.73e+00 bond pdb=" CG GLU A 466 " pdb=" CD GLU A 466 " ideal model delta sigma weight residual 1.516 1.475 0.041 2.50e-02 1.60e+03 2.65e+00 bond pdb=" C1 BMA H 3 " pdb=" C2 BMA H 3 " ideal model delta sigma weight residual 1.519 1.551 -0.032 2.00e-02 2.50e+03 2.49e+00 ... (remaining 13531 not shown) Histogram of bond angle deviations from ideal: 99.98 - 106.80: 448 106.80 - 113.61: 7430 113.61 - 120.43: 4901 120.43 - 127.25: 5481 127.25 - 134.06: 148 Bond angle restraints: 18408 Sorted by residual: angle pdb=" CG ARG A 329 " pdb=" CD ARG A 329 " pdb=" NE ARG A 329 " ideal model delta sigma weight residual 112.00 121.09 -9.09 2.20e+00 2.07e-01 1.71e+01 angle pdb=" CB ARG A 329 " pdb=" CG ARG A 329 " pdb=" CD ARG A 329 " ideal model delta sigma weight residual 111.30 103.20 8.10 2.30e+00 1.89e-01 1.24e+01 angle pdb=" N GLU A 466 " pdb=" CA GLU A 466 " pdb=" CB GLU A 466 " ideal model delta sigma weight residual 110.16 115.21 -5.05 1.48e+00 4.57e-01 1.16e+01 angle pdb=" CA PRO C 141 " pdb=" N PRO C 141 " pdb=" CD PRO C 141 " ideal model delta sigma weight residual 111.50 107.24 4.26 1.40e+00 5.10e-01 9.25e+00 angle pdb=" CA LEU C 118 " pdb=" CB LEU C 118 " pdb=" CG LEU C 118 " ideal model delta sigma weight residual 116.30 126.42 -10.12 3.50e+00 8.16e-02 8.36e+00 ... (remaining 18403 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.23: 7792 22.23 - 44.45: 415 44.45 - 66.68: 50 66.68 - 88.90: 30 88.90 - 111.13: 8 Dihedral angle restraints: 8295 sinusoidal: 3506 harmonic: 4789 Sorted by residual: dihedral pdb=" CB CYS C 143 " pdb=" SG CYS C 143 " pdb=" SG CYS C 151 " pdb=" CB CYS C 151 " ideal model delta sinusoidal sigma weight residual 93.00 177.02 -84.02 1 1.00e+01 1.00e-02 8.60e+01 dihedral pdb=" CB CYS A 571 " pdb=" SG CYS A 571 " pdb=" SG CYS A 624 " pdb=" CB CYS A 624 " ideal model delta sinusoidal sigma weight residual -86.00 -153.50 67.50 1 1.00e+01 1.00e-02 5.93e+01 dihedral pdb=" CB CYS A 647 " pdb=" SG CYS A 647 " pdb=" SG CYS A 650 " pdb=" CB CYS A 650 " ideal model delta sinusoidal sigma weight residual -86.00 -151.22 65.22 1 1.00e+01 1.00e-02 5.58e+01 ... (remaining 8292 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1772 0.057 - 0.114: 300 0.114 - 0.171: 41 0.171 - 0.228: 7 0.228 - 0.285: 3 Chirality restraints: 2123 Sorted by residual: chirality pdb=" C1 NAG A 801 " pdb=" ND2 ASN A 62 " pdb=" C2 NAG A 801 " pdb=" O5 NAG A 801 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 2120 not shown) Planarity restraints: 2339 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 602 " -0.049 5.00e-02 4.00e+02 7.35e-02 8.63e+00 pdb=" N PRO A 603 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 603 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 603 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 369 " 0.046 5.00e-02 4.00e+02 6.90e-02 7.61e+00 pdb=" N PRO C 370 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 370 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 370 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 253 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO A 254 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 254 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 254 " -0.029 5.00e-02 4.00e+02 ... (remaining 2336 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 271 2.69 - 3.24: 12878 3.24 - 3.80: 20311 3.80 - 4.35: 27706 4.35 - 4.90: 45861 Nonbonded interactions: 107027 Sorted by model distance: nonbonded pdb=" O TRP C 332 " pdb=" OG1 THR C 335 " model vdw 2.138 2.440 nonbonded pdb=" OE2 GLU A 491 " pdb=" OH TYR A 519 " model vdw 2.204 2.440 nonbonded pdb=" O THR C 174 " pdb=" OG SER C 320 " model vdw 2.212 2.440 nonbonded pdb=" OE1 GLU A 499 " pdb=" OG1 THR A 520 " model vdw 2.244 2.440 nonbonded pdb=" O PHE G 49 " pdb=" OG SER G 53 " model vdw 2.248 2.440 ... (remaining 107022 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 'H' selection = chain 'J' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.290 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 37.320 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 13536 Z= 0.214 Angle : 0.638 10.118 18408 Z= 0.319 Chirality : 0.046 0.285 2123 Planarity : 0.006 0.073 2329 Dihedral : 14.091 111.126 5160 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.47 % 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: -0.22 (0.21), residues: 1607 helix: -0.32 (0.27), residues: 372 sheet: 0.53 (0.29), residues: 350 loop : -0.25 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 332 HIS 0.009 0.001 HIS A 670 PHE 0.028 0.002 PHE A 488 TYR 0.028 0.002 TYR C 384 ARG 0.014 0.001 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.7781 (tt0) cc_final: 0.7562 (tt0) REVERT: A 151 GLN cc_start: 0.7086 (pm20) cc_final: 0.6647 (pm20) REVERT: A 231 GLU cc_start: 0.7387 (mp0) cc_final: 0.7074 (mp0) REVERT: A 296 ASP cc_start: 0.7871 (p0) cc_final: 0.7668 (p0) REVERT: A 426 LEU cc_start: 0.8319 (tp) cc_final: 0.8093 (tm) REVERT: A 596 LEU cc_start: 0.7600 (mt) cc_final: 0.7398 (mt) REVERT: A 684 GLU cc_start: 0.7007 (mp0) cc_final: 0.6568 (mp0) REVERT: F 19 ARG cc_start: 0.7482 (ttt90) cc_final: 0.7247 (ttt90) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 1.1159 time to fit residues: 321.8800 Evaluate side-chains 240 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 0.9980 chunk 120 optimal weight: 0.0970 chunk 66 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 ASN ** A 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 GLN ** C 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13536 Z= 0.273 Angle : 0.626 11.119 18408 Z= 0.316 Chirality : 0.045 0.292 2123 Planarity : 0.005 0.049 2329 Dihedral : 8.213 70.959 2109 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.45 % Allowed : 10.50 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.47 % 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: 0.05 (0.22), residues: 1607 helix: 0.31 (0.27), residues: 381 sheet: 0.59 (0.28), residues: 359 loop : -0.25 (0.22), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 167 HIS 0.008 0.001 HIS A 586 PHE 0.033 0.002 PHE A 462 TYR 0.021 0.002 TYR A 682 ARG 0.007 0.000 ARG B 204 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 257 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 PHE cc_start: 0.8281 (m-80) cc_final: 0.8062 (m-80) REVERT: A 113 GLU cc_start: 0.7738 (tt0) cc_final: 0.7533 (tt0) REVERT: A 151 GLN cc_start: 0.7086 (pm20) cc_final: 0.6630 (pm20) REVERT: A 296 ASP cc_start: 0.7837 (p0) cc_final: 0.7451 (p0) REVERT: A 426 LEU cc_start: 0.8254 (tp) cc_final: 0.7983 (tm) REVERT: A 445 ASP cc_start: 0.7533 (m-30) cc_final: 0.7247 (m-30) REVERT: A 466 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6765 (mp0) REVERT: A 596 LEU cc_start: 0.7633 (mt) cc_final: 0.7400 (mt) REVERT: A 682 TYR cc_start: 0.7980 (t80) cc_final: 0.7611 (t80) REVERT: A 684 GLU cc_start: 0.7058 (mp0) cc_final: 0.6553 (mp0) REVERT: B 244 ARG cc_start: 0.6732 (tpm170) cc_final: 0.6525 (tpm170) REVERT: C 250 MET cc_start: 0.8162 (tpp) cc_final: 0.7901 (mmm) outliers start: 21 outliers final: 9 residues processed: 260 average time/residue: 1.0891 time to fit residues: 312.1577 Evaluate side-chains 265 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 256 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 667 MET Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 237 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 120 optimal weight: 0.0870 chunk 98 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 144 optimal weight: 0.9980 chunk 156 optimal weight: 0.5980 chunk 128 optimal weight: 0.0970 chunk 143 optimal weight: 0.5980 chunk 49 optimal weight: 0.2980 chunk 116 optimal weight: 2.9990 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 ASN ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13536 Z= 0.185 Angle : 0.579 9.578 18408 Z= 0.288 Chirality : 0.042 0.276 2123 Planarity : 0.004 0.051 2329 Dihedral : 7.010 55.137 2109 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.28 % Allowed : 13.06 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.47 % 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: 0.16 (0.22), residues: 1607 helix: 0.58 (0.27), residues: 380 sheet: 0.63 (0.28), residues: 357 loop : -0.26 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 167 HIS 0.005 0.001 HIS A 586 PHE 0.026 0.002 PHE A 462 TYR 0.020 0.001 TYR F 27 ARG 0.006 0.000 ARG A 329 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 254 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 PHE cc_start: 0.8345 (m-80) cc_final: 0.8092 (m-80) REVERT: A 113 GLU cc_start: 0.7740 (tt0) cc_final: 0.7532 (tt0) REVERT: A 151 GLN cc_start: 0.7073 (pm20) cc_final: 0.6682 (pm20) REVERT: A 231 GLU cc_start: 0.7428 (mp0) cc_final: 0.7020 (mp0) REVERT: A 296 ASP cc_start: 0.7797 (p0) cc_final: 0.7459 (p0) REVERT: A 595 TYR cc_start: 0.7145 (p90) cc_final: 0.6898 (p90) REVERT: A 682 TYR cc_start: 0.8021 (t80) cc_final: 0.7465 (t80) REVERT: A 684 GLU cc_start: 0.7033 (mp0) cc_final: 0.6579 (mp0) REVERT: B 244 ARG cc_start: 0.6717 (tpm170) cc_final: 0.6477 (tpm170) REVERT: C 250 MET cc_start: 0.8169 (tpp) cc_final: 0.7936 (mmm) REVERT: E 73 GLU cc_start: 0.6583 (mp0) cc_final: 0.6295 (mp0) REVERT: E 100 MET cc_start: 0.7460 (mpp) cc_final: 0.7218 (mtm) outliers start: 33 outliers final: 12 residues processed: 269 average time/residue: 1.0537 time to fit residues: 313.1198 Evaluate side-chains 258 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 246 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 667 MET Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain E residue 7 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 0.9990 chunk 108 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 145 optimal weight: 0.0970 chunk 153 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 315 ASN A 432 GLN ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 GLN ** C 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13536 Z= 0.283 Angle : 0.614 8.989 18408 Z= 0.305 Chirality : 0.045 0.261 2123 Planarity : 0.004 0.064 2329 Dihedral : 6.321 55.513 2109 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.90 % Allowed : 15.07 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.47 % 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: 0.10 (0.22), residues: 1607 helix: 0.55 (0.27), residues: 380 sheet: 0.66 (0.28), residues: 356 loop : -0.35 (0.22), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 36 HIS 0.006 0.001 HIS D 90 PHE 0.021 0.002 PHE A 462 TYR 0.020 0.002 TYR E 27 ARG 0.006 0.000 ARG A 255 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 253 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.6689 (p0) cc_final: 0.6439 (p0) REVERT: A 84 TYR cc_start: 0.7676 (t80) cc_final: 0.7469 (t80) REVERT: A 105 PHE cc_start: 0.8414 (m-80) cc_final: 0.8184 (m-80) REVERT: A 113 GLU cc_start: 0.7729 (tt0) cc_final: 0.7497 (tt0) REVERT: A 151 GLN cc_start: 0.7090 (pm20) cc_final: 0.6680 (pm20) REVERT: A 168 MET cc_start: 0.6961 (tmm) cc_final: 0.6625 (tmm) REVERT: A 226 LYS cc_start: 0.7959 (ttmm) cc_final: 0.7747 (ttmm) REVERT: A 231 GLU cc_start: 0.7418 (mp0) cc_final: 0.6976 (mp0) REVERT: A 296 ASP cc_start: 0.7810 (p0) cc_final: 0.7459 (p0) REVERT: A 303 ASP cc_start: 0.7599 (t70) cc_final: 0.7187 (t0) REVERT: A 561 SER cc_start: 0.8015 (m) cc_final: 0.7623 (p) REVERT: A 682 TYR cc_start: 0.8073 (t80) cc_final: 0.7540 (t80) REVERT: A 684 GLU cc_start: 0.7043 (mp0) cc_final: 0.6586 (mp0) REVERT: C 250 MET cc_start: 0.8179 (tpp) cc_final: 0.7914 (mmm) REVERT: C 379 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.7677 (mmt) outliers start: 42 outliers final: 23 residues processed: 269 average time/residue: 1.0570 time to fit residues: 314.3208 Evaluate side-chains 276 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 252 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 593 ASN Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 667 MET Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain G residue 107 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 114 optimal weight: 0.0570 chunk 63 optimal weight: 2.9990 chunk 131 optimal weight: 0.3980 chunk 106 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 ASN A 465 GLN A 617 GLN ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 GLN ** C 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13536 Z= 0.324 Angle : 0.620 11.516 18408 Z= 0.309 Chirality : 0.045 0.284 2123 Planarity : 0.005 0.076 2329 Dihedral : 6.187 59.560 2109 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.97 % Allowed : 17.07 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.47 % 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: -0.08 (0.21), residues: 1607 helix: 0.37 (0.27), residues: 383 sheet: 0.53 (0.28), residues: 357 loop : -0.44 (0.22), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 36 HIS 0.006 0.001 HIS D 90 PHE 0.021 0.002 PHE A 317 TYR 0.029 0.002 TYR A 595 ARG 0.007 0.000 ARG B 133 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 250 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.6666 (p0) cc_final: 0.6412 (p0) REVERT: A 84 TYR cc_start: 0.7737 (t80) cc_final: 0.7495 (t80) REVERT: A 113 GLU cc_start: 0.7733 (tt0) cc_final: 0.7496 (tt0) REVERT: A 151 GLN cc_start: 0.7065 (pm20) cc_final: 0.6648 (pm20) REVERT: A 168 MET cc_start: 0.6981 (tmm) cc_final: 0.6722 (tmm) REVERT: A 231 GLU cc_start: 0.7450 (mp0) cc_final: 0.7026 (mp0) REVERT: A 296 ASP cc_start: 0.7790 (p0) cc_final: 0.7499 (p0) REVERT: A 561 SER cc_start: 0.8156 (m) cc_final: 0.7715 (p) REVERT: A 676 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8358 (mm) REVERT: A 682 TYR cc_start: 0.8085 (t80) cc_final: 0.7520 (t80) REVERT: A 684 GLU cc_start: 0.7042 (mp0) cc_final: 0.6605 (mp0) REVERT: B 244 ARG cc_start: 0.6729 (tpm170) cc_final: 0.6481 (tpm170) REVERT: C 156 LEU cc_start: 0.8489 (mt) cc_final: 0.8130 (mp) REVERT: C 335 THR cc_start: 0.6795 (OUTLIER) cc_final: 0.6545 (p) REVERT: C 379 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.7657 (mmt) outliers start: 43 outliers final: 24 residues processed: 268 average time/residue: 1.1154 time to fit residues: 329.7300 Evaluate side-chains 278 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 251 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 593 ASN Chi-restraints excluded: chain A residue 667 MET Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 349 ARG Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain G residue 107 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 0.8980 chunk 30 optimal weight: 0.0770 chunk 90 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 127 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 148 optimal weight: 0.0980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 ASN A 617 GLN ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 GLN C 341 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13536 Z= 0.225 Angle : 0.583 11.082 18408 Z= 0.290 Chirality : 0.043 0.269 2123 Planarity : 0.004 0.077 2329 Dihedral : 5.909 55.074 2109 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.97 % Allowed : 17.69 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.47 % 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: -0.02 (0.21), residues: 1607 helix: 0.51 (0.27), residues: 383 sheet: 0.52 (0.28), residues: 355 loop : -0.42 (0.22), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 36 HIS 0.005 0.001 HIS D 90 PHE 0.020 0.002 PHE A 105 TYR 0.020 0.001 TYR E 59 ARG 0.007 0.000 ARG B 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 241 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.6630 (p0) cc_final: 0.6375 (p0) REVERT: A 84 TYR cc_start: 0.7730 (t80) cc_final: 0.7478 (t80) REVERT: A 113 GLU cc_start: 0.7721 (tt0) cc_final: 0.7487 (tt0) REVERT: A 151 GLN cc_start: 0.7054 (pm20) cc_final: 0.6632 (pm20) REVERT: A 231 GLU cc_start: 0.7447 (mp0) cc_final: 0.7001 (mp0) REVERT: A 296 ASP cc_start: 0.7790 (p0) cc_final: 0.7492 (p0) REVERT: A 317 PHE cc_start: 0.7408 (t80) cc_final: 0.7205 (t80) REVERT: A 667 MET cc_start: 0.7202 (OUTLIER) cc_final: 0.6650 (tmm) REVERT: A 676 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8339 (mm) REVERT: A 682 TYR cc_start: 0.8060 (t80) cc_final: 0.7663 (t80) REVERT: A 684 GLU cc_start: 0.7007 (mp0) cc_final: 0.6776 (mp0) REVERT: B 171 ARG cc_start: 0.7786 (tpp80) cc_final: 0.7558 (tpp80) REVERT: B 244 ARG cc_start: 0.6717 (tpm170) cc_final: 0.6488 (tpm170) REVERT: C 156 LEU cc_start: 0.8501 (mt) cc_final: 0.8156 (mp) REVERT: C 335 THR cc_start: 0.6785 (OUTLIER) cc_final: 0.6538 (p) REVERT: C 379 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.7646 (mmt) outliers start: 43 outliers final: 27 residues processed: 259 average time/residue: 1.1119 time to fit residues: 316.5095 Evaluate side-chains 276 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 245 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 593 ASN Chi-restraints excluded: chain A residue 595 TYR Chi-restraints excluded: chain A residue 667 MET Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 349 ARG Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain F residue 61 GLN Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 107 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 129 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 ASN A 432 GLN A 617 GLN ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 GLN ** G 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13536 Z= 0.285 Angle : 0.610 11.154 18408 Z= 0.303 Chirality : 0.045 0.305 2123 Planarity : 0.005 0.081 2329 Dihedral : 5.872 55.170 2109 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.25 % Allowed : 18.38 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.47 % 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: -0.11 (0.21), residues: 1607 helix: 0.41 (0.27), residues: 381 sheet: 0.47 (0.28), residues: 355 loop : -0.47 (0.22), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 36 HIS 0.006 0.001 HIS D 90 PHE 0.022 0.002 PHE A 462 TYR 0.024 0.002 TYR A 424 ARG 0.008 0.000 ARG B 133 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 247 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.6651 (p0) cc_final: 0.6398 (p0) REVERT: A 84 TYR cc_start: 0.7749 (t80) cc_final: 0.7539 (t80) REVERT: A 113 GLU cc_start: 0.7723 (tt0) cc_final: 0.7483 (tt0) REVERT: A 151 GLN cc_start: 0.7058 (pm20) cc_final: 0.6636 (pm20) REVERT: A 231 GLU cc_start: 0.7445 (mp0) cc_final: 0.6995 (mp0) REVERT: A 296 ASP cc_start: 0.7800 (p0) cc_final: 0.7539 (p0) REVERT: A 303 ASP cc_start: 0.7575 (t70) cc_final: 0.7075 (t0) REVERT: A 667 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.6599 (tmm) REVERT: A 676 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8336 (mm) REVERT: A 682 TYR cc_start: 0.8095 (t80) cc_final: 0.7708 (t80) REVERT: A 684 GLU cc_start: 0.7015 (mp0) cc_final: 0.6781 (mp0) REVERT: B 171 ARG cc_start: 0.7799 (tpp80) cc_final: 0.7562 (tpp80) REVERT: C 250 MET cc_start: 0.8171 (tpp) cc_final: 0.7965 (mmm) REVERT: C 379 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.7694 (mmt) outliers start: 47 outliers final: 32 residues processed: 266 average time/residue: 1.1023 time to fit residues: 322.4983 Evaluate side-chains 283 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 248 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 593 ASN Chi-restraints excluded: chain A residue 667 MET Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 349 ARG Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain F residue 61 GLN Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain G residue 107 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 139 optimal weight: 0.5980 chunk 146 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 ASN A 617 GLN ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 GLN ** C 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13536 Z= 0.298 Angle : 0.629 11.286 18408 Z= 0.313 Chirality : 0.045 0.279 2123 Planarity : 0.005 0.084 2329 Dihedral : 5.822 55.126 2109 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.25 % Allowed : 18.45 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.47 % 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: -0.18 (0.21), residues: 1607 helix: 0.39 (0.27), residues: 375 sheet: 0.43 (0.28), residues: 355 loop : -0.52 (0.22), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 36 HIS 0.006 0.001 HIS D 90 PHE 0.027 0.002 PHE A 317 TYR 0.029 0.002 TYR A 595 ARG 0.008 0.000 ARG B 133 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 242 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.6598 (p0) cc_final: 0.6358 (p0) REVERT: A 84 TYR cc_start: 0.7771 (t80) cc_final: 0.7562 (t80) REVERT: A 92 MET cc_start: 0.7758 (mmm) cc_final: 0.7500 (mmt) REVERT: A 113 GLU cc_start: 0.7722 (tt0) cc_final: 0.7506 (tt0) REVERT: A 151 GLN cc_start: 0.7058 (pm20) cc_final: 0.6640 (pm20) REVERT: A 226 LYS cc_start: 0.7948 (ttmm) cc_final: 0.7747 (ttmm) REVERT: A 231 GLU cc_start: 0.7446 (mp0) cc_final: 0.6998 (mp0) REVERT: A 296 ASP cc_start: 0.7789 (p0) cc_final: 0.7567 (p0) REVERT: A 303 ASP cc_start: 0.7557 (t70) cc_final: 0.7078 (t0) REVERT: A 667 MET cc_start: 0.7089 (OUTLIER) cc_final: 0.6556 (tmm) REVERT: A 676 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8331 (mm) REVERT: A 682 TYR cc_start: 0.8085 (t80) cc_final: 0.7690 (t80) REVERT: A 684 GLU cc_start: 0.7004 (mp0) cc_final: 0.6776 (mp0) REVERT: B 244 ARG cc_start: 0.6737 (tpm170) cc_final: 0.6509 (tpm170) REVERT: C 250 MET cc_start: 0.8181 (tpp) cc_final: 0.7956 (mmm) REVERT: C 379 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.7696 (mmt) outliers start: 47 outliers final: 30 residues processed: 263 average time/residue: 1.0823 time to fit residues: 314.7179 Evaluate side-chains 282 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 249 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 593 ASN Chi-restraints excluded: chain A residue 667 MET Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain G residue 107 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 62 optimal weight: 0.0070 chunk 112 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 129 optimal weight: 0.0980 chunk 135 optimal weight: 0.0370 chunk 93 optimal weight: 0.5980 chunk 151 optimal weight: 0.6980 overall best weight: 0.2276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 ASN ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13536 Z= 0.169 Angle : 0.590 10.956 18408 Z= 0.291 Chirality : 0.042 0.266 2123 Planarity : 0.004 0.078 2329 Dihedral : 5.452 54.348 2109 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.28 % Allowed : 19.90 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.47 % 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: 0.01 (0.22), residues: 1607 helix: 0.52 (0.27), residues: 381 sheet: 0.59 (0.29), residues: 337 loop : -0.40 (0.22), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 332 HIS 0.005 0.001 HIS A 451 PHE 0.022 0.002 PHE A 317 TYR 0.022 0.001 TYR A 424 ARG 0.007 0.000 ARG B 133 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 245 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.6635 (p0) cc_final: 0.6400 (p0) REVERT: A 84 TYR cc_start: 0.7730 (t80) cc_final: 0.7508 (t80) REVERT: A 92 MET cc_start: 0.7711 (mmm) cc_final: 0.7424 (mmt) REVERT: A 113 GLU cc_start: 0.7726 (tt0) cc_final: 0.7503 (tt0) REVERT: A 151 GLN cc_start: 0.7044 (pm20) cc_final: 0.6625 (pm20) REVERT: A 231 GLU cc_start: 0.7438 (mp0) cc_final: 0.6990 (mp0) REVERT: A 293 LYS cc_start: 0.7731 (mtpp) cc_final: 0.7421 (mtpp) REVERT: A 296 ASP cc_start: 0.7784 (p0) cc_final: 0.7564 (p0) REVERT: A 303 ASP cc_start: 0.7450 (t70) cc_final: 0.6995 (t0) REVERT: A 469 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7975 (mm) REVERT: A 676 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8316 (mm) REVERT: A 682 TYR cc_start: 0.8081 (t80) cc_final: 0.7597 (t80) REVERT: A 684 GLU cc_start: 0.6981 (mp0) cc_final: 0.6545 (mp0) REVERT: B 244 ARG cc_start: 0.6709 (tpm170) cc_final: 0.6508 (tpm170) REVERT: C 237 VAL cc_start: 0.7237 (OUTLIER) cc_final: 0.6922 (p) outliers start: 33 outliers final: 19 residues processed: 263 average time/residue: 1.0550 time to fit residues: 306.1352 Evaluate side-chains 265 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 243 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 593 ASN Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain F residue 80 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 0.1980 chunk 71 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 158 optimal weight: 0.0070 chunk 145 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 134 optimal weight: 0.3980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 ASN A 431 GLN ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 GLN ** C 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13536 Z= 0.213 Angle : 0.607 11.110 18408 Z= 0.300 Chirality : 0.043 0.264 2123 Planarity : 0.004 0.081 2329 Dihedral : 5.428 54.655 2109 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.73 % Allowed : 20.87 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.47 % 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: 0.01 (0.22), residues: 1607 helix: 0.58 (0.27), residues: 381 sheet: 0.51 (0.28), residues: 354 loop : -0.41 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 96 HIS 0.004 0.001 HIS A 451 PHE 0.023 0.002 PHE A 462 TYR 0.032 0.001 TYR A 595 ARG 0.008 0.000 ARG B 133 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 241 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.6627 (p0) cc_final: 0.6336 (p0) REVERT: A 84 TYR cc_start: 0.7733 (t80) cc_final: 0.7509 (t80) REVERT: A 92 MET cc_start: 0.7723 (mmm) cc_final: 0.7459 (mmt) REVERT: A 113 GLU cc_start: 0.7724 (tt0) cc_final: 0.7496 (tt0) REVERT: A 151 GLN cc_start: 0.7051 (pm20) cc_final: 0.6629 (pm20) REVERT: A 231 GLU cc_start: 0.7444 (mp0) cc_final: 0.6970 (mp0) REVERT: A 296 ASP cc_start: 0.7812 (p0) cc_final: 0.7578 (p0) REVERT: A 303 ASP cc_start: 0.7492 (t70) cc_final: 0.7027 (t0) REVERT: A 676 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8329 (mm) REVERT: A 682 TYR cc_start: 0.8096 (t80) cc_final: 0.7491 (t80) REVERT: A 684 GLU cc_start: 0.6989 (mp0) cc_final: 0.6624 (mp0) REVERT: B 244 ARG cc_start: 0.6708 (tpm170) cc_final: 0.6506 (tpm170) REVERT: E 82 MET cc_start: 0.6528 (mtt) cc_final: 0.6314 (mtt) REVERT: G 4 MET cc_start: 0.7872 (mmp) cc_final: 0.7646 (mmp) outliers start: 25 outliers final: 21 residues processed: 254 average time/residue: 1.0589 time to fit residues: 297.1804 Evaluate side-chains 263 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 241 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 593 ASN Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain F residue 80 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 129 optimal weight: 0.0980 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 ASN ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.151222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.133052 restraints weight = 19417.928| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 2.25 r_work: 0.3773 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3601 r_free = 0.3601 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3601 r_free = 0.3601 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13536 Z= 0.274 Angle : 0.637 11.478 18408 Z= 0.314 Chirality : 0.045 0.277 2123 Planarity : 0.005 0.083 2329 Dihedral : 5.598 55.480 2109 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.80 % Allowed : 21.01 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.11 (0.21), residues: 1607 helix: 0.42 (0.27), residues: 380 sheet: 0.53 (0.28), residues: 353 loop : -0.49 (0.22), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 35 HIS 0.005 0.001 HIS D 90 PHE 0.021 0.002 PHE A 105 TYR 0.020 0.002 TYR E 27 ARG 0.009 0.000 ARG A 329 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5527.92 seconds wall clock time: 98 minutes 0.09 seconds (5880.09 seconds total)