Starting phenix.real_space_refine on Thu May 15 15:00:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tco_41156/05_2025/8tco_41156.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tco_41156/05_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_41156/05_2025/8tco_41156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tco_41156/05_2025/8tco_41156.map" model { file = "/net/cci-nas-00/data/ceres_data/8tco_41156/05_2025/8tco_41156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tco_41156/05_2025/8tco_41156.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 1.180 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 8420 2.51 5 N 2238 2.21 5 O 2499 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13222 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5165 Classifications: {'peptide': 643} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 612} Chain breaks: 3 Chain: "B" Number of atoms: 1817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1817 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 210} Chain: "C" Number of atoms: 2455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2455 Classifications: {'peptide': 295} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 276} Chain breaks: 3 Chain: "D" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 851 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "E" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 949 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "F" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 977 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 804 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 9.14, per 1000 atoms: 0.69 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: 3.57 Conformation dependent library (CDL) restraints added in 1.8 seconds 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3090 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 25 sheets defined 30.2% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 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: 5.33 Time building geometry restraints manager: 4.17 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: 2.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 34.920 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.240 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.21), residues: 1607 helix: -0.32 (0.27), residues: 372 sheet: 0.53 (0.29), residues: 350 loop : -0.25 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 332 HIS 0.009 0.001 HIS A 670 PHE 0.028 0.002 PHE A 488 TYR 0.028 0.002 TYR C 384 ARG 0.014 0.001 ARG A 47 Details of bonding type rmsd link_NAG-ASN : bond 0.00460 ( 10) link_NAG-ASN : angle 2.77203 ( 30) link_BETA1-4 : bond 0.00371 ( 5) link_BETA1-4 : angle 1.65275 ( 15) hydrogen bonds : bond 0.20829 ( 496) hydrogen bonds : angle 8.13092 ( 1335) SS BOND : bond 0.00237 ( 15) SS BOND : angle 1.31313 ( 30) covalent geometry : bond 0.00321 (13536) covalent geometry : angle 0.63774 (18408) *********************** 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 : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.7781 (tt0) cc_final: 0.7562 (tt0) REVERT: A 151 GLN cc_start: 0.7086 (pm20) cc_final: 0.6647 (pm20) REVERT: A 231 GLU cc_start: 0.7387 (mp0) cc_final: 0.7074 (mp0) REVERT: A 296 ASP cc_start: 0.7871 (p0) cc_final: 0.7668 (p0) REVERT: A 426 LEU cc_start: 0.8319 (tp) cc_final: 0.8093 (tm) REVERT: A 596 LEU cc_start: 0.7600 (mt) cc_final: 0.7398 (mt) REVERT: A 684 GLU cc_start: 0.7007 (mp0) cc_final: 0.6568 (mp0) REVERT: F 19 ARG cc_start: 0.7482 (ttt90) cc_final: 0.7247 (ttt90) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 1.1305 time to fit residues: 325.9302 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 : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 0.9980 chunk 120 optimal weight: 0.0980 chunk 66 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 48 optimal weight: 0.0980 chunk 75 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.153106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.134415 restraints weight = 19517.817| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.35 r_work: 0.3793 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3613 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 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 = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3613 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13566 Z= 0.159 Angle : 0.642 11.206 18483 Z= 0.322 Chirality : 0.045 0.289 2123 Planarity : 0.005 0.048 2329 Dihedral : 8.212 71.797 2109 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.45 % Allowed : 10.30 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.22), residues: 1607 helix: 0.32 (0.27), residues: 382 sheet: 0.59 (0.28), residues: 360 loop : -0.18 (0.22), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 167 HIS 0.005 0.001 HIS A 586 PHE 0.033 0.002 PHE A 462 TYR 0.021 0.002 TYR A 682 ARG 0.005 0.000 ARG B 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00435 ( 10) link_NAG-ASN : angle 2.39908 ( 30) link_BETA1-4 : bond 0.00314 ( 5) link_BETA1-4 : angle 2.54317 ( 15) hydrogen bonds : bond 0.04549 ( 496) hydrogen bonds : angle 5.76500 ( 1335) SS BOND : bond 0.00428 ( 15) SS BOND : angle 1.23229 ( 30) covalent geometry : bond 0.00371 (13536) covalent geometry : angle 0.63036 (18408) *********************** 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 277 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 256 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.7922 (tt0) cc_final: 0.7717 (tt0) REVERT: A 151 GLN cc_start: 0.7267 (pm20) cc_final: 0.6850 (pm20) REVERT: A 231 GLU cc_start: 0.7604 (mp0) cc_final: 0.7286 (mp0) REVERT: A 255 ARG cc_start: 0.7589 (mtp85) cc_final: 0.7369 (mtp85) REVERT: A 296 ASP cc_start: 0.8034 (p0) cc_final: 0.7591 (p0) REVERT: A 426 LEU cc_start: 0.8264 (tp) cc_final: 0.7990 (tm) REVERT: A 595 TYR cc_start: 0.7296 (p90) cc_final: 0.7096 (p90) REVERT: A 682 TYR cc_start: 0.8149 (t80) cc_final: 0.7625 (t80) REVERT: A 684 GLU cc_start: 0.7301 (mp0) cc_final: 0.6816 (mp0) REVERT: B 244 ARG cc_start: 0.7124 (tpm170) cc_final: 0.6906 (tpm170) outliers start: 21 outliers final: 8 residues processed: 261 average time/residue: 1.0701 time to fit residues: 308.6221 Evaluate side-chains 253 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 245 time to evaluate : 1.401 ------------------------------------------------------------------------------- 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 C residue 237 VAL 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 54 optimal weight: 7.9990 chunk 99 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 0.0060 chunk 152 optimal weight: 0.3980 chunk 124 optimal weight: 0.0980 chunk 133 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- 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 C 325 GLN ** C 341 GLN ** 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 = 0.4151 r_free = 0.4151 target = 0.153624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.134604 restraints weight = 19785.204| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.40 r_work: 0.3799 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3634 ------------------------------------------------------------------------------- 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: 0.7355 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13566 Z= 0.129 Angle : 0.608 9.396 18483 Z= 0.300 Chirality : 0.043 0.269 2123 Planarity : 0.004 0.052 2329 Dihedral : 6.960 55.145 2109 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.14 % Allowed : 13.55 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.22), residues: 1607 helix: 0.42 (0.27), residues: 389 sheet: 0.68 (0.29), residues: 352 loop : -0.25 (0.22), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 167 HIS 0.004 0.001 HIS A 451 PHE 0.025 0.002 PHE A 462 TYR 0.016 0.001 TYR A 682 ARG 0.005 0.000 ARG A 329 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 10) link_NAG-ASN : angle 2.21283 ( 30) link_BETA1-4 : bond 0.00340 ( 5) link_BETA1-4 : angle 2.65601 ( 15) hydrogen bonds : bond 0.03815 ( 496) hydrogen bonds : angle 5.33174 ( 1335) SS BOND : bond 0.00260 ( 15) SS BOND : angle 1.10595 ( 30) covalent geometry : bond 0.00299 (13536) covalent geometry : angle 0.59580 (18408) *********************** 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 288 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 257 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.7937 (tt0) cc_final: 0.7721 (tt0) REVERT: A 151 GLN cc_start: 0.7255 (pm20) cc_final: 0.6821 (pm20) REVERT: A 231 GLU cc_start: 0.7598 (mp0) cc_final: 0.7246 (mp0) REVERT: A 296 ASP cc_start: 0.7947 (p0) cc_final: 0.7564 (p0) REVERT: A 303 ASP cc_start: 0.7646 (t0) cc_final: 0.7311 (t0) REVERT: A 486 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7942 (tm-30) REVERT: A 561 SER cc_start: 0.7977 (m) cc_final: 0.7655 (p) REVERT: A 682 TYR cc_start: 0.8228 (t80) cc_final: 0.7647 (t80) REVERT: A 684 GLU cc_start: 0.7291 (mp0) cc_final: 0.6798 (mp0) REVERT: B 178 VAL cc_start: 0.7585 (t) cc_final: 0.7358 (p) REVERT: C 335 THR cc_start: 0.6593 (OUTLIER) cc_final: 0.6380 (p) REVERT: G 79 GLN cc_start: 0.7488 (mp10) cc_final: 0.6918 (mp10) outliers start: 31 outliers final: 10 residues processed: 270 average time/residue: 1.1049 time to fit residues: 328.8487 Evaluate side-chains 255 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 244 time to evaluate : 1.384 ------------------------------------------------------------------------------- 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 667 MET Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 212 THR 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 73 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 158 optimal weight: 0.3980 chunk 104 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 315 ASN A 432 GLN A 594 GLN ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 GLN ** C 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.150910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.132451 restraints weight = 19441.092| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.28 r_work: 0.3760 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3592 r_free = 0.3592 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 = 0.3592 r_free = 0.3592 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13566 Z= 0.201 Angle : 0.645 10.340 18483 Z= 0.317 Chirality : 0.046 0.310 2123 Planarity : 0.005 0.061 2329 Dihedral : 6.400 55.526 2109 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.18 % Allowed : 15.48 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.21), residues: 1607 helix: 0.26 (0.26), residues: 389 sheet: 0.64 (0.28), residues: 361 loop : -0.38 (0.22), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 36 HIS 0.007 0.001 HIS D 90 PHE 0.021 0.002 PHE A 462 TYR 0.028 0.002 TYR A 595 ARG 0.006 0.000 ARG B 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00423 ( 10) link_NAG-ASN : angle 2.29417 ( 30) link_BETA1-4 : bond 0.00267 ( 5) link_BETA1-4 : angle 2.88768 ( 15) hydrogen bonds : bond 0.03957 ( 496) hydrogen bonds : angle 5.32682 ( 1335) SS BOND : bond 0.00320 ( 15) SS BOND : angle 1.31040 ( 30) covalent geometry : bond 0.00479 (13536) covalent geometry : angle 0.63242 (18408) *********************** 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 305 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 259 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.6752 (p0) cc_final: 0.6519 (p0) REVERT: A 113 GLU cc_start: 0.7932 (tt0) cc_final: 0.7722 (tt0) REVERT: A 151 GLN cc_start: 0.7252 (pm20) cc_final: 0.6804 (pm20) REVERT: A 231 GLU cc_start: 0.7689 (mp0) cc_final: 0.7293 (mp0) REVERT: A 296 ASP cc_start: 0.7988 (p0) cc_final: 0.7597 (p0) REVERT: A 303 ASP cc_start: 0.7697 (t0) cc_final: 0.7273 (OUTLIER) REVERT: A 486 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7938 (tm-30) REVERT: A 561 SER cc_start: 0.8092 (m) cc_final: 0.7713 (p) REVERT: A 682 TYR cc_start: 0.8230 (t80) cc_final: 0.7731 (t80) REVERT: A 684 GLU cc_start: 0.7320 (mp0) cc_final: 0.6820 (mp0) REVERT: B 204 ARG cc_start: 0.7617 (ptp90) cc_final: 0.7338 (ptp90) REVERT: D 100 GLN cc_start: 0.6942 (OUTLIER) cc_final: 0.6404 (pm20) REVERT: E 73 GLU cc_start: 0.6752 (mp0) cc_final: 0.6344 (mp0) outliers start: 46 outliers final: 23 residues processed: 276 average time/residue: 1.0724 time to fit residues: 327.2061 Evaluate side-chains 278 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 255 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 392 THR Chi-restraints excluded: chain A residue 472 SER 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 696 MET Chi-restraints excluded: chain B residue 178 VAL 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 331 THR Chi-restraints excluded: chain D residue 100 GLN Chi-restraints excluded: chain E residue 2 VAL 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 10 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 26 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 134 optimal weight: 0.5980 chunk 56 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 A 665 ASN C 325 GLN ** C 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.150502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.132100 restraints weight = 19630.741| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.28 r_work: 0.3750 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3583 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3583 r_free = 0.3583 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3583 r_free = 0.3583 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3583 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13566 Z= 0.208 Angle : 0.640 10.299 18483 Z= 0.318 Chirality : 0.046 0.287 2123 Planarity : 0.005 0.069 2329 Dihedral : 6.227 59.345 2109 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.04 % Allowed : 16.79 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.21), residues: 1607 helix: 0.23 (0.26), residues: 381 sheet: 0.51 (0.28), residues: 358 loop : -0.44 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 36 HIS 0.007 0.001 HIS C 131 PHE 0.021 0.002 PHE A 503 TYR 0.020 0.002 TYR E 59 ARG 0.006 0.000 ARG A 255 Details of bonding type rmsd link_NAG-ASN : bond 0.00456 ( 10) link_NAG-ASN : angle 2.07131 ( 30) link_BETA1-4 : bond 0.00344 ( 5) link_BETA1-4 : angle 2.81658 ( 15) hydrogen bonds : bond 0.03891 ( 496) hydrogen bonds : angle 5.29654 ( 1335) SS BOND : bond 0.00437 ( 15) SS BOND : angle 1.36335 ( 30) covalent geometry : bond 0.00494 (13536) covalent geometry : angle 0.62849 (18408) *********************** 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 302 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 258 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.6669 (p0) cc_final: 0.6455 (p0) REVERT: A 151 GLN cc_start: 0.7238 (pm20) cc_final: 0.6795 (pm20) REVERT: A 231 GLU cc_start: 0.7739 (mp0) cc_final: 0.7274 (mp0) REVERT: A 296 ASP cc_start: 0.7966 (p0) cc_final: 0.7708 (p0) REVERT: A 303 ASP cc_start: 0.7662 (t0) cc_final: 0.7230 (OUTLIER) REVERT: A 329 ARG cc_start: 0.7587 (mmp-170) cc_final: 0.7382 (mmp-170) REVERT: A 486 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7943 (tm-30) REVERT: A 561 SER cc_start: 0.8138 (m) cc_final: 0.7751 (p) REVERT: A 667 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.6951 (tmm) REVERT: A 676 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8379 (mm) REVERT: A 682 TYR cc_start: 0.8255 (t80) cc_final: 0.7746 (t80) REVERT: A 684 GLU cc_start: 0.7351 (mp0) cc_final: 0.6866 (mp0) REVERT: B 204 ARG cc_start: 0.7656 (ptp90) cc_final: 0.6986 (ptp90) REVERT: C 123 LYS cc_start: 0.7602 (ptpp) cc_final: 0.7374 (ptpp) REVERT: C 379 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.7879 (mmt) REVERT: D 100 GLN cc_start: 0.6915 (OUTLIER) cc_final: 0.6375 (pm20) outliers start: 44 outliers final: 27 residues processed: 277 average time/residue: 1.0957 time to fit residues: 335.4325 Evaluate side-chains 292 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 262 time to evaluate : 1.415 ------------------------------------------------------------------------------- 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 312 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 595 TYR Chi-restraints excluded: chain A residue 667 MET Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 182 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 D residue 10 SER Chi-restraints excluded: chain D residue 100 GLN Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 10 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 115 optimal weight: 0.9990 chunk 144 optimal weight: 0.0170 chunk 143 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 138 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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 325 GLN ** C 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.151216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.132932 restraints weight = 19824.048| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 2.29 r_work: 0.3771 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3601 r_free = 0.3601 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3601 r_free = 0.3601 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13566 Z= 0.146 Angle : 0.596 11.472 18483 Z= 0.296 Chirality : 0.043 0.265 2123 Planarity : 0.004 0.067 2329 Dihedral : 5.954 55.101 2109 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.56 % Allowed : 18.24 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.21), residues: 1607 helix: 0.38 (0.27), residues: 381 sheet: 0.60 (0.28), residues: 353 loop : -0.42 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 36 HIS 0.007 0.001 HIS C 131 PHE 0.019 0.002 PHE A 105 TYR 0.020 0.002 TYR E 59 ARG 0.009 0.000 ARG B 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00385 ( 10) link_NAG-ASN : angle 1.96008 ( 30) link_BETA1-4 : bond 0.00333 ( 5) link_BETA1-4 : angle 2.52589 ( 15) hydrogen bonds : bond 0.03561 ( 496) hydrogen bonds : angle 5.19310 ( 1335) SS BOND : bond 0.00327 ( 15) SS BOND : angle 1.14851 ( 30) covalent geometry : bond 0.00345 (13536) covalent geometry : angle 0.58579 (18408) *********************** 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 291 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 254 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLN cc_start: 0.7241 (pm20) cc_final: 0.6789 (pm20) REVERT: A 231 GLU cc_start: 0.7717 (mp0) cc_final: 0.7248 (mp0) REVERT: A 253 LEU cc_start: 0.6599 (OUTLIER) cc_final: 0.6295 (pp) REVERT: A 293 LYS cc_start: 0.7889 (mtpp) cc_final: 0.7648 (mtpp) REVERT: A 296 ASP cc_start: 0.7948 (p0) cc_final: 0.7745 (p0) REVERT: A 303 ASP cc_start: 0.7610 (t0) cc_final: 0.7184 (OUTLIER) REVERT: A 445 ASP cc_start: 0.7781 (m-30) cc_final: 0.7576 (m-30) REVERT: A 486 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7986 (tm-30) REVERT: A 561 SER cc_start: 0.8103 (m) cc_final: 0.7716 (p) REVERT: A 667 MET cc_start: 0.7436 (OUTLIER) cc_final: 0.6870 (tmm) REVERT: A 676 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8367 (mm) REVERT: A 682 TYR cc_start: 0.8249 (t80) cc_final: 0.7742 (t80) REVERT: A 684 GLU cc_start: 0.7324 (mp0) cc_final: 0.6831 (mp0) REVERT: B 178 VAL cc_start: 0.7575 (t) cc_final: 0.7358 (p) REVERT: C 250 MET cc_start: 0.8173 (mmm) cc_final: 0.7959 (tpp) REVERT: C 379 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.7893 (mmt) REVERT: D 100 GLN cc_start: 0.6849 (OUTLIER) cc_final: 0.6342 (pm20) outliers start: 37 outliers final: 23 residues processed: 270 average time/residue: 1.0316 time to fit residues: 308.3611 Evaluate side-chains 277 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 250 time to evaluate : 1.331 ------------------------------------------------------------------------------- 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 340 MET 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 706 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 182 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 39 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 128 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 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 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 GLN ** C 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.150191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.131839 restraints weight = 19687.325| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.29 r_work: 0.3747 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3580 r_free = 0.3580 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 = 0.3580 r_free = 0.3580 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13566 Z= 0.211 Angle : 0.644 11.521 18483 Z= 0.320 Chirality : 0.046 0.269 2123 Planarity : 0.005 0.071 2329 Dihedral : 6.001 55.320 2109 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.70 % Allowed : 19.14 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.21), residues: 1607 helix: 0.24 (0.27), residues: 381 sheet: 0.51 (0.28), residues: 353 loop : -0.51 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 36 HIS 0.007 0.001 HIS D 90 PHE 0.026 0.002 PHE G 52 TYR 0.026 0.002 TYR A 595 ARG 0.012 0.000 ARG B 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00428 ( 10) link_NAG-ASN : angle 2.09141 ( 30) link_BETA1-4 : bond 0.00278 ( 5) link_BETA1-4 : angle 2.59903 ( 15) hydrogen bonds : bond 0.03824 ( 496) hydrogen bonds : angle 5.25664 ( 1335) SS BOND : bond 0.00374 ( 15) SS BOND : angle 1.41574 ( 30) covalent geometry : bond 0.00505 (13536) covalent geometry : angle 0.63302 (18408) *********************** 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 296 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 257 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLN cc_start: 0.7267 (pm20) cc_final: 0.6804 (pm20) REVERT: A 231 GLU cc_start: 0.7717 (mp0) cc_final: 0.7221 (mp0) REVERT: A 303 ASP cc_start: 0.7583 (t0) cc_final: 0.7173 (OUTLIER) REVERT: A 486 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7943 (tm-30) REVERT: A 561 SER cc_start: 0.8203 (m) cc_final: 0.7815 (p) REVERT: A 667 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.6960 (tmm) REVERT: A 676 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8365 (mm) REVERT: A 682 TYR cc_start: 0.8266 (t80) cc_final: 0.7819 (t80) REVERT: A 684 GLU cc_start: 0.7323 (mp0) cc_final: 0.6836 (mp0) REVERT: C 379 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.7894 (mmt) REVERT: D 100 GLN cc_start: 0.6892 (OUTLIER) cc_final: 0.6354 (pm20) REVERT: E 83 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7675 (mtp180) outliers start: 39 outliers final: 28 residues processed: 272 average time/residue: 1.0536 time to fit residues: 317.0891 Evaluate side-chains 283 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 251 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 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 279 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 340 MET 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 A residue 706 VAL 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 182 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain 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 107 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 36 optimal weight: 0.1980 chunk 13 optimal weight: 2.9990 chunk 64 optimal weight: 0.4980 chunk 106 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 119 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 ASN A 465 GLN A 594 GLN C 341 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.151450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.133174 restraints weight = 19662.401| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 2.28 r_work: 0.3770 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3604 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3598 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3598 r_free = 0.3598 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 = 0.3598 r_free = 0.3598 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3598 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13566 Z= 0.153 Angle : 0.618 11.683 18483 Z= 0.305 Chirality : 0.044 0.261 2123 Planarity : 0.004 0.069 2329 Dihedral : 5.785 54.891 2109 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.90 % Allowed : 18.87 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.21), residues: 1607 helix: 0.34 (0.27), residues: 381 sheet: 0.51 (0.28), residues: 353 loop : -0.46 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 47 HIS 0.004 0.001 HIS C 131 PHE 0.021 0.002 PHE A 105 TYR 0.017 0.001 TYR E 59 ARG 0.006 0.000 ARG B 171 Details of bonding type rmsd link_NAG-ASN : bond 0.00373 ( 10) link_NAG-ASN : angle 1.95591 ( 30) link_BETA1-4 : bond 0.00273 ( 5) link_BETA1-4 : angle 2.31926 ( 15) hydrogen bonds : bond 0.03570 ( 496) hydrogen bonds : angle 5.18428 ( 1335) SS BOND : bond 0.00345 ( 15) SS BOND : angle 1.38529 ( 30) covalent geometry : bond 0.00366 (13536) covalent geometry : angle 0.60770 (18408) *********************** 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 292 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 250 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 GLN cc_start: 0.7271 (pm20) cc_final: 0.6783 (pm20) REVERT: A 231 GLU cc_start: 0.7696 (mp0) cc_final: 0.7223 (mp0) REVERT: A 293 LYS cc_start: 0.7877 (mtpp) cc_final: 0.7639 (mtpp) REVERT: A 296 ASP cc_start: 0.8070 (p0) cc_final: 0.7870 (p0) REVERT: A 303 ASP cc_start: 0.7534 (t0) cc_final: 0.7115 (t0) REVERT: A 486 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7953 (tm-30) REVERT: A 667 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.6867 (tmm) REVERT: A 676 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8444 (mm) REVERT: A 682 TYR cc_start: 0.8264 (t80) cc_final: 0.7913 (t80) REVERT: A 684 GLU cc_start: 0.7297 (mp0) cc_final: 0.7029 (mp0) REVERT: C 338 ARG cc_start: 0.8491 (ttt90) cc_final: 0.8201 (ptm-80) REVERT: C 341 GLN cc_start: 0.7583 (mt0) cc_final: 0.7364 (mt0) REVERT: C 379 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.7885 (mmt) REVERT: D 100 GLN cc_start: 0.6842 (OUTLIER) cc_final: 0.6337 (pm20) outliers start: 42 outliers final: 24 residues processed: 271 average time/residue: 1.0310 time to fit residues: 309.8328 Evaluate side-chains 278 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 250 time to evaluate : 1.364 ------------------------------------------------------------------------------- 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 340 MET Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 595 TYR Chi-restraints excluded: chain A residue 667 MET Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 706 VAL 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 40 optimal weight: 0.0050 chunk 110 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 68 optimal weight: 0.2980 chunk 16 optimal weight: 0.0470 chunk 44 optimal weight: 0.9990 overall best weight: 0.4492 ------------------------------------------------------------------------------- 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 325 GLN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.151869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.133703 restraints weight = 19479.358| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.26 r_work: 0.3776 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3613 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 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 = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3613 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13566 Z= 0.142 Angle : 0.624 11.765 18483 Z= 0.306 Chirality : 0.044 0.259 2123 Planarity : 0.004 0.063 2329 Dihedral : 5.668 54.726 2109 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.42 % Allowed : 19.83 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.21), residues: 1607 helix: 0.41 (0.27), residues: 381 sheet: 0.53 (0.29), residues: 342 loop : -0.45 (0.22), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 36 HIS 0.004 0.001 HIS C 131 PHE 0.021 0.002 PHE A 105 TYR 0.016 0.001 TYR E 27 ARG 0.008 0.000 ARG F 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00367 ( 10) link_NAG-ASN : angle 1.92125 ( 30) link_BETA1-4 : bond 0.00265 ( 5) link_BETA1-4 : angle 2.19998 ( 15) hydrogen bonds : bond 0.03478 ( 496) hydrogen bonds : angle 5.12634 ( 1335) SS BOND : bond 0.00405 ( 15) SS BOND : angle 1.53634 ( 30) covalent geometry : bond 0.00339 (13536) covalent geometry : angle 0.61378 (18408) *********************** 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 288 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 253 time to evaluate : 1.488 Fit side-chains revert: symmetry clash REVERT: A 151 GLN cc_start: 0.7247 (pm20) cc_final: 0.6763 (pm20) REVERT: A 231 GLU cc_start: 0.7713 (mp0) cc_final: 0.7362 (mp0) REVERT: A 293 LYS cc_start: 0.7871 (mtpp) cc_final: 0.7650 (mtpp) REVERT: A 296 ASP cc_start: 0.8106 (p0) cc_final: 0.7844 (p0) REVERT: A 303 ASP cc_start: 0.7476 (t0) cc_final: 0.7042 (t0) REVERT: A 486 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7972 (tm-30) REVERT: A 566 PHE cc_start: 0.6697 (m-10) cc_final: 0.6411 (m-10) REVERT: A 595 TYR cc_start: 0.7302 (OUTLIER) cc_final: 0.7096 (p90) REVERT: A 667 MET cc_start: 0.7207 (OUTLIER) cc_final: 0.6782 (tmm) REVERT: A 676 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8417 (mm) REVERT: A 682 TYR cc_start: 0.8246 (t80) cc_final: 0.7790 (t80) REVERT: A 684 GLU cc_start: 0.7266 (mp0) cc_final: 0.6829 (mp0) REVERT: C 338 ARG cc_start: 0.8467 (ttt90) cc_final: 0.8192 (ptm-80) REVERT: C 341 GLN cc_start: 0.7624 (mt0) cc_final: 0.7398 (mt0) REVERT: C 379 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.7853 (mmt) REVERT: D 100 GLN cc_start: 0.6811 (OUTLIER) cc_final: 0.6329 (pm20) REVERT: E 83 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7682 (mtp180) REVERT: F 19 ARG cc_start: 0.7845 (mmm-85) cc_final: 0.7625 (mmm-85) outliers start: 35 outliers final: 23 residues processed: 268 average time/residue: 1.1073 time to fit residues: 329.6259 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 : 1.565 ------------------------------------------------------------------------------- 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 340 MET Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 595 TYR Chi-restraints excluded: chain A residue 667 MET Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 706 VAL 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 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 G residue 7 SER Chi-restraints excluded: chain G residue 79 GLN 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 109 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 23 optimal weight: 0.3980 chunk 158 optimal weight: 0.0020 chunk 131 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 152 optimal weight: 0.8980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 315 ASN C 325 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.151272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.133110 restraints weight = 19501.081| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.26 r_work: 0.3774 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3610 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3610 r_free = 0.3610 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3610 r_free = 0.3610 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3610 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13566 Z= 0.153 Angle : 0.640 11.026 18483 Z= 0.318 Chirality : 0.045 0.313 2123 Planarity : 0.005 0.083 2329 Dihedral : 5.686 54.665 2109 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.00 % Allowed : 20.87 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.21), residues: 1607 helix: 0.44 (0.27), residues: 380 sheet: 0.53 (0.29), residues: 342 loop : -0.47 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 36 HIS 0.005 0.001 HIS D 90 PHE 0.021 0.002 PHE A 105 TYR 0.018 0.001 TYR A 424 ARG 0.014 0.001 ARG A 537 Details of bonding type rmsd link_NAG-ASN : bond 0.00367 ( 10) link_NAG-ASN : angle 1.94445 ( 30) link_BETA1-4 : bond 0.00286 ( 5) link_BETA1-4 : angle 2.20160 ( 15) hydrogen bonds : bond 0.03513 ( 496) hydrogen bonds : angle 5.14951 ( 1335) SS BOND : bond 0.00475 ( 15) SS BOND : angle 1.49872 ( 30) covalent geometry : bond 0.00365 (13536) covalent geometry : angle 0.63054 (18408) ********************** 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 274 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 245 time to evaluate : 1.343 Fit side-chains revert: symmetry clash REVERT: A 151 GLN cc_start: 0.7256 (pm20) cc_final: 0.6777 (pm20) REVERT: A 231 GLU cc_start: 0.7712 (mp0) cc_final: 0.7354 (mp0) REVERT: A 293 LYS cc_start: 0.7901 (mtpp) cc_final: 0.7649 (mtpp) REVERT: A 296 ASP cc_start: 0.8119 (p0) cc_final: 0.7805 (p0) REVERT: A 303 ASP cc_start: 0.7458 (t0) cc_final: 0.7044 (t0) REVERT: A 486 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7972 (tm-30) REVERT: A 561 SER cc_start: 0.8114 (m) cc_final: 0.7802 (p) REVERT: A 566 PHE cc_start: 0.6741 (m-10) cc_final: 0.6443 (m-10) REVERT: A 667 MET cc_start: 0.7179 (OUTLIER) cc_final: 0.6777 (tmm) REVERT: A 676 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8405 (mm) REVERT: A 682 TYR cc_start: 0.8247 (t80) cc_final: 0.7782 (t80) REVERT: A 684 GLU cc_start: 0.7266 (mp0) cc_final: 0.6829 (mp0) REVERT: C 379 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.7927 (mmt) REVERT: D 100 GLN cc_start: 0.6814 (OUTLIER) cc_final: 0.6337 (pm20) REVERT: F 19 ARG cc_start: 0.7833 (mmm-85) cc_final: 0.7610 (mmm-85) outliers start: 29 outliers final: 22 residues processed: 258 average time/residue: 1.0318 time to fit residues: 294.7703 Evaluate side-chains 273 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 247 time to evaluate : 1.332 ------------------------------------------------------------------------------- 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 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 A residue 706 VAL Chi-restraints excluded: chain B residue 175 THR 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 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 109 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 137 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 67 optimal weight: 0.0570 chunk 3 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 37 optimal weight: 0.1980 chunk 42 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 C 325 GLN ** C 341 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 = 0.4123 r_free = 0.4123 target = 0.151637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.133246 restraints weight = 19738.641| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 2.29 r_work: 0.3770 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 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 = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13566 Z= 0.157 Angle : 0.638 9.927 18483 Z= 0.317 Chirality : 0.045 0.297 2123 Planarity : 0.005 0.072 2329 Dihedral : 5.657 54.843 2109 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.00 % Allowed : 21.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.21), residues: 1607 helix: 0.41 (0.27), residues: 379 sheet: 0.53 (0.28), residues: 352 loop : -0.48 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 36 HIS 0.004 0.001 HIS D 90 PHE 0.022 0.002 PHE A 105 TYR 0.031 0.002 TYR A 595 ARG 0.014 0.000 ARG A 537 Details of bonding type rmsd link_NAG-ASN : bond 0.00375 ( 10) link_NAG-ASN : angle 1.93931 ( 30) link_BETA1-4 : bond 0.00244 ( 5) link_BETA1-4 : angle 2.19108 ( 15) hydrogen bonds : bond 0.03520 ( 496) hydrogen bonds : angle 5.17521 ( 1335) SS BOND : bond 0.00378 ( 15) SS BOND : angle 1.50092 ( 30) covalent geometry : bond 0.00378 (13536) covalent geometry : angle 0.62841 (18408) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12039.57 seconds wall clock time: 207 minutes 32.88 seconds (12452.88 seconds total)