Starting phenix.real_space_refine on Sat Aug 23 16:20:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tco_41156/08_2025/8tco_41156.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tco_41156/08_2025/8tco_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/cci-nas-00/data/ceres_data/8tco_41156/08_2025/8tco_41156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tco_41156/08_2025/8tco_41156.map" model { file = "/net/cci-nas-00/data/ceres_data/8tco_41156/08_2025/8tco_41156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tco_41156/08_2025/8tco_41156.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 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. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.34, per 1000 atoms: 0.25 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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: 1.03 Conformation dependent library (CDL) restraints added in 495.1 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.42 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: 2.02 Time building geometry restraints manager: 1.40 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: 0.00 - 2.02: 18045 2.02 - 4.05: 310 4.05 - 6.07: 45 6.07 - 8.09: 4 8.09 - 10.12: 4 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 3.040 nonbonded pdb=" OE2 GLU A 491 " pdb=" OH TYR A 519 " model vdw 2.204 3.040 nonbonded pdb=" O THR C 174 " pdb=" OG SER C 320 " model vdw 2.212 3.040 nonbonded pdb=" OE1 GLU A 499 " pdb=" OG1 THR A 520 " model vdw 2.244 3.040 nonbonded pdb=" O PHE G 49 " pdb=" OG SER G 53 " model vdw 2.248 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 4.270 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: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 12.800 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.740 ------------------------------------------------------------------------------- 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 13566 Z= 0.143 Angle : 0.650 10.118 18483 Z= 0.322 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (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 ARG 0.014 0.001 ARG A 47 TYR 0.028 0.002 TYR C 384 PHE 0.028 0.002 PHE A 488 TRP 0.018 0.001 TRP C 332 HIS 0.009 0.001 HIS A 670 Details of bonding type rmsd covalent geometry : bond 0.00321 (13536) covalent geometry : angle 0.63774 (18408) SS BOND : bond 0.00237 ( 15) SS BOND : angle 1.31313 ( 30) hydrogen bonds : bond 0.20829 ( 496) hydrogen bonds : angle 8.13092 ( 1335) link_BETA1-4 : bond 0.00371 ( 5) link_BETA1-4 : angle 1.65275 ( 15) link_NAG-ASN : bond 0.00460 ( 10) link_NAG-ASN : angle 2.77203 ( 30) *********************** 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 to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.459 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: 0.5799 time to fit residues: 166.5646 Evaluate side-chains 240 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 ASN A 586 HIS A 594 GLN B 197 ASN C 233 ASN C 325 GLN ** C 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN ** G 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.151345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.133207 restraints weight = 19528.780| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.27 r_work: 0.3755 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3588 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3588 r_free = 0.3588 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3588 r_free = 0.3588 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13566 Z= 0.215 Angle : 0.677 11.219 18483 Z= 0.341 Chirality : 0.047 0.294 2123 Planarity : 0.005 0.049 2329 Dihedral : 8.315 71.918 2109 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.80 % Allowed : 10.50 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.22), residues: 1607 helix: 0.12 (0.26), residues: 383 sheet: 0.54 (0.29), residues: 357 loop : -0.27 (0.22), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 329 TYR 0.021 0.002 TYR A 682 PHE 0.034 0.002 PHE A 462 TRP 0.019 0.002 TRP A 167 HIS 0.007 0.001 HIS A 586 Details of bonding type rmsd covalent geometry : bond 0.00512 (13536) covalent geometry : angle 0.66411 (18408) SS BOND : bond 0.00384 ( 15) SS BOND : angle 1.25090 ( 30) hydrogen bonds : bond 0.04793 ( 496) hydrogen bonds : angle 5.84104 ( 1335) link_BETA1-4 : bond 0.00338 ( 5) link_BETA1-4 : angle 2.76079 ( 15) link_NAG-ASN : bond 0.00476 ( 10) link_NAG-ASN : angle 2.54648 ( 30) *********************** 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 287 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 261 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 PHE cc_start: 0.8325 (m-80) cc_final: 0.8067 (m-80) REVERT: A 113 GLU cc_start: 0.7912 (tt0) cc_final: 0.7709 (tt0) REVERT: A 151 GLN cc_start: 0.7264 (pm20) cc_final: 0.6849 (pm20) REVERT: A 231 GLU cc_start: 0.7611 (mp0) cc_final: 0.7298 (mp0) REVERT: A 296 ASP cc_start: 0.8038 (p0) cc_final: 0.7608 (p0) REVERT: A 426 LEU cc_start: 0.8294 (tp) cc_final: 0.8011 (tm) REVERT: A 466 GLU cc_start: 0.7037 (mt-10) cc_final: 0.6691 (mp0) REVERT: A 596 LEU cc_start: 0.7735 (mt) cc_final: 0.7509 (mt) REVERT: A 682 TYR cc_start: 0.8178 (t80) cc_final: 0.7703 (t80) REVERT: A 684 GLU cc_start: 0.7335 (mp0) cc_final: 0.6830 (mp0) REVERT: B 204 ARG cc_start: 0.7439 (ptp90) cc_final: 0.7185 (ptp90) REVERT: C 250 MET cc_start: 0.8191 (tpp) cc_final: 0.7934 (mmm) REVERT: F 19 ARG cc_start: 0.7599 (ttt90) cc_final: 0.7385 (ttt90) outliers start: 26 outliers final: 11 residues processed: 267 average time/residue: 0.4503 time to fit residues: 132.5644 Evaluate side-chains 265 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 254 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 667 MET Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 349 ARG Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain G residue 7 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 143 optimal weight: 0.4980 chunk 11 optimal weight: 0.3980 chunk 94 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 142 optimal weight: 3.9990 chunk 119 optimal weight: 0.0070 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 overall best weight: 0.4198 ------------------------------------------------------------------------------- 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 433 HIS A 594 GLN C 325 GLN ** C 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.153342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.135088 restraints weight = 19593.835| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 2.27 r_work: 0.3799 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13566 Z= 0.136 Angle : 0.615 9.847 18483 Z= 0.304 Chirality : 0.043 0.276 2123 Planarity : 0.004 0.057 2329 Dihedral : 7.212 55.915 2109 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.35 % Allowed : 13.48 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.22), residues: 1607 helix: 0.33 (0.27), residues: 387 sheet: 0.63 (0.28), residues: 363 loop : -0.26 (0.22), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 255 TYR 0.018 0.001 TYR E 27 PHE 0.025 0.002 PHE A 462 TRP 0.014 0.002 TRP A 167 HIS 0.006 0.001 HIS C 131 Details of bonding type rmsd covalent geometry : bond 0.00314 (13536) covalent geometry : angle 0.60331 (18408) SS BOND : bond 0.00402 ( 15) SS BOND : angle 1.03843 ( 30) hydrogen bonds : bond 0.03938 ( 496) hydrogen bonds : angle 5.44458 ( 1335) link_BETA1-4 : bond 0.00196 ( 5) link_BETA1-4 : angle 2.70982 ( 15) link_NAG-ASN : bond 0.00389 ( 10) link_NAG-ASN : angle 2.26573 ( 30) *********************** 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 292 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 258 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 PHE cc_start: 0.8382 (m-80) cc_final: 0.8138 (m-80) REVERT: A 113 GLU cc_start: 0.7896 (tt0) cc_final: 0.7693 (tt0) REVERT: A 151 GLN cc_start: 0.7224 (pm20) cc_final: 0.6824 (pm20) REVERT: A 231 GLU cc_start: 0.7554 (mp0) cc_final: 0.7201 (mp0) REVERT: A 296 ASP cc_start: 0.7960 (p0) cc_final: 0.7581 (p0) REVERT: A 303 ASP cc_start: 0.7615 (t0) cc_final: 0.7242 (t0) REVERT: A 561 SER cc_start: 0.8000 (m) cc_final: 0.7656 (p) REVERT: A 585 GLU cc_start: 0.8348 (pp20) cc_final: 0.8058 (pp20) REVERT: A 595 TYR cc_start: 0.7384 (p90) cc_final: 0.7145 (p90) REVERT: A 596 LEU cc_start: 0.7766 (mt) cc_final: 0.7562 (mt) REVERT: A 682 TYR cc_start: 0.8217 (t80) cc_final: 0.7805 (t80) REVERT: A 684 GLU cc_start: 0.7282 (mp0) cc_final: 0.6777 (mp0) REVERT: B 178 VAL cc_start: 0.7653 (t) cc_final: 0.7412 (p) REVERT: B 244 ARG cc_start: 0.7130 (tpm170) cc_final: 0.6879 (tpm170) REVERT: C 250 MET cc_start: 0.8180 (tpp) cc_final: 0.7973 (mmm) REVERT: C 335 THR cc_start: 0.6595 (OUTLIER) cc_final: 0.6367 (p) REVERT: F 19 ARG cc_start: 0.7547 (ttt90) cc_final: 0.7246 (ttt90) outliers start: 34 outliers final: 11 residues processed: 273 average time/residue: 0.4658 time to fit residues: 139.5700 Evaluate side-chains 269 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 257 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 520 THR 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 C residue 237 VAL Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain G residue 7 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 106 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 ASN A 594 GLN ** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 GLN ** C 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.150496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.132003 restraints weight = 19701.988| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.28 r_work: 0.3743 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3575 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3575 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 13566 Z= 0.252 Angle : 0.680 9.788 18483 Z= 0.336 Chirality : 0.047 0.277 2123 Planarity : 0.005 0.074 2329 Dihedral : 6.803 59.584 2109 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.90 % Allowed : 15.96 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.21), residues: 1607 helix: 0.06 (0.26), residues: 390 sheet: 0.54 (0.28), residues: 361 loop : -0.46 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 133 TYR 0.023 0.002 TYR E 27 PHE 0.035 0.003 PHE A 462 TRP 0.020 0.002 TRP E 36 HIS 0.007 0.001 HIS D 90 Details of bonding type rmsd covalent geometry : bond 0.00600 (13536) covalent geometry : angle 0.66600 (18408) SS BOND : bond 0.00460 ( 15) SS BOND : angle 1.30588 ( 30) hydrogen bonds : bond 0.04245 ( 496) hydrogen bonds : angle 5.47204 ( 1335) link_BETA1-4 : bond 0.00308 ( 5) link_BETA1-4 : angle 3.04325 ( 15) link_NAG-ASN : bond 0.00393 ( 10) link_NAG-ASN : angle 2.50396 ( 30) *********************** 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 302 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 260 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.7931 (tt0) cc_final: 0.7720 (tt0) REVERT: A 151 GLN cc_start: 0.7237 (pm20) cc_final: 0.6798 (pm20) REVERT: A 231 GLU cc_start: 0.7738 (mp0) cc_final: 0.7317 (mp0) REVERT: A 296 ASP cc_start: 0.7986 (p0) cc_final: 0.7654 (p0) REVERT: A 303 ASP cc_start: 0.7711 (t0) cc_final: 0.7310 (t0) REVERT: A 529 ASP cc_start: 0.7524 (m-30) cc_final: 0.7268 (m-30) REVERT: A 561 SER cc_start: 0.8129 (m) cc_final: 0.7756 (p) REVERT: A 594 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8221 (pm20) REVERT: A 596 LEU cc_start: 0.7833 (mt) cc_final: 0.7624 (mt) REVERT: A 671 ASP cc_start: 0.7498 (p0) cc_final: 0.7225 (p0) REVERT: A 682 TYR cc_start: 0.8204 (t80) cc_final: 0.7697 (t80) REVERT: A 684 GLU cc_start: 0.7307 (mp0) cc_final: 0.6815 (mp0) REVERT: B 178 VAL cc_start: 0.7700 (OUTLIER) cc_final: 0.7486 (p) REVERT: B 204 ARG cc_start: 0.7736 (ptp90) cc_final: 0.7471 (ptp90) REVERT: C 250 MET cc_start: 0.8246 (tpp) cc_final: 0.8005 (mmm) REVERT: C 379 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.7749 (mmt) REVERT: E 73 GLU cc_start: 0.6742 (mp0) cc_final: 0.6286 (mp0) REVERT: F 19 ARG cc_start: 0.7591 (ttt90) cc_final: 0.7293 (ttt90) outliers start: 42 outliers final: 22 residues processed: 281 average time/residue: 0.4784 time to fit residues: 148.1976 Evaluate side-chains 279 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 254 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 236 VAL 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 392 THR Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 667 MET Chi-restraints excluded: chain B residue 178 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 C residue 331 THR Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain G residue 7 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 100 optimal weight: 0.7980 chunk 123 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 57 optimal weight: 0.3980 chunk 130 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 ** C 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN ** G 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.151174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.132819 restraints weight = 19613.925| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.27 r_work: 0.3766 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3600 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 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 = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13566 Z= 0.154 Angle : 0.615 11.428 18483 Z= 0.304 Chirality : 0.044 0.269 2123 Planarity : 0.004 0.072 2329 Dihedral : 6.263 56.492 2109 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.56 % Allowed : 17.76 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.21), residues: 1607 helix: 0.26 (0.26), residues: 389 sheet: 0.58 (0.28), residues: 348 loop : -0.45 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 133 TYR 0.018 0.001 TYR E 27 PHE 0.021 0.002 PHE A 317 TRP 0.013 0.002 TRP E 36 HIS 0.005 0.001 HIS D 90 Details of bonding type rmsd covalent geometry : bond 0.00362 (13536) covalent geometry : angle 0.60272 (18408) SS BOND : bond 0.00342 ( 15) SS BOND : angle 1.14223 ( 30) hydrogen bonds : bond 0.03706 ( 496) hydrogen bonds : angle 5.26088 ( 1335) link_BETA1-4 : bond 0.00276 ( 5) link_BETA1-4 : angle 2.72507 ( 15) link_NAG-ASN : bond 0.00352 ( 10) link_NAG-ASN : angle 2.25079 ( 30) *********************** 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 292 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 255 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.7924 (tt0) cc_final: 0.7714 (tt0) REVERT: A 151 GLN cc_start: 0.7218 (pm20) cc_final: 0.6771 (pm20) REVERT: A 231 GLU cc_start: 0.7716 (mp0) cc_final: 0.7285 (mp0) REVERT: A 296 ASP cc_start: 0.7955 (p0) cc_final: 0.7653 (p0) REVERT: A 303 ASP cc_start: 0.7657 (t0) cc_final: 0.7239 (OUTLIER) REVERT: A 500 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7338 (tp) REVERT: A 529 ASP cc_start: 0.7393 (m-30) cc_final: 0.7137 (m-30) REVERT: A 561 SER cc_start: 0.8131 (m) cc_final: 0.7749 (p) REVERT: A 595 TYR cc_start: 0.7502 (p90) cc_final: 0.7272 (p90) REVERT: A 667 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.7164 (tmm) REVERT: A 671 ASP cc_start: 0.7487 (p0) cc_final: 0.7195 (p0) REVERT: A 676 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8449 (mm) REVERT: A 682 TYR cc_start: 0.8222 (t80) cc_final: 0.7691 (t80) REVERT: A 684 GLU cc_start: 0.7292 (mp0) cc_final: 0.6804 (mp0) REVERT: B 178 VAL cc_start: 0.7544 (t) cc_final: 0.7341 (p) REVERT: B 204 ARG cc_start: 0.7576 (ptp90) cc_final: 0.6929 (ptp90) REVERT: C 156 LEU cc_start: 0.8425 (mt) cc_final: 0.8119 (mp) REVERT: C 250 MET cc_start: 0.8223 (tpp) cc_final: 0.7980 (mmm) REVERT: C 379 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.7723 (mmt) REVERT: E 83 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7719 (mtp180) outliers start: 37 outliers final: 18 residues processed: 269 average time/residue: 0.4740 time to fit residues: 140.7179 Evaluate side-chains 272 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 250 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 667 MET Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 212 THR 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 7 SER Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain F residue 61 GLN Chi-restraints excluded: chain G residue 7 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 118 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 137 optimal weight: 0.0980 chunk 43 optimal weight: 0.5980 chunk 131 optimal weight: 0.7980 chunk 8 optimal weight: 0.0370 chunk 143 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- 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 C 341 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.153028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.134942 restraints weight = 19410.205| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.26 r_work: 0.3776 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3609 r_free = 0.3609 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 = 0.3609 r_free = 0.3609 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13566 Z= 0.136 Angle : 0.600 11.328 18483 Z= 0.297 Chirality : 0.043 0.263 2123 Planarity : 0.004 0.070 2329 Dihedral : 5.903 55.119 2109 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.04 % Allowed : 18.31 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.21), residues: 1607 helix: 0.28 (0.27), residues: 389 sheet: 0.61 (0.29), residues: 342 loop : -0.40 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 204 TYR 0.021 0.001 TYR E 59 PHE 0.020 0.002 PHE A 488 TRP 0.012 0.002 TRP F 47 HIS 0.005 0.001 HIS D 90 Details of bonding type rmsd covalent geometry : bond 0.00319 (13536) covalent geometry : angle 0.58840 (18408) SS BOND : bond 0.00377 ( 15) SS BOND : angle 1.28106 ( 30) hydrogen bonds : bond 0.03494 ( 496) hydrogen bonds : angle 5.12952 ( 1335) link_BETA1-4 : bond 0.00328 ( 5) link_BETA1-4 : angle 2.51342 ( 15) link_NAG-ASN : bond 0.00333 ( 10) link_NAG-ASN : angle 2.15743 ( 30) *********************** 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 296 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 252 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLN cc_start: 0.7209 (pm20) cc_final: 0.6752 (pm20) REVERT: A 231 GLU cc_start: 0.7697 (mp0) cc_final: 0.7232 (mp0) REVERT: A 253 LEU cc_start: 0.6686 (OUTLIER) cc_final: 0.6457 (pp) REVERT: A 296 ASP cc_start: 0.7951 (p0) cc_final: 0.7653 (p0) REVERT: A 303 ASP cc_start: 0.7580 (t0) cc_final: 0.7176 (OUTLIER) REVERT: A 529 ASP cc_start: 0.7388 (m-30) cc_final: 0.7141 (m-30) REVERT: A 671 ASP cc_start: 0.7480 (p0) cc_final: 0.7149 (p0) REVERT: A 676 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8447 (mm) REVERT: A 682 TYR cc_start: 0.8238 (t80) cc_final: 0.7688 (t80) REVERT: A 684 GLU cc_start: 0.7302 (mp0) cc_final: 0.6802 (mp0) REVERT: C 379 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.7742 (mmt) REVERT: D 100 GLN cc_start: 0.6878 (OUTLIER) cc_final: 0.6393 (pm20) REVERT: E 83 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7707 (mtp180) outliers start: 44 outliers final: 26 residues processed: 268 average time/residue: 0.4852 time to fit residues: 143.7011 Evaluate side-chains 277 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 247 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR 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 274 LYS Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 696 MET 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 C residue 379 MET Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain D residue 100 GLN Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 83 ARG 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 7 SER 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 58 optimal weight: 2.9990 chunk 24 optimal weight: 0.0670 chunk 31 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 136 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.0522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN A 315 ASN A 594 GLN C 325 GLN ** G 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.149197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.130893 restraints weight = 19609.014| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.26 r_work: 0.3738 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3571 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3571 r_free = 0.3571 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3571 r_free = 0.3571 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13566 Z= 0.246 Angle : 0.666 11.701 18483 Z= 0.331 Chirality : 0.046 0.277 2123 Planarity : 0.005 0.078 2329 Dihedral : 6.056 55.709 2109 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.90 % Allowed : 18.52 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.21), residues: 1607 helix: 0.10 (0.26), residues: 390 sheet: 0.51 (0.28), residues: 352 loop : -0.52 (0.22), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 204 TYR 0.028 0.002 TYR A 595 PHE 0.019 0.002 PHE A 488 TRP 0.022 0.002 TRP D 35 HIS 0.006 0.001 HIS D 90 Details of bonding type rmsd covalent geometry : bond 0.00583 (13536) covalent geometry : angle 0.65262 (18408) SS BOND : bond 0.00434 ( 15) SS BOND : angle 1.42238 ( 30) hydrogen bonds : bond 0.04019 ( 496) hydrogen bonds : angle 5.34828 ( 1335) link_BETA1-4 : bond 0.00383 ( 5) link_BETA1-4 : angle 2.70610 ( 15) link_NAG-ASN : bond 0.00411 ( 10) link_NAG-ASN : angle 2.41877 ( 30) *********************** 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 300 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 258 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLN cc_start: 0.7230 (pm20) cc_final: 0.6785 (pm20) REVERT: A 231 GLU cc_start: 0.7707 (mp0) cc_final: 0.7215 (mp0) REVERT: A 253 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6649 (pp) REVERT: A 296 ASP cc_start: 0.7970 (p0) cc_final: 0.7739 (p0) REVERT: A 303 ASP cc_start: 0.7665 (t0) cc_final: 0.7268 (OUTLIER) REVERT: A 529 ASP cc_start: 0.7473 (m-30) cc_final: 0.7203 (m-30) REVERT: A 561 SER cc_start: 0.8238 (m) cc_final: 0.7845 (p) REVERT: A 671 ASP cc_start: 0.7511 (p0) cc_final: 0.7269 (p0) REVERT: A 676 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8407 (mm) REVERT: A 682 TYR cc_start: 0.8270 (t80) cc_final: 0.7932 (t80) REVERT: A 684 GLU cc_start: 0.7321 (mp0) cc_final: 0.7050 (mp0) REVERT: B 204 ARG cc_start: 0.7518 (ptp90) cc_final: 0.7312 (ptp-110) REVERT: C 379 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.7911 (mmt) REVERT: D 100 GLN cc_start: 0.6841 (OUTLIER) cc_final: 0.6315 (pm20) REVERT: E 83 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7708 (mtm110) outliers start: 42 outliers final: 25 residues processed: 280 average time/residue: 0.4808 time to fit residues: 148.4379 Evaluate side-chains 281 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 252 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR 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 274 LYS Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 590 VAL 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 379 MET Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain D residue 100 GLN Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain G residue 7 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 135 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 81 optimal weight: 0.0770 chunk 111 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 122 optimal weight: 0.5980 chunk 128 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 D 89 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.151306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.133140 restraints weight = 19398.315| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 2.25 r_work: 0.3772 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3602 r_free = 0.3602 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 = 0.3602 r_free = 0.3602 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13566 Z= 0.152 Angle : 0.632 11.669 18483 Z= 0.311 Chirality : 0.044 0.298 2123 Planarity : 0.004 0.074 2329 Dihedral : 5.817 54.997 2109 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.76 % Allowed : 19.14 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.21), residues: 1607 helix: 0.16 (0.27), residues: 389 sheet: 0.67 (0.30), residues: 327 loop : -0.49 (0.22), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 204 TYR 0.019 0.002 TYR A 424 PHE 0.020 0.002 PHE A 97 TRP 0.012 0.002 TRP E 36 HIS 0.004 0.001 HIS D 90 Details of bonding type rmsd covalent geometry : bond 0.00361 (13536) covalent geometry : angle 0.62090 (18408) SS BOND : bond 0.00406 ( 15) SS BOND : angle 1.38806 ( 30) hydrogen bonds : bond 0.03597 ( 496) hydrogen bonds : angle 5.20459 ( 1335) link_BETA1-4 : bond 0.00241 ( 5) link_BETA1-4 : angle 2.34749 ( 15) link_NAG-ASN : bond 0.00325 ( 10) link_NAG-ASN : angle 2.18931 ( 30) *********************** 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 299 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 259 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLN cc_start: 0.7213 (pm20) cc_final: 0.6749 (pm20) REVERT: A 231 GLU cc_start: 0.7733 (mp0) cc_final: 0.7226 (mp0) REVERT: A 253 LEU cc_start: 0.6715 (OUTLIER) cc_final: 0.6465 (pp) REVERT: A 303 ASP cc_start: 0.7573 (t0) cc_final: 0.7343 (t70) REVERT: A 424 TYR cc_start: 0.7873 (t80) cc_final: 0.7589 (t80) REVERT: A 506 LEU cc_start: 0.5842 (OUTLIER) cc_final: 0.5612 (mm) REVERT: A 671 ASP cc_start: 0.7480 (p0) cc_final: 0.7204 (p0) REVERT: A 676 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8425 (mm) REVERT: A 682 TYR cc_start: 0.8267 (t80) cc_final: 0.7813 (t80) REVERT: A 684 GLU cc_start: 0.7276 (mp0) cc_final: 0.6787 (mp0) REVERT: C 379 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.7828 (mmt) REVERT: E 83 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7719 (mtp180) outliers start: 40 outliers final: 21 residues processed: 279 average time/residue: 0.5561 time to fit residues: 170.6119 Evaluate side-chains 274 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 248 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 253 LEU 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 332 MET Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 595 TYR 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 C residue 379 MET Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 22 THR 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 58 optimal weight: 5.9990 chunk 92 optimal weight: 0.4980 chunk 150 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 47 optimal weight: 0.0980 chunk 0 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 594 GLN A 617 GLN ** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 GLN E 31 GLN ** G 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.151053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.132800 restraints weight = 19729.056| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 2.28 r_work: 0.3764 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3596 r_free = 0.3596 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3596 r_free = 0.3596 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13566 Z= 0.170 Angle : 0.652 11.657 18483 Z= 0.320 Chirality : 0.045 0.299 2123 Planarity : 0.005 0.075 2329 Dihedral : 5.786 54.962 2109 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.56 % Allowed : 19.90 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.21), residues: 1607 helix: 0.11 (0.26), residues: 387 sheet: 0.63 (0.30), residues: 326 loop : -0.54 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 255 TYR 0.019 0.002 TYR E 27 PHE 0.020 0.002 PHE A 503 TRP 0.016 0.002 TRP E 36 HIS 0.005 0.001 HIS D 90 Details of bonding type rmsd covalent geometry : bond 0.00405 (13536) covalent geometry : angle 0.64123 (18408) SS BOND : bond 0.00560 ( 15) SS BOND : angle 1.32338 ( 30) hydrogen bonds : bond 0.03629 ( 496) hydrogen bonds : angle 5.24477 ( 1335) link_BETA1-4 : bond 0.00236 ( 5) link_BETA1-4 : angle 2.33106 ( 15) link_NAG-ASN : bond 0.00329 ( 10) link_NAG-ASN : angle 2.20308 ( 30) *********************** 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 295 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 258 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLN cc_start: 0.7226 (pm20) cc_final: 0.6763 (pm20) REVERT: A 231 GLU cc_start: 0.7745 (mp0) cc_final: 0.7250 (mp0) REVERT: A 253 LEU cc_start: 0.6692 (OUTLIER) cc_final: 0.6429 (pp) REVERT: A 293 LYS cc_start: 0.7914 (mtpp) cc_final: 0.7671 (mtpp) REVERT: A 303 ASP cc_start: 0.7569 (t0) cc_final: 0.7351 (t70) REVERT: A 500 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7471 (tp) REVERT: A 595 TYR cc_start: 0.7327 (p90) cc_final: 0.7112 (p90) REVERT: A 671 ASP cc_start: 0.7462 (p0) cc_final: 0.7191 (p0) REVERT: A 676 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8418 (mm) REVERT: A 682 TYR cc_start: 0.8257 (t80) cc_final: 0.8042 (t80) REVERT: C 123 LYS cc_start: 0.7585 (ptpp) cc_final: 0.7366 (ptpp) REVERT: C 379 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.7891 (mmt) REVERT: D 100 GLN cc_start: 0.6890 (OUTLIER) cc_final: 0.6381 (pm20) REVERT: E 83 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7727 (mtp180) outliers start: 37 outliers final: 23 residues processed: 276 average time/residue: 0.5781 time to fit residues: 175.7456 Evaluate side-chains 282 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 253 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR 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 274 LYS Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 75 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 C residue 379 MET Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain D residue 100 GLN Chi-restraints excluded: chain E residue 83 ARG 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 7 SER Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 107 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 126 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 139 optimal weight: 0.8980 chunk 106 optimal weight: 0.5980 chunk 54 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 76 optimal weight: 0.0770 chunk 124 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 ASN ** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 GLN ** C 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.151500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.133168 restraints weight = 19621.085| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.28 r_work: 0.3766 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3602 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3602 ------------------------------------------------------------------------------- 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: 0.7395 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13566 Z= 0.166 Angle : 0.665 11.736 18483 Z= 0.326 Chirality : 0.045 0.288 2123 Planarity : 0.004 0.075 2329 Dihedral : 5.778 54.774 2109 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.14 % Allowed : 20.94 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.21), residues: 1607 helix: 0.14 (0.27), residues: 386 sheet: 0.57 (0.30), residues: 327 loop : -0.53 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 218 TYR 0.034 0.002 TYR A 424 PHE 0.020 0.002 PHE G 49 TRP 0.015 0.002 TRP E 36 HIS 0.006 0.001 HIS D 90 Details of bonding type rmsd covalent geometry : bond 0.00396 (13536) covalent geometry : angle 0.65416 (18408) SS BOND : bond 0.00432 ( 15) SS BOND : angle 1.55728 ( 30) hydrogen bonds : bond 0.03606 ( 496) hydrogen bonds : angle 5.25098 ( 1335) link_BETA1-4 : bond 0.00243 ( 5) link_BETA1-4 : angle 2.28147 ( 15) link_NAG-ASN : bond 0.00328 ( 10) link_NAG-ASN : angle 2.19478 ( 30) ********************** 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 285 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 254 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLN cc_start: 0.7201 (pm20) cc_final: 0.6735 (pm20) REVERT: A 231 GLU cc_start: 0.7755 (mp0) cc_final: 0.7249 (mp0) REVERT: A 253 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6410 (pp) REVERT: A 293 LYS cc_start: 0.7894 (mtpp) cc_final: 0.7662 (mtpp) REVERT: A 303 ASP cc_start: 0.7522 (t0) cc_final: 0.7319 (t70) REVERT: A 500 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7480 (tp) REVERT: A 671 ASP cc_start: 0.7447 (p0) cc_final: 0.7189 (p0) REVERT: A 676 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8416 (mm) REVERT: A 682 TYR cc_start: 0.8254 (t80) cc_final: 0.7818 (t80) REVERT: A 684 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6888 (mp0) REVERT: C 379 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.7904 (mmt) REVERT: D 100 GLN cc_start: 0.6883 (OUTLIER) cc_final: 0.6371 (pm20) REVERT: E 83 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7723 (mtp180) outliers start: 31 outliers final: 22 residues processed: 270 average time/residue: 0.5589 time to fit residues: 166.2270 Evaluate side-chains 282 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 254 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR 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 279 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 75 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 379 MET Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain D residue 100 GLN Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 107 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 100 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 ** C 131 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.150154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.131885 restraints weight = 19509.540| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 2.26 r_work: 0.3755 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3588 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3588 r_free = 0.3588 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3588 r_free = 0.3588 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13566 Z= 0.201 Angle : 0.693 11.830 18483 Z= 0.340 Chirality : 0.047 0.320 2123 Planarity : 0.005 0.076 2329 Dihedral : 5.863 54.904 2109 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.21 % Allowed : 21.01 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.21), residues: 1607 helix: 0.09 (0.27), residues: 386 sheet: 0.55 (0.29), residues: 327 loop : -0.58 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 218 TYR 0.031 0.002 TYR A 595 PHE 0.029 0.002 PHE A 317 TRP 0.017 0.002 TRP E 36 HIS 0.007 0.001 HIS D 90 Details of bonding type rmsd covalent geometry : bond 0.00482 (13536) covalent geometry : angle 0.68171 (18408) SS BOND : bond 0.00392 ( 15) SS BOND : angle 1.55792 ( 30) hydrogen bonds : bond 0.03781 ( 496) hydrogen bonds : angle 5.32335 ( 1335) link_BETA1-4 : bond 0.00277 ( 5) link_BETA1-4 : angle 2.39182 ( 15) link_NAG-ASN : bond 0.00586 ( 10) link_NAG-ASN : angle 2.29587 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5683.48 seconds wall clock time: 97 minutes 23.99 seconds (5843.99 seconds total)